diff --git a/Codes/Create_GCMs.m b/Codes/Create_GCMs.m
new file mode 100755
index 0000000000000000000000000000000000000000..484c402c4e5822536446c8af6c6d88b1eda5a66a
--- /dev/null
+++ b/Codes/Create_GCMs.m
@@ -0,0 +1,59 @@
+%% CODE TO CREATE GCM - GIT
+
+% This code needs the usual your_paths.txt file.
+
+% Once the NMM model is run, this code
+% will create a GCM file to input in the PEB analysis. 
+
+%-----------------------------------------------------------------------
+% Written by I. Paparella
+% Cyclotron Research Centre, University of Liege, Belgium
+% 14th December 2023
+
+
+function Create_GCMs 
+
+%% Path info
+paths_txt = fileread('your_paths.txt') ;
+paths_txt = char(strsplit(paths_txt, '\n')) ;
+
+pathtodata = (strtrim(paths_txt(2,:)));
+
+%% Pre define variables
+GCM = [];
+
+%%  Select the subject to analyse
+cd(pathtodata);
+[subdir] = spm_select(Inf,'dir','Select subject_ID directory');
+IDs = str2num(subdir(:,end-2:end));
+
+%% Loop across subjects
+for isub = 1:size(subdir,1)
+    subject_ID = sprintf('sub-%03d', IDs(isub));
+    subject_Path = strcat (pathtodata, '/', subject_ID, '/TMS_EEG');
+    
+    % Go in the session folder and load DCM
+    DCMfile_sess=spm_select('List',subject_Path,'DCM_DefaultCodes_.*.mat$');
+    if isempty(DCMfile_sess)
+        warning('No DCM for subject %s, session %s was found. Please check the subjects you selected', subject_ID, session)
+        return
+    end
+    
+    Loaded_DCMfile_sess = load(strcat(subject_Path, '/', DCMfile_sess));
+    
+    % Fill the GCM according to the session with all subjects together
+    GCM = [GCM; {Loaded_DCMfile_sess.DCM}];
+
+end
+
+% Make PEB directory
+mkdir(strcat(pathtodata,'/PEB'));
+
+% Save GCM with the correct naming
+nameTosav= 'allFemale';
+
+GCM = GCM;
+save(strcat(pathtodata,'/PEB/', sprintf('GCM_%s_%s', session, nameTosav)), 'GCM')
+
+fprintf('GCM has been created. \n')
+end
\ No newline at end of file
diff --git a/Codes/MRS_QC.m b/Codes/MRS_QC.m
new file mode 100755
index 0000000000000000000000000000000000000000..0407614e57ddd7cc4478808813db620bbea23272
--- /dev/null
+++ b/Codes/MRS_QC.m
@@ -0,0 +1,57 @@
+%% CODE TO PERFORM ADDITIONAL QC MRS ANALYSIS REQUIRED IN 1ST ROUND REV
+
+% This code extracts QC MRS metric (linewidth, CRLB and SNR across
+% participants)
+
+% It needs;
+% a "your_paths.txt" file with all the info on your paths. An example is
+% provided on GIT + the fitted MRS data.
+%-----------------------------------------------------------------------
+% Written by I. Paparella
+% Cyclotron Research Centre, University of Liege, Belgium
+% 06th November 2024
+
+%% Path info
+paths_txt = fileread('your_paths.txt') ;
+paths_txt = char(strsplit(paths_txt, '\n')) ;
+
+pathtodata = (strtrim(paths_txt(2,:)));
+
+%%  Select the subject to analyse (all except 001, 007 and 011 which are males)
+cd(pathtodata);
+[subdir] = spm_select(Inf,'dir','Select subject_ID directory');
+IDs = str2num(subdir(:,end-2:end));
+
+%% Variables needed
+%Metrics= ['SNR', 'FWHM', '%CRLB'];
+Metabs ={'GABA', 'NAA', 'Cr'};
+%% Initalize variables
+%MRS_QC_metrics = zeros(size(subdir,1),(length(Metrics)*length(Metabs)));
+MRS_QC_metrics = [];
+%% Loop across subjects to analyse and get subjective parameters
+for isub = 1:size(subdir,1)
+    
+    % Extract path info per subject
+    subject_ID = sprintf('sub-%03d', IDs(isub));
+    subject_MRSfit = fullfile (pathtodata, subject_ID, 'MRS');
+    
+    % Load .csv summary table
+    SubMRS= readtable(fullfile(subject_MRSfit, '/summary.csv'));
+    SubMRS.Metab = categorical(SubMRS.Metab); %convert to categorical
+    
+    % Extract needed info
+    MRS_QC_metrics_Sbj = [];
+    for metabi= 1: length(Metabs)
+        MRS_QC_metrics_Sbj= [MRS_QC_metrics_Sbj table2array(SubMRS(SubMRS.Metab== Metabs(metabi), end-2:end))];
+    end
+    MRS_QC_metrics = [MRS_QC_metrics; MRS_QC_metrics_Sbj];
+end
+
+MRS_QC_metrics=array2table(MRS_QC_metrics);
+IDs_table = table(IDs);
+
+MRS_QC_metrics_full = [IDs_table MRS_QC_metrics];
+
+MRS_QC_metrics_full.Properties.VariableNames = {'Sbj_number'; 'GABA_CRLB'; 'GABA_SNR';'GABA_FWHM';...
+    'NAA_CRLB'; 'NAA_SNR';'NAA_FWHM';'Cr_CRLB'; 'Cr_SNR';'Cr_FWHM'};
+writetable(MRS_QC_metrics_full,fullfile(pathtodata,'MRS_QC_1stRev_AllFemale.csv'),'WriteRowNames',true);
\ No newline at end of file
diff --git a/Codes/NMM_QCfit.m b/Codes/NMM_QCfit.m
new file mode 100755
index 0000000000000000000000000000000000000000..7818e689ebf7092ff832869d9e19a1caf95c81b7
--- /dev/null
+++ b/Codes/NMM_QCfit.m
@@ -0,0 +1,68 @@
+%% CODE TO PERFORM ADDITIONAL QC MRS ANALYSIS REQUIRED IN 1ST ROUND REV
+
+% This code extracts QC NMM fit metrics (R2 and correlations between
+% observed and modeled data)
+
+% It needs
+% a "your_paths.txt" file with all the info on your paths. An example is
+% provided on GIT + the DCM estimated.
+%-----------------------------------------------------------------------
+% Written by I. Paparella
+% Cyclotron Research Centre, University of Liege, Belgium
+% 07th November 2024
+
+%% Path info
+paths_txt = fileread('your_paths.txt') ;
+paths_txt = char(strsplit(paths_txt, '\n')) ;
+
+pathtodata = (strtrim(paths_txt(2,:)));
+
+%%  Select the subject to analyse (all except 001, 007 and 011 which are males)
+cd(pathtodata);
+[subdir] = spm_select(Inf,'dir','Select subject_ID directory');
+IDs = str2num(subdir(:,end-2:end));
+
+%% Initalize variables
+%MRS_QC_metrics = zeros(size(subdir,1),(length(Metrics)*length(Metabs)));
+R2 = [];
+r = [];
+modes= [1 2 3];
+%% Loop across subjects to analyse and get subjective parameters
+for isub = 1:size(subdir,1)
+    
+    % Extract path info per subject
+    subject_ID = sprintf('sub-%03d', IDs(isub));
+    subject_DCMest = fullfile (pathtodata, subject_ID, 'TMS_EEG');
+    
+    % Load DCM file
+    DCMfile = spm_select('List',subject_DCMest,'DCM_DefaultCodes_.*.mat$');
+    SubDCM=load(fullfile(subject_DCMest, '/', DCMfile(1,:)));
+    
+% Compute R2    
+    for m = 1:length(modes)
+        % compute and store R2 for ERP
+        MSE_1 = sum(SubDCM.DCM.R{1}(:,m).^2); % for condition 1
+        SS_1  = sum((SubDCM.DCM.H{1}(:,m)+SubDCM.DCM.R{1}(:,m)).^2);
+        R2(isub,m,1) = 1-(MSE_1/SS_1);
+        clear MSE_1 SS_1
+    end
+    
+% Compute correlations between observed and modeled data    
+    for m = 1:length(modes)
+        % correlation
+        y1 = SubDCM.DCM.H{1}(:,m)+SubDCM.DCM.R{1}(:,m);        
+        yhat1 = SubDCM.DCM.H{1}(:,m);
+        r(isub,m,1) = corr(y1(:,1),yhat1(:,1),'type','Pearson');
+    end    
+end
+
+% Convert to table and save
+r=array2table(r);
+R2=array2table(R2);
+IDs_table = table(IDs);
+
+QC_metrics_full = [IDs_table r R2];
+
+QC_metrics_full.Properties.VariableNames = {'Sbj_number'; 'Mode1_r'; 'Mode2_r'; 'Mode3_r';
+    'Mode1_R2'; 'Mode2_R2'; 'Mode3_R2'};
+writetable(QC_metrics_full,fullfile(pathtodata,'DCM_QC_1stRev_AllFemale.csv'),'WriteRowNames',true);
\ No newline at end of file
diff --git a/Codes/PEB_analysis.m b/Codes/PEB_analysis.m
new file mode 100755
index 0000000000000000000000000000000000000000..b35f6d51cdc0db99534e1b0c0ffcd387dd08d53e
--- /dev/null
+++ b/Codes/PEB_analysis.m
@@ -0,0 +1,88 @@
+%% CODE TO RUN PEB MODEL AND TEST MRS-GABA EFFECTS
+
+% This code needs the usual your_paths.txt file with all the info on your paths. 
+% An example is provided on GIT.
+
+% This code is an authomatized script to run PEB analysis with a regressor.
+% In this case we regress the MRS-derived metrics to the NMM output. We
+% will just focus on the T and H output of the NMM because they store
+% receptors and connections info respectively. 
+
+%-----------------------------------------------------------------------
+% Written by I. Paparella
+% Cyclotron Research Centre, University of Liege, Belgium
+% 14th December 2023
+
+
+function PEB_analysis
+
+
+%% Path info
+paths_txt = fileread('your_paths.txt') ;
+paths_txt = char(strsplit(paths_txt, '\n')) ;
+
+paths = [];
+paths.data = (strtrim(paths_txt(2,:)));
+paths.spm = (strtrim(paths_txt(4,:)));
+paths.codes = (strtrim(paths_txt(8,:)));
+
+addpath(paths.spm)
+%% Define folder to store analysis into
+PEB_path= strcat(paths.data, '/PEB');
+
+%% Start the PEB analysis
+% To test whether TMS-EEG and MRS GABA metrics are related we will
+% conduct a PEB analysis putting the MRS derived GABA metric as regressor
+% as described here: (https://en.wikibooks.org/wiki/SPM/Parametric_Empirical_Bayes_(PEB))
+
+
+% First let's create a folder to store the output of this PEB analysis
+PEB_MRS_NMM = strcat(PEB_path, '/PEB_MRS_NMM_FHK_AllFemale_GABA_withoutCycle');
+mkdir(PEB_MRS_NMM);
+
+% We load the GCMs 
+GCM_all = load(strcat(PEB_path, '/GCM_FHK_allFemale.mat'));
+
+% Load the MRS info
+MRS = load(strcat(paths.data, '/MRS_GABA_FHK_AllSubjects.txt'));
+
+% We define a design matrix X1 with regressors:
+% Mean
+% MRS-derived GABA
+% Interpret: as correlation (if positive = higher MRS, higher NMM; if
+% negative the other way around)
+    
+% Then we create the design matrix
+X1= [ones(size(GCM_all.GCM,1),1) MRS(:,2)];
+X1(:,2) = X1(:,2) - mean(X1(:,2)); % mean center the 2nd column so that the
+%first column can be taken as mean connectivity across subjects. If we
+%don't mean center the first column will be taken as baseline
+
+X1_labels = {'Mean_connectivity', 'MRS'};
+
+% Fit to all DCMs from old in a single column vector:
+GCM = GCM_all.GCM;
+
+% PEB setting and Run PEB
+M = struct();
+M.Q = 'all';
+M.X= X1;
+M.Xnames = X1_labels;
+
+[PEB ,RCM] = spm_dcm_peb(GCM, M, {'T', 'H'}); % need to set the field otherwise the
+% default will be matrix A and B (set on the MRI) which we don't have in
+% NMM
+
+% Save the output in the respective folder & run BMA
+save(strcat(PEB_MRS_NMM, '/PEB_MRS_NMM_FHK_allFemale_GABA.mat'),'PEB','RCM');
+
+BMA = spm_dcm_peb_bmc(PEB);
+save(strcat(PEB_MRS_NMM,'/BMA_PEB_MRS_NMM_FHK_allFemale_GABA.mat'),'BMA');
+
+% LOO cross-validation
+spm_dcm_loo(GCM,M,{'H(3,3)'}); % on IIfeedbackLoop
+spm_dcm_loo(GCM,M,{'H(3,4)'}); % on II-DP connection
+    
+end
+
+% spm_dcm_peb_review(BMA); to review results
\ No newline at end of file
diff --git a/Codes/PEB_analysis_withCycle.m b/Codes/PEB_analysis_withCycle.m
new file mode 100755
index 0000000000000000000000000000000000000000..c0755e7b1d48c7f415b030c4f8ded305e2c809f0
--- /dev/null
+++ b/Codes/PEB_analysis_withCycle.m
@@ -0,0 +1,95 @@
+%% CODE TO RUN PEB MODEL AND TEST MRS-GABA EFFECTS
+
+% This code needs the usual your_paths.txt file with all the info on your paths. 
+% An example is provided on GIT.
+
+% This code is an authomatized script to run PEB analysis with a regressor.
+% In this case we regress the MRS-derived metrics to the NMM output. We
+% will just focus on the T and H output of the NMM because they store
+% receptors and connections info respectively. 
+
+%-----------------------------------------------------------------------
+% Written by I. Paparella
+% Cyclotron Research Centre, University of Liege, Belgium
+% 26th February 2025
+
+
+function PEB_analysis_withCycle
+
+
+%% Path info
+paths_txt = fileread('your_paths.txt') ;
+paths_txt = char(strsplit(paths_txt, '\n')) ;
+
+paths = [];
+paths.data = (strtrim(paths_txt(2,:)));
+paths.spm = (strtrim(paths_txt(4,:)));
+paths.codes = (strtrim(paths_txt(8,:)));
+
+addpath(paths.spm)
+%% Define folder to store analysis into
+PEB_path= strcat(paths.data, '/PEB');
+
+%% Start the PEB analysis
+% To test whether TMS-EEG and MRS GABA metrics are related we will
+% conduct a PEB analysis putting the MRS derived GABA metric as regressor
+% as described here: (https://en.wikibooks.org/wiki/SPM/Parametric_Empirical_Bayes_(PEB))
+
+
+% First let's create a folder to store the output of this PEB analysis
+PEB_MRS_NMM = strcat(PEB_path, '/PEB_MRS_NMM_FHK_AllFemale_GABA_withCycle');
+mkdir(PEB_MRS_NMM);
+
+% We load the GCMs 
+GCM_all = load(strcat(PEB_path, '/GCM_FHK_allFemale.mat'));
+GCM_all.GCM{11,1}= []; % remove STR7T_HS_015 -> no menstrual cycle due to contracceptive pill
+
+% Load the MRS info
+subjToExclude = 15; %015 who has no cycle due to contracceptive pill
+MRS = load(strcat(paths.data, '/MRS_GABA_FHK_AllSubjects.txt'));
+MRS(ismember(MRS(:,1), subjToExclude),:) = [];
+
+% Load table with cycle info
+MensCycle = load(strcat(paths.data, '/MensCycle.txt'));
+
+% We define a design matrix X1 with regressors:
+% Mean
+% MRS-derived GABA
+% Interpret: as correlation (if positive = higher MRS, higher NMM; if
+% negative the other way around)
+    
+% Then we create the design matrix
+X1= [ones(size(GCM_all.GCM,1),1) MRS(:,2) MensCycle];
+X1(:,2) = X1(:,2) - mean(X1(:,2)); % mean center the 2nd column so that the
+%first column can be taken as mean connectivity across subjects. If we
+%don't mean center the first column will be taken as baseline
+X1(:,3) = X1(:,3) - mean(X1(:,3));
+
+X1_labels = {'Mean_connectivity', 'MRS', 'Cycle'};
+
+% Fit to all DCMs from old in a single column vector:
+GCM = GCM_all.GCM;
+
+% PEB setting and Run PEB
+M = struct();
+M.Q = 'all';
+M.X= X1;
+M.Xnames = X1_labels;
+
+[PEB ,RCM] = spm_dcm_peb(GCM, M, {'T', 'H'}); % need to set the field otherwise the
+% default will be matrix A and B (set on the MRI) which we don't have in
+% NMM
+
+% Save the output in the respective folder & run BMA
+save(strcat(PEB_MRS_NMM, '/PEB_MRS_NMM_FHK_allFemale_GABA.mat'),'PEB','RCM');
+
+BMA = spm_dcm_peb_bmc(PEB);
+save(strcat(PEB_MRS_NMM,'/BMA_PEB_MRS_NMM_FHK_allFemale_GABA.mat'),'BMA');
+
+% LOO cross-validation
+spm_dcm_loo(GCM,M,{'H(3,3)'}); % on IIfeedbackLoop
+spm_dcm_loo(GCM,M,{'H(3,4)'}); % on II-DP connection
+    
+end
+
+% spm_dcm_peb_review(BMA); to review results
\ No newline at end of file
diff --git a/Codes/RegressionPlots.R b/Codes/RegressionPlots.R
new file mode 100755
index 0000000000000000000000000000000000000000..729c3321ac0ea11d0a7a800457068670d41836d0
--- /dev/null
+++ b/Codes/RegressionPlots.R
@@ -0,0 +1,85 @@
+#### STR7T_HS -- CORRELATION ANALYSIS TMS-EEG DERIVED GABA MEASURES AND MRS ONES
+## -------------------------------------------------------------------------------------------------------------------
+## Created: Thursday Dec 21 14:37 2023 -- author: ipaparella@uliege.be
+# To check citation (for referencing) for any of the package used in this script just run citation("package")
+## -------------------------------------------------------------------------------------------------------------------
+
+
+### WHAT IS THIS SCRIPT DOING?
+## 1. Regression plots of the relationships shown by PEB analysis.
+## --------------------------------------------------------------------------------------------------------------------
+## --------------------------------------------------------------------------------------------------------------------
+## --------------------------------------------------------------------------------------------------------------------
+## --------------------------------------------------------------------------------------------------------------------
+
+# Import Libraries
+library("ggpubr")
+library("tidyverse")
+library("ggplot2")
+library(viridis)
+
+# Import data
+GABAmetrix_onlyFem <- read.csv("/mnt/data/STR7T_HS/Prepared/STR7T_NMM_perSess_DefaultCodes_AllSubjects.txt")
+
+### 1. 
+
+EI_MRS = GABAmetrix_onlyFem$MRS_GABA/GABAmetrix_onlyFem$MRS_GLU
+data.frame(EI_MRS)
+GABAmetrix_onlyFem = cbind(GABAmetrix_onlyFem, EI_MRS)
+
+# Average of tonic and phasic inhib (just the significant values)
+TonicInhib_sign = rowMeans(subset(GABAmetrix_onlyFem, select = c(SC, II, DP)), na.rm = TRUE)
+PhasicInhib_sign = rowMeans(subset(GABAmetrix_onlyFem, select = c(II.DP)), na.rm = TRUE)
+# Add this to table
+GABAmetrix_onlyFem = cbind(GABAmetrix_onlyFem, TonicInhib_sign, PhasicInhib_sign)
+
+# Check colors in virdis palette
+# library(scales)
+# v_colors =  viridis(30, option = 'D') -> number means how many colors you want to see
+# show_col(v_colors)
+# Plots
+ggplot(GABAmetrix_onlyFem, aes(x=MRS_GABA, y=GABAa)) +
+  geom_point(alpha=0.7, color="#3C508BFF", size = 4) +
+  geom_smooth(method=lm , color="#3C508BFF", fill="#3C508BFF", se=TRUE)+
+  theme_classic()+
+  xlab("GABA:Cr") +
+  ylab("GABAa")+
+  font("xy.text", size = 20, color = "black")+
+  scale_y_continuous(labels = scales::label_number(accuracy = 0.1))
+
+# 
+GABA_MRS_Tonic = cor.test(GABAmetrix_onlyFem$TonicInhib_sign, GABAmetrix_onlyFem$MRS_GABA, 
+                          method="spearman",exact=FALSE)
+GABA_MRS_Tonic
+ggplot(GABAmetrix_onlyFem, aes(x=MRS_GABA, y=TonicInhib_sign)) +
+  geom_point(alpha=0.7, color="#1F948CFF", size = 4) +
+  geom_smooth(method=lm , color="#1F948CFF", fill="#1F948CFF", se=TRUE)+
+  theme_classic()+
+  xlab("GABA:Cr") +
+  ylab("Tonic Inhibition")+
+  font("xy.text", size = 20, color = "black")
+
+#### -> 3rd round revision menstrual cycle effect. Plot linear regression with menstrual cycle category
+# Create extra column with cycle factor
+Cycle=c('M', 'M', 'M', 'M', 'L', 'L', 'M', 'F', 'L', 'F', 'None', 'M', 'F', 'F', 'M', 'F', 'F', 'M', 'L', 'L')
+data.frame(Cycle)
+GABAmetrix_onlyFem_cycle = cbind(GABAmetrix_onlyFem, Cycle)
+
+# Plots
+ggplot(GABAmetrix_onlyFem_cycle, aes(x=MRS_GABA, y=GABAa, col=Cycle)) +
+  geom_point(alpha=0.7, size = 4) +
+  geom_smooth(method=lm , color="#3C508BFF", fill="#3C508BFF", se=TRUE)+
+  theme_classic()+
+  xlab("GABA:Cr") +
+  ylab("GABAa")+
+  font("xy.text", size = 20, color = "black")+
+  scale_y_continuous(labels = scales::label_number(accuracy = 0.1))
+
+# 
+ggplot(GABAmetrix_onlyFem_cycle, aes(x=MRS_GABA, y=TonicInhib_sign, col=Cycle)) +
+  geom_point(alpha=0.7, size = 4) +
+  geom_smooth(method=lm , color="#1F948CFF", fill="#1F948CFF", se=TRUE)+
+  theme_classic()+
+  xlab("GABA:Cr") +
+  ylab("Tonic Inhibition")+
+  font("xy.text", size = 20, color = "black")
diff --git a/Data/DCM_QC_1stRev_AllFemale.csv b/Data/DCM_QC_1stRev_AllFemale.csv
new file mode 100755
index 0000000000000000000000000000000000000000..112475e0774aa12f1059a3ef5135414288b8a0e8
--- /dev/null
+++ b/Data/DCM_QC_1stRev_AllFemale.csv
@@ -0,0 +1,21 @@
+Sbj_number,Mode1_r,Mode2_r,Mode3_r,Mode1_R2,Mode2_R2,Mode3_R2
+2,0.814922555503975,0.711756698424267,0.947713403401497,0.662752604514475,0.50448606801357,0.897857212544311
+3,0.791874350491316,0.905186996445252,0.66616857852364,0.626902357648098,0.815887552689512,0.440862359149716
+4,0.81011230920811,0.886246173596499,0.967352644495842,0.6549819892586,0.785247363371429,0.9354721869336
+5,0.862267348517587,0.973618616153802,0.947306982789012,0.743503828854095,0.947896907440254,0.897092983027956
+6,0.0128485839337502,0.997498438339493,0.381051333452898,-6.57393748666468e-05,0.994977330002448,0.140278050346107
+8,0.164937867912563,0.974405638758539,0.98922523447755,0.0133302844856542,0.949173563410989,0.978480863653342
+9,0.992842315142799,0.902129314649765,0.749791525935589,0.985449234741821,0.812685608868223,0.559075597871756
+10,0.973761878496147,0.902568306038386,0.526929891338071,0.948150344951642,0.814079553697573,0.276642161323963
+13,0.991277308412225,0.908348620509626,0.794014437691387,0.98253722389758,0.823517419160016,0.630031645932489
+14,0.858485264260853,0.698665545533499,0.817232074255248,0.732451490706415,0.487927117184329,0.664870746020384
+15,0.872503571690131,0.754255862955138,0.357190823558097,0.761003693923247,0.567949404610925,0.127585258265384
+16,0.882101926935536,0.911651013735556,0.696833527903331,0.773528202254237,0.830843194276447,0.48332024268214
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diff --git a/Data/MRS_GABA_FHK_AllSubjects.txt b/Data/MRS_GABA_FHK_AllSubjects.txt
new file mode 100755
index 0000000000000000000000000000000000000000..568040c06e6336a80a703dd95692fff78e77cfab
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diff --git a/Data/MRS_QC_1stRev_AllFemale.csv b/Data/MRS_QC_1stRev_AllFemale.csv
new file mode 100755
index 0000000000000000000000000000000000000000..fa6a8dc31773b443f095bdc86c64c49fe86b8296
--- /dev/null
+++ b/Data/MRS_QC_1stRev_AllFemale.csv
@@ -0,0 +1,21 @@
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diff --git a/Data/MensCycle.txt b/Data/MensCycle.txt
new file mode 100755
index 0000000000000000000000000000000000000000..62a2d019a8f59b09dff0efad193d28ca56d81f92
--- /dev/null
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diff --git a/Data/PEB/PEB_MRS_NMM_FHK_allFemale_GABA_withCycle/LOO_MRS-II.fig b/Data/PEB/PEB_MRS_NMM_FHK_allFemale_GABA_withCycle/LOO_MRS-II.fig
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diff --git a/Data/PEB/PEB_MRS_NMM_FHK_allFemale_GABA_withCycle/LOO_MRS_II-DP.fig b/Data/PEB/PEB_MRS_NMM_FHK_allFemale_GABA_withCycle/LOO_MRS_II-DP.fig
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diff --git a/Data/PEB/PEB_MRS_NMM_FHK_allFemale_GABA_withoutCycle/LOO_MRS-II.fig b/Data/PEB/PEB_MRS_NMM_FHK_allFemale_GABA_withoutCycle/LOO_MRS-II.fig
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diff --git a/Data/STR7T_NMM_perSess_DefaultCodes_AllSubjects.txt b/Data/STR7T_NMM_perSess_DefaultCodes_AllSubjects.txt
new file mode 100755
index 0000000000000000000000000000000000000000..22476a1a59bf3ae78fa15058880634e9999e7581
--- /dev/null
+++ b/Data/STR7T_NMM_perSess_DefaultCodes_AllSubjects.txt
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diff --git a/Data/sub-001/MRS/all_parameters.csv b/Data/sub-001/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..0f01712cea9ab8cf9512a7d5c453cdde4d8c998f
--- /dev/null
+++ b/Data/sub-001/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.012981309290373211,0.00792548800282787
+Asc,0.0406335947447854,0.016303206194450116
+Asp,0.16341914325235038,0.034078706865317464
+Cr,0.22067515532976498,0.01990350021468042
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+gamma_0,21.344302841231958,0.851915337342758
+gamma_1,4.115707833413542,3.816513817704548
+sigma_0,5.056961767208421,1.1411691601726184
+sigma_1,11.814065260827414,5.954765753972853
+eps_0,-0.8578218826185353,0.38287183133792224
+eps_1,-2.480931482026929,4.7235917841277395
+Phi0,-0.01361071456673646,0.011344638311605502
+Phi1,0.0003371186577898101,1.7800356872878433e-05
+B_real_0,0.06526461735248107,0.0
+B_imag_0,-0.2414915762965351,2.803736533363884e-17
+B_real_1,-0.17447966456048583,2.803736533363884e-17
+B_imag_1,0.175751149090185,2.803736533363884e-17
+B_real_2,0.32327866187363896,0.0
+B_imag_2,0.20798330403628248,2.803736533363884e-17
diff --git a/Data/sub-001/MRS/all_samples.csv b/Data/sub-001/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..9e77683f7f8d4cbbfa6c91cfdb4ce2e276190414
--- /dev/null
+++ b/Data/sub-001/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-001/MRS/concentration_samples.csv b/Data/sub-001/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..e4efcce8a1b3872dd3927ee9961cfae6df90b6c2
--- /dev/null
+++ b/Data/sub-001/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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diff --git a/Data/sub-001/MRS/concentrations.csv b/Data/sub-001/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..83653ca84d6bb3780faa60dac3ff20b733084ed5
--- /dev/null
+++ b/Data/sub-001/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.012981309290373211,0.030525185137124797,0.33751426221676567,0.24731478974374518,0.00792548800282787,0.026934991117499748,0.20606282279754318,0.15099327465292964
+Asc,0.0406335947447854,0.0955487597303689,1.0564741540879659,0.7741352367508559,0.016303206194450116,0.04298676541628559,0.423883638191124,0.31060226067639085
+Asp,0.16341914325235038,0.3842755373240859,4.248900502495249,3.113397127324439,0.034078706865317464,0.08246096316383736,0.8860469577963787,0.6492540956084412
+Cr,0.22067515532976498,0.5189114457507225,5.73755778979321,4.204216109581661,0.01990350021468042,0.05068183541735011,0.5174913439178958,0.3791936437727967
+GABA,0.10482068764421683,0.24648291054225843,2.7253396605786255,1.9970024398655222,0.016652118489465906,0.04372004279431479,0.4329553637926351,0.31724960024365856
+GPC,0.05713047681976751,0.13434071578503176,1.485393368465185,1.0884273339915542,0.007275789495629796,0.0259014251001616,0.18917065056627919,0.1386154746860438
+GSH,0.0791350005863118,0.18608373698599384,2.0575113604464823,1.5076488506354804,0.009194868565859602,0.029080242147286155,0.23906673901435188,0.17517701298229843
+Glc,0.13603986385110672,0.3198939288168594,3.5370387726472137,2.5917778840732715,0.016697914097695457,0.04381651678390553,0.4341460503850752,0.3181220801274001
+Gln,0.046825298184102394,0.11010837691316616,1.2174585487619183,0.8920971310403556,0.020826922749153834,0.052693620433847024,0.5415003455113067,0.3967863260554143
+Glu,0.4787656312910137,1.1258039698113116,12.44791455202165,9.121254165562242,0.02152138038072216,0.05421469291205536,0.5595562557370499,0.4100168592239466
+Ins,0.38020220859305737,0.8940348424987841,9.885263886411977,7.243462671984159,0.011012367979770624,0.032384217184911274,0.286321754671401,0.2098032956904783
+Lac,0.05579020757584604,0.13118911020433452,1.4505463453402185,1.062893052445219,0.010550620881903379,0.031522738328374,0.2743163222776924,0.20100627191811432
+Mac,0.02383256683308892,0.05604161326103216,0.6196471427860499,0.4540486728677031,0.0008791738609790047,0.01955623206929665,0.022858535330380608,0.016749673989931414
+NAA,0.6860731595727563,1.6132818150401265,17.837913811332267,13.070795511697186,0.013683491137151064,0.03759640292007101,0.3557710021692593,0.2606924816169774
+NAAG,0.08916779912110252,0.20967558168112602,2.318364292896872,1.698789775227208,0.008555958428115401,0.02798124928938345,0.2224550645722782,0.16300474877944687
+PCh,0.018874085142609815,0.04438188247307813,0.49072653454520887,0.3595816334267382,0.007213445187293195,0.025804824719874896,0.18754969748974729,0.13742771548833171
+PCr,0.20459038301369667,0.48108855424927754,5.319353436153134,3.8977753650895406,0.023258733512182918,0.05804666743518768,0.6047274666879991,0.44311622653788124
+PE,0.0921163487586094,0.2166090135528746,2.395026633593943,1.7549643811423288,0.017176979181535795,0.04482878672676848,0.4466017507084696,0.3272490393449427
+Scyllo,0.01785141502757761,0.04197710234672268,0.4641370941701767,0.34009812534454764,0.003780410937667914,0.021382142468559916,0.0982907486419264,0.07202289963830104
+Tau,0.08561281696306393,0.2013161407259846,2.225934696357333,1.6310616558756352,0.012584682582832359,0.03541030939226846,0.32720196107851374,0.2397584139893393
+Cr+PCr,0.42526553834346176,1.0000000000000002,11.056911225946347,8.101991474671204,0.008269990839176053,0.027501718693270276,0.2150199023987409,0.15755660695106374
diff --git a/Data/sub-001/MRS/fit_summary.png b/Data/sub-001/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..b9e006e75fe2423aa75c38a56335abccf465d67d
Binary files /dev/null and b/Data/sub-001/MRS/fit_summary.png differ
diff --git a/Data/sub-001/MRS/options.txt b/Data/sub-001/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..d43caf2dcc9422a130d1d827e6635dcd0e23db8d
--- /dev/null
+++ b/Data/sub-001/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.10149899799599198, "GM": 0.3867224448897795, "WM": 0.5117785571142284}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_002/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-001/MRS/qc.csv b/Data/sub-001/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..f7acc51cccf78ea0cd4aa34301478f9b025cd95f
--- /dev/null
+++ b/Data/sub-001/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,3.6661116261104976,17.53944235342507
+Asc,9.034610520099092,15.010158281252309
+Asp,12.139225450111946,22.316531987342422
+Cr,107.01130642899045,9.13915765231335
+GABA,16.59064856409528,20.867592741700633
+GPC,83.50945225362366,9.179769299202912
+GSH,32.57105824543444,10.000010907494392
+Glc,19.088715911262785,41.22623565183228
+Gln,6.757753555497556,24.052741141925495
+Glu,83.02101146731697,20.948289913225313
+Ins,86.08667453983426,30.316106275577148
+Lac,16.338204669922924,16.913948613408305
+Mac,53.69832830431279,34.648518247669024
+NAA,319.77717218174877,9.248581249809533
+NAAG,47.98916496345125,9.951481542064696
+PCh,26.475644229341334,9.39646159315912
+PCr,98.45281845089339,9.342927852092132
+PE,16.61313583934157,18.33774926925616
+Scyllo,16.66131181755178,9.681284813979621
+Tau,18.726315977997086,18.26979992409654
diff --git a/Data/sub-001/MRS/summary.csv b/Data/sub-001/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..2faa89473b43c986ff18d5dd6f8d1c5ab4e0d200
--- /dev/null
+++ b/Data/sub-001/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.030525185137124797,0.026934991117499748,0.33751426221676567,0.20606282279754318,0.24731478974374518,0.15099327465292964,61.05307119294445,3.6661116261104976,17.53944235342507
+Asc,0.0955487597303689,0.04298676541628559,1.0564741540879659,0.423883638191124,0.7741352367508559,0.31060226067639085,40.12248066371814,9.034610520099092,15.010158281252309
+Asp,0.3842755373240859,0.08246096316383736,4.248900502495249,0.8860469577963787,3.113397127324439,0.6492540956084412,20.853558638900356,12.139225450111946,22.316531987342422
+Cr,0.5189114457507225,0.05068183541735011,5.73755778979321,0.5174913439178958,4.204216109581661,0.3791936437727967,9.019366128886466,107.01130642899045,9.13915765231335
+GABA,0.24648291054225843,0.04372004279431479,2.7253396605786255,0.4329553637926351,1.9970024398655222,0.31724960024365856,15.886290067077837,16.59064856409528,20.867592741700633
+GPC,0.13434071578503176,0.0259014251001616,1.485393368465185,0.18917065056627919,1.0884273339915542,0.1386154746860438,12.735390811778288,83.50945225362366,9.179769299202912
+GSH,0.18608373698599384,0.029080242147286155,2.0575113604464823,0.23906673901435188,1.5076488506354804,0.17517701298229843,11.61921842134928,32.57105824543444,10.000010907494392
+Glc,0.3198939288168594,0.04381651678390553,3.5370387726472137,0.4341460503850752,2.5917778840732715,0.3181220801274001,12.274280218312358,19.088715911262785,41.22623565183228
+Gln,0.11010837691316616,0.052693620433847024,1.2174585487619183,0.5415003455113067,0.8920971310403556,0.3967863260554143,44.47792871978925,6.757753555497556,24.052741141925495
+Glu,1.1258039698113116,0.05421469291205536,12.44791455202165,0.5595562557370499,9.121254165562242,0.4100168592239466,4.495180726045176,83.02101146731697,20.948289913225313
+Ins,0.8940348424987841,0.032384217184911274,9.885263886411977,0.286321754671401,7.243462671984159,0.2098032956904783,2.896450291680845,86.08667453983426,30.316106275577148
+Lac,0.13118911020433452,0.031522738328374,1.4505463453402185,0.2743163222776924,1.062893052445219,0.20100627191811432,18.911241489037213,16.338204669922924,16.913948613408305
+Mac,0.05604161326103216,0.01955623206929665,0.6196471427860499,0.022858535330380608,0.4540486728677031,0.016749673989931414,3.688960014824621,53.69832830431279,34.648518247669024
+NAA,1.6132818150401265,0.03759640292007101,17.837913811332267,0.3557710021692593,13.070795511697186,0.2606924816169774,1.9944653053724317,319.77717218174877,9.248581249809533
+NAAG,0.20967558168112602,0.02798124928938345,2.318364292896872,0.2224550645722782,1.698789775227208,0.16300474877944687,9.595345531064634,47.98916496345125,9.951481542064696
+PCh,0.04438188247307813,0.025804824719874896,0.49072653454520887,0.18754969748974729,0.3595816334267382,0.13742771548833171,38.21878058083061,26.475644229341334,9.39646159315912
+PCr,0.48108855424927754,0.05804666743518768,5.319353436153134,0.6047274666879991,3.8977753650895406,0.44311622653788124,11.368439302753455,98.45281845089339,9.342927852092132
+PE,0.2166090135528746,0.04482878672676848,2.395026633593943,0.4466017507084696,1.7549643811423288,0.3272490393449427,18.647047362404706,16.61313583934157,18.33774926925616
+Scyllo,0.04197710234672268,0.021382142468559916,0.4641370941701767,0.0982907486419264,0.34009812534454764,0.07202289963830104,21.17709398290151,16.66131181755178,9.681284813979621
+Tau,0.2013161407259846,0.03541030939226846,2.225934696357333,0.32720196107851374,1.6310616558756352,0.2397584139893393,14.699531015620929,18.726315977997086,18.26979992409654
+Cr+PCr,1.0000000000000002,0.027501718693270276,11.056911225946347,0.2150199023987409,8.101991474671204,0.15755660695106374,1.9446651782296245,,
diff --git a/Data/sub-001/MRS/voxel_location.png b/Data/sub-001/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..02ed5742cc77cf32d924fbf45651ae4a4fafed22
Binary files /dev/null and b/Data/sub-001/MRS/voxel_location.png differ
diff --git a/Data/sub-001/TMS_EEG/DCM_DefaultCodes_STR7T_HS_002_FHK.mat b/Data/sub-001/TMS_EEG/DCM_DefaultCodes_STR7T_HS_002_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..b124d7b8f5dbfbba6b6c78506b485f2d8121b1cc
Binary files /dev/null and b/Data/sub-001/TMS_EEG/DCM_DefaultCodes_STR7T_HS_002_FHK.mat differ
diff --git a/Data/sub-002/MRS/all_parameters.csv b/Data/sub-002/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..2267751ebc58de6084707c332b579ff851ebbd7f
--- /dev/null
+++ b/Data/sub-002/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.08797472090566587,0.012390258005934823
+Asc,0.03369130994065298,0.017573267439498802
+Asp,0.09411335068158522,0.027057126029378018
+Cr,0.20944725500960953,0.01297821127845686
+GABA,0.07971944691790331,0.017261113281840768
+GPC,0.05518704697880727,0.004868275712146625
+GSH,0.06373720454271925,0.009564812328028239
+Glc,0.11626869041169159,0.021159093671325426
+Gln,0.07535361300092902,0.021464038736370854
+Glu,0.48560797590938715,0.02135641173085249
+Ins,0.35958358449555705,0.011354085169980497
+Lac,0.009688856847308502,0.006877893610184934
+Mac,0.028275757370328992,0.0009337332413022473
+NAA,0.6162267185453325,0.012507090223922287
+NAAG,0.06456000031073039,0.009201340640560223
+PCh,0.008402464079451513,0.004812752377980898
+PCr,0.20214435601873304,0.012306888737526906
+PE,0.09790204267919352,0.01638603983698459
+Scyllo,0.01760107460015436,0.003770866398194995
+Tau,0.08990112103473354,0.015712068648748308
+gamma_0,18.503569969011142,0.8492604007644156
+gamma_1,7.329781450538346,4.225295981054457
+sigma_0,5.371963342331742,0.8892987560198553
+sigma_1,14.568986380999748,6.335583224310898
+eps_0,-0.82182099633382,0.45325026729662915
+eps_1,-4.292695883190394,4.858019066287898
+Phi0,0.1126224603141772,0.01606115540805469
+Phi1,0.00034668691316719027,2.473950954588991e-05
+B_real_0,0.008253468174494879,1.7523353333524276e-18
+B_imag_0,-0.21730884297537248,0.0
+B_real_1,-0.1118202429741002,0.0
+B_imag_1,0.28554616207715067,5.607473066727768e-17
+B_real_2,0.4285156779575998,1.1214946133455537e-16
+B_imag_2,0.00885301134332539,0.0
diff --git a/Data/sub-002/MRS/all_samples.csv b/Data/sub-002/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..4ec91db2efcf2786d4ed000ff1ff6870838335b1
--- /dev/null
+++ b/Data/sub-002/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-002/MRS/concentration_samples.csv b/Data/sub-002/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..832b16df05efb0c6136d65daec94f95c8459404b
--- /dev/null
+++ b/Data/sub-002/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+Tau,molarity,1.7824565210417738,1.6557993094932277,1.2248527234620037,1.889247284439337,1.922834340402845,1.6928246845516575,2.051124311585404,2.1412891204306246,2.1756812220305943,1.9438478323660768,1.854934294791575,2.3354057030502684,1.9103075143950943,2.256520650526244,1.721148999954214,1.7651795370520318,1.859290231927611,2.0702380062492916,1.4761033672275385,1.815073987636665,1.3074355695630344,1.2216623202924424,1.4753710437254979,1.7135041170252532,1.62208657497476,1.94455973439132,1.5436151589996567,1.7435045896297852,1.1993360531956543,1.1741545241025664,1.3220385152411271,2.056003465597862,2.1708858668878768,2.4462518896765615,1.7443081179706357,1.4956518258445313,1.7978872664421088,1.8419521691414222,2.145008696049115,1.72984547698979,1.96929189284852,1.348801060706771,2.077938702581683,1.6627992425371463,2.275441481014118,2.054701373723492,1.6566158894554996,1.532127855178231,1.985027644980583,1.9128073664925296
+Cr+PCr,molarity,8.114872224742445,8.328813500672856,8.301090891412493,8.238021745759225,8.626297104561607,8.369225285558475,8.21953319720227,8.070395925314216,8.274633123470135,7.95482159898483,8.172324810034324,8.251921976558734,8.335468834947141,7.7615754612334795,7.8686861960072,7.776923520634433,7.975275425189778,8.084136885161486,7.954968861842504,8.141602096108889,8.25638098472785,8.489268420049722,8.330927772397757,8.38182468653169,8.292542339779931,8.278389461867564,8.395208028730938,8.582072747805064,8.09877048117159,8.16674425530887,8.09388135731026,8.098855302698368,8.117216140960906,8.213980643029386,8.118613132616124,7.992158565319803,7.974674520949989,8.255479444341814,8.424583174559746,8.379518501716072,8.267657219294321,8.24788022617838,8.410566053138506,8.154952913261488,8.474345019005723,8.490128904735432,8.139069089260845,8.204949403342871,8.325459440339369,8.261782245849213
diff --git a/Data/sub-002/MRS/concentrations.csv b/Data/sub-002/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..5e4ec5dfb84d386b1b1c446dad2c63fef5f4f501
--- /dev/null
+++ b/Data/sub-002/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.08797472090566587,0.21374274535349516,2.3731927543843185,1.7558473603326745,0.012390258005934823,0.03787149633048881,0.3342377244500365,0.2472915127163572
+Asc,0.03369130994065298,0.08185616285151391,0.9088516770926702,0.6724295003888513,0.017573267439498802,0.04848691736997694,0.4740538023757515,0.3507368358593665
+Asp,0.09411335068158522,0.22865711583976983,2.5387875020127977,1.8783654743675595,0.027057126029378018,0.06963835675670242,0.7298889361210558,0.5400208472137614
+Cr,0.20944725500960953,0.5088715352733144,5.65001744702867,4.180262307758713,0.01297821127845686,0.03901660034101573,0.3500982629308808,0.2590262041246284
+GABA,0.07971944691790331,0.19368579140553413,2.1504997328943953,1.591084109128062,0.017261113281840768,0.04782044105838692,0.4656331790696618,0.3445066932900204
+GPC,0.05518704697880727,0.1340820500226547,1.488717425616039,1.1014531193136567,0.004868275712146625,0.02584458479071768,0.1313258686981234,0.09716369623621966
+GSH,0.06373720454271925,0.15485545097353853,1.71936518181953,1.272101817422302,0.009564812328028239,0.03268141934905798,0.25801892953161415,0.19089973011968026
+Glc,0.11626869041169159,0.28248556893858856,3.1364465929099556,2.320553802809026,0.021159093671325426,0.05631006298900295,0.5707845080176276,0.4223047073905048
+Gln,0.07535361300092902,0.18307859291072892,2.0327276580080356,1.5039484196952986,0.021464038736370854,0.05698725885731442,0.5790106599326428,0.4283909669659189
+Glu,0.48560797590938715,1.1798296245545872,13.099687251467838,9.692028276750994,0.02135641173085249,0.056748068273503864,0.57610733012332,0.4262428886134729
+Ins,0.35958358449555705,0.8736416750505533,9.70007234504836,7.17676488377268,0.011354085169980497,0.035902913978256436,0.3062860828732084,0.22661101131630498
+Lac,0.009688856847308502,0.023539976490534735,0.2613651357070525,0.19337547814706568,0.006877893610184934,0.02841272347980534,0.1855370169189802,0.13727274398564662
+Mac,0.028275757370328992,0.06869857551198218,0.7627625507098601,0.5643429547601081,0.0009337332413022473,0.023090890040879376,0.025188246577813975,0.018635956216939066
+NAA,0.6162267185453325,1.4971799765445135,16.623238681006406,12.298988231909282,0.012507090223922287,0.0380975159847053,0.33738937267752916,0.249623313709225
+NAAG,0.06456000031073039,0.156854509617993,1.7415607959104906,1.2885236231692552,0.009201340640560223,0.032059500174443985,0.24821397230932435,0.18364536436067191
+PCh,0.008402464079451513,0.0204145659297048,0.22666359912310433,0.16770095116317538,0.004812752377980898,0.025783126409520945,0.12982807964025697,0.09605553131420419
+PCr,0.20214435601873304,0.4911284647266856,5.45301554929338,4.034507075074811,0.012306888737526906,0.037710691056927516,0.3319887676851024,0.2456275834835055
+PE,0.09790204267919352,0.23786209450331067,2.640990683844532,1.9539822512624507,0.01638603983698459,0.04596727716274181,0.4420273302814214,0.32704150121631664
+Scyllo,0.01760107460015436,0.042763443492395026,0.4748039241324154,0.35129182630585815,0.003770866398194995,0.024738207035934844,0.10172232116022899,0.07526100388016625
+Tau,0.08990112103473354,0.2184231131682197,2.4251590326661288,1.794295502557473,0.015712068648748308,0.04455661002932295,0.4238463855268342,0.31359001743072
+Cr+PCr,0.4115916110283425,0.9999999999999998,11.103032996322048,8.214769382833522,0.009458037554138442,0.03249746745099617,0.2551385893937011,0.18876866106990686
diff --git a/Data/sub-002/MRS/fit_summary.png b/Data/sub-002/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..f54bf6c3dadda33309485bdc65488501f5ac8d1e
Binary files /dev/null and b/Data/sub-002/MRS/fit_summary.png differ
diff --git a/Data/sub-002/MRS/options.txt b/Data/sub-002/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..679e78c7e3ded0cdd79f269a76f5eb254ce44556
--- /dev/null
+++ b/Data/sub-002/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.13403512913829774, "GM": 0.36135314607663266, "WM": 0.5046117247850697}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_003/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-002/MRS/qc.csv b/Data/sub-002/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..4ba38200f302d4dadab69f0194a695bebd7caf1d
--- /dev/null
+++ b/Data/sub-002/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,32.167929915370856,17.303949708794722
+Asc,10.013471940240178,14.728930370832877
+Asp,8.812373478673333,12.55922173416753
+Cr,140.1954117082708,8.482643272352595
+GABA,16.52713944707854,20.24084883060689
+GPC,109.6063450070847,8.5750562893883
+GSH,35.58958051437269,9.241490913951033
+Glc,21.28762494640643,40.87668302194332
+Gln,14.405213419559075,23.01698787506804
+Glu,109.25120235002265,20.658645936511178
+Ins,106.2763005099162,19.815026523752337
+Lac,3.721208922354726,16.345252599534653
+Mac,78.38295551382636,36.09724572232013
+NAA,403.80477092885326,8.465783526185385
+NAAG,47.44805606275797,9.295943123347849
+PCh,16.44245322160443,8.573820808039038
+PCr,130.13113436109802,8.690063622688927
+PE,23.355173774812723,17.753562858125175
+Scyllo,22.454367538394095,8.70859070149002
+Tau,25.41068934317038,17.38962685369976
diff --git a/Data/sub-002/MRS/summary.csv b/Data/sub-002/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..562a4edd078c1b1bafbf88ce6146e8a717a8df36
--- /dev/null
+++ b/Data/sub-002/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.21374274535349516,0.03787149633048881,2.3731927543843185,0.3342377244500365,1.7558473603326745,0.2472915127163572,14.083884414047454,32.167929915370856,17.303949708794722
+Asc,0.08185616285151391,0.04848691736997694,0.9088516770926702,0.4740538023757515,0.6724295003888513,0.3507368358593665,52.15964434287059,10.013471940240178,14.728930370832877
+Asp,0.22865711583976983,0.06963835675670242,2.5387875020127977,0.7298889361210558,1.8783654743675595,0.5400208472137614,28.749508792775536,8.812373478673333,12.55922173416753
+Cr,0.5088715352733144,0.03901660034101573,5.65001744702867,0.3500982629308808,4.180262307758713,0.2590262041246284,6.196410298077868,140.1954117082708,8.482643272352595
+GABA,0.19368579140553413,0.04782044105838692,2.1504997328943953,0.4656331790696618,1.591084109128062,0.3445066932900204,21.65232443172443,16.52713944707854,20.24084883060689
+GPC,0.1340820500226547,0.02584458479071768,1.488717425616039,0.1313258686981234,1.1014531193136567,0.09716369623621966,8.821410056631809,109.6063450070847,8.5750562893883
+GSH,0.15485545097353853,0.03268141934905798,1.71936518181953,0.25801892953161415,1.272101817422302,0.19089973011968026,15.006639209627581,35.58958051437269,9.241490913951033
+Glc,0.28248556893858856,0.05631006298900295,3.1364465929099556,0.5707845080176276,2.320553802809026,0.4223047073905048,18.198444995298356,21.28762494640643,40.87668302194332
+Gln,0.18307859291072892,0.05698725885731442,2.0327276580080356,0.5790106599326428,1.5039484196952986,0.4283909669659189,28.484418837496523,14.405213419559075,23.01698787506804
+Glu,1.1798296245545872,0.056748068273503864,13.099687251467838,0.57610733012332,9.692028276750994,0.4262428886134729,4.397870873281852,109.25120235002265,20.658645936511178
+Ins,0.8736416750505533,0.035902913978256436,9.70007234504836,0.3062860828732084,7.17676488377268,0.22661101131630498,3.1575649333126843,106.2763005099162,19.815026523752337
+Lac,0.023539976490534735,0.02841272347980534,0.2613651357070525,0.1855370169189802,0.19337547814706568,0.13727274398564662,70.98766880940724,3.721208922354726,16.345252599534653
+Mac,0.06869857551198218,0.023090890040879376,0.7627625507098601,0.025188246577813975,0.5643429547601081,0.018635956216939066,3.302239544190088,78.38295551382636,36.09724572232013
+NAA,1.4971799765445135,0.0380975159847053,16.623238681006406,0.33738937267752916,12.298988231909282,0.249623313709225,2.029624787033996,403.80477092885326,8.465783526185385
+NAAG,0.156854509617993,0.032059500174443985,1.7415607959104906,0.24821397230932435,1.2885236231692552,0.18364536436067191,14.25238630153923,47.44805606275797,9.295943123347849
+PCh,0.0204145659297048,0.025783126409520945,0.22666359912310433,0.12982807964025697,0.16770095116317538,0.09605553131420419,57.277869116401625,16.44245322160443,8.573820808039038
+PCr,0.4911284647266856,0.037710691056927516,5.45301554929338,0.3319887676851024,4.034507075074811,0.2456275834835055,6.088168366366068,130.13113436109802,8.690063622688927
+PE,0.23786209450331067,0.04596727716274181,2.640990683844532,0.4420273302814214,1.9539822512624507,0.32704150121631664,16.737178702878087,23.355173774812723,17.753562858125175
+Scyllo,0.042763443492395026,0.024738207035934844,0.4748039241324154,0.10172232116022899,0.35129182630585815,0.07526100388016625,21.42406917678722,22.454367538394095,8.70859070149002
+Tau,0.2184231131682197,0.04455661002932295,2.4251590326661288,0.4238463855268342,1.794295502557473,0.31359001743072,17.477055311332446,25.41068934317038,17.38962685369976
+Cr+PCr,0.9999999999999998,0.03249746745099617,11.103032996322048,0.2551385893937011,8.214769382833522,0.18876866106990686,2.2979179605988507,,
diff --git a/Data/sub-002/MRS/voxel_location.png b/Data/sub-002/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..7d499d36829a0f9f617243cc4fa318fce416701a
Binary files /dev/null and b/Data/sub-002/MRS/voxel_location.png differ
diff --git a/Data/sub-002/TMS_EEG/DCM_DefaultCodes_STR7T_HS_003_FHK.mat b/Data/sub-002/TMS_EEG/DCM_DefaultCodes_STR7T_HS_003_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..9711911e7040317403f88f5a61c2a41539dae634
Binary files /dev/null and b/Data/sub-002/TMS_EEG/DCM_DefaultCodes_STR7T_HS_003_FHK.mat differ
diff --git a/Data/sub-003/MRS/all_parameters.csv b/Data/sub-003/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..1f47dc1c078598f4952e0eed6add30b61d0ebcb6
--- /dev/null
+++ b/Data/sub-003/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.00976068569390006,0.0055553177424002296
+Asc,0.034481412222791316,0.012228996978178728
+Asp,0.07644478378443907,0.024648725257126827
+Cr,0.21899957398742673,0.01282297217930163
+GABA,0.058456307341704344,0.011640672217500423
+GPC,0.05579915895088136,0.004781976230320009
+GSH,0.06754046095885163,0.008151866100040442
+Glc,0.08993990084921479,0.0167057158813979
+Gln,0.06407053720028082,0.013352867299785687
+Glu,0.45097812012514604,0.014581237624970567
+Ins,0.2885401483610231,0.006793922308398563
+Lac,0.03372662841267698,0.0092027590421216
+Mac,0.03055171491288014,0.0006387732064337253
+NAA,0.6295874266028975,0.011954880911313298
+NAAG,0.06537321649217702,0.007909854364193307
+PCh,0.00647003569008183,0.003854925331002946
+PCr,0.19943100648176235,0.013951482018752815
+PE,0.11064944195158312,0.012348136110132826
+Scyllo,0.009930816460995428,0.002752559203530551
+Tau,0.05754162336920958,0.011260691595062844
+gamma_0,18.566359079851612,1.1630956375542438
+gamma_1,6.189232790374609,3.7189180694686175
+sigma_0,9.880930276404012,0.8299183797433911
+sigma_1,13.137394150543,5.328367690506499
+eps_0,-2.957074154795708,0.45319731657788204
+eps_1,1.144374532796272,4.309991164816127
+Phi0,0.07768487688468956,0.011579983629068737
+Phi1,0.00028605316342476746,1.7850590168449345e-05
+B_real_0,0.06687254248278009,0.0
+B_imag_0,-0.25392719690030274,5.607473066727768e-17
+B_real_1,-0.09196148398676339,1.401868266681942e-17
+B_imag_1,0.12556497150009663,0.0
+B_real_2,0.3013689427929744,5.607473066727768e-17
+B_imag_2,0.0011219449342614318,0.0
diff --git a/Data/sub-003/MRS/all_samples.csv b/Data/sub-003/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..b9b093497605406c3e9b2e6c397c5cd15cb9c231
--- /dev/null
+++ b/Data/sub-003/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.0017179134401764558,0.01599387930029657,0.003960604842139172,0.00768978770120593,0.013784172836070727,0.002864097891067647,0.0010902240127844474,0.01742791917719603,8.106728741047106e-05,0.008288508237373137,0.00299602712656284,0.016180208732957568,0.0033956177648197033,0.018160931994370754,0.0037953971873631604,0.009639048472096474,0.0036291427036690103,0.0074783403430921415,0.009519329745884302,0.004735325311587582,0.009682736579863275,0.006370564338968911,0.00900160671062394,0.01816993462538078,0.010708948748894949,0.007981972403152024,0.018998223791222492,0.014200113786509622,0.011450276055660144,0.007885309326547185,0.011913488049566264,0.008456554235302411,0.016624889270234824,0.008291978105888961,0.014229630694735523,0.0033540941207126735,0.009962836768613169,0.008110988769597479,0.0008406787280229649,0.011595426513288003,0.005898894933320902,0.022032565643762804,0.018332439803432528,0.0026659395588463225,0.013193853404398569,0.01268138469731665,0.015005613573054433,0.013283258027936062,0.00989778037828179,0.01478475894374328
+Asc,0.046559555266839664,0.04851323245693763,0.038243862594599276,0.03908510990308827,0.017015768193220815,0.018209770386812166,0.0034862380793711785,0.021493977367288426,0.038868880131867,0.02169997112966978,0.03574187944026003,0.01596593115738486,0.02922317515108616,0.027911425169977643,0.033609755443263986,0.0025783541793394787,0.03317367279639814,0.04691554831869325,0.02644044944330961,0.04366150335240183,0.052686434342374765,0.03022642436354251,0.05191372012741645,0.05373867107890103,0.0376680654419662,0.05169469060362806,0.039649923613246915,0.04415940016385782,0.04978020795729915,0.029335642741366887,0.028135250049262227,0.04154372563113982,0.03676274609730753,0.030874838375629692,0.03779273183529298,0.02830620268412192,0.04516694409502202,0.0388440129982288,0.05107302544668852,0.02879872981642937,0.026466703897375342,0.041259074647170706,0.04597535979705744,0.017470317628066008,0.02616748721040705,0.025356372698977513,0.027147451925016396,0.05102549565911365,0.031772507654792365,0.03488039259705754
+Asp,0.1339173990182757,0.06487215323919056,0.06907352748979516,0.12073709148066761,0.11427854341753428,0.10000843350811685,0.0881736388983014,0.07554994922119589,0.07748832058664229,0.09687878703760748,0.07174434752842511,0.06440905127158757,0.10423289362132701,0.0760672530796232,0.08152299894138298,0.06464426420859119,0.07738189094606901,0.02668417916851993,0.07208367863763726,0.11892102321337962,0.06344832680832518,0.01868054223607018,0.05828989740895063,0.08000644254916156,0.09538220466942292,0.05972761020364025,0.07291857343274219,0.05507672031744583,0.08776996433953763,0.06847090560941477,0.0621554190583812,0.0621554190583812,0.08026150367161575,0.04363088787414104,0.03633252710213452,0.08465582248359046,0.06737103483410856,0.07512396977646975,0.10155246724393518,0.08945679626018443,0.10045297680271056,0.06640250713758566,0.09907503843541732,0.08286115187521506,0.10394880533687056,0.050137804217658746,0.03079637715235352,0.11575661557376299,0.05432503087432744,0.05734642236452845
+Cr,0.2204850598950374,0.20844486215975533,0.2135330408712263,0.21353819548749609,0.20205252723112063,0.21143290613361107,0.20835536577186264,0.21856638067350287,0.22328397794631935,0.2348047345096604,0.2283243642402134,0.2403740291689417,0.23280067176866676,0.2138358894574411,0.24104192774437577,0.23789944857260534,0.24965257873880742,0.2370134631352268,0.21698704874300823,0.21906753499245638,0.2203971668604221,0.22143604825234778,0.23900489471138822,0.22940671988502195,0.23406726949191117,0.22900414649971743,0.20557847515233532,0.22361619182724896,0.23214833639609822,0.21576673930117513,0.22728520584753686,0.21980287846351076,0.2161415176862232,0.21659888952423578,0.22398752413438397,0.2112535603425855,0.1910687227693282,0.19293561607961388,0.202994640698587,0.1983956912271184,0.20938289612768382,0.21117466596723136,0.21810554823275874,0.21709702763213024,0.20160979169932175,0.2107836853186196,0.20502535512589312,0.21453196216041312,0.21856696802864906,0.22131655668651048
+GABA,0.06771096109709336,0.07038177276816002,0.06235251741109277,0.051857014152290916,0.05904336474643328,0.05585655910402562,0.07622659919615676,0.0499038558136061,0.04861857298073892,0.07654519048999228,0.06226740282564526,0.06505136461605529,0.045164408071763196,0.05607101283807823,0.04636139634330853,0.05373151545578439,0.03625583509998559,0.0490060143096685,0.07508411501407626,0.0388636788937729,0.05712527413382371,0.0489961047829756,0.054654842742650964,0.04679580223987617,0.06918419764842139,0.05984493830858066,0.049627836099011474,0.02843999076850109,0.07088389020612003,0.03954199198332041,0.06081980404691925,0.0562189621431005,0.057900354894796086,0.058300440708667176,0.0676500510106625,0.08348915419967895,0.07597824737822383,0.07158545150651083,0.06594275681531188,0.06634587681570654,0.060213152327358056,0.06516916534009719,0.058354214931706304,0.05916846370245752,0.05881959337378651,0.06728609071023123,0.03544139490114012,0.05762806151981153,0.059231732000961324,0.06582437861708065
+GPC,0.06108589129142808,0.053053542417427664,0.055115591564054545,0.05571030931047234,0.05274296815047165,0.047327757687447625,0.043943217882181446,0.04587721351885963,0.05263021888292745,0.04479869770856112,0.046884415068274114,0.05169549214515166,0.0536251739839747,0.0582820441109662,0.05885329517211269,0.05778390530844807,0.0638636896929548,0.05686652423393071,0.0540771008943063,0.054192130784284274,0.053063328850756854,0.05227238519842476,0.056753032844294005,0.05610923483740065,0.05555371762317026,0.05515318386970671,0.055075658037054415,0.05598737455768955,0.05384329998005119,0.05850981392054323,0.05629101392608137,0.06004913891436473,0.05890861775367929,0.05706124280104697,0.06033407982286646,0.05593851821982008,0.05846214251866251,0.0610527095941619,0.06462060646975529,0.06350850357630576,0.051794937931230724,0.052144922327555535,0.05149287984677395,0.05579074083949172,0.061314194370890085,0.061941555206199865,0.06145247785325596,0.059118209535316324,0.06080728201780984,0.05714396449147236
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diff --git a/Data/sub-003/MRS/concentration_samples.csv b/Data/sub-003/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..744a7b61932f9f01a4eeab915904fb068c29e568
--- /dev/null
+++ b/Data/sub-003/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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diff --git a/Data/sub-003/MRS/concentrations.csv b/Data/sub-003/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..a81a4a26f0f300e41d377725fd475907e0578c34
--- /dev/null
+++ b/Data/sub-003/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.00976068569390006,0.023326893753691083,0.24312788077162065,0.1762433075895977,0.0055553177424002296,0.022946076129311772,0.1383768181949391,0.10030930247489414
+Asc,0.034481412222791316,0.08240653009664609,0.8588938259715821,0.6226118052651791,0.012228996978178728,0.03470456447130217,0.3046107837613554,0.22081224040277783
+Asp,0.07644478378443907,0.18269406528251597,1.9041549805430833,1.380321215604869,0.024648725257126827,0.06180903054475582,0.6139724731872435,0.44506841050093227
+Cr,0.21899957398742673,0.5233832903461813,5.455037072521062,3.954354283160478,0.01282297217930163,0.03590815949271761,0.3194060488081706,0.23153732236474683
+GABA,0.058456307341704344,0.13970371686542818,1.456081935985821,1.055513237334814,0.011640672217500423,0.03352907661585697,0.28995626493399695,0.2101891853213502
+GPC,0.05579915895088136,0.13335344392924958,1.389895309613839,1.0075345772446025,0.004781976230320009,0.021928586096151947,0.11911373680483879,0.08634550215802324
+GSH,0.06754046095885163,0.16141377832164672,1.6823581512850334,1.219540779082071,0.008151866100040442,0.027014882789601798,0.2030539647921934,0.14719374125493198
+Glc,0.08993990084921479,0.21494581191547846,2.2403034147431864,1.6239950867235027,0.0167057158813979,0.04409350505739141,0.4161208983048589,0.30164587969774076
+Gln,0.06407053720028082,0.15312106760561833,1.5959261898104775,1.1568862833352773,0.013352867299785687,0.03699483120184209,0.3326051499486801,0.2411053457227844
+Glu,0.45097812012514604,1.0777848015301874,11.233365980519071,8.143062693952624,0.014581237624970567,0.0395550251264744,0.36320249559946655,0.2632853498582305
+Ins,0.2885401483610231,0.6895771050898839,7.1872158359105995,5.210010004862742,0.006793922308398563,0.024776705094710277,0.16922908746055276,0.12267410064102588
+Lac,0.03372662841267698,0.08060268533638024,0.8400929964039922,0.6089830911172822,0.0092027590421216,0.028878540578605557,0.22923054520249397,0.16616913436186254
+Mac,0.03055171491288014,0.07301501453030104,0.7610094140567787,0.5516554325835427,0.0006387732064337253,0.018777271149147862,0.01591113379165375,0.011533974787432115
+NAA,0.6295874266028975,1.5046400908292525,15.68232617981767,11.368112237305471,0.011954880911313298,0.034154705665989465,0.29778285583574937,0.21586267806639334
+NAAG,0.06537321649217702,0.15623431829211332,1.6283744896017238,1.180408043417742,0.007909854364193307,0.026600797468372444,0.1970257202299136,0.14282386908213424
+PCh,0.00647003569008183,0.015462626280390251,0.16116143016770026,0.11682585896146597,0.003854925331002946,0.02085980501225029,0.09602192465282561,0.06960625637924986
+PCr,0.19943100648176235,0.4766167096538188,4.967605707902705,3.601015473762696,0.013951482018752815,0.038235734844411895,0.34751598025152786,0.2519142008945596
+PE,0.11064944195158312,0.26443918565299684,2.756155169207348,1.9979358258280449,0.012348136110132826,0.03494468119107712,0.3075784077149751,0.22296346986937832
+Scyllo,0.009930816460995428,0.023733486328508628,0.24736564993611665,0.1793152648327637,0.002752559203530551,0.019837574751899255,0.0685632041477408,0.049701440409006176
+Tau,0.05754162336920958,0.1375177294754312,1.4332981702973715,1.0389972943194152,0.011260691595062844,0.03277951706044655,0.2804913680645828,0.20332808520825002
+Cr+PCr,0.4184305804691891,1.0,10.422642780423768,7.555369756923175,0.007830975271228401,0.02646716552781928,0.1950609293011646,0.14139959289091436
diff --git a/Data/sub-003/MRS/fit_summary.png b/Data/sub-003/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..e12b88deac51e87f015a47d6a267d8a62d4575ae
Binary files /dev/null and b/Data/sub-003/MRS/fit_summary.png differ
diff --git a/Data/sub-003/MRS/options.txt b/Data/sub-003/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..331acba6f39ddd309115b5561ab9f3f18cd702d0
--- /dev/null
+++ b/Data/sub-003/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.04303205750648602, "GM": 0.4702258333509789, "WM": 0.4867421091425351}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_004/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-003/MRS/qc.csv b/Data/sub-003/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..8ccdbd379c098a8aa7a0c7752705ff423518a06d
--- /dev/null
+++ b/Data/sub-003/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,3.508215816341954,18.629833092207313
+Asc,10.13319318768422,15.49401635695054
+Asp,7.26145201281179,23.06584296928762
+Cr,134.25161038604574,10.122210056654108
+GABA,11.786463250080397,21.467113918083058
+GPC,102.95286664670455,10.104279610200965
+GSH,35.018196012927994,11.127454101840046
+Glc,16.860319643918,41.45233176521267
+Gln,11.960255548341102,24.573185810650887
+Glu,100.28103251739076,21.52517237380944
+Ins,85.29062992619662,42.233195833267565
+Lac,12.590139335571239,17.86502610320491
+Mac,89.73348659319832,36.153039586097385
+NAA,376.350101796133,10.441311167618204
+NAAG,45.33327742267748,10.846507650614692
+PCh,11.611303814528304,10.595134977669206
+PCr,121.54451715667612,10.202977371717315
+PE,26.50897290671994,18.494390064973388
+Scyllo,11.777410030348113,10.704823303971216
+Tau,15.998634965366252,18.494357517067193
diff --git a/Data/sub-003/MRS/summary.csv b/Data/sub-003/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..e936ca33ed75b954c67dc1475912b2a72c024e1d
--- /dev/null
+++ b/Data/sub-003/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.023326893753691083,0.022946076129311772,0.24312788077162065,0.1383768181949391,0.1762433075895977,0.10030930247489414,56.91524055397076,3.508215816341954,18.629833092207313
+Asc,0.08240653009664609,0.03470456447130217,0.8588938259715821,0.3046107837613554,0.6226118052651791,0.22081224040277783,35.465476005346666,10.13319318768422,15.49401635695054
+Asp,0.18269406528251597,0.06180903054475582,1.9041549805430833,0.6139724731872435,1.380321215604869,0.44506841050093227,32.24382886166821,7.26145201281179,23.06584296928762
+Cr,0.5233832903461813,0.03590815949271761,5.455037072521062,0.3194060488081706,3.954354283160478,0.23153732236474683,5.855249828037485,134.25161038604574,10.122210056654108
+GABA,0.13970371686542818,0.03352907661585697,1.456081935985821,0.28995626493399695,1.055513237334814,0.2101891853213502,19.91345801139178,11.786463250080397,21.467113918083058
+GPC,0.13335344392924958,0.021928586096151947,1.389895309613839,0.11911373680483879,1.0075345772446025,0.08634550215802324,8.56997904669041,102.95286664670455,10.104279610200965
+GSH,0.16141377832164672,0.027014882789601798,1.6823581512850334,0.2030539647921934,1.219540779082071,0.14719374125493198,12.069603885302007,35.018196012927994,11.127454101840046
+Glc,0.21494581191547846,0.04409350505739141,2.2403034147431864,0.4161208983048589,1.6239950867235027,0.30164587969774076,18.57430987099398,16.860319643918,41.45233176521267
+Gln,0.15312106760561833,0.03699483120184209,1.5959261898104775,0.3326051499486801,1.1568862833352773,0.2411053457227844,20.84088550412086,11.960255548341102,24.573185810650887
+Glu,1.0777848015301874,0.0395550251264744,11.233365980519071,0.36320249559946655,8.143062693952624,0.2632853498582305,3.233247240669744,100.28103251739076,21.52517237380944
+Ins,0.6895771050898839,0.024776705094710277,7.1872158359105995,0.16922908746055276,5.210010004862742,0.12267410064102588,2.3545847421891417,85.29062992619662,42.233195833267565
+Lac,0.08060268533638024,0.028878540578605557,0.8400929964039922,0.22923054520249397,0.6089830911172822,0.16616913436186254,27.286329749648253,12.590139335571239,17.86502610320491
+Mac,0.07301501453030104,0.018777271149147862,0.7610094140567787,0.01591113379165375,0.5516554325835427,0.011533974787432115,2.0907932934541367,89.73348659319832,36.153039586097385
+NAA,1.5046400908292525,0.034154705665989465,15.68232617981767,0.29778285583574937,11.368112237305471,0.21586267806639334,1.8988436563638134,376.350101796133,10.441311167618204
+NAAG,0.15623431829211332,0.026600797468372444,1.6283744896017238,0.1970257202299136,1.180408043417742,0.14282386908213424,12.099533706039768,45.33327742267748,10.846507650614692
+PCh,0.015462626280390251,0.02085980501225029,0.16116143016770026,0.09602192465282561,0.11682585896146597,0.06960625637924986,59.58120659075051,11.611303814528304,10.595134977669206
+PCr,0.4766167096538188,0.038235734844411895,4.967605707902705,0.34751598025152786,3.601015473762696,0.2519142008945596,6.995643388095048,121.54451715667612,10.202977371717315
+PE,0.26443918565299684,0.03494468119107712,2.756155169207348,0.3075784077149751,1.9979358258280449,0.22296346986937832,11.159691266708784,26.50897290671994,18.494390064973388
+Scyllo,0.023733486328508628,0.019837574751899255,0.24736564993611665,0.0685632041477408,0.1793152648327637,0.049701440409006176,27.71735047507508,11.777410030348113,10.704823303971216
+Tau,0.1375177294754312,0.03277951706044655,1.4332981702973715,0.2804913680645828,1.0389972943194152,0.20332808520825002,19.56964530320919,15.998634965366252,18.494357517067193
+Cr+PCr,1.0,0.02646716552781928,10.422642780423768,0.1950609293011646,7.555369756923175,0.14139959289091436,1.871511222350784,,
diff --git a/Data/sub-003/MRS/voxel_location.png b/Data/sub-003/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..86cf759a8d54300c547ad8c46754a256b6ca574f
Binary files /dev/null and b/Data/sub-003/MRS/voxel_location.png differ
diff --git a/Data/sub-003/TMS_EEG/DCM_DefaultCodes_STR7T_HS_004_FHK.mat b/Data/sub-003/TMS_EEG/DCM_DefaultCodes_STR7T_HS_004_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..0a50c189b27acfc111b91b679889a0a8b87a6e26
Binary files /dev/null and b/Data/sub-003/TMS_EEG/DCM_DefaultCodes_STR7T_HS_004_FHK.mat differ
diff --git a/Data/sub-004/MRS/all_parameters.csv b/Data/sub-004/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..3cddab179efac0b3a198ba2569233072915d5805
--- /dev/null
+++ b/Data/sub-004/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.004618863303638881,0.0037222567658482778
+Asc,0.0534688042315967,0.020848972307100613
+Asp,0.15601884347675105,0.031195205634388202
+Cr,0.28319291385776685,0.018013021685157605
+GABA,0.09705743341145975,0.01916314850059785
+GPC,0.06547661717713461,0.011070228958150295
+GSH,0.08634278399529151,0.010886089377749075
+Glc,0.11118350172093262,0.02191845771574447
+Gln,0.10310930103898068,0.026807561659818138
+Glu,0.4946160580262162,0.02538383620073176
+Ins,0.4161541928999091,0.01309523599984825
+Lac,0.003239452658758779,0.003515147661871871
+Mac,0.026945833212412933,0.0008703706650589666
+NAA,0.7263346283912208,0.01392402032930184
+NAAG,0.10308216230372402,0.012005099892076265
+PCh,0.028324019237685447,0.011154051915633886
+PCr,0.2534922155153886,0.02113591694404285
+PE,0.11577796312640856,0.01975677607664918
+Scyllo,0.016624511639861908,0.006133372250028753
+Tau,0.09218126217776028,0.018116952479725265
+gamma_0,29.939071417662575,1.3082202568016017
+gamma_1,8.293551981398517,5.014853452156921
+sigma_0,5.1956942206002505,2.045992818680973
+sigma_1,13.948368744339554,6.717802420934299
+eps_0,3.368914226698875,0.6618697990924399
+eps_1,5.097679603421766,5.369529398272485
+Phi0,0.06178206419873499,0.01395289027647882
+Phi1,0.000400240937062252,2.2672642085953646e-05
+B_real_0,0.04156820759464561,7.00934133340971e-18
+B_imag_0,-0.3864758660325089,0.0
+B_real_1,-0.5022535686731566,1.1214946133455537e-16
+B_imag_1,0.026185588127209752,0.0
+B_real_2,-0.15279557663193313,0.0
+B_imag_2,0.07248431946073852,0.0
diff --git a/Data/sub-004/MRS/all_samples.csv b/Data/sub-004/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..aa021aa5d1b700c7b805940b0b2f24c328552c0d
--- /dev/null
+++ b/Data/sub-004/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-004/MRS/concentration_samples.csv b/Data/sub-004/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..4da739889b5c4ccd58241d1e4926dd05e4554a49
--- /dev/null
+++ b/Data/sub-004/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+PCh,molarity,0.3002576499454425,0.4587206105049048,0.64563711484046,0.4896250278393126,0.44078498335906824,0.3721317051590376,0.45211125656534645,0.5359306339684726,0.46575340390660575,0.6824574328009382,0.6569647580800976,0.7023809278067167,0.6647199149314871,0.6276061072177689,0.5514667786027647,0.6084627544841942,0.7738421152175254,0.9815409280974386,1.0566545344414686,0.790088149061721,0.7107131413347988,0.6047798911407425,0.49758231795194335,0.7017080104613493,0.7052268107256489,0.45245479050686477,0.5367975889754107,0.6308927428479312,0.4668135582232854,0.40148147856894034,0.3866100936209542,0.33787972181090775,0.3092168028647962,0.31306610119556655,0.45891422725270725,0.39730594515407935,0.3885389421529584,0.37440739130547723,0.27352898020384103,0.41089673096254486,0.4390713090543254,0.43100310125499103,0.4681989129655321,0.3294935437266559,0.2936071562248394,0.28954930905240533,0.09404591616787474,0.24336523680762412,0.35445098292000726,0.11273210324248496
+PCr,molarity,4.466762679658183,4.440763097542608,4.348020779416098,4.241706326058921,4.26817985696503,4.490096750562278,4.3803226928519905,4.151306695617189,4.18258547752651,4.5132288645796095,4.5451338732147955,4.847942354746659,4.808517971691131,4.593709002730793,4.704919210906354,4.8084865999046125,5.142121210058183,4.713469455629367,4.656151587271777,3.963563514792122,3.8639113471774698,3.469951286762461,3.4806202520275864,3.66579530653623,4.20981922724914,4.22608151305824,4.3903919559240006,4.0003404718593565,4.0494028452667665,4.143653838838578,4.396737217672498,4.11237796944638,4.160112886645602,4.04943048624834,4.507675382768192,4.460697813700735,4.388314929174769,4.703140209089056,4.751532389428735,4.75764935374523,4.419652239250422,4.355296891862753,4.36512488010404,4.763714414651415,5.099729301630182,4.615144696351633,4.687468239657156,4.82645323990403,4.950739420594687,4.6649487454289
+PE,molarity,1.8829886021697722,1.76844047946098,1.9628898890637998,1.8442428529307124,2.4313925598522212,2.0210044225213166,2.368693799706593,1.6100896175017014,1.6385855140925984,2.1436422307973366,2.0951919428756667,1.9681863262716757,2.3369772787703793,1.7758463938170075,2.067447477067521,1.8478494450048633,2.075721654546908,2.2078121414110377,1.3638512704631713,2.2765691450234176,2.186639289357041,2.964648531737802,2.6073570055794026,2.0281112261355387,2.235140576706864,2.681666975948404,2.398948821778038,1.9336754581864652,2.361619129271622,1.9988024412698042,1.3247117187829838,1.8636170132461236,2.0331769038313374,2.381808780363063,2.0288584529954345,2.253160511935933,2.224553385007544,2.4404225364418646,2.4073633757944393,1.7307815546100263,1.589238393985684,1.7324928648570812,1.5494350629080553,1.7695037002073506,1.9772404758327022,1.7105099593018125,1.534847178911101,1.671394877253688,1.6300456506817236,1.9105158966947737
+Scyllo,molarity,0.2559660891282951,0.3527182851447135,0.33747295747999984,0.2888505075588714,0.4091152275349403,0.07242730525733668,0.2630281021443369,0.17639049674083987,0.3236901488950406,0.5147499627220191,0.332294695838425,0.2185082224268136,0.38070969849184844,0.2130332817616203,0.19085519007318386,0.2473079029187478,0.04310379258315359,0.5026002222456784,0.14956024139959523,0.26357328309974687,0.34908453926435734,0.38780123166322233,0.27372443198677776,0.33718062379900865,0.16267253753884334,0.40880429922579153,0.3698175209148271,0.39529903338940914,0.3309392862038415,0.22334627175376762,0.42062003931718434,0.10490859760524882,0.4414247937836548,0.11527554690411011,0.24690733466025838,0.2486198392534446,0.2713360329147014,0.2749212187277861,0.3853176462478394,0.3633704396275558,0.3493167712884613,0.27666004603066696,0.2381448298107367,0.23396493771840052,0.07722271045715129,0.26299609258111256,0.38410633732229665,0.2996211280952334,0.3602478953506673,0.3510750234130197
+Tau,molarity,1.46094085075613,1.8388317401346113,1.7313276815087675,1.9150662317839735,1.3907675371915187,2.3154632564252533,1.8412854418981217,1.0918640552943406,1.4929466109577143,1.2651805687031599,1.8112897274180226,1.664506858144586,1.546218176775564,1.6226610252011753,1.5932459675975406,1.7049020412969542,2.0541186013312096,1.7915474688638153,1.8465045775617022,1.4708611198476782,1.3517812051722244,0.6952106558102177,1.0471980048680263,1.4067348125839285,1.4994176609114573,1.817482491472518,1.4687311904257094,1.3684281221331323,1.215446148513829,1.692740999832065,1.5999315158824063,1.8961536777697607,1.754601220915654,1.8645614250315206,1.3855746203930726,1.727446376638163,1.5969111701875807,1.6346487789678277,1.5004593662525345,1.2205281900492864,1.2738999372869855,1.82798359285474,1.630852498270779,2.1222426191744903,1.7378499418197757,1.6123426101172142,1.6182826189575885,2.3665569260119685,1.0535754544109448,1.8568404638558609
+Cr+PCr,molarity,9.112231912871774,9.470031953360255,9.208580400998017,9.12385743226676,9.260766669610538,9.399934429349413,9.359830438895667,9.18958862460604,8.869406551181894,9.358252936184174,9.423917422086122,9.46484040127698,9.36155577887282,9.497447560674384,9.423078009933059,9.583379958121458,9.795645180617017,9.659374888143523,9.55397981545071,9.36533333671891,9.292795035317544,9.49193752598347,9.05633210263405,9.45445152822344,9.343108047507437,8.644344009491945,9.493543395709906,9.127166983751478,8.9833606057277,9.322638010931819,9.468147333755667,9.128354287241978,9.253979862358085,9.276206365394417,9.575761520400654,9.05982407034247,9.22878087529658,9.482278126969447,9.195723845364915,9.296498885407322,9.260884176517457,9.139635882651381,9.39863565041295,9.507538903572591,9.705705528028098,9.389294607837524,9.401905554175572,9.851627954790338,9.689421959139061,9.47549499796547
diff --git a/Data/sub-004/MRS/concentrations.csv b/Data/sub-004/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..13cabd1978ac6c0b1d23b67a2035c45577070cd0
--- /dev/null
+++ b/Data/sub-004/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.004618863303638881,0.008606281506315785,0.1104655318424586,0.0804646718700742,0.0037222567658482778,0.025294222552925332,0.08902213515816303,0.06484499531392973
+Asc,0.0534688042315967,0.09962788477863715,1.278769149061056,0.9314737209025304,0.020848972307100613,0.04583488632650168,0.498627619582964,0.36320748314795237
+Asp,0.15601884347675105,0.29070834077139424,3.7313735846061045,2.7179858377741577,0.031195205634388202,0.06301026121552429,0.7460699212775347,0.5434479914815824
+Cr,0.28319291385776685,0.5276705061467499,6.772890598140896,4.933470291606829,0.018013021685157605,0.04145119862602429,0.43080253511140615,0.3138027224453356
+GABA,0.09705743341145975,0.1808461388241224,2.321242326572901,1.6908260796226573,0.01916314850059785,0.04320473132267703,0.45830916650571185,0.33383894580368073
+GPC,0.06547661717713461,0.12200192178533223,1.5659500756428382,1.1406604114414627,0.011070228958150295,0.03189309608305212,0.2647575061414867,0.19285315067505615
+GSH,0.08634278399529151,0.16088164040643216,2.0649889221194635,1.504167438134906,0.010886089377749075,0.03167227172330092,0.2603535921598275,0.1896452768019315
+Glc,0.11118350172093262,0.2071670997308873,2.6590838139837656,1.9369146465738594,0.02191845771574447,0.04753563103398948,0.5242056171761201,0.3818388620866975
+Gln,0.10310930103898068,0.1921225228644059,2.4659798371174486,1.7962549505021987,0.026807561659818138,0.0555582847113582,0.6411342708103748,0.46701136422345496
+Glu,0.4946160580262162,0.9216131227707473,11.82932299915454,8.616647905426017,0.02538383620073176,0.053185928491255786,0.6070842070399832,0.4422088112212471
+Ins,0.4161541928999091,0.7754159191740125,9.952815492708012,7.249773023736313,0.01309523599984825,0.03445381472538545,0.3131879240041794,0.22813055908340746
+Lac,0.003239452658758779,0.006036039535029483,0.07747530881598762,0.056434122010129095,0.003515147661871871,0.025191141840251747,0.08406887808685189,0.06123697208456992
+Mac,0.026945833212412933,0.050207899823655415,0.6444411971236157,0.4694201766037089,0.0008703706650589666,0.02437877407329839,0.020815935024547365,0.015162624517190844
+NAA,0.7263346283912208,1.3533720027599325,17.371144315446443,12.653389741005686,0.01392402032930184,0.03556418065087731,0.33300927304987615,0.24256871296165794
+NAAG,0.10308216230372402,0.19207195553214468,2.465330782441746,1.7957821698018746,0.012005099892076265,0.033046420224932184,0.28711604072700436,0.20913942675513827
+PCh,0.028324019237685447,0.052775859973552296,0.6774021319362202,0.4934293925101653,0.011154051915633886,0.03199433236007483,0.2667622304579084,0.19431342051326128
+PCr,0.2534922155153886,0.4723294938532502,6.062563571164703,4.416057935075576,0.02113591694404285,0.04628891174304224,0.5054902370378241,0.3682063117641282
+PE,0.11577796312640856,0.2157279134259532,2.768965745818748,2.0169542158592475,0.01975677607664918,0.0441232615543206,0.47250646605627394,0.34418046166589866
+Scyllo,0.016624511639861908,0.03097628521826052,0.39759468925432134,0.2896136530058917,0.006133372250028753,0.026875629458836398,0.1466867891616163,0.10684875327805703
+Tau,0.09218126217776028,0.1717604180414452,2.2046229738717407,1.6058788767052619,0.018116952479725265,0.04160815690126819,0.43328816192951985,0.3156132885375372
+Cr+PCr,0.5366851293731555,1.0000000000000002,12.835454169305601,9.349528226682407,0.013054743518060675,0.03440042275459985,0.31221949882200056,0.22742514434258254
diff --git a/Data/sub-004/MRS/fit_summary.png b/Data/sub-004/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..768733b9646382858e6ce8845915e413d7aacb5b
Binary files /dev/null and b/Data/sub-004/MRS/fit_summary.png differ
diff --git a/Data/sub-004/MRS/options.txt b/Data/sub-004/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..959f3fd230a6b173f47fffa1bcf295789969037f
--- /dev/null
+++ b/Data/sub-004/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.13678490566037738, "GM": 0.266485534591195, "WM": 0.5967295597484277}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_005/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-004/MRS/qc.csv b/Data/sub-004/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..4c58c3f80fbe23456d213af1217f420a86495f39
--- /dev/null
+++ b/Data/sub-004/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,0.7964628501490516,20.35348493565759
+Asc,7.3237151192259615,17.062225734121245
+Asp,7.1956899563803995,24.40696572385475
+Cr,76.39310261653634,11.424588233927464
+GABA,9.274736663061942,23.544627706908532
+GPC,52.25539253646868,11.887292976061724
+GSH,20.091220480229406,12.9975106058198
+Glc,10.458551816227319,43.483508764145334
+Gln,9.39790456994752,26.246771547034363
+Glu,52.388964243032895,23.954477095708384
+Ins,59.50435673100131,44.197833694076245
+Lac,0.5661047640700767,19.54159842963198
+Mac,42.789154751933495,35.285311280605995
+NAA,192.67421739494176,11.701078834036672
+NAAG,31.32069379463844,13.189602921072094
+PCh,22.874546036241956,11.587680140485952
+PCr,66.20701283144396,12.259763363746309
+PE,13.126331788663785,19.77535484998636
+Scyllo,8.922158112174857,11.829840720982652
+Tau,12.185031057433857,20.4544747232284
diff --git a/Data/sub-004/MRS/summary.csv b/Data/sub-004/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..45f7cc619c2052cf989022d0e0ca7bde4422b456
--- /dev/null
+++ b/Data/sub-004/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.008606281506315785,0.025294222552925332,0.1104655318424586,0.08902213515816303,0.0804646718700742,0.06484499531392973,80.58815602782119,0.7964628501490516,20.35348493565759
+Asc,0.09962788477863715,0.04583488632650168,1.278769149061056,0.498627619582964,0.9314737209025304,0.36320748314795237,38.99277832508582,7.3237151192259615,17.062225734121245
+Asp,0.29070834077139424,0.06301026121552429,3.7313735846061045,0.7460699212775347,2.7179858377741577,0.5434479914815824,19.994511521319357,7.1956899563803995,24.40696572385475
+Cr,0.5276705061467499,0.04145119862602429,6.772890598140896,0.43080253511140615,4.933470291606829,0.3138027224453356,6.360689411248692,76.39310261653634,11.424588233927464
+GABA,0.1808461388241224,0.04320473132267703,2.321242326572901,0.45830916650571185,1.6908260796226573,0.33383894580368073,19.744132754220576,9.274736663061942,23.544627706908532
+GPC,0.12200192178533223,0.03189309608305212,1.5659500756428382,0.2647575061414867,1.1406604114414627,0.19285315067505615,16.907148590468385,52.25539253646868,11.887292976061724
+GSH,0.16088164040643216,0.03167227172330092,2.0649889221194635,0.2603535921598275,1.504167438134906,0.1896452768019315,12.607989775199652,20.091220480229406,12.9975106058198
+Glc,0.2071670997308873,0.04753563103398948,2.6590838139837656,0.5242056171761201,1.9369146465738594,0.3818388620866975,19.713768118905957,10.458551816227319,43.483508764145334
+Gln,0.1921225228644059,0.0555582847113582,2.4659798371174486,0.6411342708103748,1.7962549505021987,0.46701136422345496,25.999169221100125,9.39790456994752,26.246771547034363
+Glu,0.9216131227707473,0.053185928491255786,11.82932299915454,0.6070842070399832,8.616647905426017,0.4422088112212471,5.132028325571738,52.388964243032895,23.954477095708384
+Ins,0.7754159191740125,0.03445381472538545,9.952815492708012,0.3131879240041794,7.249773023736313,0.22813055908340746,3.1467269159529616,59.50435673100131,44.197833694076245
+Lac,0.006036039535029483,0.025191141840251747,0.07747530881598762,0.08406887808685189,0.056434122010129095,0.06123697208456992,108.51054274146195,0.5661047640700767,19.54159842963198
+Mac,0.050207899823655415,0.02437877407329839,0.6444411971236157,0.020815935024547365,0.4694201766037089,0.015162624517190844,3.2300751592940893,42.789154751933495,35.285311280605995
+NAA,1.3533720027599325,0.03556418065087731,17.371144315446443,0.33300927304987615,12.653389741005686,0.24256871296165794,1.9170255396114801,192.67421739494176,11.701078834036672
+NAAG,0.19207195553214468,0.033046420224932184,2.465330782441746,0.28711604072700436,1.7957821698018746,0.20913942675513827,11.646146747197754,31.32069379463844,13.189602921072094
+PCh,0.052775859973552296,0.03199433236007483,0.6774021319362202,0.2667622304579084,0.4934293925101653,0.19431342051326128,39.3801876140279,22.874546036241956,11.587680140485952
+PCr,0.4723294938532502,0.04628891174304224,6.062563571164703,0.5054902370378241,4.416057935075576,0.3682063117641282,8.337895860458785,66.20701283144396,12.259763363746309
+PE,0.2157279134259532,0.0441232615543206,2.768965745818748,0.47250646605627394,2.0169542158592475,0.34418046166589866,17.064366605826674,13.126331788663785,19.77535484998636
+Scyllo,0.03097628521826052,0.026875629458836398,0.39759468925432134,0.1466867891616163,0.2896136530058917,0.10684875327805703,36.893548411505094,8.922158112174857,11.829840720982652
+Tau,0.1717604180414452,0.04160815690126819,2.2046229738717407,0.43328816192951985,1.6058788767052619,0.3156132885375372,19.653617288065487,12.185031057433857,20.4544747232284
+Cr+PCr,1.0000000000000002,0.03440042275459985,12.835454169305601,0.31221949882200056,9.349528226682407,0.22742514434258254,2.4324772205461564,,
diff --git a/Data/sub-004/MRS/voxel_location.png b/Data/sub-004/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..6723fbeb6ef559b4e08347288e140d38bf16540e
Binary files /dev/null and b/Data/sub-004/MRS/voxel_location.png differ
diff --git a/Data/sub-004/TMS_EEG/DCM_DefaultCodes_STR7T_HS_005_FHK.mat b/Data/sub-004/TMS_EEG/DCM_DefaultCodes_STR7T_HS_005_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..9449659ca2e3cecb6ad653c7d5fbe12f9f41c36b
Binary files /dev/null and b/Data/sub-004/TMS_EEG/DCM_DefaultCodes_STR7T_HS_005_FHK.mat differ
diff --git a/Data/sub-005/MRS/all_parameters.csv b/Data/sub-005/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..96f2d1683bc209a09dfe9f74ca5223c8d8d8706c
--- /dev/null
+++ b/Data/sub-005/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.04139192381102556,0.009661572074995767
+Asc,0.03695350723115995,0.014661670099029894
+Asp,0.06416804292473298,0.02162420898825048
+Cr,0.2229290561673066,0.01357414248931729
+GABA,0.05025729926474188,0.014284309527474203
+GPC,0.07469911051235062,0.004393381651178706
+GSH,0.06861669616329763,0.008385312383754336
+Glc,0.07303282573135256,0.016418794957875227
+Gln,0.04677607914442284,0.016272345199826645
+Glu,0.41091543249344303,0.014675732051883435
+Ins,0.3126591309245602,0.010716564583507804
+Lac,0.041611841320509255,0.009378890835176658
+Mac,0.027426069776383177,0.0005902888657413123
+NAA,0.6203669587379067,0.009499281844355488
+NAAG,0.09768464449536668,0.007170011604595953
+PCh,0.004477933455525159,0.0034795266397417723
+PCr,0.22941643298255576,0.012255344972249517
+PE,0.07936623238202856,0.01791669530655046
+Scyllo,0.008634883087727864,0.0037368865634965945
+Tau,0.06469085128489672,0.012299719221044916
+gamma_0,21.22729626635268,0.9261745144308022
+gamma_1,3.899041009769456,2.9710893866052306
+sigma_0,7.913528876074015,0.8421183792181637
+sigma_1,9.493502017847224,5.499890046335926
+eps_0,-0.5646522264474001,0.3847938780634869
+eps_1,-0.07028988439657347,4.826457977447859
+Phi0,0.0006401349939650235,0.011341158668759108
+Phi1,0.00035571598642902,1.5280168246380067e-05
+B_real_0,0.2623042224756872,0.0
+B_imag_0,-0.21341658134512137,5.607473066727768e-17
+B_real_1,-0.09890354793973166,0.0
+B_imag_1,-0.003471247806565505,4.380838333381069e-19
+B_real_2,0.1372841414317492,2.803736533363884e-17
+B_imag_2,0.046348611270348845,7.00934133340971e-18
diff --git a/Data/sub-005/MRS/all_samples.csv b/Data/sub-005/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..1139af63ba61ffb94bd5b4abb1e6edc8adec6436
--- /dev/null
+++ b/Data/sub-005/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.06476262452881386,0.041441646448566044,0.035734747304362005,0.05537090298898801,0.04757236520598591,0.03210357740115838,0.04594125346405727,0.04331166654232505,0.03205999248313049,0.0338430766335725,0.05341864297017339,0.045488588057779764,0.05121312149690155,0.05177309228808757,0.044425513278977966,0.04851447732300257,0.044263591133519756,0.03863425548105133,0.020789859143997665,0.04642759386363607,0.03728560996333639,0.02939622861625129,0.036644002620710096,0.04390766005450159,0.03551402003895576,0.026907610237025457,0.03807456334341528,0.05396757096506168,0.04558173513673744,0.02942077281430426,0.03674720713838665,0.03762093981755427,0.028431937734276838,0.026689823895304773,0.0514446373310921,0.04817344669794624,0.038400294162847876,0.029448687002321644,0.047739452018468576,0.04006537116625795,0.05474539969887956,0.03657707007548358,0.03530120297296347,0.05120423476323975,0.049930937374058584,0.022578276300207225,0.031860733078377564,0.04588575206486358,0.048716978656381506,0.0542434467739801
+Asc,0.03441424102120652,0.04342675266888127,0.04715964530713303,0.04805876504333335,0.056711906180731436,0.03565989472729042,0.030657910662992595,0.05321279844053843,0.05091924028564597,0.04072395245405327,0.02817745531504492,0.020733104100762366,0.04377632629381447,0.05383657086509724,0.040427144788126694,0.055371842697604944,0.03874087404474539,0.050717155302487056,0.049293418072920314,0.0370170570613265,0.025713451367540302,0.04141914957592942,0.017697894672549112,0.017874927074676198,0.01746878331961799,0.019549773271483318,0.036375833522651405,0.03509548784280652,0.04237538295820824,0.0274586149300121,0.04931672587038344,0.046597350205162924,0.06680112947527345,0.07374510209882261,0.05190451236903758,0.043107171681684785,0.04629953939874212,0.034161592894439125,0.04798587846135616,0.020159852693581944,0.039139648466053056,0.011449739872498577,0.03363030373630271,0.01721498539373298,0.03899091583052429,0.010615748635008278,0.01827767438334227,0.022908763668322698,0.01858464175917412,0.01671873079534316
+Asp,0.040754678633076045,0.0599009507211133,0.0822419650324976,0.06637629340261586,0.04383028711694342,0.05390157626221151,0.05182107749712155,0.037785838918469365,0.06727129966560574,0.07810549234611203,0.06976884309511928,0.037557608640134243,0.07234320705817326,0.044576481737114995,0.06516968022590608,0.07313008869324064,0.03611546891105798,0.03679550235458124,0.05096077922441765,0.03949751867886005,0.01572605400437093,0.069947989407705,0.07556764014122686,0.08609231873083037,0.09009066055077816,0.03178012062096346,0.055268352061421555,0.06070971378866853,0.0804655492837817,0.06261148310961989,0.07787025021969601,0.08267166526514529,0.08460578032893099,0.09081017463026812,0.04977373140250796,0.1128794903373775,0.10544854868497765,0.07817444771182065,0.08434171452967408,0.05269843653921199,0.08458468100694384,0.08907104712063822,0.06444805140001496,0.049915905766971774,0.038277263415909785,0.03685092390593065,0.10298437067479968,0.05412887347212623,0.045959480431052996,0.0867427894789126
+Cr,0.22755225044856645,0.2064672648051209,0.20088407508067158,0.22268625579169796,0.23542646860750233,0.2298471257500587,0.23601887152459816,0.24656512094178973,0.23517259075794467,0.2270873437958346,0.2341305692528562,0.22099529294981954,0.21493612857188044,0.224276789583639,0.22324467658030328,0.2237763358409998,0.23414896045874573,0.22084143716287427,0.2213606278420947,0.24185209724520593,0.2521841616711656,0.23533899966914112,0.23507851495306997,0.21982273891771778,0.2334936168951239,0.22552870234287936,0.22637430110049717,0.24908863316262786,0.23526247256310878,0.23734374364806668,0.22980463510755045,0.21978058382770135,0.2122205018088766,0.20162373981954398,0.20998804260846715,0.2098860814101341,0.21092791655558185,0.21602122631297482,0.19886933560724376,0.2083294721040042,0.20741426114120448,0.2089774366024585,0.21529669511417532,0.22715526652845414,0.23305073701246076,0.23672075197025044,0.20097120044011121,0.20273915676724405,0.20149985179256388,0.21838974791872784
+GABA,0.024324275001336496,0.05360894188229088,0.05848550018966859,0.07601142285100507,0.03764313737934098,0.03569251525813825,0.05062029828444453,0.06868005295121704,0.04250745595093294,0.02676540480630183,0.05759337050585987,0.04583765993304055,0.0671614691177438,0.04622342374645459,0.052427606209694534,0.05952801831826811,0.048462064123646786,0.03713222465691327,0.03328786706853148,0.02121882706392061,0.03457725255020849,0.058964661508703275,0.03615592267300152,0.05999081201867845,0.05222419301955589,0.03498569896284875,0.034861403025726115,0.05404752665084861,0.037009103254870716,0.06635720265908736,0.06612946295880788,0.03054548654927961,0.05386616475537175,0.06029677817793324,0.05334149881568913,0.05422432233973327,0.07001877955522999,0.09232444273691262,0.05252952383168215,0.044937390565988035,0.04891673263397372,0.05269469892852523,0.054411744173296125,0.059851942426108196,0.07463391241674472,0.050847457399728464,0.04711138184686301,0.0398051385606843,0.05487635421588685,0.03911643872637594
+GPC,0.07669015780648888,0.07246035364148805,0.07576058968934585,0.07797739753849259,0.0814859674848328,0.0749132889545873,0.07553702058893808,0.08000068399192443,0.07943570843504796,0.07482498263635964,0.07133649840656392,0.07920180639490643,0.08497971719223141,0.08199939765620318,0.07571693006774081,0.08150950160819181,0.07569925828725892,0.07634335677490911,0.07759397662615262,0.07375328196994868,0.07488653884549429,0.07736824208013363,0.07626113225303371,0.06689759782279947,0.0707285187051212,0.07837533970205533,0.06861513855510219,0.06618367885237514,0.06607266803188003,0.07322148620747462,0.07219594515545137,0.07189470691586089,0.07181602495454179,0.07267924205421282,0.07782792843793096,0.07062912403709862,0.07556652459051734,0.07034439958451566,0.08028949791452898,0.07741750698870892,0.07916893481211866,0.06987683703681752,0.07654104943490497,0.07176797421365118,0.0769147242154081,0.06874934842131859,0.06680412446545565,0.07226954451127683,0.07082325818298968,0.07554861288314046
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diff --git a/Data/sub-005/MRS/concentration_samples.csv b/Data/sub-005/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..6481efa1917b20a099d3fd06ca228b407bd7145c
--- /dev/null
+++ b/Data/sub-005/MRS/concentration_samples.csv
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+Cr+PCr,molarity,8.345586981964555,8.109497200189974,7.995731074976077,8.094748119377428,8.180075158258349,8.215881541290956,8.162261001185408,8.163020928450091,8.021642127524645,7.980114790564333,8.04439213753481,8.014628236582322,7.908426436752777,8.115865480655646,8.157690482794353,8.011061110833495,8.17662647027438,8.165785203613998,8.080842844700712,8.211241211571421,8.142683754574955,8.073087167459533,8.078509576178693,7.869928020356092,7.937152421088077,8.089942623709943,7.956608102268549,8.114828819068746,7.991895675473931,7.929808622706559,7.85629865522161,8.125504552835832,8.069259179199344,7.81809323339364,7.987275839854758,8.058014558791665,7.908896072080016,7.691289881480982,7.758792504644654,7.956416812011148,7.903871140685458,7.989651110357324,8.007280324649027,8.004490084279299,7.686308387575425,7.858426437094958,7.761413864073487,7.791916074269987,7.924840886021925,8.047491814068335
diff --git a/Data/sub-005/MRS/concentrations.csv b/Data/sub-005/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..b6711e9b9e0ced192f9d00f56864f44b25dc8bd2
--- /dev/null
+++ b/Data/sub-005/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.04139192381102556,0.09150511015113137,1.0236775231866426,0.7330384602836432,0.009661572074995767,0.027735751012785914,0.2389435730741853,0.17110352130788922
+Asc,0.03695350723115995,0.08169310431416112,0.9139095570469024,0.654435444133535,0.014661670099029894,0.03692756973813724,0.362602671025324,0.25965374607006725
+Asp,0.06416804292473298,0.1418562679719219,1.586961349001799,1.1363966458701196,0.02162420898825048,0.05097406015980383,0.5347955509153253,0.3829582054211387
+Cr,0.2229290561673066,0.49282917927683817,5.513333110718974,3.948006206028028,0.01357414248931729,0.03483637860126211,0.335706661673588,0.24039396079941194
+GABA,0.05025729926474188,0.11110379227876327,1.2429300911033478,0.8900415800733439,0.014284309527474203,0.036197544817050425,0.35327004041356375,0.2529708044023196
+GPC,0.07469911051235062,0.16513729506342606,1.8474087066511184,1.3228986699078118,0.004393381651178706,0.020184244768372456,0.10865419224351891,0.07780546117454437
+GSH,0.06861669616329763,0.1516909039863662,1.6969824813744157,1.2151809501518314,0.008385312383754336,0.02562630604271493,0.20737996743851367,0.14850134791626507
+Glc,0.07303282573135256,0.16145363993484352,1.806199259964774,1.2933892700588603,0.016418794957875227,0.04038002030434497,0.4060587140844616,0.29077189624193733
+Gln,0.04677607914442284,0.10340786028912048,1.156834871013905,0.8283902239160984,0.016272345199826645,0.04008925128728785,0.402436816095982,0.28817831529027715
+Glu,0.41091543249344303,0.908410589582129,10.162487109671588,7.277188113241204,0.014675732051883435,0.03695485861129478,0.3629504418884035,0.25990277900497993
+Ins,0.3126591309245602,0.6911954212523959,7.732477625533488,5.537098709712835,0.010716564583507804,0.02956925048874369,0.26503494594742183,0.18978711976978158
+Lac,0.041611841320509255,0.0919912817053056,1.0291163767282523,0.7369331329081226,0.009378890835176658,0.027257423710524233,0.23195248870829568,0.16609732198905314
+Mac,0.027426069776383177,0.06063080197379154,0.6782833121651985,0.4857074064085054,0.0005902888657413123,0.017741899716545117,0.014598631530283235,0.010453837401738024
+NAA,0.6203669587379067,1.3714449986089694,15.34250291643827,10.98651133782163,0.009499281844355488,0.027460418326943375,0.23492991905564517,0.1682294103742984
+NAAG,0.09768464449536668,0.21595140625576942,2.4158716416980917,1.7299655295356144,0.007170011604595953,0.023755381005294417,0.1773239570627827,0.12697873843324137
+PCh,0.004477933455525159,0.009899365778889455,0.11074527121944425,0.07930284807434869,0.0034795266397417723,0.01929357061238008,0.08605333805441563,0.061621365128064355
+PCr,0.22941643298255576,0.5071708207231617,5.673774598303171,4.062895688663366,0.012255344972249517,0.03235887209857771,0.3030910388284129,0.21703845536915348
+PE,0.07936623238202856,0.1754548995971848,1.962832859869373,1.405551987615976,0.01791669530655046,0.04338087079320414,0.4431037890104989,0.3172992586874283
+Scyllo,0.008634883087727864,0.019089132742223767,0.21355218405907858,0.15292116965269592,0.0037368865634965945,0.019527376614594832,0.09241819247673323,0.06617913159258657
+Tau,0.06469085128489672,0.14301204021394495,1.5998910975604088,1.1456554239135737,0.012299719221044916,0.03244105038362159,0.30418847322908316,0.21782430990352422
+Cr+PCr,0.4523454891498624,0.9999999999999999,11.187107709022147,8.010901894691393,0.008003730416576574,0.02502287383471766,0.1979429360785659,0.14174364660793684
diff --git a/Data/sub-005/MRS/fit_summary.png b/Data/sub-005/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..c0a8804fb0c0364c762ec777fcef24642e614287
Binary files /dev/null and b/Data/sub-005/MRS/fit_summary.png differ
diff --git a/Data/sub-005/MRS/options.txt b/Data/sub-005/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..f9babbbd910246ec186a7f3e047e81919d694685
--- /dev/null
+++ b/Data/sub-005/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.08002110112222334, "GM": 0.31135867002869877, "WM": 0.608620228849078}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-005/MRS/qc.csv b/Data/sub-005/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..05ccc56be0d5428c6ba60d98e02a69f3946cb594
--- /dev/null
+++ b/Data/sub-005/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,15.280636157794806,18.341222561675778
+Asc,10.886125240871396,15.519414832070975
+Asp,6.335592049747118,22.75348210624978
+Cr,137.88505076010384,9.980885629683193
+GABA,10.393492750717419,21.580970036274397
+GPC,139.07471562922458,9.983527251123986
+GSH,36.25555302373578,10.970122900428661
+Glc,13.795320689448536,41.45595934732467
+Gln,8.899759382019143,24.635961230541767
+Glu,93.54148461823348,21.57952933887058
+Ins,93.30731555233187,41.99623174689981
+Lac,15.938860226015816,17.75382651357546
+Mac,84.0924258498793,34.326588323152194
+NAA,369.6840839072808,10.371563847245843
+NAAG,67.41258709805024,10.769625850288595
+PCh,8.078691200989322,10.428035497828803
+PCr,141.02278640915887,10.147073611690494
+PE,19.078956382763632,18.603879366710824
+Scyllo,10.360900904672672,10.672960308394613
+Tau,18.579221861148927,18.804844869498478
diff --git a/Data/sub-005/MRS/summary.csv b/Data/sub-005/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..2e2c0573e33430132651acfdc8d26ab3347e528c
--- /dev/null
+++ b/Data/sub-005/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.09150511015113137,0.027735751012785914,1.0236775231866426,0.2389435730741853,0.7330384602836432,0.17110352130788922,23.34168404229188,15.280636157794806,18.341222561675778
+Asc,0.08169310431416112,0.03692756973813724,0.9139095570469024,0.362602671025324,0.654435444133535,0.25965374607006725,39.67599071805253,10.886125240871396,15.519414832070975
+Asp,0.1418562679719219,0.05097406015980383,1.586961349001799,0.5347955509153253,1.1363966458701196,0.3829582054211387,33.69934316621589,6.335592049747118,22.75348210624978
+Cr,0.49282917927683817,0.03483637860126211,5.513333110718974,0.335706661673588,3.948006206028028,0.24039396079941194,6.088996527724945,137.88505076010384,9.980885629683193
+GABA,0.11110379227876327,0.036197544817050425,1.2429300911033478,0.35327004041356375,0.8900415800733439,0.2529708044023196,28.42235801854039,10.393492750717419,21.580970036274397
+GPC,0.16513729506342606,0.020184244768372456,1.8474087066511184,0.10865419224351891,1.3228986699078118,0.07780546117454437,5.881437705275369,139.07471562922458,9.983527251123986
+GSH,0.1516909039863662,0.02562630604271493,1.6969824813744157,0.20737996743851367,1.2151809501518314,0.14850134791626507,12.220513158777752,36.25555302373578,10.970122900428661
+Glc,0.16145363993484352,0.04038002030434497,1.806199259964774,0.4060587140844616,1.2933892700588603,0.29077189624193733,22.481390790315178,13.795320689448536,41.45595934732467
+Gln,0.10340786028912048,0.04008925128728785,1.156834871013905,0.402436816095982,0.8283902239160984,0.28817831529027715,34.78774941692994,8.899759382019143,24.635961230541767
+Glu,0.908410589582129,0.03695485861129478,10.162487109671588,0.3629504418884035,7.277188113241204,0.25990277900497993,3.571472592993356,93.54148461823348,21.57952933887058
+Ins,0.6911954212523959,0.02956925048874369,7.732477625533488,0.26503494594742183,5.537098709712835,0.18978711976978158,3.427555290586906,93.30731555233187,41.99623174689981
+Lac,0.0919912817053056,0.027257423710524233,1.0291163767282523,0.23195248870829568,0.7369331329081226,0.16609732198905314,22.538995001295646,15.938860226015816,17.75382651357546
+Mac,0.06063080197379154,0.017741899716545117,0.6782833121651985,0.014598631530283235,0.4857074064085054,0.010453837401738024,2.1522911250288406,84.0924258498793,34.326588323152194
+NAA,1.3714449986089694,0.027460418326943375,15.34250291643827,0.23492991905564517,10.98651133782163,0.1682294103742984,1.5312359419787789,369.6840839072808,10.371563847245843
+NAAG,0.21595140625576942,0.023755381005294417,2.4158716416980917,0.1773239570627827,1.7299655295356144,0.12697873843324137,7.3399577196967085,67.41258709805024,10.769625850288595
+PCh,0.009899365778889455,0.01929357061238008,0.11074527121944425,0.08605333805441563,0.07930284807434869,0.061621365128064355,77.70384875747787,8.078691200989322,10.428035497828803
+PCr,0.5071708207231617,0.03235887209857771,5.673774598303171,0.3030910388284129,4.062895688663366,0.21703845536915348,5.341964746344645,141.02278640915887,10.147073611690494
+PE,0.1754548995971848,0.04338087079320414,1.962832859869373,0.4431037890104989,1.405551987615976,0.3172992586874283,22.574708120587893,19.078956382763632,18.603879366710824
+Scyllo,0.019089132742223767,0.019527376614594832,0.21355218405907858,0.09241819247673323,0.15292116965269592,0.06617913159258657,43.27663183775542,10.360900904672672,10.672960308394613
+Tau,0.14301204021394495,0.03244105038362159,1.5998910975604088,0.30418847322908316,1.1456554239135737,0.21782430990352422,19.013073683135335,18.579221861148927,18.804844869498478
+Cr+PCr,0.9999999999999999,0.02502287383471766,11.187107709022147,0.1979429360785659,8.010901894691393,0.14174364660793684,1.7693843773304285,,
diff --git a/Data/sub-005/MRS/voxel_location.png b/Data/sub-005/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..4d267b6bd2bb0854aa2d32d0b019809c49f7ac08
Binary files /dev/null and b/Data/sub-005/MRS/voxel_location.png differ
diff --git a/Data/sub-005/TMS_EEG/DCM_DefaultCodes_STR7T_HS_006_FHK.mat b/Data/sub-005/TMS_EEG/DCM_DefaultCodes_STR7T_HS_006_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..ecb2a2e9c6a1da82ec712f708c28ddb34c5f168f
Binary files /dev/null and b/Data/sub-005/TMS_EEG/DCM_DefaultCodes_STR7T_HS_006_FHK.mat differ
diff --git a/Data/sub-006/MRS/all_parameters.csv b/Data/sub-006/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..11d6cde36062c9a6aefdb04d898eac9f47071fd9
--- /dev/null
+++ b/Data/sub-006/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.04434342303637762,0.010593791302762971
+Asc,0.03520630000907257,0.020028933391989998
+Asp,0.08042925377986443,0.030402177453576977
+Cr,0.2439263461601319,0.022343899231234667
+GABA,0.08108513629013697,0.01271986561846092
+GPC,0.06022190562981053,0.007291975210387328
+GSH,0.06147485341194607,0.008099916415210453
+Glc,0.10926677476252562,0.024456236893354612
+Gln,0.05193177113931373,0.015255620178141329
+Glu,0.5007067213116707,0.016032898166717737
+Ins,0.36685860336673715,0.01109920437951204
+Lac,0.0029910848572646865,0.0027661877150363663
+Mac,0.02791352617986361,0.0007467574535314674
+NAA,0.6592279438484537,0.012394729008168166
+NAAG,0.05556281718450519,0.009460360450766906
+PCh,0.015758195082386912,0.005354518801916109
+PCr,0.19919698740830077,0.018009603780301656
+PE,0.1045067391801879,0.026722265978546954
+Scyllo,0.02003976255818434,0.0037680236044412875
+Tau,0.06547174417696523,0.016810539813700603
+gamma_0,23.95921711348108,0.8242016874136087
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diff --git a/Data/sub-006/MRS/all_samples.csv b/Data/sub-006/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..a450c1a4b70aa986de7a4cfc6b0b8ac1be8747dd
--- /dev/null
+++ b/Data/sub-006/MRS/all_samples.csv
@@ -0,0 +1,36 @@
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diff --git a/Data/sub-006/MRS/concentration_samples.csv b/Data/sub-006/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..99be751469eed23db7e9629e821836300ca1332a
--- /dev/null
+++ b/Data/sub-006/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+PE,internal,0.1813636046067198,0.22924648973474646,0.30677817800253043,0.24188351385029838,0.31738579024129576,0.2773065119557506,0.29311050282116646,0.2824775656499135,0.26860268524709424,0.2799214842605794,0.27456052966432604,0.3055546017634849,0.2740471492759749,0.31163527878565833,0.24879393931830815,0.15700499868937304,0.22811705782293307,0.2180689179311798,0.20052969571407558,0.2723521628637503,0.2957516578965625,0.32545450614287813,0.3126055831200265,0.329629037597147,0.31604996931880486,0.24564517741006278,0.3328574762740551,0.24868771422024827,0.2558796835616447,0.2493582707110305,0.23844040349533455,0.18860003044405682,0.22944772137692993,0.24305998430542242,0.18288419026541092,0.20366830551532045,0.10105716791432545,0.11594890516709311,0.16814342595735382,0.1462087053874175,0.18151506388289118,0.17705221906642388,0.1748016397026003,0.17661625058817587,0.18254411092763267,0.286065327344835,0.20292009238132602,0.20818900099720727,0.12790691430503787,0.17633085655575687
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diff --git a/Data/sub-006/MRS/concentrations.csv b/Data/sub-006/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..6ddea80be0af4101728d1e8893e0e60cd680b7d0
--- /dev/null
+++ b/Data/sub-006/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
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diff --git a/Data/sub-006/MRS/fit_summary.png b/Data/sub-006/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..dca5c9007e48a873ac0c9a12e040b3d91a74624f
Binary files /dev/null and b/Data/sub-006/MRS/fit_summary.png differ
diff --git a/Data/sub-006/MRS/options.txt b/Data/sub-006/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..8ae8022bc8c4f58ad38c676ed896d5c612177007
--- /dev/null
+++ b/Data/sub-006/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.06329827385636227, "GM": 0.4140922678936483, "WM": 0.5226094582499895}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_008/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-006/MRS/qc.csv b/Data/sub-006/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..91432866330d52547496fd098f189e4133ec588f
--- /dev/null
+++ b/Data/sub-006/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,15.538997977196605,18.06073367984862
+Asc,9.642812953073816,15.574289696859028
+Asp,7.5100124281497065,22.645797501878643
+Cr,142.40330101992595,9.627682455112536
+GABA,15.90392262024073,21.427536103362044
+GPC,106.27106401297313,9.627963383874167
+GSH,30.69408989397825,10.638593211399488
+Glc,19.35080969908528,41.628469416005515
+Gln,9.32983138550995,24.6524419168923
+Glu,108.0430061847157,21.4898801029411
+Ins,103.6574025987154,41.66176994166725
+Lac,1.0850153286969586,17.515622816242555
+Mac,80.67545982099102,35.18845215167511
+NAA,369.9711050568352,9.99692979362318
+NAAG,36.33348183414149,10.46542515145158
+PCh,26.689167236858733,10.148597278968778
+PCr,116.34593020795924,9.806545143477951
+PE,23.529943156808116,18.71457304033315
+Scyllo,22.85131063418766,10.195979993839337
+Tau,17.826085644092977,18.790091229975836
diff --git a/Data/sub-006/MRS/summary.csv b/Data/sub-006/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..b3be83f4599ea8156cd9296c45eb88c646a42737
--- /dev/null
+++ b/Data/sub-006/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.10007016033049758,0.03187804590564381,1.0580682107017922,0.2527760159396633,0.7661339046355113,0.1830319388970321,23.890332719853934,15.538997977196605,18.06073367984862
+Asc,0.07945034111735749,0.049876361450425705,0.8400494212066332,0.4779057696773467,0.6082692369416907,0.34604556650264817,56.89019688757011,9.642812953073816,15.574289696859028
+Asp,0.18150534554832584,0.0717762735521943,1.9191039123237976,0.72541935865789,1.3895990436899217,0.5252670481217173,37.799899942859106,7.5100124281497065,22.645797501878643
+Cr,0.5504705522857819,0.05465533731750424,5.8202704020605065,0.5331426367400449,4.21438470985485,0.38604188830359193,9.160100818534142,142.40330101992595,9.627682455112536
+GABA,0.18298548089798294,0.03561795920748263,1.9347537739392477,0.3035057858355087,1.400930911961909,0.21976472823750975,15.68704968682175,15.90392262024073,21.427536103362044
+GPC,0.1359032600356404,0.026748008502477428,1.4369410291693834,0.17399214212684763,1.040470954777401,0.12598552520080247,12.108509576584567,106.27106401297313,9.627963383874167
+GSH,0.13873079739876154,0.027906770838450026,1.4668373278123497,0.19327024125415593,1.0621184892008129,0.13994455469338954,13.175983293416754,30.69408989397825,10.638593211399488
+Glc,0.2465832116819713,0.05908182079513574,2.607189363060625,0.5835446395065826,1.887833077908032,0.4225373455816866,22.382134868084506,19.35080969908528,41.628469416005515
+Gln,0.11719484668322881,0.040372169966655096,1.2391320382026432,0.36401084173836334,0.8972399484126592,0.2635756794221198,29.376275531246844,9.32983138550995,24.6524419168923
+Glu,1.129948895445257,0.04187799785356734,11.947247831318476,0.38255729292045304,8.650852126617686,0.27700493182527225,3.2020537141417504,108.0430061847157,21.4898801029411
+Ins,0.8278927683912682,0.03274211550804449,8.75352869638344,0.26483556103482836,6.338320206266341,0.1917641040622237,3.0254720150086025,103.6574025987154,41.66176994166725
+Lac,0.006750005316077009,0.021991570841705086,0.07136958733174514,0.06600336838481687,0.05167782196048395,0.047792210207521134,92.48108452416204,1.0850153286969586,17.515622816242555
+Mac,0.06299267961151689,0.021154209977005786,0.6660382234198978,0.0178182077201862,0.48226991377685574,0.012901940457334397,2.675253025073438,80.67545982099102,35.18845215167511
+NAA,1.4876850165838704,0.03502932248598386,15.729686235998207,0.2957477760128597,11.38966827732551,0.2141472507464466,1.8801886545964623,369.9711050568352,9.99692979362318
+NAAG,0.12538905757244326,0.030007533348560985,1.3257715921419007,0.2257314832579651,0.9599745614404295,0.16344933239500967,17.026423299150352,36.33348183414149,10.46542515145158
+PCh,0.035561645909023956,0.024303779535740738,0.3760026658526749,0.1277629407018211,0.2722588086754843,0.0925115409739771,33.97926459167209,26.689167236858733,10.148597278968778
+PCr,0.44952944771421804,0.04578719036713483,4.7529934680817405,0.42972301059482265,3.4415828843333913,0.31115703570790687,9.041102485845714,116.34593020795924,9.806545143477951
+PE,0.2358412010006434,0.0638848625179265,2.4936112496310585,0.6376138379444383,1.8055925922353617,0.46168817319442707,25.569897394342288,23.529943156808116,18.71457304033315
+Scyllo,0.04522389375618278,0.022736914112253426,0.4781641619193989,0.08990794395287602,0.34623266508034733,0.0651012131936939,18.802735778435693,22.85131063418766,10.195979993839337
+Tau,0.14775061301720926,0.043403193738067954,1.5622062184062275,0.40111242127207725,1.1311739052812015,0.2904404672579207,25.67602257282618,17.826085644092977,18.790091229975836
+Cr+PCr,0.9999999999999998,0.029821490740244632,10.573263870142245,0.2229581860808273,7.65596759418824,0.16144122273483383,2.108697832751882,,
diff --git a/Data/sub-006/MRS/voxel_location.png b/Data/sub-006/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..82326d040a3cb9d763455df86bc15cc71ef1efea
Binary files /dev/null and b/Data/sub-006/MRS/voxel_location.png differ
diff --git a/Data/sub-006/TMS_EEG/DCM_DefaultCodes_STR7T_HS_008_FHK.mat b/Data/sub-006/TMS_EEG/DCM_DefaultCodes_STR7T_HS_008_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..7454165c460d8db8a9fd683336896fc6da39de05
Binary files /dev/null and b/Data/sub-006/TMS_EEG/DCM_DefaultCodes_STR7T_HS_008_FHK.mat differ
diff --git a/Data/sub-007/MRS/all_parameters.csv b/Data/sub-007/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..bda9f118796d937265b2a6109c1a66ff1be0bd45
--- /dev/null
+++ b/Data/sub-007/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.03261509127502805,0.009249278125737014
+Asc,0.037288560734053774,0.01447326629339646
+Asp,0.09125928310433862,0.02415231856360308
+Cr,0.24442028261166793,0.01735278405971481
+GABA,0.05363861382777404,0.012531944508181877
+GPC,0.04651674501094056,0.00733274495122228
+GSH,0.05751914100154348,0.006595865084913773
+Glc,0.10535290564474335,0.020020633988319558
+Gln,0.04731934028868356,0.01682227855054057
+Glu,0.43632121596428486,0.01741349589652221
+Ins,0.33209926064352624,0.011381138254425919
+Lac,0.04043432280437051,0.009911017560273648
+Mac,0.02845902824010465,0.0006844932712729928
+NAA,0.594302691230806,0.011244287809408242
+NAAG,0.049511406541513765,0.00805170005176558
+PCh,0.02002202943496213,0.007710905763604808
+PCr,0.1816203835758765,0.015217915684289776
+PE,0.10318883589700553,0.017847528251911462
+Scyllo,0.012043322851310377,0.003579508466894661
+Tau,0.07882025026088521,0.013166499975104424
+gamma_0,14.492264865638635,0.9351138777499621
+gamma_1,5.157291086887326,3.094704172541708
+sigma_0,17.086944583090933,0.5098539701464841
+sigma_1,12.842352995685587,5.501206132268463
+eps_0,0.014285570425265499,0.6231246380628037
+eps_1,-2.5079323046436315,4.488090713536053
+Phi0,-0.03577656433842362,0.009275280667755632
+Phi1,0.00034878738050585825,1.2496647270875084e-05
+B_real_0,0.3673079202636655,5.607473066727768e-17
+B_imag_0,-0.3624564269479681,0.0
+B_real_1,-0.2607686065328329,5.607473066727768e-17
+B_imag_1,-0.06696910097902571,0.0
+B_real_2,0.16387631907316882,2.803736533363884e-17
+B_imag_2,0.31232661945971396,0.0
diff --git a/Data/sub-007/MRS/all_samples.csv b/Data/sub-007/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..09893f44014634493ebd1c0328cd6a86b56ec00a
--- /dev/null
+++ b/Data/sub-007/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.021167232689294737,0.025903059799518083,0.024197496644834372,0.029231961539044907,0.032026277962018956,0.03146644913755276,0.024938585927082098,0.037501095264369136,0.04833744234921574,0.018537855605551143,0.03787672432547705,0.029086399875904362,0.03115762694688707,0.03372995493428757,0.035808018680073744,0.03869671346426617,0.03804468594705062,0.03316909378479521,0.02218600585470943,0.024216389852559077,0.04560836112507588,0.031245278005481852,0.024813959183251553,0.044973202130653575,0.036581866653818504,0.04246206349027666,0.04898809239183181,0.03719098156887754,0.023719111255400587,0.031831545135914935,0.023018101971371177,0.029766496684207333,0.019987544711174803,0.028584280283566233,0.019497680154514148,0.023054476173548902,0.025978155827287946,0.03270233716652993,0.04408446398716988,0.02658621553404221,0.051715625874999706,0.025990020872435952,0.03354807932836935,0.02849114451193233,0.04786885001844121,0.02120657452018529,0.028754109162648832,0.04216424825536348,0.05662989112305564,0.036432736065483015
+Asc,0.041878540200556647,0.037701283546980616,0.039817317016293874,0.03190203513190287,0.027570621146071624,0.029400149255912,0.03420564119804407,0.02580464612899796,0.03552457463029624,0.04665135053997967,0.0432846451711196,0.0385514652771309,0.05395801974399309,0.05530210953000892,0.04660470650248786,0.03651137345537447,0.06017908851645627,0.020699432390678625,0.04301996612883367,0.01367880802411265,0.053211780936545314,0.05469736740773896,0.056594654428348753,0.04551248283304017,0.040309220772632624,0.03736297871788645,0.049366699857911055,0.046264553506898905,0.045881166219686326,0.06515969086996104,0.05926396092041207,0.039301128493154425,0.04540623222824778,0.03944892071069594,0.027408549979703975,0.059389204918677496,0.04507567109359716,0.021558605477139968,0.02118492848830925,0.015275777874727108,0.0010427077738394096,0.025390508732334803,0.019101168498614193,0.013902609766858991,0.008044830976203053,0.036604370283289556,0.040951793541965015,0.03582660823715038,0.026718368189394187,0.026925721432492868
+Asp,0.08023813961809174,0.07735314192302142,0.07446025350522745,0.06602762005960826,0.03394541807130878,0.0861665243233488,0.09527480800941793,0.06412392190794843,0.10838820508753189,0.10172925407202792,0.11998674182685404,0.08649243824912098,0.15304760487206476,0.07178956177899484,0.06076945885803334,0.12158156788116406,0.09814288127546353,0.13566994670074473,0.06748341956213622,0.0537042354422718,0.06159462812466608,0.08919381664246664,0.1297778038179564,0.14170887736491986,0.11132090174911952,0.10259359191095255,0.08944664594246757,0.09617982114871282,0.08652625158834627,0.06650110452832445,0.08161783727415325,0.09359887995793789,0.09313920051821781,0.10714400036447769,0.07934307553070226,0.05657687836160251,0.08823228907480439,0.11681324758140474,0.09520503291618011,0.1177082140283178,0.10335480489504069,0.10547415075738706,0.08924033466049339,0.12430459936061243,0.09093022826545209,0.06469063607248773,0.0850281636942192,0.09116334127288316,0.07808840687408793,0.07009224791415608
+Cr,0.2570571541989839,0.2735151793366029,0.2685079222529433,0.24939619051527595,0.25466510023368427,0.25282711567277866,0.24873554216628535,0.24479670609642473,0.24855592177371832,0.26413337694065003,0.2593892511873501,0.25315773947516107,0.2282757317380854,0.24226218895965917,0.21633397847334293,0.2257233052943308,0.23638238979542342,0.2411037869315678,0.22796383076326118,0.2237865579571976,0.22749503917338196,0.23642653450697362,0.24379718104330608,0.23543956581193223,0.25446404190859145,0.2518130610018353,0.28679721531108604,0.2672762836963826,0.267908746747623,0.282939426954276,0.28625189306588944,0.2430281806304965,0.23057163656192445,0.23781476765524845,0.23006964820502174,0.23386325022332688,0.22536531310118266,0.23631444144223596,0.24103820089226174,0.23416757847201117,0.23607128359572185,0.2185621902816401,0.22282212329147877,0.23132250009500693,0.24378868030088943,0.24975191927032656,0.2432835131227308,0.2551230128952915,0.22962640082193128,0.22125153074066448
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diff --git a/Data/sub-007/MRS/concentration_samples.csv b/Data/sub-007/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..817ec3e8197204a176c56863ce42d1c103c6708b
--- /dev/null
+++ b/Data/sub-007/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+PE,molarity,1.5606081020417069,2.1789045004976377,2.114547731138691,1.5315791379687937,2.1747737612844,2.230808370249478,2.0636906033107496,1.5811308763055967,1.8106297901822441,1.7446688894137938,1.8783785555671138,1.9460012126366963,1.7667497222623472,2.02075233855883,1.3155868490521132,1.7386323814056457,1.7723104280118949,1.6913483807883898,1.7491727442709224,2.332261961925654,2.354438474975289,1.7745656045080545,1.327727186561644,1.687468671653124,1.6834296549637382,1.810364202153387,1.4171330629672878,1.687832719942087,1.2857566433559704,1.3921646368259983,2.252785259712583,1.706708381290131,1.3178866723199576,1.6499416799114275,2.179234535578108,1.6551292532990258,1.6819787153125108,2.318351142920261,1.9084068540490546,2.1316142811132215,2.053404943291931,2.700348515260011,2.3835352777889596,2.063659879683805,2.1769778884968405,2.038805685057818,1.9387345107109046,1.9939713456141632,1.8428308402988807,1.4678276468783844
+Scyllo,molarity,0.4017925523864863,0.32743205780912243,0.20818659671391027,0.23409653465433214,0.19635973833470566,0.12150222016496112,0.21528045772271076,0.27800323145526684,0.19902941710588137,0.22222228085731352,0.2288763256478236,0.17843650638843478,0.2356545733294396,0.17109624374005508,0.2503389448400332,0.17305287132892658,0.4003644669990329,0.16032054477881655,0.2011335264051865,0.16872454914197627,0.20514924850651411,0.2602530222653754,0.18269485787546155,0.21551187928179408,0.2800723586094066,0.08272971611111812,0.1959236559870195,0.21337958402188476,0.22001192805553152,0.22116055405346385,0.24037376733359445,0.27283386118650765,0.3221232886513343,0.20541430695896176,0.16226553934595125,0.2701317200811256,0.13660568125433611,0.2231516265944495,0.2008894717165238,0.17303501671022076,0.18083914211107222,0.1789153527374688,0.16726685174884948,0.24070455319619014,0.16861088477846203,0.1302521918829219,0.13025340420053802,0.3209012242714982,0.18685610031649055,0.3039389233649866
+Tau,molarity,1.3577228989524521,1.3417664009107966,1.5020286371595937,1.5996907634534678,1.3124966434010679,1.1078430839420503,1.2404800067880202,1.4279135473692586,1.6322579117917375,1.4497827909710723,1.523326853968427,1.4488986735062004,1.4548085363441436,1.5679203311016523,1.8010871986112635,1.6184597037997366,1.4832003233550664,1.983944121810603,1.5345081149606647,1.1595002800121763,1.6422741498749518,1.555766072681019,1.4618787952604737,1.6645766494783791,1.3713437797527457,1.5854670280495033,1.6252648328018362,1.7805919375982173,1.5169176223813843,1.5470913602544656,1.4439640758142782,1.4234022328902647,1.790221892141305,1.377517582419924,1.110390211144922,1.192270314247445,1.4106188921348264,0.9457023783544837,1.643069537178914,1.0597181904999111,1.3171005162149727,0.9024860756611338,1.2137865164514088,0.8712707033262641,1.2101757405013795,1.3944754034762938,1.2244348856012546,1.707431258586299,1.4115056832204722,1.1545576441382575
+Cr+PCr,molarity,7.602199982818639,8.003008551473108,7.985314275207827,7.890571820516626,7.615002263988563,7.420013753839138,7.3198148483343415,7.6078347226044984,7.662943740598162,7.601587100458002,7.705239270300685,7.688340449068102,7.675429807812391,7.739319675099358,7.47717299878818,7.590317953318913,7.8083108329930475,7.814691710498158,7.796814714786417,7.410520457855502,7.521887665163168,7.56635982778751,7.89878864976163,7.689025935767117,7.6903878146504105,7.596124475086312,8.334717046170377,7.941627307161384,7.7261852420482535,7.634366833680517,7.944063500462163,7.425014960743615,7.416891906314094,7.6469273242309015,7.419496429831782,7.622271768326673,7.463435073193872,7.600777827073083,7.820490354644801,7.799487237086916,7.508066915910712,7.488688036499791,7.6319482438942,7.703216728997156,7.996119937449235,7.718798362065406,7.6857612791260195,7.772795496365889,7.7477772457967005,7.900801763640995
diff --git a/Data/sub-007/MRS/concentrations.csv b/Data/sub-007/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..6773941e91c45180a9c3ea4b0a9dbe80b1c0dfbd
--- /dev/null
+++ b/Data/sub-007/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.03261509127502805,0.07655393924454804,0.7968709412599911,0.588434533573735,0.009249278125737014,0.0331842034046346,0.22598376021332053,0.1668735069271128
+Asc,0.037288560734053774,0.08752347767111798,0.9110558740985839,0.672752274649581,0.01447326629339646,0.04223672312475024,0.3536192873743666,0.2611235893478542
+Asp,0.09125928310433862,0.21420322130509015,2.2297000554999604,1.6464805581853685,0.02415231856360308,0.06199717278200422,0.5901035402628347,0.4357509898977223
+Cr,0.24442028261166793,0.5737017660752445,5.971818966421867,4.409778705867921,0.01735278405971481,0.04784177044116428,0.42397334566816774,0.3130752358863434
+GABA,0.05363861382777404,0.12590022053003305,1.3105299117021316,0.9677364519121912,0.012531944508181877,0.03866665646033065,0.3061877807375316,0.2260986749741233
+GPC,0.04651674501094056,0.10918381436964457,1.136524257088326,0.8392452108462674,0.00733274495122228,0.030431977006312987,0.17915790337750392,0.13229582339054582
+GSH,0.05751914100154348,0.13500856975991907,1.4053412159376728,1.0377480970816637,0.006595865084913773,0.029488288576980173,0.1611540245071606,0.11900119371207193
+Glc,0.10535290564474335,0.24728368441327778,2.5740436651753464,1.900754695761585,0.020020633988319558,0.053274297897039254,0.48915581184067236,0.361208016357365
+Gln,0.04731934028868356,0.11106766101021313,1.1561337332364299,0.8537254639881245,0.01682227855054057,0.04678622369165226,0.4110117255128085,0.3035039684256188
+Glu,0.43632121596428486,1.0241304424498645,10.660454546186596,7.872014492899746,0.01741349589652221,0.04796314891585135,0.4254566926910038,0.31417058592148256
+Ins,0.33209926064352624,0.7795013175980133,8.11404291924755,5.9916641621229845,0.011381138254425919,0.03665375275582504,0.27807061083892903,0.205336073531364
+Lac,0.04043432280437051,0.09490719082335487,0.9879149685838597,0.7295074442418262,0.009911017560273648,0.03422053017325658,0.24215176420942794,0.17881246893170638
+Mac,0.02845902824010465,0.06679885395629556,0.6953275840868348,0.5134517290543235,0.0006844932712729928,0.02514866080039265,0.01672393901233904,0.012349481883077672
+NAA,0.594302691230806,1.394943577919372,14.520350133652386,10.722282638030546,0.011244287809408242,0.036420311501941735,0.2747270009126683,0.20286704693553806
+NAAG,0.049511406541513765,0.1162128652754446,1.2096915750179278,0.8932742566672509,0.00805170005176558,0.03141722909253479,0.19672383391139348,0.14526705826096825
+PCh,0.02002202943496213,0.0469955828727119,0.48918990620730063,0.3612331927086229,0.007710905763604808,0.030942645214430735,0.18839734900621,0.13911852026340582
+PCr,0.1816203835758765,0.4262982339247556,4.437455188816879,3.276756296517886,0.015217915684289776,0.04365488716907133,0.37181299580296046,0.27455839513488467
+PE,0.10318883589700553,0.24220419337054902,2.5211698503425035,1.8617110100673453,0.017847528251911462,0.0488342155623078,0.43606122446004836,0.32200130527914783
+Scyllo,0.012043322851310377,0.028268012439002406,0.29424949130127515,0.21728306706026934,0.003579508466894661,0.026466282255509403,0.08745663954178227,0.06458072974191251
+Tau,0.07882025026088521,0.18500640083542705,1.9257823467699506,1.4220581756869286,0.013166499975104424,0.03981144644228144,0.32169161017477754,0.237547189622038
+Cr+PCr,0.4260406661875444,0.9999999999999999,10.409274155238744,7.6865350023858054,0.010692465199911098,0.035492924739395935,0.26124454892348076,0.19291118088884357
diff --git a/Data/sub-007/MRS/fit_summary.png b/Data/sub-007/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..26e969deb53c03e518255c28af287a62f2383bcd
Binary files /dev/null and b/Data/sub-007/MRS/fit_summary.png differ
diff --git a/Data/sub-007/MRS/options.txt b/Data/sub-007/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..8b9dd81c63b32199ca601016d72ebe244e2be356
--- /dev/null
+++ b/Data/sub-007/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.11580879345603272, "GM": 0.39517382413087937, "WM": 0.48901738241308795}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_009/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-007/MRS/qc.csv b/Data/sub-007/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..d39c0e6fe5c7fd9c27f137d8eb402343c3c57b4e
--- /dev/null
+++ b/Data/sub-007/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,13.733136277091448,19.866419387149026
+Asc,12.220322243997911,16.876802269506346
+Asp,10.341527855394345,23.535092659299004
+Cr,156.22908399338905,12.627691268555234
+GABA,12.305830839554995,22.846344076885345
+GPC,89.75650949806167,12.497551528329195
+GSH,32.06665715599614,13.844745637668083
+Glc,22.659588794725583,41.61169471373995
+Gln,10.277770461242055,25.544816108510034
+Glu,110.97635760678673,22.716699321725834
+Ins,109.30687964348903,44.79157088104375
+Lac,17.23742775474548,19.08377617862354
+Mac,98.86632927047614,34.60195480561308
+NAA,368.04250172302056,12.886361231752295
+NAAG,35.67701731739374,13.59002274247567
+PCh,37.733739963188235,12.892855400201547
+PCr,116.55600270091423,12.586005150374637
+PE,28.300526632411614,19.166512408385465
+Scyllo,15.30748295952868,12.870222078402001
+Tau,25.467004065861133,19.664112213059113
diff --git a/Data/sub-007/MRS/summary.csv b/Data/sub-007/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..5aa9c13ed10acbfd3f74c66baf2f6edafd035cbb
--- /dev/null
+++ b/Data/sub-007/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.07655393924454804,0.0331842034046346,0.7968709412599911,0.22598376021332053,0.588434533573735,0.1668735069271128,28.358890820639164,13.733136277091448,19.866419387149026
+Asc,0.08752347767111798,0.04223672312475024,0.9110558740985839,0.3536192873743666,0.672752274649581,0.2611235893478542,38.814226155365525,12.220322243997911,16.876802269506346
+Asp,0.21420322130509015,0.06199717278200422,2.2297000554999604,0.5901035402628347,1.6464805581853685,0.4357509898977223,26.465601900454594,10.341527855394345,23.535092659299004
+Cr,0.5737017660752445,0.04784177044116428,5.971818966421867,0.42397334566816774,4.409778705867921,0.3130752358863434,7.099567954957613,156.22908399338905,12.627691268555234
+GABA,0.12590022053003305,0.03866665646033065,1.3105299117021316,0.3061877807375316,0.9677364519121912,0.2260986749741233,23.363662134185958,12.305830839554995,22.846344076885345
+GPC,0.10918381436964457,0.030431977006312987,1.136524257088326,0.17915790337750392,0.8392452108462674,0.13229582339054582,15.763667362145926,89.75650949806167,12.497551528329195
+GSH,0.13500856975991907,0.029488288576980173,1.4053412159376728,0.1611540245071606,1.0377480970816637,0.11900119371207193,11.467252413829994,32.06665715599614,13.844745637668083
+Glc,0.24728368441327778,0.053274297897039254,2.5740436651753464,0.48915581184067236,1.900754695761585,0.361208016357365,19.003399921242227,22.659588794725583,41.61169471373995
+Gln,0.11106766101021313,0.04678622369165226,1.1561337332364299,0.4110117255128085,0.8537254639881245,0.3035039684256188,35.550534829758874,10.277770461242055,25.544816108510034
+Glu,1.0241304424498645,0.04796314891585135,10.660454546186596,0.4254566926910038,7.872014492899746,0.31417058592148256,3.990980786491848,110.97635760678673,22.716699321725834
+Ins,0.7795013175980133,0.03665375275582504,8.11404291924755,0.27807061083892903,5.9916641621229845,0.205336073531364,3.427029085331924,109.30687964348903,44.79157088104375
+Lac,0.09490719082335487,0.03422053017325658,0.9879149685838597,0.24215176420942794,0.7295074442418262,0.17881246893170638,24.51139742892485,17.23742775474548,19.08377617862354
+Mac,0.06679885395629556,0.02514866080039265,0.6953275840868348,0.01672393901233904,0.5134517290543235,0.012349481883077672,2.405188488862035,98.86632927047614,34.60195480561308
+NAA,1.394943577919372,0.036420311501941735,14.520350133652386,0.2747270009126683,10.722282638030546,0.20286704693553806,1.8920136111315977,368.04250172302056,12.886361231752295
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diff --git a/Data/sub-007/MRS/voxel_location.png b/Data/sub-007/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..6e4abd1d1ea1ec073e77576842f613cb609fe7a4
Binary files /dev/null and b/Data/sub-007/MRS/voxel_location.png differ
diff --git a/Data/sub-007/TMS_EEG/DCM_DefaultCodes_STR7T_HS_009_FHK.mat b/Data/sub-007/TMS_EEG/DCM_DefaultCodes_STR7T_HS_009_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..e2eb5beb1bb097419213b7096d80a7fd9cd418ca
Binary files /dev/null and b/Data/sub-007/TMS_EEG/DCM_DefaultCodes_STR7T_HS_009_FHK.mat differ
diff --git a/Data/sub-008/MRS/all_parameters.csv b/Data/sub-008/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..48bc70703b2a52b1573a0cf2109606119440fa95
--- /dev/null
+++ b/Data/sub-008/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.0258235301603147,0.01172323683990432
+Asc,0.03396258194764648,0.01556429897238425
+Asp,0.10747827666488168,0.031213214397414406
+Cr,0.23519521236113541,0.01737377854603258
+GABA,0.06166336238512016,0.022639302201461965
+GPC,0.05180950405968116,0.01005689981851864
+GSH,0.0752256606689045,0.009504424944021482
+Glc,0.1385358473662409,0.020226545138690245
+Gln,0.050936742065912276,0.017555186143995233
+Glu,0.47399733947108563,0.018265102215611714
+Ins,0.37401178576040267,0.01084517720499261
+Lac,0.053453842611721356,0.01134996284683435
+Mac,0.029664978537618028,0.0008048043402801883
+NAA,0.6473431918796827,0.014007653905972457
+NAAG,0.04270789450775375,0.010789689708168633
+PCh,0.01606094030987417,0.010158408547967152
+PCr,0.22578619582690923,0.019172750305275852
+PE,0.11293684349298666,0.020863093615932617
+Scyllo,0.014723253338911972,0.0040491285548714265
+Tau,0.08332705663928315,0.016916485648007868
+gamma_0,22.496227080602498,1.3159771974903118
+gamma_1,4.399706709925626,3.2396453704561865
+sigma_0,9.374682009993396,1.2155466108643402
+sigma_1,13.863324368405515,6.210055659336948
+eps_0,4.06149509762854,0.5048835424556208
+eps_1,1.7838773197555429,4.822820485022923
+Phi0,-0.12302303781848002,0.02065894783514817
+Phi1,0.0002993083984879259,2.3015817147459753e-05
+B_real_0,0.13723997954173936,2.803736533363884e-17
+B_imag_0,-0.4945723265952192,1.1214946133455537e-16
+B_real_1,-0.4441470952770819,5.607473066727768e-17
+B_imag_1,0.13138119346678911,0.0
+B_real_2,0.2839935422387886,0.0
+B_imag_2,0.4738049274969443,5.607473066727768e-17
diff --git a/Data/sub-008/MRS/all_samples.csv b/Data/sub-008/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..e263f4fb033832c75fcf3052f5767720bf9c1ade
--- /dev/null
+++ b/Data/sub-008/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-008/MRS/concentration_samples.csv b/Data/sub-008/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..354bf2cdc8603117a02ae6c4496aacaee8bb0071
--- /dev/null
+++ b/Data/sub-008/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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diff --git a/Data/sub-008/MRS/concentrations.csv b/Data/sub-008/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..863c0f4356f02378fc5cc3a6a532d22456013509
--- /dev/null
+++ b/Data/sub-008/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
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+GPC,0.05180950405968116,0.11238957393818995,1.249336549829089,0.9130330736133461,0.01005689981851864,0.0300537066981431,0.24251250324209703,0.17723161645682203
+GSH,0.0752256606689045,0.16318588848211915,1.8139947305892299,1.3256933727063966,0.009504424944021482,0.029195360560822572,0.22919010098986853,0.167495413767539
+Glc,0.1385358473662409,0.30052371940720224,3.340659223003066,2.441401685310915,0.020226545138690245,0.04850235532910374,0.4877437562309897,0.3564501342318212
+Gln,0.050936742065912276,0.11049630453888942,1.2282907305743602,0.8976524869783961,0.017555186143995233,0.043330464239786315,0.42332649360012814,0.30937307457030755
+Glu,0.47399733947108563,1.0282352629668994,11.429991687255264,8.353201899854225,0.018265102215611714,0.04468998450928083,0.44044543947075215,0.3218838458011777
+Ins,0.37401178576040267,0.8113381128113412,9.018935859317573,6.5911677117593745,0.01084517720499261,0.03131710367493756,0.26152105713968365,0.19112334034213757
+Lac,0.053453842611721356,0.11595661270121405,1.2889881985109677,0.9420110673131262,0.01134996284683435,0.03214784181763659,0.273693479239215,0.2000191210381994
+Mac,0.029664978537618028,0.0643517894880416,0.7153425343398231,0.5227825864087612,0.0008048043402801883,0.020744232274484836,0.01940708555354803,0.014182976536832412
+NAA,0.6473431918796827,1.4042718000800956,15.610060829122897,11.408056396056883,0.014007653905972457,0.036750784287288084,0.3377811526998679,0.24685531220583412
+NAAG,0.04270789450775375,0.0926455899287206,1.0298599560674915,0.7526364302783275,0.010789689708168633,0.031226780813072452,0.2601830293183622,0.19014549041495146
+PCh,0.01606094030987417,0.03484075501657228,0.3872941870015773,0.28304014798815164,0.010158408547967152,0.030213932613537647,0.24496028899354239,0.17902049339994425
+PCr,0.22578619582690923,0.4897945813354928,5.4446177783999765,3.979004781011533,0.019172750305275852,0.046444585846875365,0.46233250350235744,0.33787922618757754
+PE,0.11293684349298666,0.24499218729211134,2.7233637719361727,1.9902733139427315,0.020863093615932617,0.04975501145039423,0.5030935128594426,0.367667956583701
+Scyllo,0.014723253338911972,0.03193893089264465,0.3550371473833617,0.25946624067525353,0.0040491285548714265,0.02245949245317243,0.09764085548339148,0.07135733794423385
+Tau,0.08332705663928315,0.18076012428963767,2.0093521321727885,1.4684633643834626,0.016916485648007868,0.04211794455113547,0.40792484310156724,0.29811732743368263
+Cr+PCr,0.4609814081880447,1.0,11.116124975401876,8.123823604095875,0.009528778759606752,0.029232693369688992,0.2297773699184309,0.1679245983255
diff --git a/Data/sub-008/MRS/fit_summary.png b/Data/sub-008/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..8ec6abcd44480f97f831aa7c541e97b6c2d19c9d
Binary files /dev/null and b/Data/sub-008/MRS/fit_summary.png differ
diff --git a/Data/sub-008/MRS/options.txt b/Data/sub-008/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..ad1b27554b153d9260bf609fd9f609e0426e95e1
--- /dev/null
+++ b/Data/sub-008/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.12217970428408947, "GM": 0.32089877416908885, "WM": 0.5569215215468217}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_010/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-008/MRS/qc.csv b/Data/sub-008/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..45178673a7e1b5ec378f17a1d1f18d2a650dfac9
--- /dev/null
+++ b/Data/sub-008/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,8.509900828619214,19.449173981865368
+Asc,8.844997317855139,16.06066333467058
+Asp,9.766289166485171,22.87846328218373
+Cr,125.3736520460307,10.799159110501787
+GABA,11.355384865557435,22.44435787707749
+GPC,82.25899767951829,10.891116978970958
+GSH,34.71810546271368,11.999342222715338
+Glc,23.38186965371168,41.281167623987166
+Gln,8.732221250174204,25.166354769292578
+Glu,96.36143405370115,22.54654421627998
+Ins,97.61476368162987,45.141424750996414
+Lac,18.08090281697775,18.4905104283723
+Mac,83.43220044697411,34.531549619484416
+NAA,336.12503685012445,11.109795360612637
+NAAG,25.184394576238954,11.89853494073034
+PCh,25.39898589596025,11.134719389567993
+PCr,118.00175290005238,11.335535677521788
+PE,24.226420509272007,19.03109069649035
+Scyllo,15.337893162598329,11.389234737692107
+Tau,21.686722383998553,19.557215288539787
diff --git a/Data/sub-008/MRS/summary.csv b/Data/sub-008/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..f3fa704e38d8095f66864f023943459fc302bbfe
--- /dev/null
+++ b/Data/sub-008/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.056018593595385746,0.03277213754649785,0.6227096873525549,0.2826946239347088,0.4550851729184487,0.2065972867122041,45.39749897525805,8.509900828619214,19.449173981865368
+Asc,0.0736745155973674,0.039588410641700614,0.8189751228825307,0.37531815699813587,0.5985187688302229,0.27428789345335586,45.82778481440754,8.844997317855139,16.06066333467058
+Asp,0.2331510007905544,0.07079524869452443,2.591735662927824,0.7526767586777271,1.8940776035408817,0.550066973152165,29.04141689463213,9.766289166485171,22.87846328218373
+Cr,0.5102054186645072,0.04298501385154668,5.671507197001898,0.4189520231884761,4.144818823084342,0.3061761488372633,7.386960972383931,125.3736520460307,10.799159110501787
+GABA,0.13376539984008703,0.053283908764430905,1.4869529020070094,0.5459250810494373,1.0866865126322216,0.3989698810791785,36.714349211234385,11.355384865557435,22.44435787707749
+GPC,0.11238957393818995,0.0300537066981431,1.249336549829089,0.24251250324209703,0.9130330736133461,0.17723161645682203,19.411303005204893,82.25899767951829,10.891116978970958
+GSH,0.16318588848211915,0.029195360560822572,1.8139947305892299,0.22919010098986853,1.3256933727063966,0.167495413767539,12.634551640368988,34.71810546271368,11.999342222715338
+Glc,0.30052371940720224,0.04850235532910374,3.340659223003066,0.4877437562309897,2.441401685310915,0.3564501342318212,14.600224796126776,23.38186965371168,41.281167623987166
+Gln,0.11049630453888942,0.043330464239786315,1.2282907305743602,0.42332649360012814,0.8976524869783961,0.30937307457030755,34.46468194074677,8.732221250174204,25.166354769292578
+Glu,1.0282352629668994,0.04468998450928083,11.429991687255264,0.44044543947075215,8.353201899854225,0.3218838458011777,3.853418720871514,96.36143405370115,22.54654421627998
+Ins,0.8113381128113412,0.03131710367493756,9.018935859317573,0.26152105713968365,6.5911677117593745,0.19112334034213757,2.8996886242350093,97.61476368162987,45.141424750996414
+Lac,0.11595661270121405,0.03214784181763659,1.2889881985109677,0.273693479239215,0.9420110673131262,0.2000191210381994,21.233202876130612,18.08090281697775,18.4905104283723
+Mac,0.0643517894880416,0.020744232274484836,0.7153425343398231,0.01940708555354803,0.5227825864087612,0.014182976536832412,2.7129779961230023,83.43220044697411,34.531549619484416
+NAA,1.4042718000800956,0.036750784287288084,15.610060829122897,0.3377811526998679,11.408056396056883,0.24685531220583412,2.163868266737864,336.12503685012445,11.109795360612637
+NAAG,0.0926455899287206,0.031226780813072452,1.0298599560674915,0.2601830293183622,0.7526364302783275,0.19014549041495146,25.26392329223753,25.184394576238954,11.89853494073034
+PCh,0.03484075501657228,0.030213932613537647,0.3872941870015773,0.24496028899354239,0.28304014798815164,0.17902049339994425,63.24915199218953,25.39898589596025,11.134719389567993
+PCr,0.4897945813354928,0.046444585846875365,5.4446177783999765,0.46233250350235744,3.979004781011533,0.33787922618757754,8.491551148668957,118.00175290005238,11.335535677521788
+PE,0.24499218729211134,0.04975501145039423,2.7233637719361727,0.5030935128594426,1.9902733139427315,0.367667956583701,18.47323952986893,24.226420509272007,19.03109069649035
+Scyllo,0.03193893089264465,0.02245949245317243,0.3550371473833617,0.09764085548339148,0.25946624067525353,0.07135733794423385,27.501588552918644,15.337893162598329,11.389234737692107
+Tau,0.18076012428963767,0.04211794455113547,2.0093521321727885,0.40792484310156724,1.4684633643834626,0.29811732743368263,20.30131187909123,21.686722383998553,19.557215288539787
+Cr+PCr,1.0,0.029232693369688992,11.116124975401876,0.2297773699184309,8.123823604095875,0.1679245983255,2.067063571405411,,
diff --git a/Data/sub-008/MRS/voxel_location.png b/Data/sub-008/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..96b97647dd9af75b447a4d91306b49c071fca939
Binary files /dev/null and b/Data/sub-008/MRS/voxel_location.png differ
diff --git a/Data/sub-008/TMS_EEG/DCM_DefaultCodes_STR7T_HS_010_FHK.mat b/Data/sub-008/TMS_EEG/DCM_DefaultCodes_STR7T_HS_010_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..bc38999005803d33d1c7c1ee216f6e2de9ae6d75
Binary files /dev/null and b/Data/sub-008/TMS_EEG/DCM_DefaultCodes_STR7T_HS_010_FHK.mat differ
diff --git a/Data/sub-009/MRS/all_parameters.csv b/Data/sub-009/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..fc9e0fc3357d2bb65db98ff257659322f8688d2e
--- /dev/null
+++ b/Data/sub-009/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.0345142443801233,0.008476055324008235
+Asc,0.036712235023507886,0.017047741411815746
+Asp,0.08556815588550687,0.022711373824381043
+Cr,0.22348740890245028,0.015204439796249898
+GABA,0.054720804165556164,0.013124598626944012
+GPC,0.06739189182889826,0.005083439162779832
+GSH,0.07727361671417488,0.007523992630647853
+Glc,0.12867721625187897,0.02399425842961079
+Gln,0.03698721543707786,0.010888177582795972
+Glu,0.47523107826905336,0.012464313209794246
+Ins,0.3627671697126933,0.007620188721617494
+Lac,0.06335864790794891,0.00876559772677583
+Mac,0.02699191026441791,0.0005967266458261152
+NAA,0.6341791722462378,0.01159618615764226
+NAAG,0.06565461690215454,0.0056168706073053
+PCh,0.008309436490602869,0.004931522133298775
+PCr,0.22331746054635204,0.012435821380013442
+PE,0.1179016740672032,0.017092679429184292
+Scyllo,0.022789782574055048,0.003397540333362973
+Tau,0.07512752976162977,0.01565328736759181
+gamma_0,21.409940575484384,0.9901962000759267
+gamma_1,3.457380681541631,2.086686906510478
+sigma_0,4.888253520020265,1.2533806650492925
+sigma_1,12.642485208091664,5.027118930974434
+eps_0,0.48358368794070716,0.3555953932002337
+eps_1,-0.33212036329014333,3.5796522018554455
+Phi0,0.11480360083497869,0.01522531991805285
+Phi1,0.00038804154180300225,1.9608303576288493e-05
+B_real_0,0.09729584231652043,0.0
+B_imag_0,-0.27551540169917077,0.0
+B_real_1,-0.17115943113491697,2.803736533363884e-17
+B_imag_1,0.18617055741352917,0.0
+B_real_2,0.3045533860315782,0.0
+B_imag_2,0.11519938637129012,0.0
diff --git a/Data/sub-009/MRS/all_samples.csv b/Data/sub-009/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..b09d4b4f32c1d56d49c3c72b6759df706f428e6d
--- /dev/null
+++ b/Data/sub-009/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-009/MRS/concentration_samples.csv b/Data/sub-009/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..e55fca480d295afebdcfcff845b2fd0cfc9c4614
--- /dev/null
+++ b/Data/sub-009/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+PCr,molarity,4.3649313303742545,4.127279257815218,4.155586474902546,4.3016911445724455,4.222717922437119,3.9029604268571956,4.35905355873895,4.55914638817346,4.757249899432155,4.572157319396189,4.371227236704211,4.210232755973579,3.9762408779919145,3.879195293032943,3.5464626327683266,4.09234931028256,4.252610379584848,4.162036615134197,4.4179004008051646,4.450467112700703,4.520663860484395,4.593001673838852,4.550327549376576,4.515748468169719,4.108492248635022,4.071485265158788,4.539818886888103,4.361807348655997,4.323456308729856,4.595616437557689,4.569975902266615,4.545282847417972,4.488387198322185,4.074308849523721,4.007412067954214,4.283946697638492,4.379463997330251,4.352044903686142,4.489131907522126,4.489131907522126,4.3761915943321,4.362157647847323,4.452009261790551,4.15153187484886,3.9823982760372996,3.9823982760372996,4.011331095140599,4.126726817574722,4.180868659049961,4.185953714017954
+PE,molarity,2.6174664402665004,2.203605326117757,2.2659630489538665,2.413400468180018,2.7106524165228727,2.8195475018427567,2.609395436617937,2.5206670073486706,2.365631793564767,2.7538214901292153,2.64715615821341,2.278747788679066,2.0111991604221378,1.6821921620765508,1.9379234956838576,1.9697290344705598,1.7969518771715853,1.6289191541443693,2.122407621010955,1.9265786372850116,2.0002096338435913,2.53554730696224,2.760538867071563,2.5446277222059503,2.2564269894543596,2.3696870263082013,2.4576265381375038,2.5307329799702236,2.7325029360493036,2.5123400898842254,2.066765746573772,2.3833488876778772,2.456464493138405,2.53971334040453,2.756180760861586,1.8493282862685532,2.028610761151618,2.555783137078373,2.372944729394396,2.1524472128299283,2.0228222470325252,1.7049470046527375,2.1101559787510995,2.236566202595267,2.1773792640055483,2.0505290116294796,2.08455023833326,1.9998219321813535,2.0665323686745722,1.571522265863257
+Scyllo,molarity,0.3235161253907852,0.38700470382872615,0.4446467289600843,0.502304370472251,0.31947767248930037,0.4905185542323627,0.381370541237475,0.40128551031959203,0.46318708253000407,0.49422874433201647,0.36837577046578596,0.41453712910463975,0.3462180895251513,0.34369329357049033,0.44303978273785055,0.40598554219749544,0.2729720614302359,0.42633217530125717,0.3582871380650133,0.3757379835505953,0.45868590898427103,0.45804745303775757,0.444009718536203,0.5464374247321793,0.47223237152645164,0.4777124851789609,0.5021491936147126,0.522819353674466,0.47665179787643336,0.5253692145489176,0.5373040599851138,0.3691246629045025,0.47857754237757166,0.497222529341186,0.5090829929634829,0.49376992008924236,0.439518006155831,0.42110195553250596,0.5188807698784287,0.5095643231950392,0.5147143841387225,0.47963762127855797,0.4779033942459629,0.40162466596822366,0.41227350996350065,0.38498161216347626,0.3767618365170324,0.444653717255028,0.4122788374349533,0.34909555172446216
+Tau,molarity,1.6504280834133633,1.2096534429945984,1.1793983320686114,1.1541751278870829,1.5070135143286416,1.454367000286012,1.3151585859108723,1.2011233070578222,1.2732880157573006,1.3220870043218085,1.289440099228873,1.454168751254249,1.88025936211251,1.6961790175991558,1.7609384070554874,1.989215813639045,1.4827815378867044,2.002728835318815,1.9503370061794651,1.9985972177666602,1.4504325724842704,1.1841170376099819,1.2228597227341689,1.1310376266042816,1.3318293563458734,0.9897045839770069,0.9785500589615598,1.3149081090977908,0.8241702728207132,0.8887234831078585,1.113546025131385,1.3607799521649004,1.3190141549363101,1.4496513348343205,1.2679147658528498,1.690068485643291,1.5949793414642188,1.3423776739276474,1.2605478229135603,1.570176348916681,1.3107531034530795,1.9170875564391041,1.4149549714946499,1.3933302474155533,1.629114887132296,1.8359150143006207,1.9775555554627624,1.2832699040725977,1.5928037361852205,1.7000857503442166
+Cr+PCr,molarity,8.968942218995831,8.580657083830873,8.655075239581597,8.636006754643239,8.67544469593163,8.607787597802687,8.757227148487207,8.772249163093003,8.799388114361882,8.372060091365375,8.47130369667884,8.665423292341151,8.838854468137862,8.60714360058056,8.658668412981307,8.911251839372982,8.768579152438182,8.738005163245706,8.790920699313663,8.676398989708161,8.69360084313234,8.849333591161733,8.715651979038844,8.70669983393018,8.601278731175984,8.188342246928395,8.466446906416481,8.410470668173282,8.338947372806947,8.493726315560645,8.403117940066227,8.498465471313146,8.355522306900852,8.146703093046208,8.519601196309035,8.56956699794407,8.545514062404308,8.393291590647975,8.342844591341375,8.547693952396077,8.588228039830918,8.475238894138988,8.45574371955359,8.532924196861174,8.41880724654906,8.442093937882472,8.61416321066887,8.630506294865068,8.357590670836043,8.614758358786704
diff --git a/Data/sub-009/MRS/concentrations.csv b/Data/sub-009/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..6f218d47ea25dcde842ae40029273dc3ef6a8fb1
--- /dev/null
+++ b/Data/sub-009/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.0345142443801233,0.07724679550315008,0.8993181258012044,0.6625739781612262,0.008476055324008235,0.0279981447483239,0.22085577491490122,0.1627158234522159
+Asc,0.036712235023507886,0.08216614798490822,0.9565899236179801,0.7047690611104325,0.017047741411815746,0.04335675558787727,0.44420334650139437,0.3272674818399222
+Asp,0.08556815588550687,0.19151124290804492,2.229600994061931,1.6426618767766195,0.022711373824381043,0.05484317793737098,0.5917774098474968,0.4359928943712582
+Cr,0.22348740890245028,0.5001901818531073,5.823284887849571,4.290313876050504,0.015204439796249898,0.03977451042151267,0.3961734798776393,0.2918814055600707
+GABA,0.054720804165556164,0.12247136928713893,1.4258290143197654,1.050481665043609,0.013124598626944012,0.03587301138827191,0.3419802360173873,0.2519544518561642
+GPC,0.06739189182889826,0.1508307013574758,1.7559923719108166,1.2937300139938526,0.005083439162779832,0.0235258219795024,0.13245629630902178,0.0975873749901163
+GSH,0.07727361671417488,0.17294712300137402,2.013474882773143,1.4834306400954378,0.007523992630647853,0.02660059122837396,0.19604841631802014,0.14443896479492588
+Glc,0.12867721625187897,0.2879942119042273,3.352869374118474,2.4702315406858477,0.02399425842961079,0.05751445222225607,0.6252048077093159,0.4606205798870502
+Gln,0.03698721543707786,0.08278158535449015,0.9637549325760265,0.7100478922077866,0.010888177582795972,0.03190404476430229,0.283707079005036,0.20902161601757885
+Glu,0.47523107826905336,1.0636210810668174,12.382827157518195,9.123066482542269,0.012464313209794246,0.03467330945322042,0.324775552718947,0.23927887562901337
+Ins,0.3627671697126933,0.8119140916262136,9.45241876296471,6.964083702242396,0.007620188721617494,0.026737405288788714,0.19855494339963406,0.14628565238209557
+Lac,0.06335864790794891,0.14180384378109143,1.6509004184570666,1.216303359648872,0.00876559772677583,0.02844121561770622,0.22840021738129604,0.168274202755996
+Mac,0.02699191026441791,0.060410958138652986,0.7033129244680826,0.5181668520712468,0.0005967266458261152,0.020635035862811728,0.01554856837743883,0.01145543107493063
+NAA,0.6341791722462378,1.4193649523752694,16.52444765486731,12.174411596394977,0.01159618615764226,0.03313018826941223,0.3021552576054238,0.2226133392736825
+NAAG,0.06565461690215454,0.14694248293029774,1.7107251826913896,1.2603793444356557,0.0056168706073053,0.024125835663703493,0.14635561746033013,0.10782772069732446
+PCh,0.008309436490602869,0.018597461797705443,0.21651428230301048,0.15951722225816647,0.004931522133298775,0.023363286579738685,0.1284978802786575,0.09467100604212136
+PCr,0.22331746054635204,0.4998098181468928,5.818856639749859,4.28705135762067,0.012435821380013442,0.03462202541175576,0.32403315724081,0.23873191464690272
+PE,0.1179016740672032,0.2638773257163732,3.0720971719144687,2.2633721995537437,0.017092679429184292,0.04344529100095878,0.44537427097860466,0.32813016220489355
+Scyllo,0.022789782574055048,0.05100611952186086,0.5938204622471562,0.4374981162912859,0.003397540333362973,0.021950924302208727,0.08852778497140237,0.06522297836935817
+Tau,0.07512752976162977,0.1681439368696011,1.9575555100436395,1.442231958357917,0.01565328736759181,0.04063730449816403,0.40786884693200526,0.3004979847804254
+Cr+PCr,0.4468048694488024,1.0000000000000002,11.642141527599431,8.577365233671175,0.009200503551721015,0.029121161816247007,0.23973231224283023,0.1766231406433736
diff --git a/Data/sub-009/MRS/fit_summary.png b/Data/sub-009/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..df279db54d5c2216c45906c7a89d1763210312e3
Binary files /dev/null and b/Data/sub-009/MRS/fit_summary.png differ
diff --git a/Data/sub-009/MRS/options.txt b/Data/sub-009/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..67a9759af60c46043059d336411169f5ecdb7c5a
--- /dev/null
+++ b/Data/sub-009/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.11481, "GM": 0.38471, "WM": 0.50048}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_013/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-009/MRS/qc.csv b/Data/sub-009/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..45bfed924ab7b77f5782ca044b817a046fc8ade7
--- /dev/null
+++ b/Data/sub-009/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,11.417389071474975,17.985557171133085
+Asc,9.90622897233849,15.302416100225521
+Asp,7.381940893769273,17.30690788056707
+Cr,131.22958248323573,9.132920064266258
+GABA,10.26084350230335,21.03453630744043
+GPC,116.9361505302903,9.270017030599977
+GSH,38.159052686830066,9.984424457070553
+Glc,22.080754919436462,41.3466869241155
+Gln,6.467981975010879,23.692878022396723
+Glu,97.2140640145452,21.57788781161389
+Ins,98.04329313521062,33.83907895952486
+Lac,22.023155971425926,16.911443776376746
+Mac,73.15541337917894,35.07333473400809
+NAA,365.6239953263745,9.12252729579927
+NAAG,42.46753202230298,10.06753718592303
+PCh,14.409722200605229,9.196128360883328
+PCr,125.5577342275627,9.491188542468498
+PE,25.839131664151218,18.174055443751037
+Scyllo,25.992323745522164,9.324767722662205
+Tau,19.254530506792673,18.087378964988364
diff --git a/Data/sub-009/MRS/summary.csv b/Data/sub-009/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..d2c66c9d0b6457b1cb09a0ceed943a7c6e1ec292
--- /dev/null
+++ b/Data/sub-009/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.07724679550315008,0.0279981447483239,0.8993181258012044,0.22085577491490122,0.6625739781612262,0.1627158234522159,24.55813672365831,11.417389071474975,17.985557171133085
+Asc,0.08216614798490822,0.04335675558787727,0.9565899236179801,0.44420334650139437,0.7047690611104325,0.3272674818399222,46.43613062756761,9.90622897233849,15.302416100225521
+Asp,0.19151124290804492,0.05484317793737098,2.229600994061931,0.5917774098474968,1.6426618767766195,0.4359928943712582,26.541852619530143,7.381940893769273,17.30690788056707
+Cr,0.5001901818531073,0.03977451042151267,5.823284887849571,0.3961734798776393,4.290313876050504,0.2918814055600707,6.803264609366187,131.22958248323573,9.132920064266258
+GABA,0.12247136928713893,0.03587301138827191,1.4258290143197654,0.3419802360173873,1.050481665043609,0.2519544518561642,23.984659631894168,10.26084350230335,21.03453630744043
+GPC,0.1508307013574758,0.0235258219795024,1.7559923719108166,0.13245629630902178,1.2937300139938526,0.0975873749901163,7.543102033233033,116.9361505302903,9.270017030599977
+GSH,0.17294712300137402,0.02660059122837396,2.013474882773143,0.19604841631802014,1.4834306400954378,0.14443896479492588,9.736819564791602,38.159052686830066,9.984424457070553
+Glc,0.2879942119042273,0.05751445222225607,3.352869374118474,0.6252048077093159,2.4702315406858477,0.4606205798870502,18.646858494858385,22.080754919436462,41.3466869241155
+Gln,0.08278158535449015,0.03190404476430229,0.9637549325760265,0.283707079005036,0.7100478922077866,0.20902161601757885,29.43767854414126,6.467981975010879,23.692878022396723
+Glu,1.0636210810668174,0.03467330945322042,12.382827157518195,0.324775552718947,9.123066482542269,0.23927887562901337,2.622790002537995,97.2140640145452,21.57788781161389
+Ins,0.8119140916262136,0.026737405288788714,9.45241876296471,0.19855494339963406,6.964083702242396,0.14628565238209557,2.1005728626580464,98.04329313521062,33.83907895952486
+Lac,0.14180384378109143,0.02844121561770622,1.6509004184570666,0.22840021738129604,1.216303359648872,0.168274202755996,13.834887606047078,22.023155971425926,16.911443776376746
+Mac,0.060410958138652986,0.020635035862811728,0.7033129244680826,0.01554856837743883,0.5181668520712468,0.01145543107493063,2.210761076116759,73.15541337917894,35.07333473400809
+NAA,1.4193649523752694,0.03313018826941223,16.52444765486731,0.3021552576054238,12.174411596394977,0.2226133392736825,1.8285346894268102,365.6239953263745,9.12252729579927
+NAAG,0.14694248293029774,0.024125835663703493,1.7107251826913896,0.14635561746033013,1.2603793444356557,0.10782772069732446,8.555179928436953,42.46753202230298,10.06753718592303
+PCh,0.018597461797705443,0.023363286579738685,0.21651428230301048,0.1284978802786575,0.15951722225816647,0.09467100604212136,59.348454481550306,14.409722200605229,9.196128360883328
+PCr,0.4998098181468928,0.03462202541175576,5.818856639749859,0.32403315724081,4.28705135762067,0.23873191464690272,5.568674007661057,125.5577342275627,9.491188542468498
+PE,0.2638773257163732,0.04344529100095878,3.0720971719144687,0.44537427097860466,2.2633721995537437,0.32813016220489355,14.49740180910542,25.839131664151218,18.174055443751037
+Scyllo,0.05100611952186086,0.021950924302208727,0.5938204622471562,0.08852778497140237,0.4374981162912859,0.06522297836935817,14.908173530496477,25.992323745522164,9.324767722662205
+Tau,0.1681439368696011,0.04063730449816403,1.9575555100436395,0.40786884693200526,1.442231958357917,0.3004979847804254,20.83562099972903,19.254530506792673,18.087378964988364
+Cr+PCr,1.0000000000000002,0.029121161816247007,11.642141527599431,0.23973231224283023,8.577365233671175,0.1766231406433736,2.0591770996299013,,
diff --git a/Data/sub-009/MRS/voxel_location.png b/Data/sub-009/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..b430abb02070d1c78b6acf3dfd7672d73e08dd93
Binary files /dev/null and b/Data/sub-009/MRS/voxel_location.png differ
diff --git a/Data/sub-009/TMS_EEG/DCM_DefaultCodes_STR7T_HS_013_FHK.mat b/Data/sub-009/TMS_EEG/DCM_DefaultCodes_STR7T_HS_013_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..3d83459c1d1c78d97d7f425a8de457f9db882108
Binary files /dev/null and b/Data/sub-009/TMS_EEG/DCM_DefaultCodes_STR7T_HS_013_FHK.mat differ
diff --git a/Data/sub-010/MRS/all_parameters.csv b/Data/sub-010/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..1ee6d228c2453d12ba7c96144de776e7e14b6099
--- /dev/null
+++ b/Data/sub-010/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.002852966249329441,0.0028554871256102838
+Asc,0.05392181455686165,0.020190342757658998
+Asp,0.09103390093930798,0.029154304210040498
+Cr,0.2557190909939056,0.021626205125691196
+GABA,0.06899422228045103,0.018825397303549932
+GPC,0.05089827796552262,0.008597597600142292
+GSH,0.07434267576973232,0.010713381502930962
+Glc,0.14355321381332814,0.020180894268153716
+Gln,0.020341329168321595,0.014288827366177191
+Glu,0.4542666016102547,0.023371500560022157
+Ins,0.3770733564279852,0.011916037788561758
+Lac,0.020662428808021806,0.00938559386178874
+Mac,0.026916612242847388,0.0007357381379481863
+NAA,0.7207068352834105,0.01676912610847516
+NAAG,0.055321253844871736,0.011573351608606189
+PCh,0.03213773369939075,0.009086025148215061
+PCr,0.17656665650600145,0.016927203847485386
+PE,0.10243474821364916,0.021085674294862286
+Scyllo,0.020348875877514563,0.004825720464703358
+Tau,0.059846192625204485,0.018179464431612315
+gamma_0,26.749681124363352,1.6887671188164344
+gamma_1,3.5389527263829903,2.8589353444230206
+sigma_0,8.046155753954896,1.455720545555205
+sigma_1,11.926702733703566,5.988035470199581
+eps_0,0.2022857751385194,0.7088891212287997
+eps_1,1.896105879384987,4.197328128207004
+Phi0,-0.0860309679721255,0.017806237287489396
+Phi1,0.0002879755807667871,2.4183133343684024e-05
+B_real_0,0.23097635511339829,2.803736533363884e-17
+B_imag_0,-0.5086585429759398,0.0
+B_real_1,-0.38059287878301185,0.0
+B_imag_1,0.0009592146136736673,0.0
+B_real_2,0.2125641389853083,2.803736533363884e-17
+B_imag_2,0.45843687605774486,1.1214946133455537e-16
diff --git a/Data/sub-010/MRS/all_samples.csv b/Data/sub-010/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..440e1737ffbc14926d3a40727b066d9415af1637
--- /dev/null
+++ b/Data/sub-010/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.004080617490524233,0.0016186855419152355,0.001611597129607841,0.0002943406711799755,0.003290773440143458,0.005602362281554818,0.007725109168282896,0.00455341316317669,0.002567138658791001,0.0020155545958100663,0.0003485953058085939,0.0030398353136454597,0.0005891223545523682,0.0019410983465854151,0.010431862301867554,0.003977838864218365,0.007752819486396795,0.0021913661349422632,0.007012388491407822,0.0009356611641618173,0.00022015215630200534,0.0006154523967945839,0.0009442430173550957,0.004079242173004687,0.0003810473613901624,9.685906738320224e-06,9.685906738320224e-06,0.00025694308855328334,0.0006095582121202005,0.0005340704883527985,1.9446650206760615e-05,0.0010861618970925717,0.0021558553060805974,0.010370320828963078,0.00966197905764975,0.00011439022608990919,0.001985830920357922,0.002471386405297043,0.0010235276679728127,0.00478514401441572,0.003502226845100652,0.003214400088248219,0.0005495481483257308,0.001216167252888791,0.001864280952339516,0.0022406412203324474,0.007684021607061015,0.00260653758782886,0.006292736822216099,0.0005634483560824378
+Asc,0.05084067429796137,0.05581044222931926,0.04225581879131435,0.06476685194987696,0.05634702859813677,0.038933764407748955,0.027511602839024013,0.03546685975781379,0.04981093685118492,0.022114509752755095,0.05583020564207365,0.03684405652469621,0.022831849119413418,0.029921063646260685,0.019770387068133492,0.07135579266038593,0.07537073191205934,0.007367788264407146,0.07986639888320468,0.07540586911187341,0.060707769915660355,0.04232774044351405,0.058758250955100295,0.03416454952224248,0.05350251896026504,0.04548026755143847,0.058200456111858645,0.0451175650512943,0.10741444155641595,0.07993327367770485,0.08682468821984037,0.060294809522257665,0.06656793747764159,0.07755941527748793,0.08818000527456557,0.0421987438374104,0.07842886447390077,0.056824194776626036,0.06730455401381337,0.06804583259222798,0.050996615176967505,0.05279527764414938,0.061090720856678965,0.0474778435063503,0.02990793300126825,0.06492074951887497,0.03587897876546425,0.06776085504045408,0.058743766967087746,0.030259475846877402
+Asp,0.04528462303780664,0.11616185233740325,0.06139299866282688,0.09512301014048911,0.07987202326359338,0.07021074698249173,0.0898304299977103,0.07463971299650277,0.08473733476273107,0.054915407568519356,0.06657336533886948,0.03414190718724157,0.0775208142761202,0.14091724022407456,0.09469314285068053,0.07847953676675086,0.10411093582105532,0.06477193069435565,0.044327493226739886,0.10437371866915919,0.09345032237850465,0.08727130620469412,0.11086416716687761,0.07770646957241123,0.1420578354526702,0.12256170425364847,0.12300777791963996,0.12964376352489618,0.13724873370229657,0.13981800489980645,0.10491153622467544,0.11237882188281192,0.15194766008167976,0.10909706015716247,0.12587944166697063,0.06445535450105153,0.06630421152251516,0.05522415930664244,0.09669503694988192,0.10275378244244901,0.08525085077732711,0.07819379466614504,0.047196095081005605,0.06036829050497354,0.11274035567207724,0.07603699450678494,0.07049178652168464,0.06074551426561579,0.10806201350941777,0.11725397684396037
+Cr,0.2651343622945201,0.2768193102863615,0.26950116928043677,0.2792467453316977,0.2896879553157222,0.27298505758507663,0.26871671387506346,0.27667330884505476,0.2788368178962532,0.2839082472357311,0.300706096953279,0.30912277421533213,0.28857531318125723,0.2647003642292385,0.2705185794156188,0.275838933016886,0.27248469309848317,0.24593356181600212,0.24687655573612732,0.2493021517420047,0.2434671070598849,0.255033457963822,0.2568480414740827,0.25417462238256483,0.2561967749782277,0.23531341199589553,0.2506861086997791,0.2560617658117349,0.25660453596739424,0.2379718092707172,0.21969024056486683,0.21309068799099834,0.22539208950854991,0.2456791461846318,0.23984164240156874,0.2519209566627694,0.24696726639822414,0.2513650541748169,0.23256639419507869,0.21603294268901993,0.22813100209105627,0.23293551719654043,0.2274434207279135,0.23962850260894736,0.22986927688701492,0.25696807982674036,0.2437906955287798,0.25626013158051764,0.2693403399593554,0.27111481556363987
+GABA,0.10358747520458894,0.07740831017929202,0.05943281612557812,0.08021082169644056,0.08947868716055896,0.07125013935432052,0.08262040549578574,0.0956108266954072,0.036552703359844424,0.05879168565897352,0.06459767088111291,0.06477634947671854,0.07391012739999789,0.045141131528545965,0.06991563902703672,0.08060580398829778,0.05466363586277248,0.07005892076997929,0.06707830510401458,0.07664156887329948,0.07394060836571398,0.05695205074704025,0.05688267256783172,0.06984454828738777,0.07628308327163055,0.09280539327111373,0.07372167163253628,0.10859436904980062,0.08155169092410089,0.08657672870747292,0.08260491579392654,0.08818250650103703,0.09115631004709135,0.0605815460403862,0.07624387405973093,0.06437214156913633,0.02252196126855657,0.035324673617856094,0.06450913741170107,0.042605010142290727,0.0464852941143689,0.0334551553863403,0.06364422384227346,0.03434386936798842,0.08028594039041038,0.08002672137996829,0.07741028938095874,0.05160130103992618,0.09180957536591056,0.0630608266354993
+GPC,0.05263379659122528,0.05516041584885765,0.04528950533022818,0.056131064171502584,0.04742978873845702,0.050531867602970924,0.05174141177053622,0.0642996869352997,0.057733037978284545,0.060967358604044286,0.05877546660370483,0.051590735775227214,0.05330583655449875,0.0352440977585608,0.03667320309476372,0.0366702326134831,0.04236685610193319,0.04530713424567817,0.04823347374021164,0.0535303932762892,0.04088200391866222,0.04303815751995657,0.048333567548339215,0.04462450641218298,0.04692461987465192,0.04412442108613663,0.04754128896976202,0.043198292816065055,0.04594248247702166,0.04479387944507347,0.048386671378604744,0.04254731132171299,0.04777412700390823,0.04653102285944333,0.05506345520782034,0.06058200505681487,0.06033511855152573,0.07046022225942584,0.061364748210986884,0.05872109244337081,0.057707335114030915,0.05801964226470339,0.06645032565886674,0.06711236631979493,0.0588018026391199,0.057956408928713864,0.05268227725709455,0.04440813672348148,0.04282728250088276,0.0341639631722203
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diff --git a/Data/sub-010/MRS/concentration_samples.csv b/Data/sub-010/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..0559cf737bdb25d64ec122b35007fa05ae14ae79
--- /dev/null
+++ b/Data/sub-010/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+Scyllo,molarity,0.38033358608116263,0.3147493982574816,0.46687379224687725,0.39235654374006834,0.3800208093576715,0.29581572893492614,0.32111435537034594,0.29516027609175194,0.28743761249132643,0.3579883135114391,0.42181536959000887,0.1433769140687504,0.4097516787840575,0.3347589586029187,0.368768469793058,0.41395859663208356,0.386662986716869,0.3286963604848565,0.3093924604488664,0.279179852978459,0.3553497993131307,0.29023189160457813,0.37133582835483836,0.37196227182298597,0.4318120485695343,0.4396469324889504,0.3683301657678063,0.3072378629793971,0.45328055468326106,0.3057614446733927,0.3498587845840337,0.28366072064085857,0.3980865719473005,0.3090702284687241,0.21674471213181146,0.5190689534896337,0.4968936703605492,0.43234999804019836,0.3238223957650681,0.4336069722148572,0.36013464624974256,0.20421431433904302,0.4258438268970449,0.35540457363374167,0.24841159097009288,0.3044906619487831,0.10783618411351091,0.30465691755400504,0.3900761162319704,0.24938624709714538
+Tau,molarity,0.7005952754505839,0.7703458096024802,0.5545895343189566,0.7111220812969724,0.6119497468620627,0.5146954344196272,0.5616377945592465,0.6392088651168466,1.0241475980841688,0.6319236574695717,0.831865735821255,1.172625561003358,0.5173225011656895,0.33521724171684114,0.8064538441113375,0.8703478836338927,1.3467412458524748,1.3225222993156918,1.147961111673633,0.8921716436904399,0.7225530673663099,1.1642348854277442,1.2982993214180758,0.8004134491204828,1.1561638131824494,0.672955568607253,1.2746299847978282,1.194496008494352,1.4536196733350735,1.4083927349103158,1.4944636392002784,1.3036995853670508,1.4388595483236786,1.3514034368008605,1.2789933111769642,1.1074987222655812,0.7175226078904147,1.0138673544122194,0.8546905887976493,1.29113489507965,1.2757973784897325,1.0701595659142846,1.017395929825992,1.200180496287875,1.2734374545554468,1.1406405438955503,0.8754173272040645,1.3331550832391508,1.3728394011933402,1.3495930242280683
+Cr+PCr,molarity,7.274620223095473,7.3000113654718675,7.364562097720357,7.4741745216314746,7.287983406211243,7.318675761860878,7.101517175418433,7.380374252171882,7.410745327477665,7.423138545632953,7.689767388381527,7.897635512078304,7.734164104729506,7.410124266876199,7.4718412362441775,7.490800552698498,7.866511171881758,7.4379833790123415,7.411960591184047,7.1645026078132785,7.2844067775098305,7.46255851888062,7.350371690057059,7.400343095544003,7.424488814214065,6.885639438131682,7.201243091979531,7.076877982465983,7.4111501320329065,7.208086374997658,7.130792150738817,6.932480735097778,7.097764928231751,7.191355998610484,7.174074967870668,7.573996668685401,7.4057368031935535,7.573549366185059,7.406765248106421,7.346293194141828,7.420811646807038,7.272417840769182,7.111515322088085,7.154467096948214,7.184192062670935,7.488447899998193,7.2612715601777795,7.360063313475418,7.335288452532678,7.410321415626955
diff --git a/Data/sub-010/MRS/concentrations.csv b/Data/sub-010/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..edc11829405e90f4b21e158b0b1fd158dd903b8c
--- /dev/null
+++ b/Data/sub-010/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.002852966249329441,0.0065997231364424164,0.06891685072485021,0.04850108366347914,0.0028554871256102838,0.02819857684286252,0.0689777455406874,0.048543939141153014
+Asc,0.05392181455686165,0.12473650789718264,1.3025466549075804,0.9166832729702445,0.020190342757658998,0.054156973894443475,0.4877221517219813,0.34324047945316644
+Asp,0.09103390093930798,0.2105873290197419,2.199033992571651,1.5475972934162836,0.029154304210040498,0.07280094411606744,0.7042574834884496,0.49562988975913946
+Cr,0.2557190909939056,0.5915510573106753,6.177203962950336,4.347283473668629,0.021626205125691196,0.0570463325633205,0.5224071440531606,0.36765047058346434
+GABA,0.06899422228045103,0.15960327787689987,1.666638895183761,1.1729176774899959,0.018825397303549932,0.051458706978731124,0.454750243228319,0.32003609220134066
+GPC,0.05089827796552262,0.11774220700055249,1.2295094712481487,0.8652824541871298,0.008597597600142292,0.03386866410750365,0.2076853697587912,0.14616114039464662
+GSH,0.07434267576973232,0.17197577343155018,1.7958372587522882,1.2638426192816588,0.010713381502930962,0.03695576406427585,0.25879468920089804,0.18212995429390494
+Glc,0.14355321381332814,0.3320794512508396,3.467701522852203,2.4404377145919605,0.020180894268153716,0.05413812509014551,0.48749391202900777,0.34307985295430865
+Gln,0.020341329168321595,0.047055285273604745,0.49136941110598586,0.34580728322706883,0.014288827366177191,0.042943004074405225,0.3451639089174086,0.24291335787896476
+Glu,0.4542666016102547,1.0508479732155696,10.973359246649766,7.722636906553591,0.023371500560022157,0.060618013084957456,0.5645668663936615,0.39732089514522345
+Ins,0.3770733564279852,0.872278021213425,9.108663035664577,6.410333950386237,0.011916037788561758,0.03887629045020168,0.287846306523606,0.20257538828440455
+Lac,0.020662428808021806,0.04779808015305027,0.4991259613078061,0.35126605109474807,0.00938559386178874,0.034970241798204425,0.22672037262585717,0.159557258424997
+Mac,0.026916612242847388,0.06226578692107627,0.6502033272896195,0.4575886106730524,0.0007357381379481863,0.02746676340138027,0.017772644677262483,0.012507717885349856
+NAA,0.7207068352834105,1.6672000857108191,17.409545379402974,12.252182276302001,0.01676912610847516,0.04750081296516713,0.40507852522812005,0.28507900804706277
+NAAG,0.055321253844871736,0.12797380937219918,1.3363518036831574,0.9404740633469936,0.011573351608606189,0.03831828336948709,0.27956830733065446,0.1967496442580777
+PCh,0.03213773369939075,0.07434372723425878,0.7763258315854499,0.5463488785663423,0.009086025148215061,0.03454426678428462,0.2194839279886151,0.15446452126295981
+PCr,0.17656665650600145,0.4084489426893248,4.2651811644354565,3.0016738478385996,0.016927203847485386,0.04779991218375353,0.4088970842260928,0.2877663660369691
+PE,0.10243474821364916,0.23696073443566676,2.474435249045421,1.741414324240723,0.021085674294862286,0.05595300214401418,0.5093499680037871,0.35846132190184754
+Scyllo,0.020348875877514563,0.04707274296041634,0.4915517109951058,0.3459355790223795,0.004825720464703358,0.029599744508545762,0.11657111505752438,0.0820383599175604
+Tau,0.059846192625204485,0.13844128096130986,1.44565717332662,1.0173990653194573,0.018179464431612315,0.05020048377460836,0.43914695338075715,0.3090550845324973
+Cr+PCr,0.43228574749990706,1.0,10.442385127385792,7.348957321507228,0.011850673501754009,0.03876922449181506,0.2862673531105662,0.2014641803464167
diff --git a/Data/sub-010/MRS/fit_summary.png b/Data/sub-010/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..269e89f1de59a414a624769229b5b5aac4e83392
Binary files /dev/null and b/Data/sub-010/MRS/fit_summary.png differ
diff --git a/Data/sub-010/MRS/options.txt b/Data/sub-010/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..1cf2fe7363323599451bf8f6681a69cf01013690
--- /dev/null
+++ b/Data/sub-010/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.03594842908999875, "GM": 0.32506796845662783, "WM": 0.6389836024533734}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_014/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-010/MRS/qc.csv b/Data/sub-010/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..62f29d436a6f7aa8fcc282e65faa6ba1fa326db5
--- /dev/null
+++ b/Data/sub-010/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,1.0406812325931483,19.938570214472904
+Asc,15.470038694846174,16.92691711724526
+Asp,9.204465692591716,23.543507622638213
+Cr,146.36524989167535,11.657584034927408
+GABA,14.138838279006565,23.137844001411928
+GPC,87.96639590912712,11.32086076579629
+GSH,37.081466547988605,12.932818268412428
+Glc,27.699315374168574,42.5653839908026
+Gln,3.9049568235537144,26.334830526247142
+Glu,103.18276759805114,23.26852994385233
+Ins,112.30011031940185,44.969948641272204
+Lac,7.785229487371052,19.0998568138693
+Mac,89.68782083002026,34.544553416269395
+NAA,399.15064067415216,12.008255775724365
+NAAG,35.93116456193692,12.689176313348597
+PCh,54.018946833482815,12.067260594887076
+PCr,101.41262147419249,11.553402779607408
+PE,24.51315484572753,19.531766414343004
+Scyllo,23.054795466382014,12.093138605719796
+Tau,17.266465019525278,20.182819220487847
diff --git a/Data/sub-010/MRS/summary.csv b/Data/sub-010/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..bbd65a7499e6701440b02a5197de26087fcb88dc
--- /dev/null
+++ b/Data/sub-010/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.0065997231364424164,0.02819857684286252,0.06891685072485021,0.0689777455406874,0.04850108366347914,0.048543939141153014,100.08835983536206,1.0406812325931483,19.938570214472904
+Asc,0.12473650789718264,0.054156973894443475,1.3025466549075804,0.4877221517219813,0.9166832729702445,0.34324047945316644,37.44373761081031,15.470038694846174,16.92691711724526
+Asp,0.2105873290197419,0.07280094411606744,2.199033992571651,0.7042574834884496,1.5475972934162836,0.49562988975913946,32.025766125827765,9.204465692591716,23.543507622638213
+Cr,0.5915510573106753,0.0570463325633205,6.177203962950336,0.5224071440531606,4.347283473668629,0.36765047058346434,8.457016267982354,146.36524989167535,11.657584034927408
+GABA,0.15960327787689987,0.051458706978731124,1.666638895183761,0.454750243228319,1.1729176774899959,0.32003609220134066,27.28546924846482,14.138838279006565,23.137844001411928
+GPC,0.11774220700055249,0.03386866410750365,1.2295094712481487,0.2076853697587912,0.8652824541871298,0.14616114039464662,16.891725896829193,87.96639590912712,11.32086076579629
+GSH,0.17197577343155018,0.03695576406427585,1.7958372587522882,0.25879468920089804,1.2638426192816588,0.18212995429390494,14.410809662157439,37.081466547988605,12.932818268412428
+Glc,0.3320794512508396,0.05413812509014551,3.467701522852203,0.48749391202900777,2.4404377145919605,0.34307985295430865,14.058127806456694,27.699315374168574,42.5653839908026
+Gln,0.047055285273604745,0.042943004074405225,0.49136941110598586,0.3451639089174086,0.34580728322706883,0.24291335787896476,70.24529836737405,3.9049568235537144,26.334830526247142
+Glu,1.0508479732155696,0.060618013084957456,10.973359246649766,0.5645668663936615,7.722636906553591,0.39732089514522345,5.144886389881268,103.18276759805114,23.26852994385233
+Ins,0.872278021213425,0.03887629045020168,9.108663035664577,0.287846306523606,6.410333950386237,0.20257538828440455,3.160137831387068,112.30011031940185,44.969948641272204
+Lac,0.04779808015305027,0.034970241798204425,0.4991259613078061,0.22672037262585717,0.35126605109474807,0.159557258424997,45.42347828027341,7.785229487371052,19.0998568138693
+Mac,0.06226578692107627,0.02746676340138027,0.6502033272896195,0.017772644677262483,0.4575886106730524,0.012507717885349856,2.7333979897254554,89.68782083002026,34.544553416269395
+NAA,1.6672000857108191,0.04750081296516713,17.409545379402974,0.40507852522812005,12.252182276302001,0.28507900804706277,2.326761075032801,399.15064067415216,12.008255775724365
+NAAG,0.12797380937219918,0.03831828336948709,1.3363518036831574,0.27956830733065446,0.9404740633469936,0.1967496442580777,20.9202626553972,35.93116456193692,12.689176313348597
+PCh,0.07434372723425878,0.03454426678428462,0.7763258315854499,0.2194839279886151,0.5463488785663423,0.15446452126295981,28.272140261051792,54.018946833482815,12.067260594887076
+PCr,0.4084489426893248,0.04779991218375353,4.2651811644354565,0.4088970842260928,3.0016738478385996,0.2877663660369691,9.586863217806945,101.41262147419249,11.553402779607408
+PE,0.23696073443566676,0.05595300214401418,2.474435249045421,0.5093499680037871,1.741414324240723,0.35846132190184754,20.584493702160216,24.51315484572753,19.531766414343004
+Scyllo,0.04707274296041634,0.029599744508545762,0.4915517109951058,0.11657111505752438,0.3459355790223795,0.0820383599175604,23.714924076153817,23.054795466382014,12.093138605719796
+Tau,0.13844128096130986,0.05020048377460836,1.44565717332662,0.43914695338075715,1.0173990653194573,0.3090550845324973,30.376977438588053,17.266465019525278,20.182819220487847
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diff --git a/Data/sub-010/MRS/voxel_location.png b/Data/sub-010/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..8fac864bf7e8e25f76f46259623d333e1940403c
Binary files /dev/null and b/Data/sub-010/MRS/voxel_location.png differ
diff --git a/Data/sub-010/TMS_EEG/DCM_DefaultCodes_STR7T_HS_014_FHK.mat b/Data/sub-010/TMS_EEG/DCM_DefaultCodes_STR7T_HS_014_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..a2228371e56342b830e5a7a91c9c7af0ad48df21
Binary files /dev/null and b/Data/sub-010/TMS_EEG/DCM_DefaultCodes_STR7T_HS_014_FHK.mat differ
diff --git a/Data/sub-011/MRS/all_parameters.csv b/Data/sub-011/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..98afb9c78a312cb83c6ec19ef08d73c2329954a6
--- /dev/null
+++ b/Data/sub-011/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.027576967043938572,0.010779312758880099
+Asc,0.024109513615312234,0.012719697749955749
+Asp,0.0985095469666743,0.030960534238908474
+Cr,0.19486282794650367,0.012604022812323805
+GABA,0.08105219403001594,0.01659013345317855
+GPC,0.058720063163981824,0.004921793889000699
+GSH,0.06603380538706281,0.009610934723510399
+Glc,0.06922251638802987,0.022174657051618973
+Gln,0.08385666064650243,0.01756472554484454
+Glu,0.42997687129989054,0.0178743021131735
+Ins,0.35001086871205156,0.01107899664656889
+Lac,0.04014921085920806,0.010722079954362354
+Mac,0.025335329110725207,0.0008041826585585734
+NAA,0.5836191011851253,0.011398826143185034
+NAAG,0.08134629510530779,0.008409731446550129
+PCh,0.010023052258237703,0.0046991718685862344
+PCr,0.21671808086417202,0.011718201276185067
+PE,0.09325674667283694,0.019558853044879042
+Scyllo,0.010874666487035676,0.003405523747494423
+Tau,0.07243106401202126,0.014301408525503784
+gamma_0,11.994583670473341,1.2330603923429018
+gamma_1,4.143375352728746,3.6986872875431964
+sigma_0,10.25409747036618,0.6791475428572671
+sigma_1,9.889832564674967,4.700156485989277
+eps_0,0.18115037264069792,0.47150882413073836
+eps_1,-5.850117395623621,4.769271982651481
+Phi0,0.14591322085111494,0.01683423102838111
+Phi1,0.0003984162193899346,2.273670058941338e-05
+B_real_0,0.08592752288278227,0.0
+B_imag_0,0.10012473781462969,2.803736533363884e-17
+B_real_1,0.2014292384601339,2.803736533363884e-17
+B_imag_1,0.23861703597570205,0.0
+B_real_2,0.4196792088066278,5.607473066727768e-17
+B_imag_2,-0.26085964133415396,0.0
diff --git a/Data/sub-011/MRS/all_samples.csv b/Data/sub-011/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..3a31217c53fbb37bbe55ca7734d42aba97386772
--- /dev/null
+++ b/Data/sub-011/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-011/MRS/concentration_samples.csv b/Data/sub-011/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..590214fc7c06a948de2b0694ee2140b659b054c2
--- /dev/null
+++ b/Data/sub-011/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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diff --git a/Data/sub-011/MRS/concentrations.csv b/Data/sub-011/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..75fa760d6e586925c2fbfc7f81ea2dd49a6bb8ae
--- /dev/null
+++ b/Data/sub-011/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.027576967043938572,0.0670025417933653,0.7070707662167687,0.5079548999399415,0.010779312758880099,0.0366859723598613,0.27638053595842416,0.19854992483888
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+Asp,0.0985095469666743,0.23934430596242257,2.5257752508611335,1.8145000134662912,0.030960534238908474,0.07948905692476432,0.7938251016475443,0.570278633119975
+Cr,0.19486282794650367,0.47344962746107155,4.996264050494458,3.5892826108785765,0.012604022812323805,0.039971719545387384,0.3231659251404977,0.23216023489000398
+GABA,0.08105219403001594,0.19692894469820849,2.0781704110187946,1.492943696195149,0.01659013345317855,0.04779857441407645,0.42536941621198876,0.3055825379481625
+GPC,0.058720063163981824,0.1426695502803135,1.5055767368289918,1.0815962379547988,0.004921793889000699,0.0283362572242376,0.12619431900222877,0.09065715306650726
+GSH,0.06603380538706281,0.16043942751833978,1.6931003796337385,1.2163119662360276,0.009610934723510399,0.03471634937491246,0.24642343620255092,0.17702894513496115
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+Ins,0.35001086871205156,0.8504059863307559,8.97424480110926,6.447037323257794,0.01107899664656889,0.037209275103458325,0.2840644018365432,0.20406996259147367
+Lac,0.04014921085920806,0.09754876866185358,1.0294218809482394,0.7395297804926392,0.010722079954362354,0.03658683020075906,0.2749130923893537,0.19749572321308942
+Mac,0.025335329110725207,0.06155613287296394,0.6495953865460325,0.46666497236187415,0.0008041826585585734,0.02576356009163569,0.0206191655398243,0.014812670342271819
+NAA,0.5836191011851253,1.4179936160585767,14.963937274037946,10.749992255246545,0.011398826143185034,0.03777524159251125,0.29226479917794723,0.20996107308570056
+NAAG,0.08134629510530779,0.1976435091228357,2.0857111341273384,1.4983609011413666,0.008409731446550129,0.0328243931873228,0.21562470042899254,0.15490333975625087
+PCh,0.010023052258237703,0.024352568459020136,0.2569900899098537,0.1846199583447302,0.0046991718685862344,0.028112269750404734,0.12048631194328067,0.0865565590481773
+PCr,0.21671808086417202,0.5265503725389284,5.556630620238525,3.9918461992263548,0.011718201276185067,0.038347782615038864,0.30045354668020574,0.2158438144135579
+PE,0.09325674667283694,0.22658180852536672,2.391093959672384,1.7177458764573368,0.019558853044879042,0.05402051219336555,0.5014870992422472,0.3602649713263255
+Scyllo,0.010874666487035676,0.02642169802885086,0.2788253963203764,0.20030629613841391,0.003405523747494423,0.026989008562144368,0.087317299312636,0.06272816265999949
+Tau,0.07243106401202126,0.1759825649380133,1.8571254716762817,1.3341464931277345,0.014301408525503784,0.04321264006224988,0.36668673056015544,0.26342528984416486
+Cr+PCr,0.4115809088106756,0.9999999999999998,10.55289467073298,7.5811288101049294,0.01057325122742014,0.03633024507235766,0.271097138233611,0.1947543673206278
diff --git a/Data/sub-011/MRS/fit_summary.png b/Data/sub-011/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..802e9efe181fbd7741f41dee86f90340779ed699
Binary files /dev/null and b/Data/sub-011/MRS/fit_summary.png differ
diff --git a/Data/sub-011/MRS/options.txt b/Data/sub-011/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..1915fcabb51c3759746e8db3d6449f9e1c528377
--- /dev/null
+++ b/Data/sub-011/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.07755107755107755, "GM": 0.3352073352073352, "WM": 0.5872415872415873}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_015/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-011/MRS/qc.csv b/Data/sub-011/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..ae199583d3f449bf741f0f2bbb5bc64f8f180bd9
--- /dev/null
+++ b/Data/sub-011/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,11.34820438025344,17.50177551192791
+Asc,8.30713039352614,14.347219591554124
+Asp,10.411805029258321,11.834636909931724
+Cr,149.44691622134968,8.825037841244109
+GABA,18.812441377415915,20.228936534151547
+GPC,132.81431906094755,8.927505851147188
+GSH,42.053860058751816,9.551345117203175
+Glc,14.21824896402318,38.88367150566367
+Gln,18.015390754428978,22.846267642800175
+Glu,108.75309190950877,20.4184004902567
+Ins,116.08757574625484,19.713891850239545
+Lac,17.407372802703197,16.538184301435265
+Mac,76.88352398013552,35.006107277304736
+NAA,440.3810559519175,8.821291228566523
+NAAG,68.0553838328731,9.515623498756629
+PCh,22.785845683859833,8.877533447558484
+PCr,158.68796042532324,9.055850947943394
+PE,25.65254337428188,17.3738400169998
+Scyllo,16.224415273897034,8.958615155902327
+Tau,23.21566293468753,17.172444056367866
diff --git a/Data/sub-011/MRS/summary.csv b/Data/sub-011/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..c4258c385890bd2822ef610436396dd7b5b8eba5
--- /dev/null
+++ b/Data/sub-011/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.0670025417933653,0.0366859723598613,0.7070707662167687,0.27638053595842416,0.5079548999399415,0.19854992483888,39.088101101565464,11.34820438025344,17.50177551192791
+Asc,0.058577822972839685,0.040187445875857514,0.6181655958732201,0.32613181934681773,0.44408602137262143,0.2342909134115678,52.75800230941747,8.30713039352614,14.347219591554124
+Asp,0.23934430596242257,0.07948905692476432,2.5257752508611335,0.7938251016475443,1.8145000134662912,0.570278633119975,31.428968249526513,10.411805029258321,11.834636909931724
+Cr,0.47344962746107155,0.039971719545387384,4.996264050494458,0.3231659251404977,3.5892826108785765,0.23216023489000398,6.468151440244944,149.44691622134968,8.825037841244109
+GABA,0.19692894469820849,0.04779857441407645,2.0781704110187946,0.42536941621198876,1.492943696195149,0.3055825379481625,20.46845696371248,18.812441377415915,20.228936534151547
+GPC,0.1426695502803135,0.0283362572242376,1.5055767368289918,0.12619431900222877,1.0815962379547988,0.09065715306650726,8.381792565951578,132.81431906094755,8.927505851147188
+GSH,0.16043942751833978,0.03471634937491246,1.6931003796337385,0.24642343620255092,1.2163119662360276,0.17702894513496115,14.554567417665968,42.053860058751816,9.551345117203175
+Glc,0.1681868981436934,0.05968795151164036,1.774858621107693,0.5685560608278916,1.2750465389993375,0.40844686385965,32.033878871605815,14.21824896402318,38.88367150566367
+Gln,0.20374283367228752,0.049811693341228765,2.1500766636603195,0.4503578631251362,1.544600666205396,0.3235340707478243,20.94613046766625,18.015390754428978,22.846267642800175
+Glu,1.0446958595391918,0.050457602541386724,11.02456536866795,0.4582953763774947,7.919973878549901,0.3292363270742266,4.1570380423338955,108.75309190950877,20.4184004902567
+Ins,0.8504059863307559,0.037209275103458325,8.97424480110926,0.2840644018365432,6.447037323257794,0.20406996259147367,3.1653293188684963,116.08757574625484,19.713891850239545
+Lac,0.09754876866185358,0.03658683020075906,1.0294218809482394,0.2749130923893537,0.7395297804926392,0.19749572321308942,26.705580819413015,17.407372802703197,16.538184301435265
+Mac,0.06155613287296394,0.02576356009163569,0.6495953865460325,0.0206191655398243,0.46666497236187415,0.014812670342271819,3.1741551690289223,76.88352398013552,35.006107277304736
+NAA,1.4179936160585767,0.03777524159251125,14.963937274037946,0.29226479917794723,10.749992255246545,0.20996107308570056,1.9531276683778898,440.3810559519175,8.821291228566523
+NAAG,0.1976435091228357,0.0328243931873228,2.0857111341273384,0.21562470042899254,1.4983609011413666,0.15490333975625087,10.33818618987283,68.0553838328731,9.515623498756629
+PCh,0.024352568459020136,0.028112269750404734,0.2569900899098537,0.12048631194328067,0.1846199583447302,0.0865565590481773,46.88364130521318,22.785845683859833,8.877533447558484
+PCr,0.5265503725389284,0.038347782615038864,5.556630620238525,0.30045354668020574,3.9918461992263548,0.2158438144135579,5.407117500052728,158.68796042532324,9.055850947943394
+PE,0.22658180852536672,0.05402051219336555,2.391093959672384,0.5014870992422472,1.7177458764573368,0.3602649713263255,20.973123921527474,25.65254337428188,17.3738400169998
+Scyllo,0.02642169802885086,0.026989008562144368,0.2788253963203764,0.087317299312636,0.20030629613841391,0.06272816265999949,31.316121294886113,16.224415273897034,8.958615155902327
+Tau,0.1759825649380133,0.04321264006224988,1.8571254716762817,0.36668673056015544,1.3341464931277345,0.26342528984416486,19.744854946670674,23.21566293468753,17.172444056367866
+Cr+PCr,0.9999999999999998,0.03633024507235766,10.55289467073298,0.271097138233611,7.5811288101049294,0.1947543673206278,2.568936265283326,,
diff --git a/Data/sub-011/MRS/voxel_location.png b/Data/sub-011/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..b01b13072e7f2e0187f911c06d75d25b90ab59c5
Binary files /dev/null and b/Data/sub-011/MRS/voxel_location.png differ
diff --git a/Data/sub-011/TMS_EEG/DCM_DefaultCodes_STR7T_HS_015_FHK.mat b/Data/sub-011/TMS_EEG/DCM_DefaultCodes_STR7T_HS_015_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..cbd8c7486c75b9f79b7574b17470303271623491
Binary files /dev/null and b/Data/sub-011/TMS_EEG/DCM_DefaultCodes_STR7T_HS_015_FHK.mat differ
diff --git a/Data/sub-012/MRS/all_parameters.csv b/Data/sub-012/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..bff1a95e0d2e615b85b4d5f5724533cc3837cb09
--- /dev/null
+++ b/Data/sub-012/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.019862439627317204,0.007741815921789093
+Asc,0.029155196793795427,0.014262486916589575
+Asp,0.11109483100080374,0.020576453181372568
+Cr,0.21436001335168037,0.009304694551650587
+GABA,0.06761307100869723,0.012738401459450195
+GPC,0.06148085491614638,0.0057428949898905915
+GSH,0.07027217188011498,0.008036598703004131
+Glc,0.11120570558094302,0.013994270916836762
+Gln,0.0790277693726264,0.012231427975171261
+Glu,0.4439963112819337,0.014378799940339484
+Ins,0.36829037307033324,0.008237543289335849
+Lac,0.036829417412027,0.0073952069631079125
+Mac,0.026244154589349238,0.0005809721555463418
+NAA,0.607597284781209,0.009832376135723854
+NAAG,0.06551187723642202,0.005876485224086492
+PCh,0.013100330076264323,0.006032894675469878
+PCr,0.21664506406414033,0.007822701660797907
+PE,0.1039937902780908,0.015565078648429563
+Scyllo,0.015482256756459081,0.0033053059648477192
+Tau,0.08832257230193541,0.01269654925399221
+gamma_0,16.808807757205717,0.7532571735764936
+gamma_1,3.434374460220428,2.469346737160767
+sigma_0,7.0468734349603075,0.6784829077970017
+sigma_1,11.578268008602363,5.346586708540052
+eps_0,-1.5121563520089254,0.2838722769825247
+eps_1,-2.620669678758051,3.9802577325833757
+Phi0,0.07277654938150416,0.009648635427667874
+Phi1,0.0004203146232729771,1.5771145478740855e-05
+B_real_0,0.07008914484471865,0.0
+B_imag_0,-0.0890009542493787,0.0
+B_real_1,-0.04224315665210899,7.00934133340971e-18
+B_imag_1,0.28221594840936204,0.0
+B_real_2,0.43904509243267836,5.607473066727768e-17
+B_imag_2,0.029816141722185493,3.504670666704855e-18
diff --git a/Data/sub-012/MRS/all_samples.csv b/Data/sub-012/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..dca19a7af5bae2e5460acb33cb7b2cf858f10cba
--- /dev/null
+++ b/Data/sub-012/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.03371009318626076,0.010709142185538971,0.028332422357520454,0.01558756323959386,0.018002557751819005,0.022451229335427113,0.02025362606931914,0.023018663927767517,0.023477726860449542,0.01523358470340415,0.018331375787721226,0.0316780437046876,0.00485870050478999,0.009358039291355653,0.005763320408600338,0.03152784866574753,0.017571915071003242,0.02302249078387767,0.015077513076951678,0.027321585323431305,0.006599938340915254,0.017233427388067,0.029575579916578883,0.01914943565249478,0.020120748174135644,0.01632950967526254,0.017625884235727363,0.02032451577365591,0.027467854477010775,0.01313075609369,0.02018496714367737,0.025742881301374372,0.006789654135160989,0.014497632145080996,0.01748336000140037,0.023737401637493667,0.01146187316986429,0.02700909787799583,0.015036964021901826,0.01755209816718313,0.026449932471296615,0.026085736797708748,0.009544307764723734,0.02726478728533035,0.00847957780148103,0.022937513460265867,0.03177862123745639,0.017881193844476104,0.024462294148176113,0.03589699499100764
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diff --git a/Data/sub-012/MRS/concentration_samples.csv b/Data/sub-012/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..73abdec2f7148216e0dc73c3af54bca776cff4c8
--- /dev/null
+++ b/Data/sub-012/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+PCh,molarity,0.2272998595125497,0.2563406979954713,0.33082023203444627,0.2597191617059328,0.16451318769895165,0.12521345633933723,0.16252189629126224,0.09571856453975078,0.11270240773411849,0.05214340822704622,0.1657726363753503,0.15115127924337785,0.2693127741790293,0.2904960741833474,0.04666593095319845,0.011760960737909986,0.203790038685503,0.2653598629827774,0.2794116365171101,0.34363614108389784,0.2909793505688352,0.2782508177815878,0.21841424327127343,0.24891525816808951,0.3312256468071148,0.250749847363889,0.304072527267978,0.18671710254366963,0.2772595101529046,0.31225467909581767,0.2535981276919477,0.29412766494418685,0.3431953305687708,0.33273776553923323,0.17751962717813724,0.19949108738773283,0.1936741426665066,0.34407163108433536,0.35244097133556584,0.49710471578589943,0.30148546286798583,0.2596715669525414,0.2489395409004091,0.08174738795247159,0.015043297114776567,0.042770577549690575,0.09995688569603658,0.1715778467416683,0.2149676663674232,0.13866409002466315
+PCr,molarity,3.627856026802469,3.6432974580392963,3.8078087832918057,3.721078761918349,3.6437006317565577,3.1512923992886592,3.6599272867779926,3.800005518891218,3.6877798233781935,3.571656731567804,3.7597084173376105,3.8121311577570314,3.6629004995538867,3.6007572171997846,3.6194847353596526,3.7347454126471966,3.6795638730650926,3.8503122324522754,3.6322647256245055,3.6993675072096375,3.755182754697438,3.679158779037337,3.7070690524280354,3.7714417099645297,3.63774411867819,3.5785337126730905,3.6904433596521353,3.6614699418949033,3.6826067723104217,3.6771287866443347,3.7310961347702074,3.5967056044205217,3.772957669171745,3.4165227227995647,3.544369657901212,3.7236294529158736,3.9657294343828213,3.5817122747927175,3.6788503417187397,3.66786223064406,3.506085477782435,3.3195393824322412,3.73217588019749,3.4944320197912155,3.815538251568567,3.596094072632461,3.7487152549261813,3.644981494820823,3.6237989382317637,3.8003246320833215
+PE,molarity,1.8196529886591186,2.0128370901646204,2.0122689252032964,1.9930182587396867,2.308712722811722,2.105280196566842,1.7699168782786752,1.731898584119714,1.8174438889334197,1.8142008332282131,1.6591874335692527,1.77515903652747,1.8796135643613645,1.7225433412543003,1.6219704658799399,1.8093199262357156,1.6752903245936555,2.2532290989048263,1.7832317542158234,1.565678733577551,1.5808570890494813,1.6647103836494255,1.6183542260547077,1.8141156238523288,1.667274845432283,1.986537295281181,1.628960957628533,2.019737966661083,1.8419674015600036,1.5213884207918282,1.4502793013894049,1.94308476433117,1.5015420224663105,1.3591044553539062,1.3373649657779196,1.6041906750404478,1.5980585888363512,1.0862080104338745,1.3994700145041121,1.2365086310179765,1.8906925131455716,1.8210709605173898,1.7898468631301216,1.8549843011110907,2.1583468527686356,2.130145613009657,2.107163823160516,2.157456705793116,1.4905360882235328,1.5335221376025105
+Scyllo,molarity,0.20001360562885653,0.24135799387977366,0.29417690951993286,0.2753234026695985,0.32884577626949224,0.22039232377909745,0.29372250908631714,0.3626891675691903,0.30963125984011824,0.2543721507213497,0.19905645770864755,0.33822044395643946,0.2697898550160988,0.2194342680967944,0.22715879826929933,0.1647157484205571,0.2101514111533134,0.2545117742114173,0.3108429245613319,0.30072159521569697,0.29269637882235644,0.20158612058382114,0.28911749778143486,0.20384923819424827,0.3170159138120792,0.15716982582026823,0.2895843457917692,0.3734121395076436,0.2829405359983824,0.22577076044122943,0.2846976855639855,0.21042290745983477,0.28591716198852113,0.14255474386317188,0.28780743104617473,0.19585624740954824,0.3690249475797213,0.330559679121074,0.3484806727994526,0.27234217197638805,0.2817115692559285,0.20150898982807824,0.30348392118327183,0.24777959655320558,0.2174157024943587,0.2847516554684027,0.26391039187993415,0.22651370428565099,0.21875117368863636,0.2080676423049959
+Tau,molarity,1.5488241300364993,1.646495111354604,1.5688178013023162,1.2218093410809974,1.0900120416436667,1.286487477708126,1.2056737652512046,0.922524420023405,1.087077259599291,1.6587828862146594,1.3411311566256854,1.7028216147397925,1.507680552001107,1.4820455504357266,1.7111451014008359,1.3760615780335521,1.5099983984088854,1.5315236845352045,1.3077663052608537,1.2982717167476099,1.3163845213034666,1.3677991011806916,1.2012453850114,1.3370380914669662,1.4754962289459308,1.3824500413356249,1.2329823150471293,1.6163901379604482,1.6193098014638145,1.6570130161115784,1.6354129719304877,1.7561500558595637,1.5559383128216049,1.7072445670176646,1.8736432763141113,1.7607572871153498,1.6498232317617816,1.9430942759795962,1.6915562282005026,1.6635950881247195,1.5478250450288689,1.2582996495651835,1.559018568808903,1.3473485220129129,1.6338477285555917,1.4169355511250339,1.5687160814992782,1.627229184221177,1.5196297212356835,1.7472209380687425
+Cr+PCr,molarity,7.313550086519682,7.062443008724065,7.056292267539621,7.244418374737785,7.347863367654769,7.09088011096828,7.290448970823021,7.3369209551839845,7.349816661653644,7.258238042313907,7.370318718170279,7.688337599170099,7.3678398484435155,7.454226927220144,7.240381352192057,7.175736736205862,7.205935980822861,7.222629229981998,6.9170465613889744,7.370464820530065,7.312130988853477,7.418025559153219,7.348843881776411,7.424772478164568,7.358744634631876,7.0378634360065355,7.13614456083041,7.3006517091191645,7.244106406882972,7.224108945294637,7.339323568877378,7.234050110089121,7.545241935458885,7.288377095242093,7.381581913677182,7.213879935904284,7.309868465030488,7.441704229318005,7.309285640843177,7.432748702600933,7.11526156142365,7.090267265594366,7.388334257567808,7.251929128447841,7.447462286832206,7.295494840913991,7.396134591796997,7.370962201033969,7.265096977034214,7.116942760632666
diff --git a/Data/sub-012/MRS/concentrations.csv b/Data/sub-012/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..26c760c19a9462d0d2fb378b2ba41f7ec70401d1
--- /dev/null
+++ b/Data/sub-012/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.019862439627317204,0.046084003804332266,0.46525055208411825,0.3358631042982246,0.007741815921789093,0.026225501009959334,0.18134147664279116,0.1309099172702538
+Asc,0.029155196793795427,0.06764467130782167,0.6829207116017587,0.4929985986274532,0.014262486916589575,0.03821209509109684,0.3340792992472939,0.2411709347239738
+Asp,0.11109483100080374,0.25775759224669825,2.6022448614887015,1.8785534663173877,0.020576453181372568,0.0514227817662847,0.48197534553612337,0.34793668706427244
+Cr,0.21436001335168037,0.4973491603322164,5.0210908844987046,3.6247118114678747,0.009304694551650587,0.02883040691833771,0.21794977648041503,0.1573373490518318
+GABA,0.06761307100869723,0.15687302668006897,1.5837439511526883,1.143300437720932,0.012738401459450195,0.0351943075716032,0.2983796765593408,0.2153994744977785
+GPC,0.06148085491614638,0.14264531472521727,1.4401051547062242,1.0396079824276219,0.0057428949898905915,0.023295390294350352,0.13451948072547032,0.09710924615275467
+GSH,0.07027217188011498,0.16304256158986846,1.6460297615409043,1.1882643943180957,0.008036598703004131,0.02669859480988696,0.1882463611523741,0.13589453456048745
+Glc,0.11120570558094302,0.2580148388220845,2.6048419472742235,1.8804282954608393,0.013994270916836762,0.037674472726255494,0.3277967053512668,0.2366355473299934
+Gln,0.0790277693726264,0.18335693362698552,1.8511176884849254,1.3363168092780515,0.012231427975171261,0.034212482566536716,0.28650451429939433,0.20682682725898568
+Glu,0.4439963112819337,1.030141718849357,10.400007895461771,7.50773732744394,0.014378799940339484,0.0384460315429192,0.3368037731553124,0.24313772500552766
+Ins,0.36829037307033324,0.854491959302414,8.626699570307624,6.22759088528244,0.008237543289335849,0.02702626306108351,0.19295321396015144,0.13929239876164393
+Lac,0.036829417412027,0.08545007783399054,0.8626788604717028,0.6227655158979696,0.0073952069631079125,0.025681386268469004,0.17322263462693244,0.12504894736804043
+Mac,0.026244154589349238,0.060890592627589085,0.6147335191837602,0.44377445044256575,0.0005809721555463418,0.019155987562554943,0.013608480185973233,0.009823924720922157
+NAA,0.607597284781209,1.4097218724758025,14.2321375165056,10.274141246432208,0.009832376135723854,0.029758238537582617,0.23030999772821498,0.1662601590506653
+NAAG,0.06551187723642202,0.15199792454699584,1.534526353469357,1.1077703882239975,0.005876485224086492,0.023474051686336386,0.13764864971874993,0.09936818471230877
+PCh,0.013100330076264323,0.03039483932488693,0.3068573606680053,0.22151949152783024,0.006032894675469878,0.02368667304974462,0.14131232774484764,0.10201298388445869
+PCr,0.21664506406414033,0.5026508396677836,5.074615080189655,3.663350782317667,0.007822701660797907,0.026354392175196948,0.18323611473537604,0.13227765134052347
+PE,0.1039937902780908,0.24128205380225887,2.4359126697437223,1.7584787108679933,0.015565078648429563,0.04085726238225983,0.3645907335801276,0.2631970559305192
+Scyllo,0.015482256756459081,0.03592128623933185,0.36265074374570044,0.2617965825615378,0.0033053059648477192,0.02058994650648306,0.07742228315384633,0.055890934992819774
+Tau,0.08832257230193541,0.20492234762405004,2.068835767206063,1.4934868963495564,0.01269654925399221,0.035112802387986496,0.29739934574094096,0.21469177635441883
+Cr+PCr,0.4310050774158207,1.0,10.09570596468836,7.288062593785542,0.008235861933399802,0.027023504488345892,0.19291383049104227,0.13926396794273616
diff --git a/Data/sub-012/MRS/fit_summary.png b/Data/sub-012/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..ffa4c11e4ba6c250915ee014cbe84add85681e93
Binary files /dev/null and b/Data/sub-012/MRS/fit_summary.png differ
diff --git a/Data/sub-012/MRS/options.txt b/Data/sub-012/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..a5b49d7a4c9fa56a394ae01781f657a7982567fc
--- /dev/null
+++ b/Data/sub-012/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.11457211457211455, "GM": 0.271032271032271, "WM": 0.6143956143956144}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_016/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-012/MRS/qc.csv b/Data/sub-012/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..97f8a9965dc070d712e6cf69a4d701917363137c
--- /dev/null
+++ b/Data/sub-012/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,4.0180736677209445,16.943033852689833
+Asc,4.499984289008221,14.450181574491541
+Asp,5.350160172131061,19.01177149166299
+Cr,83.9560313750975,8.61397328821435
+GABA,7.645119765739763,20.115108703031492
+GPC,72.26313923382929,8.667617321450829
+GSH,22.629685694292238,9.374056002469466
+Glc,9.690068837800496,0.0
+Gln,7.8358548883913235,23.32654998922598
+Glu,53.70204413335331,20.130284759608216
+Ins,56.69184368785173,19.100979677396104
+Lac,7.703014867594442,16.260068057456184
+Mac,33.31812098219901,34.35788255284997
+NAA,225.87910556652892,8.605109429810948
+NAAG,27.621209100520137,9.305161136575938
+PCh,14.565897559726809,8.718249854702288
+PCr,82.7133017822099,8.753125208548841
+PE,12.487713404654974,17.800080474873926
+Scyllo,11.088619145562113,8.97626690084362
+Tau,13.344811070362248,17.505182572571673
diff --git a/Data/sub-012/MRS/summary.csv b/Data/sub-012/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..d669aefca47cae1c3ec6d260aba8f9c7a3fc22b9
--- /dev/null
+++ b/Data/sub-012/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.046084003804332266,0.026225501009959334,0.46525055208411825,0.18134147664279116,0.3358631042982246,0.1309099172702538,38.97716527803372,4.0180736677209445,16.943033852689833
+Asc,0.06764467130782167,0.03821209509109684,0.6829207116017587,0.3340792992472939,0.4929985986274532,0.2411709347239738,48.919192751340994,4.499984289008221,14.450181574491541
+Asp,0.25775759224669825,0.0514227817662847,2.6022448614887015,0.48197534553612337,1.8785534663173877,0.34793668706427244,18.521521654975743,5.350160172131061,19.01177149166299
+Cr,0.4973491603322164,0.02883040691833771,5.0210908844987046,0.21794977648041503,3.6247118114678747,0.1573373490518318,4.340685749251773,83.9560313750975,8.61397328821435
+GABA,0.15687302668006897,0.0351943075716032,1.5837439511526883,0.2983796765593408,1.143300437720932,0.2153994744977785,18.840146245999716,7.645119765739763,20.115108703031492
+GPC,0.14264531472521727,0.023295390294350352,1.4401051547062242,0.13451948072547032,1.0396079824276219,0.09710924615275467,9.340948491564268,72.26313923382929,8.667617321450829
+GSH,0.16304256158986846,0.02669859480988696,1.6460297615409043,0.1882463611523741,1.1882643943180957,0.13589453456048745,11.436388669919936,22.629685694292238,9.374056002469466
+Glc,0.2580148388220845,0.037674472726255494,2.6048419472742235,0.3277967053512668,1.8804282954608393,0.2366355473299934,12.58413032292735,9.690068837800496,0.0
+Gln,0.18335693362698552,0.034212482566536716,1.8511176884849254,0.28650451429939433,1.3363168092780515,0.20682682725898568,15.47737975179137,7.8358548883913235,23.32654998922598
+Glu,1.030141718849357,0.0384460315429192,10.400007895461771,0.3368037731553124,7.50773732744394,0.24313772500552766,3.238495360203359,53.70204413335331,20.130284759608216
+Ins,0.854491959302414,0.02702626306108351,8.626699570307624,0.19295321396015144,6.22759088528244,0.13929239876164393,2.2366979676014247,56.69184368785173,19.100979677396104
+Lac,0.08545007783399054,0.025681386268469004,0.8626788604717028,0.17322263462693244,0.6227655158979696,0.12504894736804043,20.079619724565443,7.703014867594442,16.260068057456184
+Mac,0.060890592627589085,0.019155987562554943,0.6147335191837602,0.013608480185973233,0.44377445044256575,0.009823924720922157,2.2137202155565716,33.31812098219901,34.35788255284997
+NAA,1.4097218724758025,0.029758238537582617,14.2321375165056,0.23030999772821498,10.274141246432208,0.1662601590506653,1.6182389852621568,225.87910556652892,8.605109429810948
+NAAG,0.15199792454699584,0.023474051686336386,1.534526353469357,0.13764864971874993,1.1077703882239975,0.09936818471230877,8.97010660048587,27.621209100520137,9.305161136575938
+PCh,0.03039483932488693,0.02368667304974462,0.3068573606680053,0.14131232774484764,0.22151949152783024,0.10201298388445869,46.051470767141254,14.565897559726809,8.718249854702288
+PCr,0.5026508396677836,0.026354392175196948,5.074615080189655,0.18323611473537604,3.663350782317667,0.13227765134052347,3.6108377057147742,82.7133017822099,8.753125208548841
+PE,0.24128205380225887,0.04085726238225983,2.4359126697437223,0.3645907335801276,1.7584787108679933,0.2631970559305192,14.967315458746947,12.487713404654974,17.800080474873926
+Scyllo,0.03592128623933185,0.02058994650648306,0.36265074374570044,0.07742228315384633,0.2617965825615378,0.055890934992819774,21.34899334665,11.088619145562113,8.97626690084362
+Tau,0.20492234762405004,0.035112802387986496,2.068835767206063,0.29739934574094096,1.4934868963495564,0.21469177635441883,14.375203215989208,13.344811070362248,17.505182572571673
+Cr+PCr,1.0,0.027023504488345892,10.09570596468836,0.19291383049104227,7.288062593785542,0.13926396794273616,1.9108503275134483,,
diff --git a/Data/sub-012/MRS/voxel_location.png b/Data/sub-012/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..0db62a2b6cbe5017e17b640ad6196e3244725c32
Binary files /dev/null and b/Data/sub-012/MRS/voxel_location.png differ
diff --git a/Data/sub-012/TMS_EEG/DCM_DefaultCodes_STR7T_HS_016_FHK.mat b/Data/sub-012/TMS_EEG/DCM_DefaultCodes_STR7T_HS_016_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..90ef2f694323e17c2a3dcb320a94e7c5f3835aa9
Binary files /dev/null and b/Data/sub-012/TMS_EEG/DCM_DefaultCodes_STR7T_HS_016_FHK.mat differ
diff --git a/Data/sub-013/MRS/all_parameters.csv b/Data/sub-013/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..81e2f3488b7459769d5a47317c8c714ab704b08b
--- /dev/null
+++ b/Data/sub-013/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.030784487567007416,0.00855691372844789
+Asc,0.0309390697775109,0.013962041638549081
+Asp,0.1283105909994636,0.025394657790975
+Cr,0.20446468781919822,0.010467517858802232
+GABA,0.08404975899047468,0.012598846248468127
+GPC,0.05228329327190369,0.004868703337875667
+GSH,0.0648797844711993,0.006040595373546377
+Glc,0.10327521605129836,0.018979987799307655
+Gln,0.056129658489112895,0.014064682549031855
+Glu,0.5019463342168485,0.017077154332319208
+Ins,0.33935319922179863,0.010966378270588854
+Lac,0.08663217064271626,0.009242699453902612
+Mac,0.02805861942491629,0.0006077874291506368
+NAA,0.6242851125935087,0.012208850659832177
+NAAG,0.08700063070931209,0.0075825356832487124
+PCh,0.010347137688593123,0.005142152083015035
+PCr,0.20016663330044537,0.01155552331962328
+PE,0.11205361115090787,0.013765153816324462
+Scyllo,0.0129636932533711,0.0034587117334276525
+Tau,0.10130600800667837,0.01336495448177559
+gamma_0,20.27183209705003,0.8904464968031621
+gamma_1,3.8702483320710375,2.7356379443903722
+sigma_0,9.183779938539725,0.7853105821233823
+sigma_1,11.76270739539003,4.933385356239123
+eps_0,-0.3581994080708302,0.4600028170545074
+eps_1,-0.44995827361236373,4.32956006838465
+Phi0,-0.029261018938668674,0.008070548557542773
+Phi1,0.0003114185164116585,1.2298094904748446e-05
+B_real_0,0.04694724801368583,0.0
+B_imag_0,-0.15543947260805313,0.0
+B_real_1,-0.29537214285200286,0.0
+B_imag_1,0.16514616676755445,0.0
+B_real_2,0.05544989675146105,7.00934133340971e-18
+B_imag_2,0.20441696588417954,2.803736533363884e-17
diff --git a/Data/sub-013/MRS/all_samples.csv b/Data/sub-013/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..102b36792cfa95e3f9654629ce6278ff843eea5d
--- /dev/null
+++ b/Data/sub-013/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.036777732137911995,0.028672592864954723,0.02069578574424323,0.019474806539500473,0.032893353512686484,0.046696025441348814,0.015730843449373016,0.015426476955865258,0.03109599888296427,0.023277191428056603,0.034520059009721445,0.030994403469219542,0.031562660716521904,0.050096756985068686,0.03021687633558679,0.029629897795360433,0.025307475687665747,0.023448871562490228,0.043304176943553006,0.041781630357790804,0.02245134986629064,0.011804958776158291,0.039558801418332214,0.036189917419404485,0.029495139902407125,0.02383026004189996,0.03463731880859267,0.023436422301679354,0.026581154071413725,0.0337700624646613,0.04373997255570071,0.037140814056800565,0.02882063164333353,0.03773035063307741,0.03475600947181277,0.032368721597302225,0.0339460959601029,0.031655737969107076,0.04421340574446656,0.01552916888294889,0.02722479063240827,0.021582485706957207,0.026392031549160765,0.03767755240866773,0.032335112953228266,0.019506445427113186,0.037873287561511704,0.035132999904254246,0.03740219327099801,0.030837569530695528
+Asc,0.027444708472992383,0.03644639676054225,0.003972582699750107,0.003477175123147767,0.025411109685215396,0.01931379092144585,0.012512779351153833,0.04181882835123748,0.023868770099175776,0.019009246450801497,0.02225031773669421,0.03267729137483378,0.024233907845627792,0.013806094130115996,0.02715685442985476,0.029532518388161073,0.057552847741247484,0.02872601030885562,0.021315153255222874,0.030336328140755785,0.04394414999461974,0.04341595896556845,0.038853926245097224,0.026125011344448088,0.05843903374869665,0.028841892759656228,0.02413182426648567,0.036761987035276035,0.015504971580289963,0.010824854514478979,0.02667257384807422,0.042104411434590025,0.04977280997878648,0.034459865636595866,0.023349655011529892,0.012456867992013752,0.027544301016782853,0.049593691564433995,0.057053692290317606,0.04364129934017486,0.03396247634915471,0.037741295160427846,0.053639186226269765,0.02356555119029041,0.023774748482147032,0.012972176074918022,0.024659035603644807,0.03881209555937355,0.051115348095393066,0.05235608629917774
+Asp,0.16079553022529347,0.1645520700566448,0.10282647601475343,0.1484963064581191,0.16136819867869717,0.13363876841209107,0.15054065635574315,0.13043022700532517,0.10556537355531995,0.12922533874999956,0.13128729367312153,0.13804487128274207,0.17922719197827713,0.1442390644493489,0.09986394256618555,0.08013579925296878,0.1229284243838592,0.13343186345563154,0.1180054824318453,0.09222862187587734,0.13537454376903738,0.11250031984792974,0.13873106585678127,0.09411979898548811,0.11673113337702573,0.12166457185414248,0.1033656283468492,0.13260927592577643,0.13787763020516908,0.13670756538768516,0.12851186124700184,0.12284744891453321,0.14432181126256585,0.14360318563524133,0.13493897122197127,0.14031497763693335,0.1635633108346884,0.1284641241043592,0.11253985839630241,0.1716501438250177,0.19273348655968586,0.1460538609305886,0.08577881210819246,0.10105907922913432,0.08830229652275669,0.08917837223344557,0.09052260157745298,0.11244956525100137,0.13360018758543638,0.12858256047914277
+Cr,0.20655378325957593,0.20190931970562978,0.2041153304556986,0.21028420403495623,0.21490818061914624,0.20952273608870842,0.1936871543102128,0.19648203711754086,0.18625638165883673,0.1814200755442521,0.19579779463257882,0.20487600694398095,0.19865077086299965,0.19547445833886046,0.20420645222453288,0.2293664624915344,0.20181802353814396,0.1923479536417018,0.19848684858178403,0.21673646493535192,0.20817695265762984,0.22111513587577775,0.22734124581683585,0.21556903810301578,0.208928598297011,0.21041858856369658,0.21760908679626148,0.20807503777887718,0.20332626805358864,0.2086659762615408,0.20563198972666147,0.20650406972606933,0.20399562233317314,0.19386356379879136,0.1875547476009468,0.18506155930971205,0.19896256019936168,0.21023707547367299,0.21259342186939076,0.19305896908451306,0.1927592262824977,0.1894114389431574,0.2073336059738064,0.20080270180749335,0.21041782003434237,0.208828865001817,0.20924801509122817,0.20244277890461027,0.2133375035030816,0.2190624891053229
+GABA,0.08368009878989374,0.08966522553974253,0.10027117559873522,0.07792728602824066,0.09184911758632129,0.07802616732178486,0.09482818475116196,0.06383422449919895,0.08656885460851428,0.09230929214560382,0.09160974490895239,0.09405369434737874,0.09324405114894631,0.07415737911686907,0.06324836433918833,0.08092502377183938,0.09780183388342532,0.11000817678870765,0.10062749142656867,0.11480548906821127,0.07539787136888085,0.061102724997602324,0.10501649217046605,0.07263642769201922,0.06911281885070521,0.09780087827586759,0.07858943123955535,0.09085942907929487,0.09749190490609491,0.08762045483327927,0.08933292647960406,0.08067823963048075,0.08041545884394281,0.09653628927972331,0.09303905368184005,0.08746895998663799,0.09179993466580842,0.0789914064793928,0.06718012762106625,0.076833828858573,0.07576848044871776,0.08453086955948745,0.061047253147301764,0.0767610055678185,0.06742251835206908,0.07515092407738214,0.07676154828367879,0.08149169834761218,0.07243028694840839,0.0737778301811376
+GPC,0.04946163022942332,0.05105098764333691,0.05254580022548794,0.049469517101270385,0.04638784544532337,0.049377778511944914,0.04652257676350525,0.04636377987266498,0.050714438568057664,0.04915261114889549,0.05833801497086654,0.06061433083611315,0.06121196322557505,0.05948755480438796,0.06106219589576904,0.05682530376175649,0.05276931693098362,0.05904506310880051,0.061834730700075544,0.0629496359571245,0.05330487525214212,0.05961733003164343,0.05328092730018338,0.055068537405071505,0.05598883928249325,0.053635493034629965,0.052400018412395805,0.05087023308978691,0.046232436922959246,0.0502642037665035,0.05131499509061431,0.04789925763530352,0.05008907659017993,0.05037951460424955,0.044500414206285525,0.04483944709747285,0.04422248276434185,0.048578199897844294,0.05264609281049652,0.04968464328380012,0.05003896180415019,0.057763507790122584,0.05387145801277379,0.04965852884395002,0.053564028606306685,0.05010062193493696,0.050251678197182736,0.0483032150878094,0.04901749590936797,0.051593073228823845
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diff --git a/Data/sub-013/MRS/concentration_samples.csv b/Data/sub-013/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..67af6215a1c6a72441cbd9b99e3a459931ebc3bc
--- /dev/null
+++ b/Data/sub-013/MRS/concentration_samples.csv
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diff --git a/Data/sub-013/MRS/concentrations.csv b/Data/sub-013/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..f3435eb377213adec649623a5587e822c6dc0341
--- /dev/null
+++ b/Data/sub-013/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.030784487567007416,0.07608033773021958,0.79028542257106,0.5831658288151644,0.00855691372844789,0.03185398174955467,0.2196692138230685,0.1620978642469982
+Asc,0.0309390697775109,0.07646236997150961,0.7942537870690497,0.5860941563603972,0.013962041638549081,0.041929677237222567,0.3584272095567034,0.2644898852505999
+Asp,0.1283105909994636,0.31710494047870313,3.2939313804602306,2.4306512162365577,0.025394657790975,0.06712882105769472,0.6519201536067364,0.48106360795892994
+Cr,0.20446468781919822,0.5053110749148877,5.248924863937983,3.8732760737361103,0.010467517858802232,0.03516648243376827,0.26871737774772386,0.1982913866758037
+GABA,0.08404975899047468,0.2077193598308283,2.157687346791204,1.5921963052562114,0.012598846248468127,0.03920396027952805,0.32343187489173286,0.2386661983120666
+GPC,0.05228329327190369,0.12921217548664324,1.3421930258496648,0.9904283768807254,0.004868703337875667,0.02668786090618044,0.12498714706136123,0.09223026406099206
+GSH,0.0648797844711993,0.16034296181440508,1.665564442985639,1.2290499623273154,0.006040595373546377,0.028112746738175348,0.15507142865291987,0.11442999659759034
+Glc,0.10327521605129836,0.25523287659869853,2.651234573275435,1.956393681510134,0.018979987799307655,0.05260909103706076,0.48724565077525955,0.3595473301867579
+Gln,0.056129658489112895,0.13871802690359744,1.4409351716927083,1.0632919824527598,0.014064682549031855,0.04213867484113761,0.3610621605246997,0.2664342629668683
+Glu,0.5019463342168485,1.2405029171442472,12.88573896125822,9.508618565670584,0.017077154332319208,0.048462970089751915,0.43839697180121145,0.3235010112913018
+Ins,0.33935319922179863,0.8386725928254496,8.711721637857064,6.428536101323702,0.010966378270588854,0.036083080557093805,0.28152389630596303,0.2077415470810854
+Lac,0.08663217064271626,0.21410149467173942,2.2239818491571097,1.6411162110445863,0.009242699453902612,0.03300351055562908,0.23727439437559544,0.17508904365526046
+Mac,0.02805861942491629,0.06934366659327335,0.7203081701689702,0.5315283555305002,0.0006077874291506368,0.023868776024537332,0.015602843615122163,0.011513618964505137
+NAA,0.6242851125935087,1.5428492062010115,16.026364672690995,11.826142771099324,0.012208850659832177,0.03844292797529833,0.3134200847686994,0.231278318290153
+NAAG,0.08700063070931209,0.21501210155599215,2.2334407891117354,1.6480961329826709,0.0075825356832487124,0.03030884670083158,0.1946554219410992,0.14363973727408544
+PCh,0.010347137688593123,0.02557176656508413,0.2656270325381177,0.19601096535710869,0.005142152083015035,0.026999288995228157,0.13200699940204447,0.0974103393749164
+PCr,0.20016663330044537,0.49468892508511225,5.1385871549151325,3.7918558935149678,0.01155552331962328,0.03718911609963038,0.2966481611818484,0.2189020141853267
+PE,0.11205361115090787,0.27692767539805757,2.8765895565503774,2.122687177310181,0.013765153816324462,0.041530166701447074,0.3533727945547581,0.2607601415028337
+Scyllo,0.0129636932533711,0.03203828417805038,0.33279806196292994,0.2455776762290484,0.0034587117334276525,0.025308640670354425,0.08879048117509623,0.06552009320495392
+Tau,0.10130600800667837,0.2503662042927311,2.600681956205379,1.9190899960435273,0.01336495448177559,0.040723951008777536,0.34309905848790967,0.25317896685714647
+Cr+PCr,0.4046313211196437,1.0000000000000002,10.38751201885312,7.665131967251081,0.009638911182123759,0.03368864002556656,0.24744576241877958,0.18259467909490976
diff --git a/Data/sub-013/MRS/fit_summary.png b/Data/sub-013/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..8be7ba7b1b002ce83bd672c518e3c9422d4e13fa
Binary files /dev/null and b/Data/sub-013/MRS/fit_summary.png differ
diff --git a/Data/sub-013/MRS/options.txt b/Data/sub-013/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..e0d5cd58aa09c8295bb54c93abcba65fda29b8d2
--- /dev/null
+++ b/Data/sub-013/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.09457926829268293, "GM": 0.44348170731707315, "WM": 0.4619390243902439}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_017/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-013/MRS/qc.csv b/Data/sub-013/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..9aa8b6597e720165c5276ac3f25b6317e4ac92be
--- /dev/null
+++ b/Data/sub-013/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,6.73188237439649,18.582799143949885
+Asc,5.419171920149392,15.596650937989578
+Asp,7.575879964572717,22.743838143356033
+Cr,74.65047352670089,10.211180674451342
+GABA,10.30446645985218,21.736672027993485
+GPC,57.49469501606088,10.19324249682318
+GSH,20.265646880535392,11.297196258946755
+Glc,11.563287172746762,41.33893059417781
+Gln,6.342933719223637,24.735421607881886
+Glu,67.8409423100226,21.687387818297978
+Ins,59.95639566848753,42.100319928822934
+Lac,19.676953206696876,17.93874910914871
+Mac,51.00423832534869,34.6887877896514
+NAA,220.5098177062973,10.611416278346962
+NAAG,35.526966350738775,10.991878888501876
+PCh,11.011277076718295,10.70014774741491
+PCr,72.69962640407681,10.369744611095703
+PE,16.05700166996832,18.61801860561258
+Scyllo,9.213244610222105,10.894120456558175
+Tau,17.332154914792817,18.876384001736287
diff --git a/Data/sub-013/MRS/summary.csv b/Data/sub-013/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..57fa40976e445191ff442897730b796fa8e6e787
--- /dev/null
+++ b/Data/sub-013/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.07608033773021958,0.03185398174955467,0.79028542257106,0.2196692138230685,0.5831658288151644,0.1620978642469982,27.796186991329265,6.73188237439649,18.582799143949885
+Asc,0.07646236997150961,0.041929677237222567,0.7942537870690497,0.3584272095567034,0.5860941563603972,0.2644898852505999,45.12754177469763,5.419171920149392,15.596650937989578
+Asp,0.31710494047870313,0.06712882105769472,3.2939313804602306,0.6519201536067364,2.4306512162365577,0.48106360795892994,19.791552352121236,7.575879964572717,22.743838143356033
+Cr,0.5053110749148877,0.03516648243376827,5.248924863937983,0.26871737774772386,3.8732760737361103,0.1982913866758037,5.119474648873518,74.65047352670089,10.211180674451342
+GABA,0.2077193598308283,0.03920396027952805,2.157687346791204,0.32343187489173286,1.5921963052562114,0.2386661983120666,14.989747025801641,10.30446645985218,21.736672027993485
+GPC,0.12921217548664324,0.02668786090618044,1.3421930258496648,0.12498714706136123,0.9904283768807254,0.09223026406099206,9.312158881338181,57.49469501606088,10.19324249682318
+GSH,0.16034296181440508,0.028112746738175348,1.665564442985639,0.15507142865291987,1.2290499623273154,0.11442999659759034,9.31044303365072,20.265646880535392,11.297196258946755
+Glc,0.25523287659869853,0.05260909103706076,2.651234573275435,0.48724565077525955,1.956393681510134,0.3595473301867579,18.37806641806492,11.563287172746762,41.33893059417781
+Gln,0.13871802690359744,0.04213867484113761,1.4409351716927083,0.3610621605246997,1.0632919824527598,0.2664342629668683,25.057488193625638,6.342933719223637,24.735421607881886
+Glu,1.2405029171442472,0.048462970089751915,12.88573896125822,0.43839697180121145,9.508618565670584,0.3235010112913018,3.402187279435657,67.8409423100226,21.687387818297978
+Ins,0.8386725928254496,0.036083080557093805,8.711721637857064,0.28152389630596303,6.428536101323702,0.2077415470810854,3.231552935330164,59.95639566848753,42.100319928822934
+Lac,0.21410149467173942,0.03300351055562908,2.2239818491571097,0.23727439437559544,1.6411162110445863,0.17508904365526046,10.668899769371883,19.676953206696876,17.93874910914871
+Mac,0.06934366659327335,0.023868776024537332,0.7203081701689702,0.015602843615122163,0.5315283555305002,0.011513618964505137,2.1661344770616777,51.00423832534869,34.6887877896514
+NAA,1.5428492062010115,0.03844292797529833,16.026364672690995,0.3134200847686994,11.826142771099324,0.231278318290153,1.9556530203182556,220.5098177062973,10.611416278346962
+NAAG,0.21501210155599215,0.03030884670083158,2.2334407891117354,0.1946554219410992,1.6480961329826709,0.14363973727408544,8.715495073344472,35.526966350738775,10.991878888501876
+PCh,0.02557176656508413,0.026999288995228157,0.2656270325381177,0.13200699940204447,0.19601096535710869,0.0974103393749164,49.696372443983606,11.011277076718295,10.70014774741491
+PCr,0.49468892508511225,0.03718911609963038,5.1385871549151325,0.2966481611818484,3.7918558935149678,0.2189020141853267,5.772951829728141,72.69962640407681,10.369744611095703
+PE,0.27692767539805757,0.041530166701447074,2.8765895565503774,0.3533727945547581,2.122687177310181,0.2607601415028337,12.284435704429269,16.05700166996832,18.61801860561258
+Scyllo,0.03203828417805038,0.025308640670354425,0.33279806196292994,0.08879048117509623,0.2455776762290484,0.06552009320495392,26.679987452867593,9.213244610222105,10.894120456558175
+Tau,0.2503662042927311,0.040723951008777536,2.600681956205379,0.34309905848790967,1.9190899960435273,0.25317896685714647,13.19265732087137,17.332154914792817,18.876384001736287
+Cr+PCr,1.0000000000000002,0.03368864002556656,10.38751201885312,0.24744576241877958,7.665131967251081,0.18259467909490976,2.3821465811030653,,
diff --git a/Data/sub-013/MRS/voxel_location.png b/Data/sub-013/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..059f0258b3ec8bcfef86d3cbab5a6b7f6549f2e8
Binary files /dev/null and b/Data/sub-013/MRS/voxel_location.png differ
diff --git a/Data/sub-013/TMS_EEG/DCM_DefaultCodes_STR7T_HS_017_FHK.mat b/Data/sub-013/TMS_EEG/DCM_DefaultCodes_STR7T_HS_017_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..64857461c731bdf1548d67516859c9d95a70262e
Binary files /dev/null and b/Data/sub-013/TMS_EEG/DCM_DefaultCodes_STR7T_HS_017_FHK.mat differ
diff --git a/Data/sub-014/MRS/all_parameters.csv b/Data/sub-014/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..963d886ab450381a881c8b0cbba9d5d3d862d13a
--- /dev/null
+++ b/Data/sub-014/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.03104104505414476,0.01396497206710924
+Asc,0.024896015780338683,0.018725185411125618
+Asp,0.08433843405017985,0.03797576730515113
+Cr,0.21208605960313412,0.02084017605150917
+GABA,0.10444914777745959,0.020124394401708653
+GPC,0.060910645236999766,0.009059016392038741
+GSH,0.06831528060407223,0.011683146189110248
+Glc,0.1211080239671759,0.02634549408310222
+Gln,0.04910122677002605,0.020994622586794146
+Glu,0.4393871398386618,0.028844197148562643
+Ins,0.3297764071641193,0.018488061210797366
+Lac,0.01774136264327729,0.013307937677511176
+Mac,0.027039312254609635,0.0008726257372810533
+NAA,0.6374030617576867,0.014682614917458902
+NAAG,0.08211457816983639,0.012043057809382115
+PCh,0.01558994847303476,0.00853867417214676
+PCr,0.2167698868722848,0.01824136163778078
+PE,0.07527011338238015,0.02574835943166298
+Scyllo,0.011321903324595557,0.00486499826392477
+Tau,0.05816298363779532,0.021343001515326435
+gamma_0,20.13845127331622,1.1504335966002304
+gamma_1,5.9059440929246,3.9117237555342124
+sigma_0,7.850150912173671,0.9887164499331105
+sigma_1,12.437462636793473,5.850942839471974
+eps_0,6.097686306765877,0.6225610101693727
+eps_1,6.033889015328077,5.588914203963042
+Phi0,-0.06722962686924817,0.021460408636488217
+Phi1,0.00032633672739653405,2.6032525560958642e-05
+B_real_0,0.09842603241539434,1.401868266681942e-17
+B_imag_0,-0.21839724185867176,5.607473066727768e-17
+B_real_1,-0.0983308633245802,1.401868266681942e-17
+B_imag_1,0.22265091166226625,2.803736533363884e-17
+B_real_2,0.5171608407140588,1.1214946133455537e-16
+B_imag_2,0.13801786542704175,0.0
diff --git a/Data/sub-014/MRS/all_samples.csv b/Data/sub-014/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..fc506c2acfa9305ffa9fde011c57e730ada682e9
--- /dev/null
+++ b/Data/sub-014/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-014/MRS/concentration_samples.csv b/Data/sub-014/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..37b52961748ffc4870e17e09200faf3dcebcc92e
--- /dev/null
+++ b/Data/sub-014/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+PCr,molarity,4.132107041575341,4.090474379497025,4.607839001964967,4.5939150165749565,4.569638587726444,4.4412774103595964,3.691305962425143,3.75229519751803,3.814712744093939,4.053360542431096,4.321516661787918,4.662612920235876,4.1527011267575515,4.261161504819917,3.891683718134838,4.239068831646571,4.1302043629425516,4.159986036645273,3.8499277665026095,4.111798517654374,4.542245878826859,4.004353516662061,4.0759908516244066,4.127207353698195,3.747672787216834,3.7665734096824095,4.027972099086174,4.0370953855632115,4.296455610751017,4.067253807202112,4.146731789582005,4.370386970663194,4.2137863544310425,4.260821830390331,4.176463558846782,4.212252206765771,4.337577856612317,3.7711997141890268,3.769394006984587,3.7095464947679995,4.270218520606953,4.333628269032114,4.333859317579862,3.7471377713123735,2.93098179951083,3.0393098098589735,4.14158138462599,3.982680523594114,3.7675970655674216,3.742682561229956
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+Scyllo,molarity,0.31811760538155376,0.27162091737826266,0.13865507550634198,0.220540282778522,0.26604088251733954,0.37082140258055435,0.24025425334514586,0.23061439233801903,0.16009202789193913,0.15372694797201344,0.12010557974057931,0.12932556684653265,0.1352611430025386,0.1793068327388094,0.16361213267423114,0.09558608195172828,0.07153811345976198,0.05703008107918334,0.26448881496838145,0.3051443193604051,0.3913515645479067,0.2084985749283578,0.3362693665008126,0.16831487994872912,0.13912699523866515,0.2864966923981051,0.30373951552624334,0.06963771038554052,0.10659599781567862,0.38777325638061233,0.263944540411854,0.14881304637877693,0.27087807806110087,0.05785306881085975,0.3253870601619445,0.27710852415471215,0.24702611132518054,0.2159124848376267,0.11684786473308213,0.16158863934902268,0.22205864471188316,0.25254967458996885,0.25098703035709097,0.2614187284310509,0.0634924402440282,0.24523905570782498,0.3478077285202733,0.3015328846456474,0.11653937245606627,0.19100818431905053
+Tau,molarity,0.8157173705472508,1.058243652769802,0.8105464943656253,1.0104557718858174,1.293607123777338,1.6511511231766631,1.103096033216494,0.7107782562608991,0.1866159781335615,0.8899507204395217,1.306121670852189,0.40797640008102765,0.987738082460477,0.8673516991511291,1.4711261531563506,1.2721172864316017,1.3310049060974054,1.2098982086936794,1.6532511438664168,1.3588842180137801,1.329704515550737,1.6360497774581608,1.2100665755875217,1.6931265746825594,1.2648657859920314,0.8861202187573365,1.7010563082881385,1.1009526796082338,1.2535458078665862,1.7364633660587923,1.1859491780514482,1.04282237140109,1.282924250229005,0.7119286051435084,1.1603128195472932,0.977930902074251,1.349559082522462,0.15122273654843027,1.2470909263008092,1.324126588143912,0.5361355852325278,1.0465028002246004,1.0707617989970095,1.1744783183669913,1.5882184154791936,1.5350965167156867,0.3310501778525147,0.7963149157354573,0.4057457297729058,0.47085857642744333
+Cr+PCr,molarity,7.7942972162348765,7.8629140991051925,8.629063684363004,8.203604556659164,8.250866849697347,8.032237368557622,8.096759897650974,8.471239603995823,7.9666518634266215,8.021328985491781,8.289485104848604,8.014965380868583,7.571555159997994,7.857811905095118,7.932634169780454,7.821060620746741,8.167153110245351,8.297468643022196,8.024078135054474,7.899980961804804,8.45238623568037,8.101976190710161,7.627772344059407,8.043349785930555,7.880697661904793,7.714984624601172,8.09284366108648,8.41801146497081,8.268933987812266,8.084912014504017,8.317521360836812,8.293151065496158,8.150493687821312,7.8290419160801585,7.9366532982019,7.9495346219317735,8.239864040079489,7.648375067269772,7.67216787621489,7.888055272030601,7.918176933344976,7.794662649577555,7.946835489827972,7.747308410302953,8.274649378413667,8.02261077550605,8.021901998094588,8.31641252232203,8.211918301522866,8.489501866599928
diff --git a/Data/sub-014/MRS/concentrations.csv b/Data/sub-014/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..fec76572b8c9c54b07325daad09724186cadc9f7
--- /dev/null
+++ b/Data/sub-014/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.03104104505414476,0.07238105314676793,0.8072651238796537,0.5827541350620852,0.01396497206710924,0.04460810725556069,0.3631783300487029,0.2621736866120033
+Asc,0.024896015780338683,0.058052164100668865,0.6474551751710876,0.4673894231736272,0.018725185411125618,0.05325392958896473,0.4869742334452562,0.3515403302016288
+Asp,0.08433843405017985,0.19665912235406988,2.1933371216264375,1.5833413824075069,0.03797576730515113,0.09365283154965566,0.9876121259623735,0.7129442771862274
+Cr,0.21208605960313412,0.49453916016829774,5.515590047952038,3.9816323196324652,0.02084017605150917,0.05736697504420526,0.541977477644522,0.3912464528257622
+GABA,0.10444914777745959,0.24355298937995812,2.7163439269721548,1.960893155009868,0.020124394401708653,0.05596017581201582,0.5233625901241727,0.3778086089807749
+GPC,0.060910645236999766,0.14203054834052775,1.584065210661156,1.1435159582818786,0.009059016392038741,0.03709074744311052,0.23559219662839587,0.1700709255389868
+GSH,0.06831528060407223,0.15929656838275394,1.7766329504539653,1.2825280911292638,0.011683146189110248,0.04088608897166558,0.30383630574309095,0.2193354553741014
+Glc,0.1211080239671759,0.2823979123118386,3.1495809435587305,2.273641291166715,0.02634549408310222,0.06858140211551662,0.6851508545401377,0.4946014411048803
+Gln,0.04910122677002605,0.11449351973213323,1.2769450204401354,0.9218099096516452,0.020994622586794146,0.0576723592840789,0.5459940724860337,0.3941459801105665
+Glu,0.4393871398386618,1.0245564820770101,11.426867660359985,8.248906317021472,0.028844197148562643,0.073845894597855,0.7501330687716151,0.5415112516846933
+Ins,0.3297764071641193,0.7689677848107473,8.576289610016955,6.191111303939418,0.018488061210797366,0.052801534879458385,0.48080749206722095,0.347088640252932
+Lac,0.01774136264327729,0.0413690489524183,0.4613885675252662,0.3330703725976954,0.013307937677511176,0.043502325630190374,0.3460912459319505,0.24983874406260165
+Mac,0.027039312254609635,0.06304987135385208,0.7031945515611276,0.5076269499987304,0.0008726257372810533,0.030555751368498526,0.02269383400842373,0.016382381967975448
+NAA,0.6374030617576867,1.4862871017557902,16.576544401567553,11.96639060613482,0.014682614917458902,0.045843927192183255,0.3818416206524293,0.27564647200983794
+NAAG,0.08211457816983639,0.19147356786049138,2.1355026869415057,1.5415914603996703,0.012043057809382115,0.04145000056001493,0.3131963030697821,0.22609231502893828
+PCh,0.01558994847303476,0.036352412974943654,0.4054380792724432,0.2926804468798887,0.00853867417214676,0.03641340231532535,0.22205998062638255,0.16030219578905372
+PCr,0.2167698868722848,0.5054608398317022,5.637399426278911,4.069564916755179,0.01824136163778078,0.052332921639030715,0.47439172993598755,0.3424571854793348
+PE,0.07527011338238015,0.17551374535200592,1.9575029544937732,1.4130957815261147,0.02574835943166298,0.06733700900903612,0.669621545603338,0.48339103608442796
+Scyllo,0.011321903324595557,0.026400247956558306,0.2944416875765819,0.21255360338779078,0.00486499826392477,0.03253003149324751,0.12652097954018884,0.09133384041763981
+Tau,0.05816298363779532,0.13562359136164873,1.5126084869138678,1.0919322839598735,0.021343001515326435,0.05836349491850183,0.5550541462821357,0.40068632889123945
+Cr+PCr,0.428855946475419,1.0000000000000002,11.152989474230951,8.051197236387646,0.01307492833982194,0.04311643836864081,0.34003151722350283,0.24546430516050838
diff --git a/Data/sub-014/MRS/fit_summary.png b/Data/sub-014/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..316df5585ac1f645ecc0211239f7087d095fd4b6
Binary files /dev/null and b/Data/sub-014/MRS/fit_summary.png differ
diff --git a/Data/sub-014/MRS/options.txt b/Data/sub-014/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..df775455911ef9190b5336314938b72ab990b53e
--- /dev/null
+++ b/Data/sub-014/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.07775566971557449, "GM": 0.36157774714948004, "WM": 0.5606665831349456}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_018/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-014/MRS/qc.csv b/Data/sub-014/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..5d97f2b64e34aff1d68ebc6ef0ab56d427e8799b
--- /dev/null
+++ b/Data/sub-014/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,10.728716029591801,18.59479171253124
+Asc,6.899899743047143,15.294049160580753
+Asp,7.856036251954461,22.372107692756494
+Cr,124.32629537312413,9.800657575626548
+GABA,20.024101340004233,21.902046137800653
+GPC,104.47165103321629,10.071007887082606
+GSH,34.23764484774313,10.664861022742706
+Glc,21.05932416286976,40.60492474099824
+Gln,8.840420464516429,24.152922549417298
+Glu,91.94615085135655,22.082964172841656
+Ins,90.65345386333651,42.07272184075021
+Lac,6.280192333928095,17.565107528795362
+Mac,75.02287211043974,34.6508739271107
+NAA,369.7548556333639,9.712268816296397
+NAAG,52.03876539132644,10.9753095549926
+PCh,27.503327985277586,9.692413983783428
+PCr,122.31822557482897,10.173993634539165
+PE,16.95611083284674,18.323553252368797
+Scyllo,13.265711128315647,9.745485453882763
+Tau,15.65138722956144,18.7678910826607
diff --git a/Data/sub-014/MRS/summary.csv b/Data/sub-014/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..ecce85384b38d1b233265a2ca50e777a5da33cf8
--- /dev/null
+++ b/Data/sub-014/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.07238105314676793,0.04460810725556069,0.8072651238796537,0.3631783300487029,0.5827541350620852,0.2621736866120033,44.98873038182251,10.728716029591801,18.59479171253124
+Asc,0.058052164100668865,0.05325392958896473,0.6474551751710876,0.4869742334452562,0.4673894231736272,0.3515403302016288,75.2135826725881,6.899899743047143,15.294049160580753
+Asp,0.19665912235406988,0.09365283154965566,2.1933371216264375,0.9876121259623735,1.5833413824075069,0.7129442771862274,45.02783070712012,7.856036251954461,22.372107692756494
+Cr,0.49453916016829774,0.05736697504420526,5.515590047952038,0.541977477644522,3.9816323196324652,0.3912464528257622,9.826282826182133,124.32629537312413,9.800657575626548
+GABA,0.24355298937995812,0.05596017581201582,2.7163439269721548,0.5233625901241727,1.960893155009868,0.3778086089807749,19.26716955564433,20.024101340004233,21.902046137800653
+GPC,0.14203054834052775,0.03709074744311052,1.584065210661156,0.23559219662839587,1.1435159582818786,0.1700709255389868,14.872632454952065,104.47165103321629,10.071007887082606
+GSH,0.15929656838275394,0.04088608897166558,1.7766329504539653,0.30383630574309095,1.2825280911292638,0.2193354553741014,17.10180516833568,34.23764484774313,10.664861022742706
+Glc,0.2823979123118386,0.06858140211551662,3.1495809435587305,0.6851508545401377,2.273641291166715,0.4946014411048803,21.753714758191975,21.05932416286976,40.60492474099824
+Gln,0.11449351973213323,0.0576723592840789,1.2769450204401354,0.5459940724860337,0.9218099096516452,0.3941459801105665,42.75783716184126,8.840420464516429,24.152922549417298
+Glu,1.0245564820770101,0.073845894597855,11.426867660359985,0.7501330687716151,8.248906317021472,0.5415112516846933,6.56464300688316,91.94615085135655,22.082964172841656
+Ins,0.7689677848107473,0.052801534879458385,8.576289610016955,0.48080749206722095,6.191111303939418,0.347088640252932,5.606241322653636,90.65345386333651,42.07272184075021
+Lac,0.0413690489524183,0.043502325630190374,0.4613885675252662,0.3460912459319505,0.3330703725976954,0.24983874406260165,75.01079790257225,6.280192333928095,17.565107528795362
+Mac,0.06304987135385208,0.030555751368498526,0.7031945515611276,0.02269383400842373,0.5076269499987304,0.016382381967975448,3.2272482711992385,75.02287211043974,34.6508739271107
+NAA,1.4862871017557902,0.045843927192183255,16.576544401567553,0.3818416206524293,11.96639060613482,0.27564647200983794,2.3035055521965164,369.7548556333639,9.712268816296397
+NAAG,0.19147356786049138,0.04145000056001493,2.1355026869415057,0.3131963030697821,1.5415914603996703,0.22609231502893828,14.666162912599553,52.03876539132644,10.9753095549926
+PCh,0.036352412974943654,0.03641340231532535,0.4054380792724432,0.22205998062638255,0.2926804468798887,0.16030219578905372,54.77038097281544,27.503327985277586,9.692413983783428
+PCr,0.5054608398317022,0.052332921639030715,5.637399426278911,0.47439172993598755,4.069564916755179,0.3424571854793348,8.41508103407745,122.31822557482897,10.173993634539165
+PE,0.17551374535200592,0.06733700900903612,1.9575029544937732,0.669621545603338,1.4130957815261147,0.48339103608442796,34.207945590381385,16.95611083284674,18.323553252368797
+Scyllo,0.026400247956558306,0.03253003149324751,0.2944416875765819,0.12652097954018884,0.21255360338779078,0.09133384041763981,42.96979160170102,13.265711128315647,9.745485453882763
+Tau,0.13562359136164873,0.05836349491850183,1.5126084869138678,0.5550541462821357,1.0919322839598735,0.40068632889123945,36.69516276578594,15.65138722956144,18.7678910826607
+Cr+PCr,1.0000000000000002,0.04311643836864081,11.152989474230951,0.34003151722350283,8.051197236387646,0.24546430516050838,3.0487925951077752,,
diff --git a/Data/sub-014/MRS/voxel_location.png b/Data/sub-014/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..5d19bd0bd130e958a55d73e2d71cb0ab449dcb26
Binary files /dev/null and b/Data/sub-014/MRS/voxel_location.png differ
diff --git a/Data/sub-014/TMS_EEG/DCM_DefaultCodes_STR7T_HS_018_FHK.mat b/Data/sub-014/TMS_EEG/DCM_DefaultCodes_STR7T_HS_018_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..56568d7fb873dad90229b0663f6a64b4657fbb4b
Binary files /dev/null and b/Data/sub-014/TMS_EEG/DCM_DefaultCodes_STR7T_HS_018_FHK.mat differ
diff --git a/Data/sub-015/MRS/all_parameters.csv b/Data/sub-015/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..c052d6e4734a3076d35898a307b7d173e6fc89e3
--- /dev/null
+++ b/Data/sub-015/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.011034347215502081,0.006982151063291591
+Asc,0.024983861607093066,0.013998969020276987
+Asp,0.17153237857039128,0.024631573417705395
+Cr,0.21282662139751468,0.014952227860775342
+GABA,0.11852178635220677,0.014203941759157498
+GPC,0.06156139300601305,0.009078328195479667
+GSH,0.07065903457322172,0.006986843168407146
+Glc,0.08996933297561373,0.016319506838555632
+Gln,0.07390466337532432,0.018000659772969156
+Glu,0.4985667366967391,0.015952295280485765
+Ins,0.3629812049250449,0.009438710134169923
+Lac,0.03555410744859844,0.009675661943811283
+Mac,0.026132029389851614,0.0005545058840729704
+NAA,0.6751103205640371,0.00895869914239225
+NAAG,0.05739502138246569,0.007302491486510305
+PCh,0.01803021541724638,0.008563917341843754
+PCr,0.2355927023488735,0.01403954731637382
+PE,0.12160334161807045,0.019521259132069934
+Scyllo,0.016241506787096693,0.0031511951809887304
+Tau,0.08980068431012292,0.01347459055628434
+gamma_0,20.07322954678681,0.6834192112397016
+gamma_1,2.950655281494205,2.399506529315082
+sigma_0,4.493351968067459,1.220945841489371
+sigma_1,10.593563418595618,4.691673485178501
+eps_0,-0.783205869907242,0.3809010487318606
+eps_1,1.504739765439608,4.382938115246913
+Phi0,0.024464538531819825,0.014283533263164783
+Phi1,0.00036188846769454004,1.991798400018764e-05
+B_real_0,-0.17187474214906184,5.607473066727768e-17
+B_imag_0,-0.0795961834706399,0.0
+B_real_1,-0.036139437266645584,7.00934133340971e-18
+B_imag_1,0.45300359116119465,5.607473066727768e-17
+B_real_2,0.605302875497407,0.0
+B_imag_2,0.06398143822296219,1.401868266681942e-17
diff --git a/Data/sub-015/MRS/all_samples.csv b/Data/sub-015/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..4311c4212bd865d54480d626f2c63ca3e253d3f6
--- /dev/null
+++ b/Data/sub-015/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.0023044445012059666,0.009994538649449837,0.0016325119228488456,0.013724553059822528,0.01627570842633032,0.011726779973442056,0.006649578223479661,0.016753932039419855,0.014226794444909707,0.01361482869136674,0.0024140755905046668,0.0026627938281041674,0.0011343154571268159,0.005053017293684268,0.005893316726029824,0.007231619772184353,0.01378197064485211,0.022254173527913194,0.01878936000273092,0.009963559335514743,0.02885057597183152,0.007857164170994262,0.020571234845145652,0.01506242204136024,0.00665645312872091,0.004350278225439879,0.02817509926797554,0.0010446897322859104,0.0127713372093364,0.0013398998765226655,0.007265443322694702,0.020367551847389424,0.01913034333231532,0.01050989381117916,0.019882998156047303,0.00743035054008501,0.011722861342275204,0.005823820410872056,0.003949298859370179,0.018196277448467406,0.006283143553570574,0.01834881851967276,0.012847040011539699,0.009966678696821503,0.01539322529200327,0.00812484869916172,0.012137016456405043,0.011434133510599586,0.009979969217429033,0.00016262116667148385
+Asc,0.029530120860693617,0.020039617049414215,0.04158258384343576,0.001962168905126957,0.015844292772593083,0.03556537564492748,0.0208122319805991,0.021334341371620942,0.022877557457080477,0.025230489086129043,0.022407551258551955,0.020383484083172886,0.02531466370479571,0.025689983967422836,0.002566251349265852,0.006568065609154631,0.02481505297833216,0.004524369574833612,0.01883743311468905,0.058149451931808475,0.03656455955251753,0.03725063298940663,0.06613752790390799,0.018669938915389712,0.010197179951283799,0.02234802568983135,0.020332364253832107,0.03399009583987169,0.024542875432423214,0.04887081556671083,0.01897721559479812,0.013349504570967263,0.03238701660252912,0.02963704714000294,0.017096440341379464,0.008218532576148782,0.0364678940142434,0.02831015055192286,0.009937764610989887,0.014283521096099028,0.05255017907891134,0.03292519242404854,0.04418663451091431,0.023001992203093513,0.007586033828771858,0.009024674437676884,0.014879089788841806,0.022148854470869894,0.03317685375773231,0.038109386115889377
+Asp,0.1946792827303803,0.22243724249557162,0.1467590238842422,0.17710964025440348,0.13662625372957538,0.16193257838235953,0.153823303103655,0.1694086728568312,0.2106433301295839,0.15553708331435803,0.15553708331435803,0.18341445692945987,0.16625368254895906,0.1656036937953319,0.17335320695774578,0.1808701952913129,0.15530600971899433,0.20015334394950166,0.2047418864512726,0.19463295695089408,0.20409513619117148,0.20359827528603938,0.2012074015797534,0.17749566103613018,0.2026661681239824,0.1616687164257865,0.11500217953136342,0.16860926970479836,0.15671752066242362,0.15475537155904953,0.16434564520740558,0.16417219452146076,0.16528138991109936,0.15185664522249723,0.15236717379795484,0.16257207050282196,0.23006304289280502,0.18572840690656411,0.11284770990153727,0.17696092509857012,0.18506388116307965,0.13209811732740018,0.1748696744510358,0.17391639827694425,0.16880432004545753,0.17606960242210096,0.1324569335572022,0.17906753470150594,0.16539620084062062,0.168042434882211
+Cr,0.2085453893763236,0.18892527094884515,0.20298052264698718,0.20600067951700363,0.19649437848312806,0.20849823912209672,0.2104636091434166,0.21222515049586868,0.21747363877655754,0.2392247892815769,0.2271490752402609,0.22814356047255047,0.24405565832751072,0.2462493366689483,0.22022045745619573,0.22879547774533013,0.21245231270576323,0.21419124456846056,0.20731105635037234,0.21074149547491342,0.20442341299437225,0.19034209545598124,0.2035877958098619,0.20313230041381725,0.20825458880756176,0.19741496346393897,0.20708345829091337,0.204922251734829,0.20980785109668107,0.20755310658999193,0.2078878097261512,0.21824315358159366,0.22498504142110012,0.2144819777763664,0.20304600797369982,0.2012493898193424,0.18376476764322125,0.19210191460751852,0.23835430117108797,0.24786610238833437,0.23724977125821745,0.2101966451331724,0.21734896085176283,0.22295544872425793,0.21775311979606626,0.21528964116115082,0.2053751780775962,0.2258138409037852,0.19733170625812568,0.19337312414312324
+GABA,0.12270768103930499,0.1280906886876244,0.10102476784772611,0.11408524836385854,0.11895709618370104,0.10835148021225423,0.1357805629235883,0.13785098993401113,0.13372382106565237,0.14419391775435372,0.13495884984482534,0.12875198669997223,0.10760543966867292,0.1028487171533196,0.10403208246316852,0.10476239949294382,0.13318543736484287,0.13463295255202537,0.14179019010579574,0.11103348696756642,0.14120834476515462,0.11586121705991263,0.1265146847812311,0.12532291581101956,0.1090792811895811,0.1239526335366753,0.1372552262478557,0.12032820227982866,0.12073726524435896,0.11023107802194568,0.1405000908851412,0.11723961010552765,0.11273299376230791,0.10052857537971256,0.10052857537971256,0.09530793216226911,0.11806319536555168,0.12748201597020153,0.08551771874990087,0.10502242606463194,0.11032939426599657,0.13759511755184134,0.11143479512782709,0.12479206947264679,0.11240392819544298,0.12340584345086258,0.10775849905379975,0.09655666296851984,0.10728542590120851,0.11274580253446476
+GPC,0.056379127809044326,0.06050684456786849,0.061796213880349726,0.06024156493050473,0.06198843094779072,0.05902985139718244,0.05996907893079665,0.06364323962640901,0.07151183881522598,0.06636506585930747,0.06008614519640943,0.061164002373305694,0.050159141385836076,0.04936836899370014,0.043034431374855214,0.04129599801757799,0.042316861860420024,0.045261102307790846,0.04852328988200474,0.055569272411356826,0.0572669734167655,0.061981728026749894,0.07113039831896574,0.07014271736188127,0.063782634664489,0.06345547556703664,0.06352715704036423,0.06867847059276987,0.07223715109766639,0.06953582683419428,0.06413547200537605,0.0631343885876953,0.06609989963539335,0.0608812981971961,0.06130659531971409,0.061947367312983115,0.058681124627361386,0.057388889737422503,0.04845830067725565,0.05216552476381452,0.05609423167837842,0.06349618621801065,0.06602596542952846,0.06646345131600649,0.07065519490012262,0.07353601155914155,0.07816451951655065,0.07702898553983441,0.07807660055204682,0.07438123923820086
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diff --git a/Data/sub-015/MRS/concentration_samples.csv b/Data/sub-015/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..ae0987bba6ceebfa53b0bde6e28177f5d813e0f3
--- /dev/null
+++ b/Data/sub-015/MRS/concentration_samples.csv
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diff --git a/Data/sub-015/MRS/concentrations.csv b/Data/sub-015/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..fa604789970cad374c50464c9fb5a154c45fffdb
--- /dev/null
+++ b/Data/sub-015/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.011034347215502081,0.024607207208007745,0.31102421680356823,0.233828469734891,0.006982151063291591,0.024508773661565248,0.19680530471377378,0.14795852139704738
+Asc,0.024983861607093066,0.05571539914551754,0.7042180055887687,0.5294321461488511,0.013998969020276987,0.03650794815695866,0.39458776224407127,0.29665166773787904
+Asp,0.17153237857039128,0.3825267322052441,4.834968726229409,3.6349366942841455,0.024631573417705395,0.058099201976339304,0.6942880880274005,0.5219668193269376
+Cr,0.21282662139751468,0.47461518745316766,5.998926075311071,4.510001564053871,0.014952227860775342,0.03834161097581007,0.4214571889973409,0.31685214281644436
+GABA,0.11852178635220677,0.2643101670151016,3.3407636223886596,2.511591070294336,0.014203941759157498,0.036899582513503344,0.4003653115935089,0.30099523794948746
+GPC,0.06156139300601305,0.1372853259125609,1.7352258063922676,1.3045453473786908,0.009078328195479667,0.027714689885676724,0.25589007321774193,0.19237853841665026
+GSH,0.07065903457322172,0.15757357194799268,1.9916602639943808,1.497333154786847,0.006986843168407146,0.02451542262201574,0.1969375606859871,0.148057951634068
+Glc,0.08996933297561373,0.20063661000144042,2.535958020766927,1.9065370195349058,0.016319506838555632,0.04102093285643652,0.4599965665346598,0.34582610428703275
+Gln,0.07390466337532432,0.1648115044594342,2.0831445300315115,1.5661111623392046,0.018000659772969156,0.04438079392643388,0.5073830828859305,0.3814513579034832
+Glu,0.4985667366967391,1.1118315163837873,14.053058670073609,10.565110452454824,0.015952295280485765,0.04029618162491358,0.4496460052355335,0.33804453687615665
+Ins,0.3629812049250449,0.8094682492548774,10.231320690871575,7.6919221438771945,0.009438710134169923,0.028307081722605012,0.26604812860989213,0.20001537959975613
+Lac,0.03555410744859844,0.0792876345103868,1.0021606360016173,0.7534258597387613,0.009675661943811283,0.028702180789347352,0.27272706933692986,0.20503661719245328
+Mac,0.026132029389851614,0.05827587707757007,0.7365813143026605,0.5537629298733433,0.0005545058840729704,0.018967498670124382,0.0156298107118173,0.01175051498738576
+NAA,0.6751103205640371,1.505533514755172,19.02927781848682,14.306239424652508,0.00895869914239225,0.027520414486092902,0.2525180991610262,0.18984348329531364
+NAAG,0.05739502138246569,0.12799408576541743,1.6177886398958292,1.216255910581534,0.007302491486510305,0.02496871750881177,0.20583471327744027,0.15474684421239487
+PCh,0.01803021541724638,0.040208381892667275,0.5082161653450843,0.3820776705378784,0.008563917341843754,0.026888118500989024,0.24139041775623987,0.1814776758308039
+PCr,0.2355927023488735,0.5253848125468324,6.640631684106419,4.992436797126666,0.01403954731637382,0.036585359140263014,0.39573153926288845,0.2975115610052797
+PE,0.12160334161807045,0.2711822064270483,3.4276231614609536,2.576892201221963,0.019521259132069934,0.047470009704933515,0.5502440891149072,0.41367432626529693
+Scyllo,0.016241506787096693,0.03621946229124233,0.45779798564520113,0.344173207897633,0.0031511951809887304,0.020189610940643952,0.08882247350212663,0.06677686795747892
+Tau,0.08980068431012292,0.20026051410958232,2.5312043350187063,1.9029631915046308,0.01347459055628434,0.035513158294036486,0.37980715058787456,0.2855395818661319
+Cr+PCr,0.44841932374638815,1.0,12.639557759417489,9.502438361180536,0.008487298278256096,0.026767027416963022,0.23923076265574647,0.17985404390756218
diff --git a/Data/sub-015/MRS/fit_summary.png b/Data/sub-015/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..a3ff9fffdcf01fe894b775dd51bb84e04ce3b088
Binary files /dev/null and b/Data/sub-015/MRS/fit_summary.png differ
diff --git a/Data/sub-015/MRS/options.txt b/Data/sub-015/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..670054c90f41cf776cc38dbb35cac0ec554214d3
--- /dev/null
+++ b/Data/sub-015/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.1663735933983496, "GM": 0.3735533883470868, "WM": 0.4600730182545636}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_019/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-015/MRS/qc.csv b/Data/sub-015/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..66e68c9aaaaa2f9deb1ac2e61b85a32758f1f226
--- /dev/null
+++ b/Data/sub-015/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,1.76345850487637,17.127773300986526
+Asc,3.00640817535463,14.734020770577331
+Asp,6.601661367310228,22.085081389698672
+Cr,65.44823462741289,8.64316771708372
+GABA,10.659435792621924,20.426683776307218
+GPC,56.474167202259686,8.726246149596404
+GSH,17.93891254537277,9.439671930821806
+Glc,6.2585694677910855,0.0
+Gln,5.864645161367072,23.56050933824587
+Glu,47.63716408648134,20.6043989891293
+Ins,44.20017447084096,20.117342913049757
+Lac,5.930870538148059,16.40527469526683
+Mac,27.40071717187741,34.39387745557228
+NAA,198.69334604006366,8.632628783694642
+NAAG,18.89491542750337,9.473088969897884
+PCh,15.747176972940842,8.751591864485409
+PCr,69.70697887382671,8.883343136485404
+PE,11.544903347844674,18.016011225667295
+Scyllo,9.0672314379523,9.103889182910532
+Tau,10.831988637818363,17.814693141910094
diff --git a/Data/sub-015/MRS/summary.csv b/Data/sub-015/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..635a8f12da0d8328559d289aef6f9e88adab0742
--- /dev/null
+++ b/Data/sub-015/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.024607207208007745,0.024508773661565248,0.31102421680356823,0.19680530471377378,0.233828469734891,0.14795852139704738,63.27652127424823,1.76345850487637,17.127773300986526
+Asc,0.05571539914551754,0.03650794815695866,0.7042180055887687,0.39458776224407127,0.5294321461488511,0.29665166773787904,56.032046768553165,3.00640817535463,14.734020770577331
+Asp,0.3825267322052441,0.058099201976339304,4.834968726229409,0.6942880880274005,3.6349366942841455,0.5219668193269376,14.35972241683654,6.601661367310228,22.085081389698672
+Cr,0.47461518745316766,0.03834161097581007,5.998926075311071,0.4214571889973409,4.510001564053871,0.31685214281644436,7.025543967475654,65.44823462741289,8.64316771708372
+GABA,0.2643101670151016,0.036899582513503344,3.3407636223886596,0.4003653115935089,2.511591070294336,0.30099523794948746,11.984245425518795,10.659435792621924,20.426683776307218
+GPC,0.1372853259125609,0.027714689885676724,1.7352258063922676,0.25589007321774193,1.3045453473786908,0.19237853841665026,14.746788128385813,56.474167202259686,8.726246149596404
+GSH,0.15757357194799268,0.02451542262201574,1.9916602639943808,0.1969375606859871,1.497333154786847,0.148057951634068,9.888110148415489,17.93891254537277,9.439671930821806
+Glc,0.20063661000144042,0.04102093285643652,2.535958020766927,0.4599965665346598,1.9065370195349058,0.34582610428703275,18.138966133025626,6.2585694677910855,0.0
+Gln,0.1648115044594342,0.04438079392643388,2.0831445300315115,0.5073830828859305,1.5661111623392046,0.3814513579034832,24.356595309220108,5.864645161367072,23.56050933824587
+Glu,1.1118315163837873,0.04029618162491358,14.053058670073609,0.4496460052355335,10.565110452454824,0.33804453687615665,3.1996308831547653,47.63716408648134,20.6043989891293
+Ins,0.8094682492548774,0.028307081722605012,10.231320690871575,0.26604812860989213,7.6919221438771945,0.20001537959975613,2.600330266719734,44.20017447084096,20.117342913049757
+Lac,0.0792876345103868,0.028702180789347352,1.0021606360016173,0.27272706933692986,0.7534258597387613,0.20503661719245328,27.213907585219673,5.930870538148059,16.40527469526683
+Mac,0.05827587707757007,0.018967498670124382,0.7365813143026605,0.0156298107118173,0.5537629298733433,0.01175051498738576,2.121939615942392,27.40071717187741,34.39387745557228
+NAA,1.505533514755172,0.027520414486092902,19.02927781848682,0.2525180991610262,14.306239424652508,0.18984348329531364,1.3269978060633838,198.69334604006366,8.632628783694642
+NAAG,0.12799408576541743,0.02496871750881177,1.6177886398958292,0.20583471327744027,1.216255910581534,0.15474684421239487,12.723214157981364,18.89491542750337,9.473088969897884
+PCh,0.040208381892667275,0.026888118500989024,0.5082161653450843,0.24139041775623987,0.3820776705378784,0.1814776758308039,47.49758748668161,15.747176972940842,8.751591864485409
+PCr,0.5253848125468324,0.036585359140263014,6.640631684106419,0.39573153926288845,4.992436797126666,0.2975115610052797,5.959245416517016,69.70697887382671,8.883343136485404
+PE,0.2711822064270483,0.047470009704933515,3.4276231614609536,0.5502440891149072,2.576892201221963,0.41367432626529693,16.053225900141747,11.544903347844674,18.016011225667295
+Scyllo,0.03621946229124233,0.020189610940643952,0.45779798564520113,0.08882247350212663,0.344173207897633,0.06677686795747892,19.402111037457708,9.0672314379523,9.103889182910532
+Tau,0.20026051410958232,0.035513158294036486,2.5312043350187063,0.37980715058787456,1.9029631915046308,0.2855395818661319,15.00499763426123,10.831988637818363,17.814693141910094
+Cr+PCr,1.0,0.026767027416963022,12.639557759417489,0.23923076265574647,9.502438361180536,0.17985404390756218,1.8927146598740792,,
diff --git a/Data/sub-015/MRS/voxel_location.png b/Data/sub-015/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..4d86554a27841605a0e02d55959a3dfc55a30b74
Binary files /dev/null and b/Data/sub-015/MRS/voxel_location.png differ
diff --git a/Data/sub-015/TMS_EEG/DCM_DefaultCodes_STR7T_HS_019_FHK.mat b/Data/sub-015/TMS_EEG/DCM_DefaultCodes_STR7T_HS_019_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..84d7a3c79839f07dfa6b2a63170777a78fd07cfc
Binary files /dev/null and b/Data/sub-015/TMS_EEG/DCM_DefaultCodes_STR7T_HS_019_FHK.mat differ
diff --git a/Data/sub-016/MRS/all_parameters.csv b/Data/sub-016/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..fb6b637a294f0847df0b31d2a655ec9009d1613c
--- /dev/null
+++ b/Data/sub-016/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.020372460144548906,0.00879583168424682
+Asc,0.03342552397504075,0.015247805493133816
+Asp,0.12231219326017133,0.026726008037520704
+Cr,0.23342117729486392,0.016639491475620334
+GABA,0.0622982650018679,0.01463742089136485
+GPC,0.06423528326681142,0.004801982426885376
+GSH,0.06828092523378611,0.006929352280081849
+Glc,0.10333386639585655,0.013915006325544176
+Gln,0.07488504686220761,0.015258574976924857
+Glu,0.4564532956698257,0.017654736023582952
+Ins,0.33228476350188657,0.010372434699597867
+Lac,0.022648994531558723,0.009259790004300368
+Mac,0.026274806344082715,0.0006743187595402065
+NAA,0.6016431633932251,0.010347158576304093
+NAAG,0.078204536943353,0.007308774604533593
+PCh,0.01388033823003336,0.0053793858109297075
+PCr,0.20537336928764596,0.016340647602119916
+PE,0.09818210792297784,0.015854473415427534
+Scyllo,0.027577698167413605,0.0032399693888225077
+Tau,0.06230039563911034,0.012064527429323613
+gamma_0,18.878867301187608,0.8097679221175091
+gamma_1,4.32187950314867,3.205132792170692
+sigma_0,8.166354201325166,0.7778227432780627
+sigma_1,12.412773585256632,6.08801456054732
+eps_0,4.125590065398694,0.3635680188159418
+eps_1,-0.8821645723611696,4.251783959036513
+Phi0,0.01625848241686253,0.013377610406853752
+Phi1,0.0003268485342254022,1.9673720442245157e-05
+B_real_0,0.10051624822738421,0.0
+B_imag_0,-0.08493510486758847,1.401868266681942e-17
+B_real_1,0.017552326616788294,0.0
+B_imag_1,0.19542755200887885,5.607473066727768e-17
+B_real_2,0.3984553300926812,0.0
+B_imag_2,0.05249158139289555,7.00934133340971e-18
diff --git a/Data/sub-016/MRS/all_samples.csv b/Data/sub-016/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..5e87369f05435185f5c72199bdd51640cebe1230
--- /dev/null
+++ b/Data/sub-016/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-016/MRS/concentration_samples.csv b/Data/sub-016/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..b5efd5dda78a4eb3242e6c9d444a6174fa3fbee4
--- /dev/null
+++ b/Data/sub-016/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+NAA,molarity,11.145086917137137,11.096752025215123,11.403800769052436,11.14432219576713,11.281427330168864,11.20563957686753,11.229732367379532,11.357984091860088,11.061946578660592,11.05074102751328,11.079570854324563,10.782548607379082,11.024214289392207,11.421651785239876,11.24871871050373,11.098786332406137,10.844009690807377,10.926991009083237,10.861163163295927,11.24024894494208,11.054158766532202,11.147816603711798,11.099143223841306,11.24305880419116,11.097190813245229,11.288280389378214,11.121293294131055,11.139023428461625,11.289405738155594,11.542882323979873,11.178553324424643,11.153443337180581,11.236162458281324,11.67743953447202,11.342071257946332,11.389921412506734,11.364023998811644,11.291938716631048,11.478862005304771,11.167429194151408,10.854431862923127,10.974796355353252,11.017007197757358,11.169236152623963,11.20578147337436,10.974982289686231,11.222150629237941,11.23496331612761,10.75644789021325,11.459474567682
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+PCh,molarity,0.23766978399210645,0.28237085672923196,0.29405862629671053,0.172668236322878,0.0933905200852941,0.09174875971999609,0.08719790047739388,0.08341196449584201,0.1901856306084571,0.22280049011584424,0.1578564435143906,0.14648876065008767,0.1435064349805729,0.1241238492035842,0.3090742579866707,0.22151101299103013,0.19186463583792232,0.2495046450922716,0.36445283906834747,0.2988358951367575,0.23358057334103557,0.3176861986670512,0.3053949139871374,0.2837874607536224,0.2650538639087065,0.3581683464225328,0.41408197625531895,0.35915707018512577,0.3621047096417525,0.3363489671852863,0.47023591031460116,0.3730126607852818,0.28234123890562624,0.3711259665977106,0.3323316829880842,0.3168476878199021,0.25709840971224496,0.23933061880012543,0.33608459629645626,0.34130482673833357,0.2918152529400066,0.4732827272755398,0.33958701484756176,0.29512559994298265,0.07977867672052329,0.19633175468983743,0.2131291857566218,0.16293014647773735,0.15198836804577873,0.16730338243083748
+PCr,molarity,3.9452925447723115,3.928278876931726,3.8460659260751537,3.818337360492014,3.8809210354548496,3.9183056048270286,3.949547587493591,3.3660514389674066,3.4322015407274495,3.673044920136197,3.3825742313960157,3.2525140528913563,3.74443421899754,3.721267176806022,3.5949726843135528,4.027435890062893,3.983645786763955,3.94767207497816,4.1206762985215954,3.897911105250806,3.983574026209942,4.209875839455611,4.2869046563447455,4.353921383044456,4.5649198137197375,3.9641394478999006,4.036393131679463,4.123768318939585,3.7561113906616512,3.6724365811539275,3.6363189554611073,3.5764056258659074,3.1515683095065032,3.3980752787444737,3.7590396653617164,3.750480536824433,3.924229403451271,3.7354053407892995,3.7588031131945225,3.6114822669968154,3.498673278099716,3.4505996743547653,3.4111934149152416,3.643250930725428,3.5699707078573053,3.753685717954612,3.9352468320858587,4.356972337955549,4.250848033051311,4.151148116767475
+PE,molarity,2.308202596422402,2.171263992912616,2.358738306298647,2.120448484858794,2.1695917005796455,1.6813915205605277,1.3083377264040243,1.8285441180747677,1.8578656885398324,1.2892098700092225,1.509471944658864,1.7271753921836757,1.7219577591560677,2.051931462283565,1.6544704136898225,1.758760858863823,1.4737793557997236,1.6230942109727724,1.6266718006078709,1.3312779960556556,1.698408583293817,1.8741990718181905,1.9298901054761743,1.7325896509862841,2.010873176600719,2.0285666115192664,1.5326816796122567,1.848311751833906,1.659447874418365,1.8500515176558585,1.5849555391151728,2.0442237044086875,2.41652549550955,2.364976024119795,2.0843378254565734,2.3434112920538785,1.9364487834149637,1.9466267803828043,1.9481780819134515,1.6800154138684058,1.4630313294432606,1.5485182108742745,1.819743652152498,1.4303510234649268,1.4887975346332092,1.5254974486982869,1.7483403605961232,2.2765996409036764,1.984039052349419,1.7985922781056043
+Scyllo,molarity,0.5042572261685913,0.46325080164185706,0.49386624596788437,0.43583160231576284,0.5164096892955635,0.5719604749453181,0.5512276877614112,0.5748933062637449,0.4670086803814281,0.5561991487965869,0.5595911373716007,0.40660549614820624,0.5666020232118762,0.6655727870720596,0.46990643099792934,0.4777244863758128,0.4998283664301134,0.44579154555496164,0.48806248087975324,0.41902487667288296,0.5018331573075954,0.5748323237879489,0.6170134967132356,0.4237622395604107,0.4893606940618371,0.42453516033196065,0.5194832017282295,0.41605637277230545,0.48183000310466156,0.46357566328758915,0.5178614318647305,0.46504157194025547,0.508076820022689,0.4543586464955292,0.5164297525153474,0.5472087362527788,0.4940986731967144,0.5765901755438212,0.5075942607441823,0.4471969562251003,0.5009286722810676,0.593341749415654,0.48153168104618543,0.6062491276690889,0.5375088620174151,0.5423661378713248,0.6218200693172551,0.5068367085636318,0.5273905000983405,0.6099044591350856
+Tau,molarity,1.0363861503462828,1.197259572602456,0.9627846152217509,1.2134413184184225,1.2101591696779008,1.5780134837175341,1.2508074786318384,1.1168827842111215,0.9203173969942323,1.4090273477132667,1.2616975180459151,1.2567178213970613,1.6079065072216936,1.5309165441026211,1.393651637876064,0.9188650646969296,0.9293124952834244,1.1643278951409832,0.9531042738523805,1.1315608444764012,1.2319349080216915,1.0098954744579862,0.7231744714207724,1.0959525571906659,1.151804077127382,0.8310939580648589,1.1732273536598246,1.1141225722611376,1.0697662434774886,1.2731005259031192,1.3812552039304933,0.8384638981414488,0.9155656027628039,0.9117000084548106,0.853891625370253,1.2661773494641961,1.0383092315210112,1.323473117344363,0.9136556558530584,1.5185053747367454,1.432333577859372,1.6618934521326376,1.2869621916712795,1.4233140547130085,1.1633662039648245,0.9354580636648566,1.0985383127797705,0.8536407707892498,1.1112774702045944,1.2062082413125064
+Cr+PCr,molarity,8.188362849310217,8.094751345090163,8.288690875148312,8.40784128049004,7.971637221705606,8.270635350912288,8.164175537433522,8.014737060053733,8.119746609754495,8.139483409393364,7.7038556797666615,7.710581435602356,8.18458687542373,8.22751794426029,8.290100980471662,7.9550565660508585,7.898513509791214,8.060658919825093,8.168153812686677,7.9990824145803145,8.232756987928914,8.274491086999214,8.197331042933712,8.194442046798871,8.42821030036922,8.02361911770127,8.281740561274065,8.281798677540392,7.991757874412474,8.272159646557192,8.308808169793908,8.327636917426172,8.10465224032403,8.175388829718079,8.283247087676152,8.30741510454916,8.450348678721873,8.311299411792403,8.211995853243097,8.07466176177122,8.055534006110607,8.073943949107354,8.002943253771496,8.379221479008674,8.14408518777038,8.137991092996263,8.085120033411755,8.159299017839231,7.843903292727416,7.983981240410295
diff --git a/Data/sub-016/MRS/concentrations.csv b/Data/sub-016/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..e0e0ef93ae83cd8df012628a1777fbce62b68902
--- /dev/null
+++ b/Data/sub-016/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.020372460144548906,0.046428243703612475,0.5259376782993416,0.37835114340072473,0.00879583168424682,0.028547599839181963,0.2270741609948547,0.16335351505328932
+Asc,0.03342552397504075,0.07617579624763064,0.8629170139805501,0.6207686811015248,0.015247805493133816,0.04025741928509101,0.3936390285374793,0.28317761339308145
+Asp,0.12231219326017133,0.2787459283912774,3.1576250729918542,2.271544911291366,0.026726008037520704,0.0642098515584882,0.6899615715397154,0.49634730551864903
+Cr,0.23342117729486392,0.5319600690410402,6.026026860835859,4.335027222870071,0.016639491475620334,0.0430248944623912,0.4295669473728755,0.3090235828534475
+GABA,0.0622982650018679,0.14197593267069802,1.6082988811700543,1.1569844598098233,0.01463742089136485,0.03906301153736902,0.3778812723290355,0.27184173592149014
+GPC,0.06423528326681142,0.14639034091717631,1.6583051583628656,1.1929581748216338,0.004801982426885376,0.023084789776951855,0.12396850802067201,0.08918095943795
+GSH,0.06828092523378611,0.1556102412064657,1.762747897641478,1.2680926089122753,0.006929352280081849,0.025739586538708843,0.17888892281277263,0.12868982634367243
+Glc,0.10333386639585655,0.23549487385533377,2.667678493236513,1.9190851878216173,0.013915006325544176,0.03766682707873174,0.35923133821103875,0.25842527197711346
+Gln,0.07488504686220761,0.17066084217645672,1.9332406300760459,1.3907423503544891,0.015258574976924857,0.04027860645415393,0.3939170547189691,0.283377620975733
+Glu,0.4564532956698257,1.0402437751901168,11.783848630618422,8.477111998273667,0.017654736023582952,0.04507738933641668,0.45577661261079694,0.3278783963039373
+Ins,0.33228476350188657,0.7572673044590915,8.578300107618034,6.171091724492458,0.010372434699597867,0.03117568283080577,0.2677759183481678,0.192633707495178
+Lac,0.022648994531558723,0.05161639931024042,0.584708941150133,0.4206302487323751,0.009259790004300368,0.02929971743305815,0.23905176016281365,0.17197000808540397
+Mac,0.026274806344082715,0.05987951889721597,0.6783132988515981,0.48796772468229704,0.0006743187595402065,0.020383994329936848,0.01740828747779695,0.01252324323515051
+NAA,0.6016431633932251,1.371127257799895,15.53208627110119,11.173534132546271,0.010347158576304093,0.031132028488540683,0.26712338716110384,0.19216428700884092
+NAAG,0.078204536943353,0.17822586345349575,2.0189369521710696,1.4523909121284473,0.007308774604533593,0.026278966771599296,0.18868413139343512,0.1357363425360965
+PCh,0.01388033823003336,0.031632886821722,0.3583363428332273,0.25778142663477505,0.0053793858109297075,0.023736892499772917,0.1388748174743054,0.09990431974920208
+PCr,0.20537336928764596,0.4680399309589597,5.301941555475772,3.814131849698639,0.016340647602119916,0.04242585071096172,0.4218519609702712,0.3034735451832332
+PE,0.09818210792297784,0.22375416624398703,2.5346801282300278,1.8234082938722345,0.015854473415427534,0.04145670774685191,0.4093008345386174,0.29444446582208406
+Scyllo,0.027577698167413605,0.06284877144029856,0.7119488978796906,0.5121646359825063,0.0032399693888225077,0.021625588037926732,0.08364340713039482,0.06017172762379141
+Tau,0.06230039563911034,0.1419807883309587,1.6083538859361275,1.1570240293576899,0.012064527429323613,0.03419217046079869,0.311459170907004,0.22405873984224534
+Cr+PCr,0.4387945465825098,0.9999999999999998,11.32796841631163,8.14915907256871,0.008918930825465753,0.028745281894403313,0.23025210200315516,0.16563967492310225
diff --git a/Data/sub-016/MRS/fit_summary.png b/Data/sub-016/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..d7b3774b8a658411557aacf41c341db993767a61
Binary files /dev/null and b/Data/sub-016/MRS/fit_summary.png differ
diff --git a/Data/sub-016/MRS/options.txt b/Data/sub-016/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..8668e8ccedc5145c97c823093ed4926007f01166
--- /dev/null
+++ b/Data/sub-016/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.09224406101525381, "GM": 0.30666066516629165, "WM": 0.6010952738184546}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_022/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-016/MRS/qc.csv b/Data/sub-016/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..be6e2fe8fb1bd015ab0acd0745b334af82cc4482
--- /dev/null
+++ b/Data/sub-016/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,7.692348608957945,18.49893095007144
+Asc,10.239988450988825,15.187275419421729
+Asp,12.203373397526954,22.46776153362622
+Cr,152.580051944091,9.56595622264721
+GABA,13.058155187533542,21.638813847732145
+GPC,122.88422356687664,9.79081189654669
+GSH,37.791717731555586,10.408702410834726
+Glc,19.8156138300327,40.80405880179113
+Gln,14.784510784199076,23.891691496063864
+Glu,104.39209538314896,22.048958500884687
+Ins,101.15367733485014,41.74092049892523
+Lac,8.769020843049685,17.42775158425772
+Mac,79.2449607904149,35.02416483950223
+NAA,390.525520296684,9.505449452685031
+NAAG,55.59276418638432,10.647285597206803
+PCh,27.23943507089554,9.510570032774043
+PCr,128.6968896597526,9.976725138484408
+PE,24.391292026317256,18.07119799641246
+Scyllo,35.8257157086898,9.576924916194969
+Tau,18.128266635831285,18.433086130804266
diff --git a/Data/sub-016/MRS/summary.csv b/Data/sub-016/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..f9861d2c2d697bbd590930619b3a97b33e16ad59
--- /dev/null
+++ b/Data/sub-016/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.046428243703612475,0.028547599839181963,0.5259376782993416,0.2270741609948547,0.37835114340072473,0.16335351505328932,43.175108071571486,7.692348608957945,18.49893095007144
+Asc,0.07617579624763064,0.04025741928509101,0.8629170139805501,0.3936390285374793,0.6207686811015248,0.28317761339308145,45.61725196744722,10.239988450988825,15.187275419421729
+Asp,0.2787459283912774,0.0642098515584882,3.1576250729918542,0.6899615715397154,2.271544911291366,0.49634730551864903,21.850649003302212,12.203373397526954,22.46776153362622
+Cr,0.5319600690410402,0.0430248944623912,6.026026860835859,0.4295669473728755,4.335027222870071,0.3090235828534475,7.128526926501137,152.580051944091,9.56595622264721
+GABA,0.14197593267069802,0.03906301153736902,1.6082988811700543,0.3778812723290355,1.1569844598098233,0.27184173592149014,23.49571194466808,13.058155187533542,21.638813847732145
+GPC,0.14639034091717631,0.023084789776951855,1.6583051583628656,0.12396850802067201,1.1929581748216338,0.08918095943795,7.475614931033434,122.88422356687664,9.79081189654669
+GSH,0.1556102412064657,0.025739586538708843,1.762747897641478,0.17888892281277263,1.2680926089122753,0.12868982634367243,10.14829874720727,37.791717731555586,10.408702410834726
+Glc,0.23549487385533377,0.03766682707873174,2.667678493236513,0.35923133821103875,1.9190851878216173,0.25842527197711346,13.466065686769014,19.8156138300327,40.80405880179113
+Gln,0.17066084217645672,0.04027860645415393,1.9332406300760459,0.3939170547189691,1.3907423503544891,0.283377620975733,20.375997099930284,14.784510784199076,23.891691496063864
+Glu,1.0402437751901168,0.04507738933641668,11.783848630618422,0.45577661261079694,8.477111998273667,0.3278783963039373,3.867807767205489,104.39209538314896,22.048958500884687
+Ins,0.7572673044590915,0.03117568283080577,8.578300107618034,0.2677759183481678,6.171091724492458,0.192633707495178,3.1215498990338078,101.15367733485014,41.74092049892523
+Lac,0.05161639931024042,0.02929971743305815,0.584708941150133,0.23905176016281365,0.4206302487323751,0.17197000808540397,40.88388997311971,8.769020843049685,17.42775158425772
+Mac,0.05987951889721597,0.020383994329936848,0.6783132988515981,0.01740828747779695,0.48796772468229704,0.01252324323515051,2.5664081048196503,79.2449607904149,35.02416483950223
+NAA,1.371127257799895,0.031132028488540683,15.53208627110119,0.26712338716110384,11.173534132546271,0.19216428700884092,1.719816530108453,390.525520296684,9.505449452685031
+NAAG,0.17822586345349575,0.026278966771599296,2.0189369521710696,0.18868413139343512,1.4523909121284473,0.1357363425360965,9.345716872957974,55.59276418638432,10.647285597206803
+PCh,0.031632886821722,0.023736892499772917,0.3583363428332273,0.1388748174743054,0.25778142663477505,0.09990431974920208,38.755437524498845,27.23943507089554,9.510570032774043
+PCr,0.4680399309589597,0.04242585071096172,5.301941555475772,0.4218519609702712,3.814131849698639,0.3034735451832332,7.9565562267390195,128.6968896597526,9.976725138484408
+PE,0.22375416624398703,0.04145670774685191,2.5346801282300278,0.4093008345386174,1.8234082938722345,0.29444446582208406,16.148027121056614,24.391292026317256,18.07119799641246
+Scyllo,0.06284877144029856,0.021625588037926732,0.7119488978796906,0.08364340713039482,0.5121646359825063,0.06017172762379141,11.748512762573217,35.8257157086898,9.576924916194969
+Tau,0.1419807883309587,0.03419217046079869,1.6083538859361275,0.311459170907004,1.1570240293576899,0.22405873984224534,19.365089588210996,18.128266635831285,18.433086130804266
+Cr+PCr,0.9999999999999998,0.028745281894403313,11.32796841631163,0.23025210200315516,8.14915907256871,0.16563967492310225,2.032598375465147,,
diff --git a/Data/sub-016/MRS/voxel_location.png b/Data/sub-016/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..9657b3f9d223625d14710d90dd63b93f4cacf58a
Binary files /dev/null and b/Data/sub-016/MRS/voxel_location.png differ
diff --git a/Data/sub-016/TMS_EEG/DCM_DefaultCodes_STR7T_HS_022_FHK.mat b/Data/sub-016/TMS_EEG/DCM_DefaultCodes_STR7T_HS_022_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..d410616852e782fdc82c8d9bed834c31aff13ef9
Binary files /dev/null and b/Data/sub-016/TMS_EEG/DCM_DefaultCodes_STR7T_HS_022_FHK.mat differ
diff --git a/Data/sub-017/MRS/all_parameters.csv b/Data/sub-017/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..e5d479167babbba548b89942e9d55606fdd3cb56
--- /dev/null
+++ b/Data/sub-017/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.01850284760419978,0.0074484155526091615
+Asc,0.03302071886897548,0.011166036902494588
+Asp,0.06813952053867676,0.01939538900930333
+Cr,0.1892668166740058,0.012451557958546803
+GABA,0.06012537752789348,0.011109831474502412
+GPC,0.06755954878039745,0.0038038564609805
+GSH,0.06601566947620853,0.005966627489598146
+Glc,0.07822203969265336,0.014506985506158695
+Gln,0.044587079435079426,0.013585296520983241
+Glu,0.39334429119253916,0.012670677085570495
+Ins,0.32852392873763214,0.00972459272430784
+Lac,0.05604839320100118,0.007946671040757209
+Mac,0.02773150592980716,0.0006641083045055006
+NAA,0.5743787410147124,0.010004133472621406
+NAAG,0.09224074033198885,0.005400665719600108
+PCh,0.003672128747983703,0.0035566870178914147
+PCr,0.19977326584385097,0.011307653759171568
+PE,0.10514223589078467,0.012766506938912146
+Scyllo,0.011035610429480956,0.0023995483919796567
+Tau,0.0871553055654569,0.011687498186647936
+gamma_0,13.452164814330922,1.0834526562303732
+gamma_1,2.8123453079136804,2.6558272252079904
+sigma_0,8.837389568562307,0.8141210607581912
+sigma_1,10.153319928367624,4.620832761356769
+eps_0,0.8743697856929817,0.30003050903033107
+eps_1,-0.748606892677226,3.6912168940663763
+Phi0,0.10415231270728792,0.014822866752334707
+Phi1,0.0003498541408590851,1.9902391919195482e-05
+B_real_0,0.13258086836161323,0.0
+B_imag_0,-0.0018747354087798596,0.0
+B_real_1,0.08400643577900048,1.401868266681942e-17
+B_imag_1,0.15017430343634083,0.0
+B_real_2,0.22869901224926104,2.803736533363884e-17
+B_imag_2,-0.14961861496561446,0.0
diff --git a/Data/sub-017/MRS/all_samples.csv b/Data/sub-017/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..c3fdf22ab25d953dcd25bfbbf540a896f387663e
--- /dev/null
+++ b/Data/sub-017/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.020162605573962544,0.009003559424248513,0.014991692353346301,0.0074431501674185555,0.00495204397012655,0.012510331473321173,0.012720657530986227,0.008506135665741172,0.005445053207564772,0.011917903959908327,0.026156846785044388,0.015792417566509245,0.013772942495494378,0.01931372233857026,0.025087282173021606,0.029168824310414947,0.02068235899403656,0.011991774602271903,0.02280737251324366,0.012635079960063725,0.010247969892398307,0.020750922834341212,0.01998454464339695,0.01221451719374789,0.02179378417672569,0.012372998697049081,0.019303765054979095,0.013484563107342367,0.024999134352442623,0.03386494317808497,0.011546361414641652,0.013601236597177473,0.015512929210859385,0.018751152565920786,0.015967979815390467,0.027253121176171662,0.012402805320394313,0.03542439294481112,0.018465951602108566,0.02012388883949697,0.03352625863243325,0.023855383924996042,0.02097609752696983,0.018311499843823957,0.02846151648713551,0.03162314456307787,0.016169772943504076,0.025630371662493073,0.01938127603916992,0.024078340903609947
+Asc,0.03415131311893714,0.0397433143538523,0.037791157752391814,0.03718097342944206,0.06404720198770711,0.04770278071056252,0.041435454170072966,0.039170759791269806,0.02408068851929679,0.038558077931419944,0.039861152588833965,0.019934749830235014,0.04088486640159493,0.02032939042806542,0.04166283767283589,0.037940258342503856,0.03702875738039026,0.032568283795191603,0.020634450702041646,0.03941436887778277,0.05165727667159528,0.032945111561168194,0.031371158124629685,0.03133567325900359,0.018601612237678127,0.03362450106690145,0.016388615662106667,0.015243275969987785,0.043947477088984895,0.03463648498702056,0.017789081339653456,0.02511150359643892,0.0481452887606016,0.02826648975782985,0.040969556116753236,0.028210124923962476,0.030365868200302362,0.03316210646143285,0.010444689260112487,0.015346185505929108,0.04383150858626321,0.012654086580587337,0.023684165373120406,0.02690682620383236,0.02811068484112581,0.03897034041168759,0.04784644533471199,0.04030667129166307,0.04214237189419624,0.024899924595065397
+Asp,0.059916495765162794,0.060184580242474285,0.07851705437792693,0.0610654687193476,0.07370935311152596,0.07526094776223352,0.05187243071064333,0.055351536276331915,0.07059153219545743,0.08841765930318378,0.06892898829790262,0.025705281067062,0.054855109687707085,0.04866559400774417,0.08764448019692599,0.08920208605340979,0.10009650355241012,0.07851589346869844,0.06075473275023495,0.07724509061580175,0.04952572570259976,0.06466959725302308,0.07434913055068831,0.06601613184550813,0.05032463725786482,0.0866412202565423,0.07394757403650527,0.10305809109940206,0.08642453495723902,0.04108657143403221,0.1025584978104183,0.04387224255812504,0.03524792279094503,0.05753920041586627,0.05694946942891597,0.08609022920123116,0.08194698120103375,0.0861562097840675,0.07128643035743698,0.08908852359010346,0.0765183950919145,0.06377931205274431,0.10105801857937308,0.04905820311188987,0.07323768443957872,0.06438294404665736,0.0755352438226473,0.07483630929005275,0.03282958300049566,0.02246059380475145
+Cr,0.17604632743633122,0.17886675466669794,0.19371743814632397,0.19264896113299526,0.20014614869575664,0.188684781699938,0.18453712697614802,0.18513239996467712,0.1607681250284057,0.17341835721076107,0.18132610465171328,0.18575487019239384,0.1847928866473721,0.1812342647341698,0.1701178940999078,0.1694016242626283,0.174122493003035,0.18004658164503531,0.1967558905850973,0.19852877337084956,0.2004144598614069,0.192335742946503,0.19066061592596298,0.19556409621532164,0.20118369471766515,0.1939455992774837,0.18939466385432432,0.19355185950705853,0.19880644708651093,0.20862247762269087,0.18862053229026576,0.18507895260780385,0.195950860390689,0.20423988660471376,0.19472398706838548,0.1794822349589304,0.19327378036919093,0.18281402530406118,0.18319785514814868,0.17768906109930627,0.17767322476049235,0.17106398495766037,0.17295336356655971,0.18269545468007506,0.19914027748523105,0.20703076367224024,0.2108401869205636,0.2119996564738149,0.21236250779191937,0.2119827763850718
+GABA,0.05347432024055891,0.08867250458249817,0.06129834009720788,0.05823290396446983,0.05240651741628004,0.05237048555402357,0.05694406395060532,0.04452415241623422,0.05763555832281656,0.05406207057270798,0.06507164655940227,0.052592919546797415,0.045160404637980434,0.05198377421790742,0.05839054604609065,0.06220195109740185,0.056569338778147626,0.04617021986764451,0.05383004203222848,0.05380310101971361,0.060726493417732876,0.04052834551470936,0.07818839812398597,0.05706933033039177,0.07187696665270049,0.07401685379194013,0.07637765152809875,0.06919283298128179,0.0824570837171015,0.04284162897402102,0.053945668273789917,0.07819591425543002,0.058098053537673874,0.0640551852394235,0.06351019392521962,0.07507569962917104,0.06104860649731556,0.051228517931052146,0.05080016852770483,0.05010549087703121,0.06778482572538752,0.06660930416937363,0.07054753175255249,0.057163879097069686,0.06873346990053886,0.05721055343300027,0.05288004643686488,0.08128085656664778,0.0490694886888305,0.05025497597791646
+GPC,0.06284001971346902,0.06909752831515849,0.06981575806627888,0.07181542501611607,0.07048178576050351,0.07082302900490935,0.06870793137115588,0.06612750956530573,0.06887305927457207,0.06894277795216908,0.06791929081717346,0.06802927115393007,0.07117845105062848,0.06610831129347941,0.061121498192145234,0.06015780952619397,0.057545290488863324,0.06262972410422248,0.06639285922148373,0.07131997348590349,0.06729699791460919,0.07124045102501318,0.06958851632652749,0.07008052782755338,0.06776536484029452,0.06576441770481432,0.06116015156352549,0.06268807130120166,0.06210162572155578,0.062403349760762054,0.07105853925656168,0.06885286505725491,0.07404524622093447,0.07008097724315157,0.06784252621860273,0.06860171948507078,0.062392951761564557,0.06584496246522573,0.06268236138141299,0.06785976675556563,0.06803420233615617,0.06617646615188479,0.07078349354835668,0.071837375891525,0.0734394668294444,0.07236629086309204,0.06708629633687194,0.06656959840082714,0.07036880672711665,0.07203674872973378
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diff --git a/Data/sub-017/MRS/concentration_samples.csv b/Data/sub-017/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..a78d6a524dd14a4f22fc47c24e1441bdc55b876e
--- /dev/null
+++ b/Data/sub-017/MRS/concentration_samples.csv
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+NAA,internal,1.46825524075488,1.477683922087955,1.4617114856841955,1.4592970671390848,1.4428313702140985,1.4657931354225056,1.446330203163148,1.447767370458644,1.4573102686294699,1.4481184308976016,1.4733412237005,1.4360968492440234,1.4574001316845684,1.4805181843238573,1.4939204027874178,1.5188633718939875,1.478717081484142,1.5061322579624874,1.4939025937084949,1.4946862019598481,1.4733246300660323,1.4728614340034836,1.4604949591387144,1.4696170595021938,1.5069746233603432,1.5003431810875323,1.4923216388411287,1.4593166242403124,1.4742695945634745,1.4733623589343285,1.457612649151367,1.4097134789705918,1.460227739980064,1.4472793149734586,1.4735457902928362,1.4525675204760864,1.4342497923708324,1.4770794919673311,1.4803586452204538,1.4918831105743717,1.4803771698886616,1.4864054447185917,1.4843243063134457,1.486387991518591,1.517792375826594,1.504675617890573,1.518257930260003,1.510761083175832,1.537461185428701,1.517471732590362
+NAAG,internal,0.21086550874401652,0.21983509885977476,0.23446298196584917,0.24057300903450665,0.2496433520745398,0.25059930579546147,0.2549037715273023,0.2398923060626668,0.24293926955699596,0.2602386876272908,0.25251584216082074,0.21918699579617448,0.23121351836703327,0.2138725637831282,0.2273344898770201,0.23916337359081513,0.2164038420690744,0.24240429503821947,0.23723273500728878,0.2346796228745127,0.23492316019613765,0.23555959846810268,0.21635911568672872,0.24090730165120414,0.23662615434780163,0.23589440142977786,0.2531940775382445,0.24005709298348749,0.26142365409607016,0.2400563717968014,0.2321197434333093,0.24468872383992415,0.23319372473211722,0.259500412070994,0.23816427034596674,0.2519694887274407,0.23227930497974905,0.2382726461226818,0.22881965302611773,0.2101830331475105,0.24840950877856266,0.25310531234507394,0.23334357706561482,0.244637311413709,0.24909533498167016,0.22263630149608213,0.2564815371435702,0.2103340513529391,0.212224813026178,0.24249451429008906
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diff --git a/Data/sub-017/MRS/concentrations.csv b/Data/sub-017/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..b83bbf985f2fcc3af934d1f1361c5bbf602667e3
--- /dev/null
+++ b/Data/sub-017/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
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+GPC,0.06755954878039745,0.17365703899493826,1.7159171236242299,1.224183510423871,0.0038038564609805,0.02433535570177632,0.09661258186346791,0.0689261316810742
+GSH,0.06601566947620853,0.16968860650284906,1.6767047697425017,1.1962083149053784,0.005966627489598146,0.027052290381576468,0.15154391147531107,0.1081156863458385
+Glc,0.07822203969265336,0.20106421730738502,1.986729333994354,1.417388553833151,0.014506985506158695,0.0434406732041373,0.36845694341595303,0.26286754075762037
+Gln,0.044587079435079426,0.11460793228942649,1.1324488466276648,0.8079208403212548,0.013585296520983241,0.041424854817585746,0.34504734490813577,0.24616647513832945
+Glu,0.39334429119253916,1.0110636637922388,9.990389470051499,7.127424677782744,0.012670677085570495,0.03946332556274913,0.32181730297985656,0.22959351023021646
+Ins,0.32852392873763214,0.8444475093965492,8.344043810499423,5.9528754054818025,0.00972459272430784,0.03348772993976468,0.24699092100439063,0.17621026595932174
+Lac,0.05604839320100118,0.14406842821505053,1.423550029291004,1.0156006068875256,0.007946671040757209,0.03022987221072486,0.20183422122855474,0.1439942069844097
+Mac,0.02773150592980716,0.0712818734520351,0.7043410849814594,0.502496729053672,0.0006641083045055006,0.022350015007162254,0.01686741300398808,0.01203368658002464
+NAA,0.5743787410147124,1.476399905370544,14.588408817775317,10.40778093077278,0.010004133472621406,0.034027432101087655,0.25409086121182367,0.18127556288262373
+NAAG,0.09224074033198885,0.23709829520652295,2.3427845314052833,1.6714083403777071,0.005400665719600108,0.02625490246915479,0.13716928183394064,0.09786042148884562
+PCh,0.003672128747983703,0.009438947072542721,0.09326688399444001,0.0665392167737426,0.0035566870178914147,0.02408711728164086,0.09033482709024056,0.06444740495816713
+PCr,0.19977326584385097,0.513503042028276,5.073958809554126,3.6199048437180505,0.011307653759171568,0.03662531699078116,0.28719843550829355,0.20489543703963878
+PE,0.10514223589078467,0.27026067651000635,2.6704642976165553,1.905184296671057,0.012766506938912146,0.03966686050163514,0.32425124591274734,0.2313299535366766
+Scyllo,0.011035610429480956,0.0283662556260496,0.28028891914516296,0.19996599383967645,0.0023995483919796567,0.023122538478577936,0.06094514023689807,0.04347997621289515
+Tau,0.0871553055654569,0.2240265450320444,2.213621670573713,1.5792599246924468,0.011687498186647936,0.03740486795199305,0.29684594750602106,0.21177824329037984
+Cr+PCr,0.38904008251785677,1.0,9.881068648615189,7.04943213076179,0.00866965304519423,0.03151536684403238,0.22019694306256452,0.15709468891690304
diff --git a/Data/sub-017/MRS/fit_summary.png b/Data/sub-017/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..48dc05276df3c5ea8ded1e060138018fa304136b
Binary files /dev/null and b/Data/sub-017/MRS/fit_summary.png differ
diff --git a/Data/sub-017/MRS/options.txt b/Data/sub-017/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..8615300eb67067c1f805e8e333ca6953e161964c
--- /dev/null
+++ b/Data/sub-017/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.075594, "GM": 0.301831, "WM": 0.622575}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_023/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-017/MRS/qc.csv b/Data/sub-017/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..9445cc8392235c6c7f80cb81a3b4f3d464d6dd20
--- /dev/null
+++ b/Data/sub-017/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,3.981075581593065,17.36589009845341
+Asc,5.716404858334287,14.338817745946466
+Asp,3.674961941182177,11.725323868841308
+Cr,84.00815197134558,8.551508892485536
+GABA,7.357621043703892,20.18341926968347
+GPC,87.08331819852765,8.652565207121466
+GSH,23.943784647736358,9.240408641503205
+Glc,7.5782056121427965,0.0
+Gln,4.972171340494592,22.630102047933423
+Glu,50.517716385162636,20.571893583265872
+Ins,54.45967188110977,19.540087911651415
+Lac,12.851129887964243,16.359482739363806
+Mac,37.791282795928566,35.08134840026896
+NAA,251.87219034749813,8.52840652522201
+NAAG,42.80152405521774,9.291963105586317
+PCh,4.7884237549751925,8.571093741138966
+PCr,81.42039989407444,8.782191688653908
+PE,14.188526828501901,17.36180827601135
+Scyllo,9.382862663479344,8.63474915610626
+Tau,14.346424778435287,17.081323709547675
diff --git a/Data/sub-017/MRS/summary.csv b/Data/sub-017/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..cc43b48f1db786aa6f93828b5674fb14c4c92b68
--- /dev/null
+++ b/Data/sub-017/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.04756026033217415,0.02937965507859269,0.4699461972882226,0.18917923552354285,0.3352728273330238,0.13496578445080606,40.25550937855922,3.981075581593065,17.36589009845341
+Asc,0.08487742099802748,0.036337112085824144,0.8386796235989219,0.28360156735637987,0.5983376187596904,0.20232933019209984,33.81524474618754,5.716404858334287,14.338817745946466
+Asp,0.1751478153553733,0.05460840444628064,1.730647587181421,0.4926154884277927,1.2346926371989018,0.3514457368657671,28.46422877057711,3.674961941182177,11.725323868841308
+Cr,0.486496957971724,0.03899978864901375,4.807109839061064,0.31625198661879406,3.429527287043739,0.22562305709719158,6.578838370802968,84.00815197134558,8.551508892485536
+GABA,0.1545480279018133,0.036223106633559446,1.527099673205913,0.2821740288651757,1.0894758336369124,0.20131088410436776,18.477774163410977,7.357621043703892,20.18341926968347
+GPC,0.17365703899493826,0.02433535570177632,1.7159171236242299,0.09661258186346791,1.224183510423871,0.0689261316810742,5.630375764268273,87.08331819852765,8.652565207121466
+GSH,0.16968860650284906,0.027052290381576468,1.6767047697425017,0.15154391147531107,1.1962083149053784,0.1081156863458385,9.038198865420075,23.943784647736358,9.240408641503205
+Glc,0.20106421730738502,0.0434406732041373,1.986729333994354,0.36845694341595303,1.417388553833151,0.26286754075762037,18.545905429158985,7.5782056121427965,0.0
+Gln,0.11460793228942649,0.041424854817585746,1.1324488466276648,0.34504734490813577,0.8079208403212548,0.24616647513832945,30.469132971052694,4.972171340494592,22.630102047933423
+Glu,1.0110636637922388,0.03946332556274913,9.990389470051499,0.32181730297985656,7.127424677782744,0.22959351023021646,3.2212688398643343,50.517716385162636,20.571893583265872
+Ins,0.8444475093965492,0.03348772993976468,8.344043810499423,0.24699092100439063,5.9528754054818025,0.17621026595932174,2.9600865792866355,54.45967188110977,19.540087911651415
+Lac,0.14406842821505053,0.03022987221072486,1.423550029291004,0.20183422122855474,1.0156006068875256,0.1439942069844097,14.178231679646544,12.851129887964243,16.359482739363806
+Mac,0.0712818734520351,0.022350015007162254,0.7043410849814594,0.01686741300398808,0.502496729053672,0.01203368658002464,2.39477908695786,37.791282795928566,35.08134840026896
+NAA,1.476399905370544,0.034027432101087655,14.588408817775317,0.25409086121182367,10.40778093077278,0.18127556288262373,1.7417311537240816,251.87219034749813,8.52840652522201
+NAAG,0.23709829520652295,0.02625490246915479,2.3427845314052833,0.13716928183394064,1.6714083403777071,0.09786042148884562,5.854967880962649,42.80152405521774,9.291963105586317
+PCh,0.009438947072542721,0.02408711728164086,0.09326688399444001,0.09033482709024056,0.0665392167737426,0.06444740495816713,96.85627226017947,4.7884237549751925,8.571093741138966
+PCr,0.513503042028276,0.03662531699078116,5.073958809554126,0.28719843550829355,3.6199048437180505,0.20489543703963878,5.660243732517236,81.42039989407444,8.782191688653908
+PE,0.27026067651000635,0.03966686050163514,2.6704642976165553,0.32425124591274734,1.905184296671057,0.2313299535366766,12.142129973508661,14.188526828501901,17.36180827601135
+Scyllo,0.0283662556260496,0.023122538478577936,0.28028891914516296,0.06094514023689807,0.19996599383967645,0.04347997621289515,21.743685202672708,9.382862663479344,8.63474915610626
+Tau,0.2240265450320444,0.03740486795199305,2.213621670573713,0.29684594750602106,1.5792599246924468,0.21177824329037984,13.40996754106976,14.346424778435287,17.081323709547675
+Cr+PCr,1.0,0.03151536684403238,9.881068648615189,0.22019694306256452,7.04943213076179,0.15709468891690304,2.2284729606996976,,
diff --git a/Data/sub-017/MRS/voxel_location.png b/Data/sub-017/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..d4f912c0fda8d00850ef2696ff910dc5979d56f8
Binary files /dev/null and b/Data/sub-017/MRS/voxel_location.png differ
diff --git a/Data/sub-017/TMS_EEG/DCM_DefaultCodes_STR7T_HS_023_FHK.mat b/Data/sub-017/TMS_EEG/DCM_DefaultCodes_STR7T_HS_023_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..720c2487fbf6e44495f5affac11b93827a97faf1
Binary files /dev/null and b/Data/sub-017/TMS_EEG/DCM_DefaultCodes_STR7T_HS_023_FHK.mat differ
diff --git a/Data/sub-018/MRS/all_parameters.csv b/Data/sub-018/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..dd74431c5997eceed9384194baf80c9f043c4bf4
--- /dev/null
+++ b/Data/sub-018/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.0210409473497847,0.012161739927398772
+Asc,0.046177603366392636,0.020938340645210454
+Asp,0.06656180502896718,0.033663679809333026
+Cr,0.2396672330126002,0.018152523733112238
+GABA,0.061792602156137556,0.021203046215985684
+GPC,0.07187183220493744,0.008393973890606518
+GSH,0.0753920232318504,0.012471356338291984
+Glc,0.17402202999354935,0.025004723972254703
+Gln,0.010593448368074465,0.009813834183591007
+Glu,0.4559562306096806,0.02128669182591566
+Ins,0.38128755568807265,0.01607841071328816
+Lac,0.10162445397217866,0.014310850077930586
+Mac,0.02793692132369459,0.000866730578352509
+NAA,0.6659257942491551,0.02030112207466603
+NAAG,0.07426111009496593,0.01007546506637007
+PCh,0.012957292604185157,0.007027168663083833
+PCr,0.2097903295878938,0.020178445310366323
+PE,0.11368470457031425,0.021374717517951024
+Scyllo,0.01640122426716613,0.0059625738461925055
+Tau,0.05597256014154798,0.02066062922110059
+gamma_0,24.975740151916153,2.022989917867856
+gamma_1,3.079377790852543,2.4945398462801736
+sigma_0,7.3186764734424,1.9912531224560315
+sigma_1,9.897842143814223,5.598013591325912
+eps_0,-6.015339927514787,0.6576439759283417
+eps_1,-6.058364529555083,3.724472189690892
+Phi0,0.06083963040683743,0.014809809980325677
+Phi1,0.00033987569520551583,2.0291651662537703e-05
+B_real_0,0.16416405705406834,2.803736533363884e-17
+B_imag_0,-0.7414675305257538,0.0
+B_real_1,-0.6385026248665164,0.0
+B_imag_1,0.07940691020178214,1.401868266681942e-17
+B_real_2,0.23264229954785798,0.0
+B_imag_2,0.5934916285545055,1.1214946133455537e-16
diff --git a/Data/sub-018/MRS/all_samples.csv b/Data/sub-018/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..3f858da8a9886c9a027619d2c99a3d7b286c1dfb
--- /dev/null
+++ b/Data/sub-018/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-018/MRS/concentration_samples.csv b/Data/sub-018/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..35700cf62e8f341fffb3d9ff0551dbabab7d87f5
--- /dev/null
+++ b/Data/sub-018/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+PCr,molarity,3.38800127439265,4.035873261368561,3.855605539743062,3.7268210983270613,3.8461742140009822,3.5338164520253117,3.6330194813588346,3.7005698808858565,3.82937364159257,3.3084396536534864,3.044974228559036,3.3336682679744927,3.1570930414176828,2.8650625876875164,3.4561967240248364,3.628713250856896,3.124187293484887,3.3632360795123177,3.967009327368401,3.936420937582539,4.078685324008755,3.9043939334151916,4.252457040022457,3.930597658035039,2.9404953501628714,3.4133513963586326,3.3338646515566457,2.99895459559716,3.664992504879307,3.9143026960430434,3.940770123321217,3.700708618165768,3.6996333500984133,3.4105777409417217,3.7679605673159817,3.968298211075107,4.101239855202521,3.9214309472977855,4.260956152646088,4.001630334953964,3.73267189716732,3.6942144842312254,4.111903949007644,3.975008090319,4.068313191771863,3.989033868149628,3.784542602384785,4.200684698773976,3.779175336513622,4.077752027277591
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+Tau,molarity,0.49597141330824324,0.9753353598249315,1.2354337656218723,0.9465894292771432,0.720901491841441,0.3586763495900962,1.1884618655022998,0.8797625937737784,1.067248488936497,0.7701033794843953,1.0943120307383027,1.2086591101144046,0.5883341003141529,1.1624814613525953,0.6944861936936257,1.623483062900698,1.228692630538742,1.3205556742327584,1.1539912220979518,1.1964158685246238,0.9514211848662742,0.7245610262330909,0.2354849619098342,0.628888402119505,1.1298278542328517,0.7360295430595516,0.6980470182697628,1.2762636247371804,1.3468008249282288,1.4883546198700348,1.4235222583663822,1.2334275391242837,0.6420128157508506,0.7140245698860951,1.2667935732937479,1.5981810608969549,1.430569082497759,1.3868919787488432,1.5145147010070223,1.4383192889772733,1.4957322105913706,1.0503953201915666,0.8963747050395612,0.8366459090875855,0.4180640426529128,0.6038313605311072,0.4526784581118444,0.9350986100430958,0.5520238301675637,0.4379084368520898
+Cr+PCr,molarity,7.361230809053568,7.650475592374355,7.72029790607601,7.564129649651844,7.746322829363599,7.59360376433244,7.881992986254142,7.798583997450096,7.815970781264786,7.817928038194249,7.483399588715604,7.732706732657296,7.769246217259219,7.525237861909151,8.148556671050175,8.155298285782008,7.740856857895672,8.139089956119205,8.19088672843426,8.16188658737304,8.467239324280891,8.267901349226362,8.031004805399087,7.7601011347800375,7.739740512438393,7.9350289229013296,7.84977550017729,7.538816521950087,7.893420898517965,7.716453842211987,7.878061012249358,8.029746270028458,7.903087287839699,8.047927087021405,8.035899739164845,8.281833396068116,8.454312848290327,8.470146669229077,8.256756282885725,8.412604473286436,8.249617540591066,8.403127632117892,7.948592102474103,8.19083788650178,8.073556549147762,7.711501898612504,7.873184782753262,8.035543014062286,7.8151545949699885,7.833724977974525
diff --git a/Data/sub-018/MRS/concentrations.csv b/Data/sub-018/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..5825af27df44bcc32e3bde75a7ed72ce2370acb0
--- /dev/null
+++ b/Data/sub-018/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.0210409473497847,0.04681409125267564,0.5118459662404766,0.3717997604589944,0.012161739927398772,0.04408861517707038,0.2958487287108061,0.2149015401541661
+Asc,0.046177603366392636,0.10274074174926762,1.1233248969648972,0.8159719039632934,0.020938340645210454,0.058153841684460764,0.5093499366191634,0.3699866696533382
+Asp,0.06656180502896718,0.14809363679153725,1.619194746481343,1.1761667739614166,0.033663679809333026,0.08259183931145694,0.818908884318576,0.5948471749493911
+Cr,0.2396672330126002,0.533236623333072,5.830189316963955,4.2349908653170285,0.018152523733112238,0.05331784624894452,0.4415816405706224,0.3207604611855274
+GABA,0.061792602156137556,0.13748261748810017,1.5031782377158613,1.0918935491763857,0.021203046215985684,0.058626692414038464,0.5157892131588706,0.37466409534954376
+GPC,0.07187183220493744,0.15990793833593056,1.7483674470002433,1.2699965240784754,0.008393973890606518,0.039502119786479,0.2041933571341211,0.14832400033824955
+GSH,0.0753920232318504,0.16774002598964732,1.834000263221313,1.3321993402738943,0.012471356338291984,0.04451471909367781,0.30338051463104254,0.22037255367321507
+Glc,0.17402202999354935,0.38718233816488484,4.233292000043377,3.0750207198656216,0.025004723972254703,0.06562526833125579,0.6082695274785751,0.44184086527466654
+Gln,0.010593448368074465,0.02356940732464788,0.2576981789667924,0.18718936463310495,0.009813834183591007,0.04109005586579149,0.23873314051495678,0.173413351499155
+Glu,0.4559562306096806,1.0144589134769173,11.091675367086815,8.056881399030729,0.02128669182591566,0.058776546897652424,0.5178239916944872,0.37614213800695906
+Ins,0.38128755568807265,0.8483282681506127,9.275271408282292,6.737463837257854,0.01607841071328816,0.04991326919426418,0.3911263846795576,0.284110270910546
+Lac,0.10162445397217866,0.2261046702255822,2.47213521199096,1.7957341471138062,0.014310850077930586,0.047174518715373925,0.34812837863671253,0.2528769519017697
+Mac,0.02793692132369459,0.062156972422614844,0.6795987010944614,0.4936536593832456,0.000866730578352509,0.03486188648960094,0.021084247917741526,0.015315385569711334
+NAA,0.6659257942491551,1.4816210687305125,16.199433701135295,11.767105666363207,0.02030112207466603,0.05702442683767761,0.49384884013692615,0.35872682911717224
+NAAG,0.07426111009496593,0.16522385264874018,1.8064894616561638,1.3122157707889452,0.01007546506637007,0.04140231655242082,0.24509762162734205,0.17803644654943207
+PCh,0.012957292604185157,0.028828734195095546,0.3152014898662629,0.22895919115934846,0.007027168663083833,0.038158598992181575,0.17094420106173341,0.12417214786986554
+PCr,0.2097903295878938,0.46676337666692813,5.103398253449948,3.7070571486502257,0.020178445310366323,0.05680847695325899,0.4908645825408022,0.3565590944224232
+PE,0.11368470457031425,0.2529375719312667,2.76551509255837,2.0088423408144163,0.021374717517951024,0.05893447162815038,0.5199653209153072,0.3776975780101546
+Scyllo,0.01640122426716613,0.03649115207289228,0.3989792067342586,0.2898144818478912,0.0059625738461925055,0.0372508162289969,0.14504667118117315,0.10536044270630822
+Tau,0.05597256014154798,0.12453358180847854,1.361598822160304,0.9890516860742555,0.02066062922110059,0.05766005626926434,0.5025942772923039,0.3650794266835091
+Cr+PCr,0.449457562600494,1.0000000000000002,10.933587570413904,7.942048013967256,0.015644948473504984,0.04922666822167892,0.38058190228234035,0.2764508649798025
diff --git a/Data/sub-018/MRS/fit_summary.png b/Data/sub-018/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..8255db74e7fdd7b902894419b5ec6822d7b6da52
Binary files /dev/null and b/Data/sub-018/MRS/fit_summary.png differ
diff --git a/Data/sub-018/MRS/options.txt b/Data/sub-018/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..f0eb8f93323be107ad03c5659e7db56dd5e2b808
--- /dev/null
+++ b/Data/sub-018/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.04222379032258065, "GM": 0.483679435483871, "WM": 0.4740967741935484}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_025/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-018/MRS/qc.csv b/Data/sub-018/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..0079cbc3957554803229fc15bba7317caa7f40eb
--- /dev/null
+++ b/Data/sub-018/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,4.701034520473094,19.249879688976687
+Asc,8.126266357497215,16.607610392876815
+Asp,3.958305514540109,23.491095870605434
+Cr,84.71511004061793,11.279288933524347
+GABA,7.667920189768488,22.574532068714838
+GPC,77.75804921071935,10.783027024880745
+GSH,22.953827311404307,12.561741536291297
+Glc,20.560335342649623,42.808790697247126
+Gln,1.231184152036591,25.74066443455423
+Glu,62.75021946544241,22.41709444992081
+Ins,70.5780978167377,42.610650514074734
+Lac,23.41785491163281,18.712589229236077
+Mac,55.28035147932172,34.84329234037037
+NAA,233.893791148461,11.352754264398168
+NAAG,30.310385085873662,11.98921288980138
+PCh,13.877301396957911,11.220484500091832
+PCr,76.08448361408995,10.717192298331083
+PE,16.720840575306838,19.117758951504165
+Scyllo,11.803528139634578,10.941319166624341
+Tau,9.587197397971856,19.5286492573445
diff --git a/Data/sub-018/MRS/summary.csv b/Data/sub-018/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..a62e58d890d50ae2ccbad5b7be20ba6f8bb23254
--- /dev/null
+++ b/Data/sub-018/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.04681409125267564,0.04408861517707038,0.5118459662404766,0.2958487287108061,0.3717997604589944,0.2149015401541661,57.80034389717351,4.701034520473094,19.249879688976687
+Asc,0.10274074174926762,0.058153841684460764,1.1233248969648972,0.5093499366191634,0.8159719039632934,0.3699866696533382,45.34306485998592,8.126266357497215,16.607610392876815
+Asp,0.14809363679153725,0.08259183931145694,1.619194746481343,0.818908884318576,1.1761667739614166,0.5948471749493911,50.575070484766535,3.958305514540109,23.491095870605434
+Cr,0.533236623333072,0.05331784624894452,5.830189316963955,0.4415816405706224,4.2349908653170285,0.3207604611855274,7.574053200738497,84.71511004061793,11.279288933524347
+GABA,0.13748261748810017,0.058626692414038464,1.5031782377158613,0.5157892131588706,1.0918935491763857,0.37466409534954376,34.31324378023412,7.667920189768488,22.574532068714838
+GPC,0.15990793833593056,0.039502119786479,1.7483674470002433,0.2041933571341211,1.2699965240784754,0.14832400033824955,11.679087109775768,77.75804921071935,10.783027024880745
+GSH,0.16774002598964732,0.04451471909367781,1.834000263221313,0.30338051463104254,1.3321993402738943,0.22037255367321507,16.542010419244573,22.953827311404307,12.561741536291297
+Glc,0.38718233816488484,0.06562526833125579,4.233292000043377,0.6082695274785751,3.0750207198656216,0.44184086527466654,14.368711808028891,20.560335342649623,42.808790697247126
+Gln,0.02356940732464788,0.04109005586579149,0.2576981789667924,0.23873314051495678,0.18718936463310495,0.173413351499155,92.64060051651373,1.231184152036591,25.74066443455423
+Glu,1.0144589134769173,0.058776546897652424,11.091675367086815,0.5178239916944872,8.056881399030729,0.37614213800695906,4.668582288578932,62.75021946544241,22.41709444992081
+Ins,0.8483282681506127,0.04991326919426418,9.275271408282292,0.3911263846795576,6.737463837257854,0.284110270910546,4.216872665637621,70.5780978167377,42.610650514074734
+Lac,0.2261046702255822,0.047174518715373925,2.47213521199096,0.34812837863671253,1.7957341471138062,0.2528769519017697,14.082092959484353,23.41785491163281,18.712589229236077
+Mac,0.062156972422614844,0.03486188648960094,0.6795987010944614,0.021084247917741526,0.4936536593832456,0.015315385569711334,3.1024555938359426,55.28035147932172,34.84329234037037
+NAA,1.4816210687305125,0.05702442683767761,16.199433701135295,0.49384884013692615,11.767105666363207,0.35872682911717224,3.0485561980004032,233.893791148461,11.352754264398168
+NAAG,0.16522385264874018,0.04140231655242082,1.8064894616561638,0.24509762162734205,1.3122157707889452,0.17803644654943207,13.567619785760613,30.310385085873662,11.98921288980138
+PCh,0.028828734195095546,0.038158598992181575,0.3152014898662629,0.17094420106173341,0.22895919115934846,0.12417214786986554,54.23330998031243,13.877301396957911,11.220484500091832
+PCr,0.46676337666692813,0.05680847695325899,5.103398253449948,0.4908645825408022,3.7070571486502257,0.3565590944224232,9.618386772166424,76.08448361408995,10.717192298331083
+PE,0.2529375719312667,0.05893447162815038,2.76551509255837,0.5199653209153072,2.0088423408144163,0.3776975780101546,18.801753145895464,16.720840575306838,19.117758951504165
+Scyllo,0.03649115207289228,0.0372508162289969,0.3989792067342586,0.14504667118117315,0.2898144818478912,0.10536044270630822,36.354443723625415,11.803528139634578,10.941319166624341
+Tau,0.12453358180847854,0.05766005626926434,1.361598822160304,0.5025942772923039,0.9890516860742555,0.3650794266835091,36.912067571775,9.587197397971856,19.5286492573445
+Cr+PCr,1.0000000000000002,0.04922666822167892,10.933587570413904,0.38058190228234035,7.942048013967256,0.2764508649798025,3.480851091476948,,
diff --git a/Data/sub-018/MRS/voxel_location.png b/Data/sub-018/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..1d451a9ef36401f4f081c2e58554ff62e27d3594
Binary files /dev/null and b/Data/sub-018/MRS/voxel_location.png differ
diff --git a/Data/sub-018/TMS_EEG/DCM_DefaultCodes_STR7T_HS_025_FHK.mat b/Data/sub-018/TMS_EEG/DCM_DefaultCodes_STR7T_HS_025_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..263da86e8b5c387a13d1858486d0aa96e3901c84
Binary files /dev/null and b/Data/sub-018/TMS_EEG/DCM_DefaultCodes_STR7T_HS_025_FHK.mat differ
diff --git a/Data/sub-019/MRS/all_parameters.csv b/Data/sub-019/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..d6fffc643469d8e1553a6f9042aebcddcf9d94be
--- /dev/null
+++ b/Data/sub-019/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.033000058051757875,0.017598048409174633
+Asc,0.05807650195493986,0.028171711844021657
+Asp,0.119015939840506,0.038713779551675584
+Cr,0.22155714074395758,0.029416667833515844
+GABA,0.07862380595501083,0.024004533866033004
+GPC,0.06958345040836544,0.009291914123185302
+GSH,0.08983589864740693,0.014104165767414025
+Glc,0.21865828735169995,0.03329171464252407
+Gln,0.0156380776128665,0.014134666014088769
+Glu,0.473139582515015,0.03100588219031364
+Ins,0.4049499087292471,0.01604929781465461
+Lac,0.0032165088485545655,0.0030456154207282034
+Mac,0.025709752726156068,0.0009735090944366674
+NAA,0.6593560258263345,0.02358242549741061
+NAAG,0.03875267187989862,0.01334451774549617
+PCh,0.009183531506179295,0.006812405696902117
+PCr,0.2136657972826102,0.024759377133493538
+PE,0.0790968280273501,0.026295306983152338
+Scyllo,0.015308162791008755,0.00592434715447655
+Tau,0.09688575037586106,0.023028107286668615
+gamma_0,19.309104396801548,2.247190672260562
+gamma_1,6.62349117737444,5.377550354262089
+sigma_0,9.375847448250134,1.6985508725263025
+sigma_1,13.362370709812335,6.020065773797626
+eps_0,-1.5351654909561583,0.7820328611215192
+eps_1,-2.627753202654161,6.939446985406568
+Phi0,-0.11020372182640582,0.026432377275775572
+Phi1,0.0002330998734846463,3.560665648153158e-05
+B_real_0,0.2775706195016199,0.0
+B_imag_0,-1.0013298199882277,0.0
+B_real_1,-0.8394637564375143,1.1214946133455537e-16
+B_imag_1,-0.14306678412866505,0.0
+B_real_2,0.1309104747305345,0.0
+B_imag_2,0.7809550544995415,1.1214946133455537e-16
diff --git a/Data/sub-019/MRS/all_samples.csv b/Data/sub-019/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..f6e081d4affe0546c017028ddabbb1a4e38825d8
--- /dev/null
+++ b/Data/sub-019/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
+Ala,0.03856001656347464,0.0193735199458524,0.00018471532749718758,0.04989622185221658,0.04025960362134299,0.02254437018316828,0.013736064644432434,0.052980097579961916,0.041204676191816655,0.05606078905289519,0.055351173666218,0.040231128987398626,0.0378513967976232,0.049266384546027234,0.03132833221296957,0.05354307452573817,0.022607270520167456,0.013038650381004104,0.021757888643959368,0.021035294916340576,0.029495028656225372,0.042468930343869005,0.030092642560165042,0.034261324153098995,0.030569941401419172,0.07343880397581753,0.03501252809547951,0.007112252317841815,0.019185089598980815,0.025579905683893248,0.04248740658753828,0.0036242552034608244,0.07012769096162332,0.04404735582069777,0.03801621842321029,0.03801621842321029,0.027324452603896,0.014016350028856874,0.01819373186287867,0.008732427832017133,0.012537273592487363,0.08030091198045049,0.051718129734097035,0.03028496583987117,0.030840287086260153,0.02615706084681295,0.024280191291268093,0.03126430345058134,0.011335969800140764,0.0386705842716397
+Asc,0.0726060004496869,0.0795298306655798,0.06692049640462072,0.06121180177816625,0.03275253184004881,0.033260490560961885,0.01065596969915985,0.03852699730766965,0.04398723467141458,0.07454616336164259,0.11513325884031178,0.03693836899709664,0.02723400875933603,0.035895308083889646,0.02648072992701195,0.07343032766021976,0.10190043305021712,0.05736409464386271,0.07880600455426465,0.07369628670598158,0.07136585013062542,0.07766398193420453,0.027229449975427745,0.07746884374075794,0.052903039227455206,0.04150066486819372,0.06653956025676575,0.07556306935031545,0.01580065052561777,0.08139131540933187,0.0947493893354717,0.07646555503673494,0.06240150023492813,0.07550111556081077,0.11239903801216497,0.08594153327941059,0.07089401532769078,0.11617413969318174,0.0511167786148096,0.07298667380497278,0.05868190283325747,0.0003327923173367525,0.02819083595266322,0.020072862285541795,0.015727075870139055,0.039890246626028185,0.009250322112861933,0.07011024894499171,0.05344376423447698,0.061192544289681614
+Asp,0.10118841939054411,0.14416975320961892,0.05341357681674665,0.07820050352946963,0.16700723186774538,0.12442592311001842,0.08804674556516291,0.09673898274430288,0.10924635273830097,0.09007407211758525,0.19751856639804716,0.11795171698581214,0.14208671442746038,0.16018610510750828,0.177789746952473,0.0890059557858418,0.10096373860667215,0.1246191700761131,0.17977967505040643,0.1297598603441267,0.10089466419006321,0.16632579803218772,0.17348962545346028,0.06547455305541967,0.13494984274887692,0.036849764830400415,0.1252859447964665,0.10642530557729225,0.15010281296878672,0.12187147121375944,0.06102250604666015,0.1414280690475729,0.15818140569059483,0.1638952279260092,0.0731705235838479,0.10754228235363025,0.1204585543780356,0.1329828948047609,0.10619801368776316,0.12051407106047801,0.18652462980287965,0.1509276899263916,0.1335317720168159,0.12889160801186073,0.12410097504931786,0.06057659210922517,0.0740082652415098,0.0461902753454025,0.07935829086807147,0.127450751383803
+Cr,0.18222965685834053,0.22594886921181387,0.20728204848677173,0.21921419636464393,0.20402540855030135,0.19743199044768078,0.2264285089846284,0.21981958594063847,0.2108230631764185,0.25206441372585237,0.23736080374295648,0.22133100624970709,0.17772706147131945,0.18898747545458788,0.19877707127294908,0.22650882015015553,0.20186425302724367,0.18341846959785452,0.2106494592687712,0.24760953417952422,0.26403057568589317,0.22038966603484314,0.2130377658705564,0.21126521486612465,0.23390706826227323,0.23009800867903296,0.19415442507227743,0.21990277758076412,0.20745871129731697,0.19512417831255205,0.22932607912044553,0.19579815522332242,0.20805320889952136,0.21383211114822445,0.2173843578866654,0.23745625909736057,0.19410833619420986,0.19726787377666233,0.17086555207023318,0.19483580193875766,0.20410107012636974,0.22968480848795933,0.23325072783719206,0.2508051281563106,0.2731586600040724,0.2701406239202953,0.31093189501302165,0.28446178916237114,0.25942270891721525,0.2741018023938765
+GABA,0.05823240314854096,0.041556379816994574,0.0658942351221877,0.07017643175962868,0.09954091867654834,0.10038627265568147,0.06898632941497873,0.061106782091197354,0.09049659163799562,0.10805948449752097,0.10705033496959034,0.07735581060444574,0.0822594044548847,0.10865796636234135,0.10089054453874892,0.04006417324021008,0.057373911354178096,0.06941141998542968,0.07196383517782705,0.06540782589626307,0.06726489980453569,0.13573673324181024,0.07524995161776613,0.06961399728820541,0.07313486466796638,0.06182737600395797,0.08951794983705313,0.08757197472495984,0.057452043433748566,0.08283698419148865,0.045619102902817954,0.0057337849137113865,0.06241440357628068,0.06938255990261644,0.07781603838086631,0.06103787102544076,0.07787992756096018,0.08670909468011992,0.11173471603479147,0.07034907215808996,0.08075190017412867,0.1327556021107999,0.1075045796213885,0.12321897153594329,0.06807479940813524,0.09763192576524579,0.06328843968064513,0.09225097331067637,0.07858324235979353,0.07337546243140486
+GPC,0.0587860656867417,0.07869638372799286,0.08056506943562815,0.07681334084337625,0.06366391986125283,0.0650581386484676,0.05931021323761496,0.06404567878178034,0.06185305102574714,0.0792514866229316,0.07078647045704016,0.07433891883094679,0.06886677557180393,0.06205417314212705,0.05183303574874681,0.05067541160397929,0.049613955951807405,0.0568541493587075,0.08015542464553935,0.06260508769628767,0.08211609298842464,0.06991656937037265,0.07470864732908386,0.0704417747089729,0.06997454817631861,0.06800328234697516,0.09034571066659926,0.07018890547279773,0.0684574096671026,0.06798916779782767,0.06552614357149221,0.05301245759537171,0.06442611424943719,0.06852318604490377,0.07607011157945803,0.06496379404985493,0.08189815077194512,0.08409072708737308,0.08110645080104088,0.06754992743548746,0.07730874773982345,0.06835028543444446,0.06716981912840177,0.060594932278777464,0.06624307994211057,0.07859896207851301,0.0736422715622587,0.07594504225037527,0.08490218733862688,0.07128127007558177
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diff --git a/Data/sub-019/MRS/concentration_samples.csv b/Data/sub-019/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..1c777bbff6421b1f9fad3534b7fa0ef833be32ae
--- /dev/null
+++ b/Data/sub-019/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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diff --git a/Data/sub-019/MRS/concentrations.csv b/Data/sub-019/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..dc7af6b2cda07c9dad05aab850a91f4e4558c0b4
--- /dev/null
+++ b/Data/sub-019/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.033000058051757875,0.0758233428628328,0.8420995606272699,0.6140822329230442,0.017598048409174633,0.053879610620423,0.44906917466692087,0.32747363187193324
+Asc,0.05807650195493986,0.13344081131908225,1.482003355943141,1.080717735251052,0.028171711844021657,0.07387795088111215,0.718889225248044,0.5242338570225592
+Asp,0.119015939840506,0.27345971326823953,3.037063464862387,2.214710470389595,0.038713779551675584,0.09581464936521873,0.9879030121569857,0.7204061324588199
+Cr,0.22155714074395758,0.5090658634596894,5.653722505023968,4.12285043543574,0.029416667833515844,0.0763966695759704,0.7506581660816949,0.5474006451754904
+GABA,0.07862380595501083,0.1806517972410069,2.0063319993472395,1.46307264811582,0.024004533866033004,0.06565123974497852,0.6125506624850324,0.44668884320175184
+GPC,0.06958345040836544,0.1598800162598916,1.7756390889952576,1.294845013128175,0.009291914123185302,0.0415195356751944,0.2371122132042387,0.17290876773445096
+GSH,0.08983589864740693,0.20641352005652558,2.292443566641165,1.6717130967322427,0.014104165767414025,0.04814828019576077,0.35991184552237027,0.2624576476315925
+Glc,0.21865828735169995,0.5024052462472742,5.5797492058220595,4.068907064753115,0.03329171464252407,0.08437600570732083,0.8495420895632205,0.6195095303606282
+Gln,0.0156380776128665,0.03593118892991778,0.39905439760729566,0.29100147654502034,0.014134666014088769,0.04819547595219856,0.3606901545872677,0.26302521207506574
+Glu,0.473139582515015,1.0871200508419265,12.073634353198967,8.804427278867172,0.03100588219031364,0.07964541905012883,0.7912119344872837,0.5769735719650468
+Ins,0.4049499087292471,0.9304424775160341,10.333561828349175,7.53551838558637,0.01604929781465461,0.051263056260166875,0.4095479655490157,0.2986536758030049
+Lac,0.0032165088485545655,0.007390485582260871,0.08207927040229071,0.05985446852363645,0.0030456154207282034,0.03629088486378783,0.07771839078623193,0.056674394792042046
+Mac,0.025709752726156068,0.05907260504864898,0.6560646481462326,0.4784204420857447,0.0009735090944366674,0.03567999469670687,0.0248421254109915,0.018115563237644502
+NAA,0.6593560258263345,1.5149845474966321,16.82552857253904,12.269639647168177,0.02358242549741061,0.06483857437609192,0.6017792489561075,0.4388340312758881
+NAAG,0.03875267187989862,0.08904096841865675,0.9888954713962096,0.7211298611177611,0.01334451774549617,0.04699123737114092,0.3405270533960933,0.24832172239160522
+PCh,0.009183531506179295,0.021100752519663143,0.23434649218589246,0.17089192766233033,0.006812405696902117,0.03889813795702907,0.17383981068089044,0.1267687861448618
+PCr,0.2136657972826102,0.49093413654031076,5.452350227098368,3.9760042145622365,0.024759377133493538,0.0671149138507352,0.6318128462931335,0.46073535907339286
+PE,0.0790968280273501,0.1817386472918891,2.018402635061248,1.471874888704258,0.026295306983152338,0.07013127356910072,0.6710068940588491,0.48931674005800563
+Scyllo,0.015308162791008755,0.03517315254664791,0.39063559040110557,0.28486225005750754,0.00592434715447655,0.0381228416286725,0.15117822301898548,0.11024333119433555
+Tau,0.09688575037586106,0.222611774129301,2.4723425545068056,1.8029004020513884,0.023028107286668615,0.06377804532507372,0.5876340883330139,0.42851898988812853
+Cr+PCr,0.43522293802656775,1.0,11.106072732122335,8.098854649997975,0.015498207072702282,0.05035987931625112,0.39548516387345645,0.2883986928320499
diff --git a/Data/sub-019/MRS/fit_summary.png b/Data/sub-019/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..4d88bfd2837ed2bf7eab2d24f05d163cbf99d093
Binary files /dev/null and b/Data/sub-019/MRS/fit_summary.png differ
diff --git a/Data/sub-019/MRS/options.txt b/Data/sub-019/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..64888f9123852d4c4fa72c72252cc9ab83e8ea4d
--- /dev/null
+++ b/Data/sub-019/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.08475079222978223, "GM": 0.40082566333266834, "WM": 0.5144235444375495}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_027/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-019/MRS/qc.csv b/Data/sub-019/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..e3bb941489b733f73552cb187abf8c28b70e6031
--- /dev/null
+++ b/Data/sub-019/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,8.431070891355084,18.42659901669211
+Asc,11.657103097072495,15.531573113979766
+Asp,8.22386666003693,22.510538898637822
+Cr,92.9916170605851,10.265819190847951
+GABA,11.15047302606245,21.64923084497567
+GPC,88.78248266760986,10.07010256788008
+GSH,32.33585605279421,11.453044998879731
+Glc,27.804521085501356,41.04397113743172
+Gln,2.0325714299560627,24.858374127418305
+Glu,74.1713452688553,21.429832516895075
+Ins,82.40447546104892,41.89885215118728
+Lac,0.8458581842295309,17.807288951200473
+Mac,52.85146648178449,35.353522252204186
+NAA,268.1019763943585,10.661648873808318
+NAAG,18.45831299862577,10.884103589280558
+PCh,11.39885578454418,10.721199476734864
+PCr,91.14090371448121,10.170449625686778
+PE,13.196452808402405,18.42470479429921
+Scyllo,12.878473080243337,10.449829486918848
+Tau,19.291525114560464,18.76565539057844
diff --git a/Data/sub-019/MRS/summary.csv b/Data/sub-019/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..efd477239ff8aa6581a65f0ad2d76d5d95ad87c7
--- /dev/null
+++ b/Data/sub-019/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.0758233428628328,0.053879610620423,0.8420995606272699,0.44906917466692087,0.6140822329230442,0.32747363187193324,53.32732561128694,8.431070891355084,18.42659901669211
+Asc,0.13344081131908225,0.07387795088111215,1.482003355943141,0.718889225248044,1.080717735251052,0.5242338570225592,48.50793504381411,11.657103097072495,15.531573113979766
+Asp,0.27345971326823953,0.09581464936521873,3.037063464862387,0.9879030121569857,2.214710470389595,0.7204061324588199,32.528230759305146,8.22386666003693,22.510538898637822
+Cr,0.5090658634596894,0.0763966695759704,5.653722505023968,0.7506581660816949,4.12285043543574,0.5474006451754904,13.277237526508435,92.9916170605851,10.265819190847951
+GABA,0.1806517972410069,0.06565123974497852,2.0063319993472395,0.6125506624850324,1.46307264811582,0.44668884320175184,30.53087239222252,11.15047302606245,21.64923084497567
+GPC,0.1598800162598916,0.0415195356751944,1.7756390889952576,0.2371122132042387,1.294845013128175,0.17290876773445096,13.353626571625446,88.78248266760986,10.07010256788008
+GSH,0.20641352005652558,0.04814828019576077,2.292443566641165,0.35991184552237027,1.6717130967322427,0.2624576476315925,15.699921723687387,32.33585605279421,11.453044998879731
+Glc,0.5024052462472742,0.08437600570732083,5.5797492058220595,0.8495420895632205,4.068907064753115,0.6195095303606282,15.225452941088925,27.804521085501356,41.04397113743172
+Gln,0.03593118892991778,0.04819547595219856,0.39905439760729566,0.3606901545872677,0.29100147654502034,0.26302521207506574,90.38621219311015,2.0325714299560627,24.858374127418305
+Glu,1.0871200508419265,0.07964541905012883,12.073634353198967,0.7912119344872837,8.804427278867172,0.5769735719650468,6.553220938628544,74.1713452688553,21.429832516895075
+Ins,0.9304424775160341,0.051263056260166875,10.333561828349175,0.4095479655490157,7.53551838558637,0.2986536758030049,3.9632797708284726,82.40447546104892,41.89885215118728
+Lac,0.007390485582260871,0.03629088486378783,0.08207927040229071,0.07771839078623193,0.05985446852363645,0.056674394792042046,94.68699027819687,0.8458581842295309,17.807288951200473
+Mac,0.05907260504864898,0.03567999469670687,0.6560646481462326,0.0248421254109915,0.4784204420857447,0.018115563237644502,3.7865362020625675,52.85146648178449,35.353522252204186
+NAA,1.5149845474966321,0.06483857437609192,16.82552857253904,0.6017792489561075,12.269639647168177,0.4388340312758881,3.5765845118130315,268.1019763943585,10.661648873808318
+NAAG,0.08904096841865675,0.04699123737114092,0.9888954713962096,0.3405270533960933,0.7211298611177611,0.24832172239160522,34.43509079026393,18.45831299862577,10.884103589280558
+PCh,0.021100752519663143,0.03889813795702907,0.23434649218589246,0.17383981068089044,0.17089192766233033,0.1267687861448618,74.1806754005066,11.39885578454418,10.721199476734864
+PCr,0.49093413654031076,0.0671149138507352,5.452350227098368,0.6318128462931335,3.9760042145622365,0.46073535907339286,11.587899162328236,91.14090371448121,10.170449625686778
+PE,0.1817386472918891,0.07013127356910072,2.018402635061248,0.6710068940588491,1.471874888704258,0.48931674005800563,33.244451944469816,13.196452808402405,18.42470479429921
+Scyllo,0.03517315254664791,0.0381228416286725,0.39063559040110557,0.15117822301898548,0.28486225005750754,0.11024333119433555,38.700575865029435,12.878473080243337,10.449829486918848
+Tau,0.222611774129301,0.06377804532507372,2.4723425545068056,0.5876340883330139,1.8029004020513884,0.42851898988812853,23.76831184909317,19.291525114560464,18.76565539057844
+Cr+PCr,1.0,0.05035987931625112,11.106072732122335,0.39548516387345645,8.098854649997975,0.2883986928320499,3.560981216425732,,
diff --git a/Data/sub-019/MRS/voxel_location.png b/Data/sub-019/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..b6885eaac0fbfdb23db0df61fd3b17686a879708
Binary files /dev/null and b/Data/sub-019/MRS/voxel_location.png differ
diff --git a/Data/sub-019/TMS_EEG/DCM_DefaultCodes_STR7T_HS_027_FHK.mat b/Data/sub-019/TMS_EEG/DCM_DefaultCodes_STR7T_HS_027_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..e1e6545f263791b2facc11909dfe799ebce7e071
Binary files /dev/null and b/Data/sub-019/TMS_EEG/DCM_DefaultCodes_STR7T_HS_027_FHK.mat differ
diff --git a/Data/sub-020/MRS/all_parameters.csv b/Data/sub-020/MRS/all_parameters.csv
new file mode 100755
index 0000000000000000000000000000000000000000..c291f262bfd82ad8ab25b4f33b1c99bb5f2427bb
--- /dev/null
+++ b/Data/sub-020/MRS/all_parameters.csv
@@ -0,0 +1,35 @@
+parameter,mean,std
+Ala,0.032155039434923406,0.007817960405599598
+Asc,0.019706161980971026,0.011502084170388595
+Asp,0.08914414678158769,0.02226572477165603
+Cr,0.20440680267551112,0.010962574567319073
+GABA,0.07610988908991549,0.010926717446281441
+GPC,0.07232157891375411,0.0042219100469870156
+GSH,0.07006909154620118,0.006226220586692762
+Glc,0.07733810866726132,0.014956957870672614
+Gln,0.07733380790661312,0.011676727549569936
+Glu,0.4632541614042658,0.014521072255444111
+Ins,0.3132695008237455,0.007516803839189814
+Lac,0.018424784207775796,0.007711993524010868
+Mac,0.02712691515647049,0.0006398883572209173
+NAA,0.6033047468789536,0.008114570777978338
+NAAG,0.06673828995077394,0.00668767129266184
+PCh,0.005002129162983077,0.0037575886050814724
+PCr,0.21829117435523432,0.010053675417062475
+PE,0.09616727570992303,0.013489740948018634
+Scyllo,0.018750226685413568,0.0028944461893392697
+Tau,0.09963660213028104,0.011171101798701299
+gamma_0,16.634928442190752,0.8247118146317943
+gamma_1,3.017913183439824,1.9595349616039248
+sigma_0,7.01951853719027,0.7554390623354946
+sigma_1,11.580298793559214,5.406366330924038
+eps_0,-0.7644123212669015,0.2926465315194847
+eps_1,-4.682618445722482,3.5154478563480778
+Phi0,0.1570711330975136,0.012019450570622795
+Phi1,0.0004038212826313106,1.762479342416081e-05
+B_real_0,0.1071448973299502,1.401868266681942e-17
+B_imag_0,-0.1015875292200255,1.401868266681942e-17
+B_real_1,-0.00627909915299929,0.0
+B_imag_1,0.1883518203401546,2.803736533363884e-17
+B_real_2,0.28275004020581695,5.607473066727768e-17
+B_imag_2,-0.09297852876516188,0.0
diff --git a/Data/sub-020/MRS/all_samples.csv b/Data/sub-020/MRS/all_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..7f2e6f8d9bee78161376ac44bd014682735ae0a9
--- /dev/null
+++ b/Data/sub-020/MRS/all_samples.csv
@@ -0,0 +1,36 @@
+parameter,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
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diff --git a/Data/sub-020/MRS/concentration_samples.csv b/Data/sub-020/MRS/concentration_samples.csv
new file mode 100755
index 0000000000000000000000000000000000000000..9df9b391fe5add9099314f572611fa4272aa5127
--- /dev/null
+++ b/Data/sub-020/MRS/concentration_samples.csv
@@ -0,0 +1,85 @@
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+PCr,molarity,4.306168979442702,4.214133759266556,4.539758034796334,4.477745232079771,4.396286680501389,4.10775021742408,4.020913684060323,4.023997415416733,4.3185605783711445,4.545953144872869,4.701692455151229,4.2197854939635375,4.333955191957853,4.402385292387153,4.3188200823651,4.0726600574491645,3.934774440219257,4.031284419094921,4.129731240269926,3.983294997656667,4.109108967032848,4.127099756121198,4.165187312125596,3.966907989195234,4.1671562966522355,4.116024343606802,4.102551306745936,4.318219490684842,4.358152144662214,4.30070672496777,4.16185083269648,4.032965525325495,4.04691854673183,4.183792078430126,4.102951089972237,4.14076691906775,4.102282277867146,4.233172152198856,4.081425532085253,4.091788397994868,4.190204382184437,3.7320751359329294,3.957572723286713,3.87326934118423,3.843651472386469,3.932752241186568,3.9816418603791255,4.016766926191781,3.9605641456469414,4.108437878865152
+PE,molarity,1.6833104296046213,1.7046938577979178,2.0341022078229276,1.3773023807648448,1.7247632465880522,2.0499046062023383,1.8551066318489475,2.1409895152857454,2.0472782946418224,1.715553309819866,1.6229946736724679,2.1502697061194485,1.9414866203749361,1.5711547593401145,1.901050193550121,2.0787005422125095,2.1010807117448693,1.7165447824663187,1.8697301145454455,1.6018080010859277,2.0092139407613145,1.4856087423399627,1.6139460792954983,1.5992925044564372,1.3084113908534325,1.4483117862350756,2.1369860372664635,2.281893937174521,1.868173469741024,2.1234361097288965,1.5180790142818537,1.4548637927264454,2.227409070731549,1.7366209972185938,1.7930709627159829,1.7484972787529078,1.8589783510177356,1.8718478398122578,2.1244535367655164,2.4928654888706827,1.7718389524205929,2.0355328432154827,1.8051255654735947,1.7847248164027796,1.8549693234624358,1.9286915158515041,1.6342219277758805,1.4766073064679237,1.9732743719248773,1.5962142744554078
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+Tau,molarity,1.5612189409052653,1.8105310694826149,1.8071041053795434,2.15964115075238,1.8245487939609104,2.187249845632357,1.8150145208907527,2.1311520220048346,1.696751575524308,1.7506822980832897,1.944078843485603,1.8312125543122417,1.6174581772293548,1.814220168083629,1.8561203086619034,2.036038855989511,1.8755013925630786,1.710435117288784,2.1003898224480624,1.964306262156957,1.8963551246884716,1.9774351169139828,1.9969353009306192,2.2209985217782964,2.0389660795066122,2.2125128448397136,1.7769662077260886,1.8548141895338837,1.6693772037885863,1.707235715271181,1.5070927958199942,1.8592090497895568,1.6104199318586225,2.0805166739813967,1.7805550802453967,1.8322413688257488,1.9136619519658444,1.7529342901854987,1.6652103882153975,1.806692265762082,2.0791750486508542,1.6572864848484723,1.8413137449852823,2.4175778288196197,2.5199220444390176,2.0997737392913147,1.8583837612227816,1.931758886563767,2.0596207142759737,1.6315693870568282
+Cr+PCr,molarity,8.051359760041782,7.922898310508223,8.119707745211468,8.145417410749387,8.230159426643638,8.168092295483538,8.361217916467863,8.407837268826663,8.134387247947314,8.208419517632704,8.150609594488973,8.144765117027333,8.059820578568575,8.097714187094015,8.103368801154907,8.068708214104928,7.98544759428205,8.042486721952233,7.800313755254111,7.884711418043366,8.06121300261807,8.064456239616765,8.148003869442878,7.9631350815819655,8.106287541177377,7.895998426691142,8.0454066533164,7.907860249291457,8.00533857454695,7.813495131328551,7.873000251602053,7.805819011013014,8.14618729050879,8.306228389430265,7.902833541463592,8.158252243356962,8.010604916568402,8.006892643420723,7.840340493659337,7.751682204686332,8.080367850779473,8.089989402361313,8.032930836381563,7.9307008665897785,8.0589509077532,7.962016272659987,7.967238704545377,7.896785693467759,7.92967626026807,8.11864846937053
diff --git a/Data/sub-020/MRS/concentrations.csv b/Data/sub-020/MRS/concentrations.csv
new file mode 100755
index 0000000000000000000000000000000000000000..aecdf495e4d3e8f718cd707fa27d84923d1b1c93
--- /dev/null
+++ b/Data/sub-020/MRS/concentrations.csv
@@ -0,0 +1,23 @@
+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.032155039434923406,0.07607095652739443,0.841173658334587,0.6115614762908923,0.007817960405599598,0.02551909881370339,0.2045173158130456,0.14869095144195155
+Asc,0.019706161980971026,0.04661995810672564,0.5155118655293552,0.3747944249143417,0.011502084170388595,0.032397378881935744,0.30089374449872025,0.21875984913348026
+Asp,0.08914414678158769,0.21089324204431592,2.3320048547644436,1.6954457828849379,0.02226572477165603,0.0555322249823676,0.582469855138884,0.4234751302233348
+Cr,0.20440680267551112,0.48357648671841963,5.347268142619378,3.8876433742565077,0.010962574567319073,0.031333010177687186,0.2867802097465987,0.20849883577058073
+GABA,0.07610988908991549,0.18005737719530074,1.9910295545049264,1.4475452977243617,0.010926717446281441,0.031262832126209734,0.2858421898837522,0.20781686385380868
+GPC,0.07232157891375411,0.171095162133917,1.8919276163394632,1.3754948631829935,0.0042219100469870156,0.020221412696223844,0.11044488148027287,0.08029713495852474
+GSH,0.07006909154620118,0.1657663280964901,1.8330026990445683,1.3326544710069814,0.006226220586692762,0.022937082549562917,0.16287750973236972,0.11841741514317758
+Glc,0.07733810866726132,0.18296304422965345,2.023159695635839,1.47090498849542,0.014956957870672614,0.039512128775707756,0.391273006991414,0.28446860575996097
+Gln,0.07733380790661312,0.18295286968214697,2.0230471880279604,1.4708231916891523,0.011676727549569936,0.03274516977752868,0.3054624034943715,0.22208141753064323
+Glu,0.4632541614042658,1.0959460101001866,12.118697552083276,8.810699779101887,0.014521072255444111,0.038591382227551506,0.3798702687575134,0.27617843243012874
+Ins,0.3132695008237455,0.7411189971248892,8.195108968405084,5.958119217624186,0.007516803839189814,0.02500754818490729,0.19663908039022518,0.14296320992507344
+Lac,0.018424784207775796,0.04358853178622061,0.4819911095878589,0.3504237105120915,0.007711993524010868,0.025337994645242397,0.20174522935273514,0.14667555156432113
+Mac,0.02712691515647049,0.06417564462225327,0.7096382670492779,0.5159308329844812,0.0006398883572209173,0.017647575214933407,0.01673943617635965,0.012170131813875357
+NAA,0.6033047468789536,1.4272714317605346,15.782411402413517,11.47434268899925,0.008114570777978338,0.02603216273354501,0.2122766231072804,0.1543322282185591
+NAAG,0.06673828995077394,0.15788646640700543,1.745869154429188,1.2693054601916134,0.00668767129266184,0.023652944305253516,0.17494902901215978,0.1271938147351937
+PCh,0.005002129162983077,0.011833813821681104,0.13085536082156646,0.09513623833995907,0.0037575886050814724,0.0197020075283954,0.09829826394241115,0.07146613641287029
+PCr,0.21829117435523432,0.5164235132815804,5.710482367349117,4.151712303763115,0.010053675417062475,0.02957785376619658,0.26300346940622843,0.1912123476835296
+PE,0.09616727570992303,0.2275082468703847,2.5157294328530346,1.8290197162737174,0.013489740948018634,0.0364364113509037,0.352890711460505,0.2565633889408921
+Scyllo,0.018750226685413568,0.04435844906835158,0.49050466280697624,0.35661334938579653,0.0028944461893392697,0.018868869186111966,0.07571851668434808,0.05504990246332403
+Tau,0.09963660213028104,0.23571582440536226,2.606486777526039,1.8950033513323254,0.011171101798701299,0.03174254881964847,0.2922352680256957,0.2124648461910954
+Cr+PCr,0.4226979770307455,1.0000000000000002,11.057750509968498,8.039355678019625,0.0074320986706432335,0.02486544840065372,0.1944231989060685,0.14135218972929184
diff --git a/Data/sub-020/MRS/fit_summary.png b/Data/sub-020/MRS/fit_summary.png
new file mode 100755
index 0000000000000000000000000000000000000000..9bebdf59bcfec9d9b5c645ab8b2ca82e7261151e
Binary files /dev/null and b/Data/sub-020/MRS/fit_summary.png differ
diff --git a/Data/sub-020/MRS/options.txt b/Data/sub-020/MRS/options.txt
new file mode 100755
index 0000000000000000000000000000000000000000..2dae8eba6f109fcbe5dc7d7dc5d6c2332de001b1
--- /dev/null
+++ b/Data/sub-020/MRS/options.txt
@@ -0,0 +1,9 @@
+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.08016935988976574, "GM": 0.3952258549417512, "WM": 0.524604785168483}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_029/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0
diff --git a/Data/sub-020/MRS/qc.csv b/Data/sub-020/MRS/qc.csv
new file mode 100755
index 0000000000000000000000000000000000000000..cfe46e8930aaf6156dc5e513ef487c80c1907e58
--- /dev/null
+++ b/Data/sub-020/MRS/qc.csv
@@ -0,0 +1,21 @@
+Metab,SNR,FWHM
+Ala,8.170006276884772,17.311891207882393
+Asc,3.9261356873245585,14.631656523904407
+Asp,5.504033897581304,12.188746120567993
+Cr,104.16344042151728,8.57361761388005
+GABA,10.933787021980672,20.213536874321232
+GPC,108.15497320790027,8.660854560737775
+GSH,29.16720874771298,9.319257206114566
+Glc,8.778545012082821,0.0
+Gln,10.012467071453786,22.940536652570916
+Glu,70.41400584787392,20.564841864506704
+Ins,61.11905008952274,19.840719218845138
+Lac,4.936061613683964,16.371563928503576
+Mac,44.250093703138894,35.08204540014326
+NAA,299.84421500940994,8.56127029517265
+NAAG,36.12362761047487,9.326679034716248
+PCh,7.411445511283577,8.653160677884257
+PCr,104.04198165128244,8.749565697255495
+PE,15.023847522395059,17.61916916218459
+Scyllo,17.87734359906399,8.758871437702199
+Tau,19.21633701801727,17.389077260527817
diff --git a/Data/sub-020/MRS/summary.csv b/Data/sub-020/MRS/summary.csv
new file mode 100755
index 0000000000000000000000000000000000000000..3b421a4de473bf6d2a71e64c2c33701b59122ce1
--- /dev/null
+++ b/Data/sub-020/MRS/summary.csv
@@ -0,0 +1,22 @@
+Metab,/Cr+PCr,/Cr+PCr CRLB,mMol/kg,mMol/kg CRLB,mM,mM CRLB,%CRLB,SNR,FWHM
+Ala,0.07607095652739443,0.02551909881370339,0.841173658334587,0.2045173158130456,0.6115614762908923,0.14869095144195155,24.313328619676813,8.170006276884772,17.311891207882393
+Asc,0.04661995810672564,0.032397378881935744,0.5155118655293552,0.30089374449872025,0.3747944249143417,0.21875984913348026,58.36795709634082,3.9261356873245585,14.631656523904407
+Asp,0.21089324204431592,0.0555322249823676,2.3320048547644436,0.582469855138884,1.6954457828849379,0.4234751302233348,24.977214517751058,5.504033897581304,12.188746120567993
+Cr,0.48357648671841963,0.031333010177687186,5.347268142619378,0.2867802097465987,3.8876433742565077,0.20849883577058073,5.3631163072012775,104.16344042151728,8.57361761388005
+GABA,0.18005737719530074,0.031262832126209734,1.9910295545049264,0.2858421898837522,1.4475452977243617,0.20781686385380868,14.356501601746816,10.933787021980672,20.213536874321232
+GPC,0.171095162133917,0.020221412696223844,1.8919276163394632,0.11044488148027287,1.3754948631829935,0.08029713495852474,5.837690645584195,108.15497320790027,8.660854560737775
+GSH,0.1657663280964901,0.022937082549562917,1.8330026990445683,0.16287750973236972,1.3326544710069814,0.11841741514317758,8.885830327324001,29.16720874771298,9.319257206114566
+Glc,0.18296304422965345,0.039512128775707756,2.023159695635839,0.391273006991414,1.47090498849542,0.28446860575996097,19.33969957168629,8.778545012082821,0.0
+Gln,0.18295286968214697,0.03274516977752868,2.0230471880279604,0.3054624034943715,1.4708231916891523,0.22208141753064323,15.099123999778385,10.012467071453786,22.940536652570916
+Glu,1.0959460101001866,0.038591382227551506,12.118697552083276,0.3798702687575134,8.810699779101887,0.27617843243012874,3.1345799919910657,70.41400584787392,20.564841864506704
+Ins,0.7411189971248892,0.02500754818490729,8.195108968405084,0.19663908039022518,5.958119217624186,0.14296320992507344,2.39946877031575,61.11905008952274,19.840719218845138
+Lac,0.04358853178622061,0.025337994645242397,0.4819911095878589,0.20174522935273514,0.3504237105120915,0.14667555156432113,41.8566287509418,4.936061613683964,16.371563928503576
+Mac,0.06417564462225327,0.017647575214933407,0.7096382670492779,0.01673943617635965,0.5159308329844812,0.012170131813875357,2.358868870750631,44.250093703138894,35.08204540014326
+NAA,1.4272714317605346,0.02603216273354501,15.782411402413517,0.2122766231072804,11.47434268899925,0.1543322282185591,1.3450202107570082,299.84421500940994,8.56127029517265
+NAAG,0.15788646640700543,0.023652944305253516,1.745869154429188,0.17494902901215978,1.2693054601916134,0.1271938147351937,10.020741163123382,36.12362761047487,9.326679034716248
+PCh,0.011833813821681104,0.0197020075283954,0.13085536082156646,0.09829826394241115,0.09513623833995907,0.07146613641287029,75.11978364910097,7.411445511283577,8.653160677884257
+PCr,0.5164235132815804,0.02957785376619658,5.710482367349117,0.26300346940622843,4.151712303763115,0.1912123476835296,4.605626153580405,104.04198165128244,8.749565697255495
+PE,0.2275082468703847,0.0364364113509037,2.5157294328530346,0.352890711460505,1.8290197162737174,0.2565633889408921,14.027371419680023,15.023847522395059,17.61916916218459
+Scyllo,0.04435844906835158,0.018868869186111966,0.49050466280697624,0.07571851668434808,0.35661334938579653,0.05504990246332403,15.436859713226598,17.87734359906399,8.758871437702199
+Tau,0.23571582440536226,0.03174254881964847,2.606486777526039,0.2922352680256957,1.8950033513323254,0.2124648461910954,11.211845406063114,19.21633701801727,17.389077260527817
+Cr+PCr,1.0000000000000002,0.02486544840065372,11.057750509968498,0.1944231989060685,8.039355678019625,0.14135218972929184,1.7582527181346435,,
diff --git a/Data/sub-020/MRS/voxel_location.png b/Data/sub-020/MRS/voxel_location.png
new file mode 100755
index 0000000000000000000000000000000000000000..eeab54cd6f10d235d82170209c09479b517c3ffb
Binary files /dev/null and b/Data/sub-020/MRS/voxel_location.png differ
diff --git a/Data/sub-020/TMS_EEG/DCM_DefaultCodes_STR7T_HS_029_FHK.mat b/Data/sub-020/TMS_EEG/DCM_DefaultCodes_STR7T_HS_029_FHK.mat
new file mode 100755
index 0000000000000000000000000000000000000000..fcb2a3f19d6ed381cdeb01a16329ad0d81724497
Binary files /dev/null and b/Data/sub-020/TMS_EEG/DCM_DefaultCodes_STR7T_HS_029_FHK.mat differ
diff --git a/README.md b/README.md
index bf7619927ce79aad0b5921603307060caaf436fe..b3dc076a4ce3ea57b67d3dc5eda454a57b8a3a23 100644
--- a/README.md
+++ b/README.md
@@ -1,93 +1,3 @@
-# MRS-GABA-NMM
+#MRS-GABA-NMM
 
-
-
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://gitlab.uliege.be/CyclotronResearchCentre/Public/fasst/mrs-gaba-nmm.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://gitlab.uliege.be/CyclotronResearchCentre/Public/fasst/mrs-gaba-nmm/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+Here you can find the data and the codes to generate the ouput presented in "7 Tesla magnetic resonance spectroscopy estimates of GABA concentration relate to physiological measures of tonic inhibition in the human motor cortex" Paparella et.al 2025