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MRI_processing/Coregistration.m

+%% Script for coregistration of EPI to Structural/Template/MNI
+
+% using this code we get are the followings:
+
+% 1-
+% 2-
+% 3-
+
+
+
+% --> BE CAREFUL : this code only reads "prepared" data. You need to have
+% the data downloaded on your computer in the prepared format:
+
+%..../prepared
+%         --> sub-008
+%               --> ses-evening
+%                    --> MRI
+%                        --> 005-b1map_sag_p2
+%                        --> 007-cmrr_mbep2d_p3_mb2_1.4iso_VolCheck 
+%                        --> ...
+%                    --> LM
+%                    --> Physio
+%              --> ses-morning
+%                    --> MRI
+%                        --> 005-b1map_sag_p2
+%                        --> 007-cmrr_mbep2d_p3_mb2_1.4iso_VolCheck 
+%                        --> ...
+%                    --> LM
+%                    --> Physio
+%               --> ses-struct
+%                    --> MRI
+%                        --> 005-b1map_sag_p2
+%                        --> 007-cmrr_mbep2d_p3_mb2_1.4iso_VolCheck 
+%                        --> ...
+%                    --> LM
+%                    --> Physio
+
+
+%        --> sub-009
+
+
+% Written by R. Sharifpour
+% Cyclotron Research Centre, University of Liege, Belgium
+% 20th November 2022
+
+
+%%
+function Coregistration(task,overwrite)
+
+% default values
+if nargin < 2
+    overwrite = 0; 
+end
+if nargin < 1
+    warning('Task [1,2,3] must be specified as first input');
+    return;
+end
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% paths
+% load file 'your_paths.txt' which contains:
+% 1. path to the data
+% 2. path to SPM 
+% 3. path to template
+% 4. path to bash scripts
+% 5. path to ANTs
+% 6. path to edf toolbox
+% 7% path to synthstrip
+paths_txt = fileread('/home/islay/Documents/HILIGHT_CODES/MRI_processing/Functional_Preproc/Prepared/your_paths.txt') ; % better to use an absolute path
+% split data by new lines
+% the data is structured as follows:
+% path to your data (example):
+% corresponding path, for example: /mnt/data/Prepared
+
+paths_txt = char(strsplit(paths_txt, '\n')) ;
+
+% create a struct to store the paths we are interested in
+paths = [];
+paths.data = (strtrim(paths_txt(2,:))); 
+paths.spm = (strtrim(paths_txt(4,:))); 
+paths.template = (strtrim(paths_txt(6,:)));
+paths.bash = (strtrim(paths_txt(8,:)));
+paths.ANTs = (strtrim(paths_txt(10,:)));
+paths.synthstrip = (strtrim(paths_txt(14,:)));
+% add SPM path to matlab's search path
+addpath(paths.spm)
+% go to the path where the data is stored
+addpath(pwd)
+
+% go to the path where the data is stored
+cd(paths.data);
+% select directories of subjects for analyses
+% directory has to be 'sub-0ID'
+[all_subs_dir] = spm_select(Inf,'dir','Select subject directory');
+%for each subject, select the session/sessions to be analyzed
+all_subs_ses = [];
+for ii=1:size(all_subs_dir,1)
+    cd (all_subs_dir(ii,:))
+    sub_ses  = spm_select(Inf,'dir','Select subject directory');
+    all_subs_ses =[all_subs_ses; sub_ses];
+end
+all_subs_ses = string(all_subs_ses);
+
+% extract subject ID subject session/sessions name: sub-ID/ses-
+split_subs_dir = split(paths.data,filesep);
+subjects_folder = char(split_subs_dir(end));
+subs_info = extractAfter(all_subs_ses,[subjects_folder '/']);
+
+T = dir(fullfile(paths.data,'HILIGHT_participants.xlsx')) ;
+T = readtable(char([paths.data '/' T.name])) ;
+
+fprintf('\n path initialization done \n')
+
+for isub = 1:size(subs_info,1)
+    cd(paths.data);
+    
+    subject_info = char(subs_info(isub));
+    subject_ID = subject_info(5:7);
+    switch subject_info(13)
+        case 'm'
+            subject_session = 'M';
+        case 'e'
+            subject_session = 'E';
+    end
+    entry_table = ['HILIGHT_', subject_ID '_' subject_session] ;
+    index = strcmp(T.subject_Ids, entry_table) ;
+    patient_data = T(index,:) ;
+    
+        
+    fprintf('Looking for  processed functional folder (TASK : NBACK)')
+    
+   % go to where all subjects' data have been saved
+    prep_folder = dir(char([paths.data])) ; 
+    
+   % look for the subject that's beeing processed 
+   for iFile = 1:numel(prep_folder)
+        if(strncmpi(prep_folder(iFile).name,['sub-', subject_ID],7))
+            sub_folder = fullfile(char([paths.data]), prep_folder(iFile).name); % .../Prepared/sub-...
+        end
+    end
+    
+    mri_folder = dir(char([sub_folder subject_info(8:end) '/MRI'])) ; % .../Prepared/sub-.../ses-.../MRI
+   
+   for ii = 1:numel(mri_folder)
+        if (endsWith(mri_folder(ii).name,'output_preprocessing'))
+            
+            switch(task)
+                 case 1
+                      outputfolder = fullfile(char([mri_folder(ii).folder '/output_preprocessing/nback']));
+                 case 2
+                      outputfolder = fullfile(char([mri_folder(ii).folder '/output_preprocessing/oddball']));
+                 case 3
+                      outputfolder = fullfile(char([mri_folder(ii).folder '/output_preprocessing/emo']));
+                otherwise
+                      warning('Unexpected task type. No preprocessing done. Please enter a valid task type : 1 (nback), 2 (oddball) or 3 (emotional).')
+            end
+             
+        end
+    end
+    
+ 
+    if ~isempty(dir(outputfolder)) && overwrite == false
+        message =  ['Output already exists and "overwrite" set to false. No preprocessing conducted for sub-', subject_ID] ;
+        disp(message)
+        continue
+    end
+    
+    %%
+    
+    % Coregistration of meanuf to the Structural,template and MNI spaces
+    
+    input1= paths.ANTs;
+    input2= outputfolder ;
+    input3= [sub_folder '/ses-struct/MRI/output_preprocessing/mp2rage_UNI'];
+    input4= paths.template;
+    
+    PathToScript= [paths.bash '/Coreg.sh']; %Corg_DCM.sh
+    cmdStr=[PathToScript ' ' input1 ' ' input2 ' ' input3 ' ' input4];
+    system(cmdStr)    
+    
+  
+end
+end
+