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MRI_processing/nback_1stlevel_per_illuminance.m 0 → 100644
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%% This script does the 1st level analysis of fMRI data in the native space.
% % Task = 1 (nback) ; 2 (oddball) ; 3 (emotional)
% mod = 0 >> no parametric modulation
% mod = 1 >> light intensity parametric modulation
% mod = 2 >> linear time parametric modulation
% mod = 3 >> pupil size parametric modulation
% mod = 4 >> RT parametric modulation
% pupille = 0 >> no continuous pupil regressor
% pupille = 1 >> continuous pupil regressor
% Overwrite = "true" or "false"
% Make sure you've preprocessed both the structral and functional data first,
% because the main scripts for 1st level analysis
% will look for the output computed by the structural and functional preprocessing scripts.
% Therefore, this code will look for required files in the
% .../output_preprocessing/mp2rage_UNI & task folder.
% Written by R.Sharifpour
% Cyclotron Research Centre, University of Liege, Belgium
% 23th November 2022
%%
function nback_1stlevel_v07(subs_info,paths,mod,pupille,overwrite)
for id = 1:length(subs_info)
%this part of the code search for the preprocessed functional files (nback task) of the
%current subject being processed
subject_info = char(subs_info(id));
subject_ID = subject_info(5:7);
message = ['processing functional images of subject: sub-', subject_ID '/' subject_info(9:end)] ;
disp(message)
% if ~exist(fullfile(char([paths.data '/sub-' subject_ID '/' subject_info(9:end)])))
% message = ['(1) No data found for sub-', subject_ID '/' subject_info(9:end)] ;
% disp(message)
% continue
% end
fprintf('Looking for preprocessed functional files (TASK : NBACK)')
nback_folder = char([paths.data '/' char(subs_info(id)) '/MRI' '/output_preprocessing' '/nback']) ;
%We extracted the name of the .nii files but since the input in the
%batch need the entire path to the nifti files, we will change the
%content of the cell containing the names of the files to add the
%entire path before the name
list_folder = nback_folder ;
preprocessed_nifti = dir(fullfile(list_folder, 'sBET*')) ;
preprocessed_nifti = {preprocessed_nifti.name} ;
[r c] = size(preprocessed_nifti) ;
%We save the entire path to the nifti files (fith the files names)
for i = 1:c
preprocessed_nifti{i} = char([list_folder '/' preprocessed_nifti{i}]) ;
end
%Here, we reshape the cell into a format readable by spm. The input is
%put in a single 1x1 cell containing #volume x 1 cells.
preprocessed_nifti = preprocessed_nifti' ;
%preprocessed_nifti = {preprocessed_nifti} ;
fprintf('\n Preprocessed functional data found \n ')
%We will find for the "onsets_task_HILIGHT_ID" and the
%"REGRESSOR_nback_HILIGHT_ID_..." files created respectively with the
%"task_LM.m" codes and the "Merge_reg.m" code + creates output dir
output = char([paths.data '/' char(subs_info(id)) '/MRI' '/output_1stlevel_TASK-5LightConditions_RESTLight_LightOnOff']) ;%we save that path to create an output folder
if mod == 0
onsets_nback = dir(fullfile(char([paths.data '/' char(subs_info(id)) '/LM/']), 'onsets_nback_nomod_TASK-4LightDark_RESTLight_LightOnOff_HILIGHT_*')) ;
output_nback = char([output '/nback_nomod']) ;
end
onset_nback = char([onsets_nback.folder '/' onsets_nback.name]) ;
if pupille == 0
pupil_nback = dir(fullfile(char([paths.data '/' char(subs_info(id)) '/LM/']), 'REGRESSOR_Motion_Physio_noPUPIL_nback_HILIGHT_*')) ;
output_nback = char(strcat(output_nback,'_NoPUPIL')) ;
elseif pupille == 1
pupil_nback = dir(fullfile(char([paths.data '/' char(subs_info(id)) '/LM/']), 'REGRESSOR_Motion_Physio_PUPIL_nback_HILIGHT_*')) ;
output_nback = char(strcat(output_nback,'_PUPIL')) ;
end
pupil_nback = char([pupil_nback.folder '/' pupil_nback.name]) ;
if exist(output_nback)
rmdir(output_nback,'s')
end
if ~exist(output)
mkdir(output)
mkdir(output_nback)
elseif ~exist(output_nback)
mkdir(output_nback)
end
if ~isempty(dir(output_nback)) && overwrite == false
message = ['Output already exists and "overwrite" set to false. No 1st-level Analysis conducted for sub-', subject_ID] ;
disp(message)
continue
end
%%
% %set up batch
if mod==0
clear matlabbatch
spm_jobman('initcfg') ;
matlabbatch{1}.spm.stats.fmri_spec.dir = {output_nback};
matlabbatch{1}.spm.stats.fmri_spec.timing.units = 'scans';
matlabbatch{1}.spm.stats.fmri_spec.timing.RT = 2.34;
matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t = 16;
matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
%%
matlabbatch{1}.spm.stats.fmri_spec.sess.scans = preprocessed_nifti ;
%%
matlabbatch{1}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
matlabbatch{1}.spm.stats.fmri_spec.sess.multi = {onset_nback} ;
matlabbatch{1}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{1}.spm.stats.fmri_spec.sess.multi_reg = {pupil_nback};
matlabbatch{1}.spm.stats.fmri_spec.sess.hpf = 512;
matlabbatch{1}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});
matlabbatch{1}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];
matlabbatch{1}.spm.stats.fmri_spec.volt = 1;
matlabbatch{1}.spm.stats.fmri_spec.global = 'None';
matlabbatch{1}.spm.stats.fmri_spec.mthresh = -inf;
matlabbatch{1}.spm.stats.fmri_spec.mask = {''};
matlabbatch{1}.spm.stats.fmri_spec.cvi = 'AR(1)';
matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;
matlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%creation of contrasts
matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'N0B1';
matlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = [1];
matlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{2}.tcon.name = 'N0B2';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.weights = [0 1];
matlabbatch{3}.spm.stats.con.consess{2}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{3}.tcon.name = 'N0B3';
matlabbatch{3}.spm.stats.con.consess{3}.tcon.weights = [0 0 1];
matlabbatch{3}.spm.stats.con.consess{3}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{4}.tcon.name = 'N0O';
matlabbatch{3}.spm.stats.con.consess{4}.tcon.weights = [0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{4}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{5}.tcon.name = 'N0D';
matlabbatch{3}.spm.stats.con.consess{5}.tcon.weights = [0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{5}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{6}.tcon.name = 'N2B1';
matlabbatch{3}.spm.stats.con.consess{6}.tcon.weights = [0 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{6}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{7}.tcon.name = 'N2B2';
matlabbatch{3}.spm.stats.con.consess{7}.tcon.weights = [0 0 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{7}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{8}.tcon.name = 'N2B3';
matlabbatch{3}.spm.stats.con.consess{8}.tcon.weights = [0 0 0 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{8}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{9}.tcon.name = 'N2O';
matlabbatch{3}.spm.stats.con.consess{9}.tcon.weights = [0 0 0 0 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{9}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{10}.tcon.name = 'N2D';
matlabbatch{3}.spm.stats.con.consess{10}.tcon.weights = [0 0 0 0 0 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{10}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{11}.tcon.name = 'N0(B3-B1)';
matlabbatch{3}.spm.stats.con.consess{11}.tcon.weights = [-1 0 1];
matlabbatch{3}.spm.stats.con.consess{11}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{12}.tcon.name = 'N0(B3-B2)';
matlabbatch{3}.spm.stats.con.consess{12}.tcon.weights = [0 -1 1];
matlabbatch{3}.spm.stats.con.consess{12}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{13}.tcon.name = 'N0(B2-B1)';
matlabbatch{3}.spm.stats.con.consess{13}.tcon.weights = [-1 1];
matlabbatch{3}.spm.stats.con.consess{13}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{14}.tcon.name = 'N0(B3-O)';
matlabbatch{3}.spm.stats.con.consess{14}.tcon.weights = [0 0 1 -1];
matlabbatch{3}.spm.stats.con.consess{14}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{15}.tcon.name = 'N0(B2-O)';
matlabbatch{3}.spm.stats.con.consess{15}.tcon.weights = [0 1 0 -1];
matlabbatch{3}.spm.stats.con.consess{15}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{16}.tcon.name = 'N0(B1-O)';
matlabbatch{3}.spm.stats.con.consess{16}.tcon.weights = [1 0 0 -1];
matlabbatch{3}.spm.stats.con.consess{16}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{17}.tcon.name = 'N2(B3-B1)';
matlabbatch{3}.spm.stats.con.consess{17}.tcon.weights = [0 0 0 0 0 -1 0 1];
matlabbatch{3}.spm.stats.con.consess{17}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{18}.tcon.name = 'N2(B3-B2)';
matlabbatch{3}.spm.stats.con.consess{18}.tcon.weights = [0 0 0 0 0 0 -1 1];
matlabbatch{3}.spm.stats.con.consess{18}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{19}.tcon.name = 'N2(B2-B1)';
matlabbatch{3}.spm.stats.con.consess{19}.tcon.weights = [0 0 0 0 0 -1 1];
matlabbatch{3}.spm.stats.con.consess{19}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{20}.tcon.name = 'N2(B3-O)';
matlabbatch{3}.spm.stats.con.consess{20}.tcon.weights = [0 0 0 0 0 0 0 1 -1];
matlabbatch{3}.spm.stats.con.consess{20}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{21}.tcon.name = 'N2(B2-O)';
matlabbatch{3}.spm.stats.con.consess{21}.tcon.weights = [0 0 0 0 0 0 1 0 -1];
matlabbatch{3}.spm.stats.con.consess{21}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{22}.tcon.name = 'N2(B1-O)';
matlabbatch{3}.spm.stats.con.consess{22}.tcon.weights = [0 0 0 0 0 1 0 0 -1];
matlabbatch{3}.spm.stats.con.consess{22}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{23}.tcon.name = '(N2-N0)B1';
matlabbatch{3}.spm.stats.con.consess{23}.tcon.weights = [-1 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{23}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{24}.tcon.name = '(N2-N0)B2';
matlabbatch{3}.spm.stats.con.consess{24}.tcon.weights = [0 -1 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{24}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{25}.tcon.name = '(N2-N0)B3';
matlabbatch{3}.spm.stats.con.consess{25}.tcon.weights = [0 0 -1 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{25}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{26}.tcon.name = '(N2-N0)O';
matlabbatch{3}.spm.stats.con.consess{26}.tcon.weights = [0 0 0 -1 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{26}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{27}.tcon.name = '(N2-N0)D';
matlabbatch{3}.spm.stats.con.consess{27}.tcon.weights = [0 0 0 0 -1 0 0 0 0 1];
matlabbatch{3}.spm.stats.con.consess{27}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{28}.tcon.name = '(N2-N0)B3-(N2-N0)B1';
matlabbatch{3}.spm.stats.con.consess{28}.tcon.weights = [1 0 -1 0 0 -1 0 1];
matlabbatch{3}.spm.stats.con.consess{28}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{29}.tcon.name = '(N2-N0)B3-(N2-N0)B2';
matlabbatch{3}.spm.stats.con.consess{29}.tcon.weights = [0 1 -1 0 0 0 -1 1];
matlabbatch{3}.spm.stats.con.consess{29}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{30}.tcon.name = '(N2-N0)B2-(N2-N0)B1';
matlabbatch{3}.spm.stats.con.consess{30}.tcon.weights = [1 -1 0 0 0 -1 1 0];
matlabbatch{3}.spm.stats.con.consess{30}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{31}.tcon.name = '(N2-N0)B3-(N2-N0)O';
matlabbatch{3}.spm.stats.con.consess{31}.tcon.weights = [0 0 -1 1 0 0 0 1 -1];
matlabbatch{3}.spm.stats.con.consess{31}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{32}.tcon.name = '(N2-N0)B2-(N2-N0)O';
matlabbatch{3}.spm.stats.con.consess{32}.tcon.weights = [0 -1 0 1 0 0 1 0 -1];
matlabbatch{3}.spm.stats.con.consess{32}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{33}.tcon.name = '(N2-N0)B1-(N2-N0)O';
matlabbatch{3}.spm.stats.con.consess{33}.tcon.weights = [-1 0 0 1 0 1 0 0 -1];
matlabbatch{3}.spm.stats.con.consess{33}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{34}.tcon.name = 'N2';
matlabbatch{3}.spm.stats.con.consess{34}.tcon.weights = [0 0 0 0 0 1 1 1 1 1];
matlabbatch{3}.spm.stats.con.consess{34}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{35}.tcon.name = 'N0';
matlabbatch{3}.spm.stats.con.consess{35}.tcon.weights = [1 1 1 1 1];
matlabbatch{3}.spm.stats.con.consess{35}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
matlabbatch{3}.spm.stats.con.consess{36}.tcon.name = 'N2-N0';
matlabbatch{3}.spm.stats.con.consess{36}.tcon.weights = [-1 -1 -1 -1 -1 1 1 1 1 1];
matlabbatch{3}.spm.stats.con.consess{36}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 1;
if pupille==1
matlabbatch{3}.spm.stats.con.consess{37}.tcon.name = 'pupil_reg' ;
matlabbatch{3}.spm.stats.con.consess{37}.tcon.weights = [zeros(1,16) 1];
matlabbatch{3}.spm.stats.con.consess{37}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
spm_jobman('run', matlabbatch) % run batch
end
%%
% Coregistration of statistical maps to the template ans MNI spaces.
input1= paths.ANTs ;
input2= char([paths.data '/' char(subs_info(id)) '/MRI' '/output_preprocessing' '/nback']) ;
input3= char([paths.data '/sub-' subject_ID '/ses-struct/MRI/output_preprocessing/mp2rage_UNI']);
input4= paths.template;
input5= output_nback ;
PathToScript= [paths.bash '/Coreg_Stat.sh'];
cmdStr=[PathToScript ' ' input1 ' ' input2 ' ' input3 ' ' input4 ' ' input5];
system(cmdStr)
end
end
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