White matter and CSF signal regression using Matlab and FSL

wm_csf_signal_regression.m

path = '/data/nimble/work/Divyangana_Rakesh/resting_state/t3/fmriprep';

subjectNames = dir(sprintf('%s',path));
subs = startsWith({subjectNames.name},'sub') & ~contains({subjectNames.name},'.html');
subject_names = {subjectNames.name};
subject_names = subject_names(subs);

TR = 1.4;

upper=((1/TR)/2)*100; upper=num2str(upper);
lower=((1/TR)/2)*10; lower=num2str(lower);


for i = 1:length(subject_names)

    cd (sprintf('%s/%s/func',path,subject_names{i}))
    fmrifile = sprintf('%s_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii',subject_names{i});
    
    confounds = tdfread(sprintf('%s_task-rest_desc-confounds_regressors.tsv',subject_names{i}));
    csf = confounds.csf;
    wm = confounds.white_matter;
   
    
    conf = [wm csf];
    
    writetable(table(conf), 'conf.txt', 'Delimiter', ' ','WriteVariableNames',false)
    

    
    % regress white matter and csf signal
    
    output_name_wm_csf = sprintf('%s_bptf_AROMA_wm_csf.nii.gz',subject_names{i});
    
    fprintf('regressing out WM, CSF signal for %s, index: %d\n',subject_names{i},i) 
    
    system(['/usr/local/fsl/bin/fsl_regfilt -i ' , fmrifile , ' -d conf.txt -f "1" ' '-o ' , output_name_wm_csf]);
   
    
    % bandpass filter the data
    
    fprintf('calculating the mean image for %s, index: %d\n',subject_names{i},i);
    
    output_bptf_filename = sprintf('%s_AROMA_bptf_wm_csf.nii.gz',subject_names{i});
    
    system(['/usr/local/fsl/bin/fslmaths ' , output_name_wm_csf , ' -Tmean mean.nii.gz']);
    
    fprintf('bandpass filtering for %s, index: %d\n',subject_names{i},i)
    
    system(['fslmaths ' , output_name_wm_csf , ' -bptf ' upper ' ' lower ' -add mean.nii.gz ' , output_bptf_filename]);
    
    delete('mean.nii.gz');

    
end


%  gsr = confounds.global_signal;
%  conf_with_gsr = [wm csf gsr];
%  writetable(table(conf_with_gsr), 'conf_with_gsr.txt', 'Delimiter', ' ','WriteVariableNames',false)
%  output_name_gsr = sprintf('%s_bptf_AROMAnonaggr_wm_csf_gsr.nii.gz',subject_names{i});  
%  fprintf('regressing out GSR, WM, CSF signal for %s, index: %d\n',subject_names{i},i)  
%  system(['/usr/local/fsl/bin/fsl_regfilt -i ' , fmrifile , ' -d conf_with_gsr.txt -f "1" ' '-o ' , output_name_gsr]);