Bandpass filter with FSL's fslmaths using Matlab

bandpass_filter_fsl.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 = 7:length(subject_names)

    cd (sprintf('%s/%s/func',path,subject_names{i}))
    zipped_file = sprintf('%s_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz',subject_names{i});
    system(['mv ' , zipped_file , ' ' , subject_names{i}, '_bold.nii.gz'])
    fmrifile = sprintf('%s_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii',subject_names{i});
    fprintf('calculating the mean image for %s, index: %d\n',subject_names{i},i);
    system(['/usr/local/fsl/bin/fslmaths ' , fmrifile , ' -Tmean mean.nii.gz']);
    fprintf('bandpass filtering for %s, index: %d\n',subject_names{i},i)
    system(['fslmaths ' , fmrifile , ' -bptf ' upper ' ' lower ' -add mean.nii.gz ' , extractBefore(fmrifile,'_task') ,'_bptf_' extractAfter(fmrifile,'desc-')]);
    delete('mean.nii.gz');

end