This set of codes prepares the fMRI data for preprocessing, applies preprocessing, and creates folder structure for spm 1st analysis.
dicom2nifti.sh: This script converts the dicom files to nifti format to be able to apply preprocessing.
change_anat_name.sh: Some anatomical files do not comply with the BIDS folder format. This script changes the names accordingly.
to_server_copy_files.sh: This script can be used to transfer any files to a server with scp command.
fmriprep.sh: This script runs the preprocessing using fmriprep. It was originally written by Daniel Levitas of Indiana University and is adjusted according to our project.
get_derivatives_from_server.sh: After preprocessing on the server, it transfers the necessary files to the local computer.
unzip.sh: This script unzips the necessary folders.
spm_folder.sh: This creates the spm folder structure for further spm 1st level analysis.
copy_files_to_spm_folder.sh: After the preprocessing, this script copies the necessary outputs to spm folder for 1st level analysis.