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resources fmriprep
The fmriprep package contains the single module preprocess. This module contains the two functions run_freesurfer and run_fmriprep.
run_freesurfer employs a simple implementation of FreeSurfer. The required 001.mgz is made from the T1w structural file in dset and placed in the designated <subjec>/mri/orig sub-directory. Then FreeSurfer is called with its recon-all option. Output will be used by fMRIprep, and will be saved to derivatives/freesurfer if fMRIprep finishes successfully.
run_fmriprep utilizes a sinularity file (sif) of fMRIprep. The space MNIPediatricAsym cohort-5 (res=2) is hardcoded for use by the EMU project. Specific environmental variables are passed to the submit function, correcting the global TMPDIR variable and setting SINGULARITYENV_TEMPLATEFLOW_HOME to point to a templatefow directory in /scratch (so it is readable by the SIF). A path to a readable version of the FreeSurfer license is also required.