Hoffman2:Software Tools: FMRIprep

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

Official Website:[1]

Usage [2]

For using FMRIprep module in Hoffman, the following modules are needed as well (This example is for FMRIprep version 1.4.0)

module load fsl/5.0.9
module load python/3.7.2
module load freesurfer/6.0.0
module load ants/ants-2.2.0
module load afni/19.0.15
module load ica-aroma
module load itksnap/3.6.0-RC1.QT4

export PATH=/u/project/CCN/apps/c3d/c3d-1.0.0-Linux-x86_64/bin/:$PATH
export NO_FSL_JOBS=true

To load FMRIprep module

module load fmriprep/1.4.0

To get fmriprep command line help, run command

fmriprep -h

(You should run FMRIprep with a interactive mode or a batch mode in Hoffman)

Note on 7/16/2020: For the newest version fmriprep/20.1.1, python module version needs to be python/3.7.0