Hoffman2:Software Tools: FMRIprep

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

Official Website

Fmriprep Command Line Usage

For using FMRIprep module in Hoffman, the following modules are needed as well

For FMRIprep version 20.2.0rc0

module load fsl/5.0.9
module load python/3.7.0
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
module load fmriprep/20.2.0rc0

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

(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
module load fmriprep/1.4.0

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

To find all FMRIprep version in Hoffman

module av fmriprep

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: fmriprep version 20.1.1 has bug with multi echo scans.