Hoffman2:Software Tools: FMRIprep

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

Official Website

Fmriprep Command Line Usage

From version 20.2.1, FMRIprep is provided through Singularity The following command need to be run in a CentOS 7 node.

module load singularity
singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif
exit ##to stop container

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

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

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 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.