Hoffman2:Software Tools: FMRIprep: Difference between revisions

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


For FMRIprep version 20.2.0rc0
FMRIprep version '''20.2.0rc0'''
  module load fsl/5.0.9
  module load fsl/5.0.9
  module load python/3.7.0
  module load python/3.7.0
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(This example is for FMRIprep version '''1.4.0''')
FMRIprep version '''1.4.0'''


  module load fsl/5.0.9
  module load fsl/5.0.9
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  module av fmriprep
  module av fmriprep
To load FMRIprep module
module load fmriprep/1.4.0


To get fmriprep command line help, run command
To get fmriprep command line help, run command

Revision as of 22:42, 1 April 2021

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

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.