Hoffman2:Software Tools:FMRIprep: Difference between revisions

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[https://fmriprep.org/en/stable/usage.html Fmriprep Command Line Usage]
[https://fmriprep.org/en/stable/usage.html 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
Or as the instruction from FMRIPrep official site -->
module load singularity
singularity run --cleanenv /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif \
path/to/data/dir path/to/output/dir \
participant --participant-label label


From version '''23.1.3''', FMRIprep is provided through Apptainer
From version '''23.1.3''', FMRIprep is provided through Apptainer


  module load apptainer/1.2.2
  module load apptainer
  apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/23.1.3/23.1.3-fmriprep.sif \
  apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/23.1.3-fmriprep.sif \
  path/to/data/dir path/to/output/dir \
  path/to/data/dir path/to/output/dir \
  participant --participant-label label
  participant --participant-label label

Revision as of 18:06, 8 April 2026

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

Official Website

Fmriprep Command Line Usage

From version 23.1.3, FMRIprep is provided through Apptainer 

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/23.1.3-fmriprep.sif \
path/to/data/dir path/to/output/dir \
participant --participant-label label


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