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
FMRIprep is provided through Apptainer
The following command need to be run in a CentOS 7 node. 


<!-- module load singularity
module load apptainer
  singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.1.sif
  apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
  exit ##to stop container
  -w PATH/TO/WORKSPACE \
 
--output-spaces SPACE_NAME \
Or as the instruction from FMRIPrep official site -->
  --fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
 
  PATH/TO/DATA/DIR PATH/TO/OUTPUT/DIR \
  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
  participant --participant-label label


From version '''23.1.3''', FMRIprep is provided through Apptainer
module load apptainer/1.2.2
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/23.1.3/23.1.3-fmriprep.sif \
path/to/data/dir path/to/output/dir \
participant --participant-label label


* Note: By default, fmriprep uses "MNI152NLin2009cAsym" space if no SPACE_NAME specified with --output-spaces option


<!--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

Latest revision as of 18:28, 8 April 2026

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

Official Website

Fmriprep Command Line Usage

FMRIprep is provided through Apptainer 

module load apptainer
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/fmriprep-25.1.3.sif \
-w PATH/TO/WORKSPACE \
--output-spaces SPACE_NAME \
--fs-license-file /u/project/CCN/apps/freesurfer/rh7/7.2.0/.license \
PATH/TO/DATA/DIR PATH/TO/OUTPUT/DIR \
participant --participant-label label


  • Note: By default, fmriprep uses "MNI152NLin2009cAsym" space if no SPACE_NAME specified with --output-spaces option


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