Hoffman2:Software Tools:FMRIprep

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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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