Hoffman2:Software Tools:FMRIprep: Difference between revisions
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module load apptainer | module load apptainer | ||
apptainer run --cleanenv /u/project/CCN/apps/fmriprep/rh7/25.1.3/ | 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 | 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
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