Hoffman2:Software Tools: FMRIprep: Difference between revisions

From Center for Cognitive Neuroscience
Jump to navigation Jump to search
No edit summary
No edit summary
Line 10: Line 10:


  module load singularity
  module load singularity
  singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.1/fmriprep-20.2.5.sif
  singularity shell --userns /u/project/CCN/apps/fmriprep/rh7/20.2.5/fmriprep-20.2.5.sif
  exit ##to stop container
  exit ##to stop container



Revision as of 20:04, 25 February 2022

FMRIPrep: A Robust Preprocessing Pipeline for fMRI Data

Official Website

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/rh7/20.2.5/fmriprep-20.2.5.sif
exit ##to stop container

Or use the following command to run it

singularity run --cleanenv fmriprep.sif path/to/data/dir path/to/output/dir \
   participant --participant-label label

For more details, please check FMRIprep's | official site

  • FMRIprep is no longer a module in Hoffman2, please use the container version