Hoffman2:Software Tools:FMRIprep: Difference between revisions

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  module load singularity
  module load singularity
  singularity run --cleanenv fmriprep.simg path/to/data/dir path/to/output/dir \
  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



Revision as of 19:17, 17 May 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/rh7/20.2.1/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