fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

Availability and Restrictions


The following versions of fMRIPrep are available on OSC systems: 

Version Pitzer
20.2.0 X*
* Current default version

You can use module spider fMRIPrep to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


fMRIPrep is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Developed at Poldrack Lab at Stanford University, for use at the Center for Reproducible Neuroscience (CRN), as well as for open-source software distribution.

fMRIPrep uses the 3-clause BSD license; the full license may be found in the LICENSE file in the fMRIPrep distirbution.

All trademarks referenced herein are property of their respective holders.

Copyright (c) 2015-2020, the fMRIPrep developers and the CRN. All rights reserved.


Usage on Pitzer


To configure your environment for use of fMRIPrep, run the following command: module load fmriprep. The default version will be loaded. To select a particular fMRIPrep version, use module load fmriprep/version. For example, use module load fmriprep/20.2.0 to load fMRIPrep 20.2.0.

fMRIPrep is installed in a singularity container.  FMRIPREP_IMG environment variable contains the container image file path. So, an example usage would be

module load fmriprep
singularity exec $FMRIPREP_IMG fmriprep --help

For more information about singularity usages, please read OSC singularity page.

Further Reading


Fields of Science: