Welcome to fMRIprep’s documentation!

FMRIPREP: A Robust Preprocessing Pipeline for fMRI Data

This pipeline is developed by the Poldrack lab at Stanford University for use at the Center for Reproducible Neuroscience (CRN), as well as for open-source software distribution.

https://circleci.com/gh/poldracklab/preprocessing-workflow/tree/master.svg?style=shield Documentation Status Latest Version

About

fMRIprep is a functional magnetic resonance image preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. This open-source neuroimaging data processing tool is being developed as a part of the MRI image analysis and reproducibility platform offered by the CRN.

External Dependencies

fMRIprep is implemented using nipype, but it requires some other neuroimaging software tools: FSL, ANTs, AFNI, FreeSurfer, C3D.

These tools must be installed and their binaries available in the system’s $PATH.

Installation

The fMRIprep is packaged and available through the PyPi repository. Therefore, the easiest way to install the tool is:

pip install fmriprep

Execution and the BIDS format

The fmriprep workflow takes as principal input the path of the dataset that is to be processed. The only requirement to the input dataset is that it has a valid BIDS (Brain Imaging Data Structure) format. This can be easily checked online using the BIDS Validator.

The command line interface follows the BIDS-Apps definition. Example:

fmriprep data/bids_root/ out/ participant -w work/

Support and communication

The documentation of this project is found here: http://preprocessing-workflow.readthedocs.org/en/latest/.

If you have a problem or would like to ask a question about how to use fmriprep, please submit a question to NeuroStars.org with an fmriprep tag. NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.

All previous fmriprep questions are available here: http://neurostars.org/t/fmriprep/

To participate in the fmriprep development-related discussions please use the following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging Please add [fmriprep] to the subject line when posting on the mailing list.

All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/poldracklab/preprocessing-workflow/issues.

Acknowledgements

Please acknowledge this work mentioning explicitly the name of this software (fmriprep) and the version, along with the link to the GitHub repository (https://github.com/poldracklab/preprocessing-workflow).

License information

We use the 3-clause BSD license; the full license is in the file LICENSE in the fmriprep distribution.

All trademarks referenced herein are property of their respective holders.

Copyright (c) 2015-2016, the fmriprep developers and the CRN. All rights reserved.

Authors

The CRN developers team:

  • Chris F. Gorgolewski
  • Craig Moodie
  • Ross Blair
  • Shoshana Berleant
  • Oscar Esteban
  • Russell A. Poldrack

Poldrack Lab, Psychology Department, Stanford University.

Indices and tables