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.
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.