fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application
www.nipreps.org <https://www.nipreps.org>__) for the preprocessing of
task-based and resting-state functional MRI (fMRI).
.. image:: https://img.shields.io/badge/docker-nipreps/fmriprep-brightgreen.svg?logo=docker&style=flat :target: https://hub.docker.com/r/nipreps/fmriprep/tags/ :alt: Docker image available!
.. image:: https://codeocean.com/codeocean-assets/badge/open-in-code-ocean.svg :target: https://doi.org/10.24433/CO.ed5ddfef-76a3-4996-b298-e3200f69141b :alt: Available in CodeOcean!
.. image:: https://readthedocs.org/projects/fmriprep/badge/?version=latest :target: http://fmriprep.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status
.. image:: https://img.shields.io/badge/doi-10.1038%2Fs41592--018--0235--4-blue.svg :target: https://doi.org/10.1038/s41592-018-0235-4 :alt: Published in Nature Methods
.. image:: https://img.shields.io/badge/RRID-SCR__016216-blue.svg :target: https://doi.org/10.1038/s41592-018-0235-4 :alt: RRID:SCR_016216
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. It performs basic processing steps (coregistration, normalization, unwarping, noise component extraction, segmentation, skullstripping etc.) providing outputs that can be easily submitted to a variety of group level analyses, including task-based or resting-state fMRI, graph theory measures, surface or volume-based statistics, etc.
fMRIPrep performs minimal preprocessing.
Here we define 'minimal preprocessing' as motion correction, field
unwarping, normalization, bias field correction, and brain extraction.
workflows section of our documentation <https://fmriprep.readthedocs.io/en/latest/workflows.html>__ for more details.
The fMRIPrep pipeline uses a combination of tools from well-known software packages, including FSL, ANTs, FreeSurfer and AFNI. This pipeline was designed to provide the best software implementation for each state of preprocessing, and will be updated as newer and better neuroimaging software become available.
This tool allows you to easily do the following:
More information and documentation can be found at https://fmriprep.readthedocs.io/
fMRIPrep is built around three principles:
Please acknowledge this work using the citation boilerplate that fMRIPrep includes
in the visual report generated for every subject processed.
For a more detailed description of the citation boilerplate and its relevance,
please check out the
NiPreps documentation <https://www.nipreps.org/intro/transparency/#citation-boilerplates>__.
The boilerplate text is public domain, distributed under the
CC0 license <https://creativecommons.org/publicdomain/zero/1.0/>,
and we recommend fMRIPrep users to reproduce it verbatim in their works.
Therefore, if reviewers and/or editors raise concerns because the text is flagged by automated
plagiarism detection, please refer them to the NiPreps community and/or the note to this
effect in the
boilerplate documentation page <https://www.nipreps.org/intro/transparency/#citation-boilerplates>.
fMRIPrep contributors have published two relevant papers:
Esteban et al. (2019) <https://doi.org/10.1038/s41592-018-0235-4>
preprint <https://doi.org/10.1101/306951>], and
Esteban et al. (2020) <https://doi.org/10.1038/s41596-020-0327-3>
Other materials that have been generated over time include the
OHBM 2018 software demonstration <https://effigies.github.io/fmriprep-demo/>__
and some conference posters:
.. image:: _static/OHBM2018-poster_thumb.png :target: _static/OHBM2018-poster.png
.. image:: _static/OHBM2017-poster_thumb.png :target: _static/OHBM2017-poster.png
fMRIPrep adheres to the
general licensing guidelines <https://www.nipreps.org/community/licensing/>__
of the NiPreps framework.
Copyright (c) 2021, the *NiPreps* Developers. As of the 21.0.x pre-release and release series, *fMRIPrep* is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at `http://www.apache.org/licenses/LICENSE-2.0 <http://www.apache.org/licenses/LICENSE-2.0>`__. Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. Acknowledgements ---------------- This work is steered and maintained by the `NiPreps Community <https://www.nipreps.org>`__. This work was supported by the Laura and John Arnold Foundation, the NIH (grant NBIB R01EB020740, PI: Ghosh), and NIMH (R24MH114705, R24MH117179, R01MH121867, PI: Poldrack)