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A robust and easy-to-use pipeline for preprocessing of diverse fMRI data

Project description

Preprocessing of functional MRI (fMRI) involves numerous steps to clean and standardize the data before statistical analysis. Generally, researchers create ad hoc preprocessing workflows for each dataset, building upon a large inventory of available tools. The complexity of these workflows has snowballed with rapid advances in acquisition and processing. fMRIPrep is an analysis-agnostic tool that addresses the challenge of robust and reproducible preprocessing for task-based and resting fMRI data. fMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of virtually any dataset, ensuring high-quality preprocessing without manual intervention. fMRIPrep robustly produces high-quality results on diverse fMRI data. Additionally, fMRIPrep introduces less uncontrolled spatial smoothness than observed with commonly used preprocessing tools. fMRIPrep equips neuroscientists with an easy-to-use and transparent preprocessing workflow, which can help ensure the validity of inference and the interpretability of results.

The workflow is based on Nipype and encompasses a large set of tools from well-known neuroimaging packages, including FSL, ANTs, FreeSurfer, AFNI, and Nilearn. 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 becomes available.

fMRIPrep performs basic preprocessing 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 allows you to easily do the following:

  • Take fMRI data from unprocessed (only reconstructed) to ready for analysis.

  • Implement tools from different software packages.

  • Achieve optimal data processing quality by using the best tools available.

  • Generate preprocessing-assessment reports, with which the user can easily identify problems.

  • Receive verbose output concerning the stage of preprocessing for each subject, including meaningful errors.

  • Automate and parallelize processing steps, which provides a significant speed-up from typical linear, manual processing.

[Nat Meth doi:10.1038/s41592-018-0235-4] [Documentation] [Software doi:10.5281/zenodo.852659] [Support]

License information

fMRIPrep adheres to the general licensing guidelines of the NiPreps framework.


Copyright (c) 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

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.

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