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@nipreps

NeuroImaging PREProcessing toolS

NiPreps (NeuroImaging PREProcessing toolS)

Please visit www.nipreps.org for a more comprehensive description of this community. Don't forget to also learn about the sister initiative www.templateflow.org.

News and some discussions take place at the Nipreps GitHub discussions.

About

The current neuroimaging workflow has matured into a large chain of processing and analysis steps involving a large number of experts, across imaging modalities and applications. The development and fast adoption of fMRIPrep have revealed that neuroscientists need tools that simplify their research workflow, provide visual reports and checkpoints, and engender trust in the tool itself. The NiPreps framework extends fMRIPrep's approach and principles to new imaging modalities. The vision for NiPreps is to provide end-users (i.e., researchers) with applications that allow them to perform quality control smoothly and to prepare their data for modeling and statistical analysis.

Acknowledgments

This work is steered and maintained by the NiPreps Community. The development of this framework is supported the NIMH (RF1MH121867, RAP, OE).

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  1. fmriprep fmriprep Public

    fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

    HTML 691 307

  2. dmriprep dmriprep Public

    dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

    Python 70 25

  3. smriprep smriprep Public

    Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)

    Python 151 45

  4. mriqc mriqc Public

    Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain

    Python 337 133

Repositories

Showing 10 of 58 repositories
  • niworkflows Public

    Common workflows for MRI (anatomical, functional, diffusion, etc)

    nipreps/niworkflows’s past year of commit activity
    Python 103 Apache-2.0 54 73 (4 issues need help) 7 Updated Sep 23, 2025
  • nibabies Public

    fMRIPrep Lifespan - A robust, transparent workflow tailored for neonate and infant MRI

    nipreps/nibabies’s past year of commit activity
    Python 32 Apache-2.0 13 36 2 Updated Sep 23, 2025
  • sdcflows Public

    Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes

    nipreps/sdcflows’s past year of commit activity
    Python 43 Apache-2.0 28 34 (1 issue needs help) 6 Updated Sep 22, 2025
  • fmriprep Public

    fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

    nipreps/fmriprep’s past year of commit activity
    HTML 691 Apache-2.0 307 313 (24 issues need help) 9 Updated Sep 22, 2025
  • nireports Public

    The NiPreps' Reporting and Visualization system - report templates and "reportlets"

    nipreps/nireports’s past year of commit activity
    Python 10 Apache-2.0 20 19 (1 issue needs help) 4 Updated Sep 22, 2025
  • smriprep Public

    Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)

    nipreps/smriprep’s past year of commit activity
    Python 151 Apache-2.0 45 59 (1 issue needs help) 10 Updated Sep 22, 2025
  • petprep Public

    PETPrep: A Robust Preprocessing Pipeline for PET Data

    nipreps/petprep’s past year of commit activity
    Jupyter Notebook 13 Apache-2.0 12 15 7 Updated Sep 22, 2025
  • nifreeze Public

    A flexible framework for volume-wise artifact estimation and correction across multiple 4D neuroimaging modalities (diffusion MRI, functional MRI, and PET)

    nipreps/nifreeze’s past year of commit activity
    Python 5 Apache-2.0 5 32 (1 issue needs help) 24 Updated Sep 22, 2025
  • nipreps.github.io Public

    The NiPreps landing page

    nipreps/nipreps.github.io’s past year of commit activity
    Python 3 CC0-1.0 11 10 (1 issue needs help) 2 Updated Sep 22, 2025
  • Cookiecutter Public template

    Template for NiPreps repositories

    nipreps/Cookiecutter’s past year of commit activity
    0 Apache-2.0 1 4 0 Updated Sep 16, 2025