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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 763 326

  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 79 25

  3. smriprep smriprep Public

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

    Python 169 48

  4. mriqc mriqc Public

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

    Python 383 143

  5. petprep petprep Public

    PETPrep: A Robust Preprocessing Pipeline for PET Data

    HTML 27 19

Repositories

Showing 10 of 71 repositories
  • mriqc-flyte Public

    MRIQC's image quality workflows ported from nipype to the Flyte 2 orchestrator

    nipreps/mriqc-flyte's past year of commit activity
    Python 0 Apache-2.0 0 48 0 Updated Nov 13, 2026
  • mriqc Public

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

    nipreps/mriqc's past year of commit activity
    Python 383 Apache-2.0 143 55 (10 issues need help) 3 Updated Nov 13, 2026
  • nipost Public

    Library for post-preprocessing utilities (resampling, etc.)

    nipreps/nipost's past year of commit activity
    Python 2 Apache-2.0 0 0 0 Updated Nov 13, 2026
  • nifreeze Public

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

    Python 5 Apache-2.0 9 47 (1 issue needs help) 6 Updated Nov 12, 2026
  • smriprep Public

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

    nipreps/smriprep's past year of commit activity
    Python 169 Apache-2.0 48 67 18 Updated Nov 12, 2026
  • nireports Public

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

    nipreps/nireports's past year of commit activity
    Python 13 Apache-2.0 27 24 (1 issue needs help) 12 Updated Nov 12, 2026
  • migas-server Public
    nipreps/migas-server's past year of commit activity
    Python 4 Apache-2.0 2 3 0 Updated Nov 11, 2026
  • 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 763 Apache-2.0 326 330 (24 issues need help) 17 Updated Nov 11, 2026
  • skills-comm Public

    Neuroimaging community skills repo - making LLMs leverage neuroimaging tools more effectively

    nipreps/skills-comm's past year of commit activity
    Python 16 Apache-2.0 7 5 0 Updated Nov 10, 2026
  • fmriprep_stats Public

    Automatic reports summarizing usage stats from Sentry.io

    nipreps/fmriprep_stats's past year of commit activity
    Jupyter Notebook 5 Apache-2.0 1 0 4 Updated Nov 10, 2026