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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 757 323

  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 78 25

  3. smriprep smriprep Public

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

    Python 169 47

  4. mriqc mriqc Public

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

    Python 380 141

  5. petprep petprep Public

    PETPrep: A Robust Preprocessing Pipeline for PET Data

    HTML 27 19

Repositories

Showing 10 of 69 repositories
  • 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 Oct 13, 2026
  • sdcflows Public

    Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes

    nipreps/sdcflows's past year of commit activity
    Python 46 Apache-2.0 32 40 (1 issue needs help) 19 Updated Oct 13, 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 4 0 Updated Oct 12, 2026
  • nibabies Public

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

    nipreps/nibabies's past year of commit activity
    Python 39 Apache-2.0 18 31 (1 issue needs help) 5 Updated Oct 9, 2026
  • petprep Public

    PETPrep: A Robust Preprocessing Pipeline for PET Data

    nipreps/petprep's past year of commit activity
    HTML 27 Apache-2.0 19 27 15 Updated Oct 9, 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 26 24 (1 issue needs help) 7 Updated Oct 9, 2026
  • niworkflows Public

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

    nipreps/niworkflows's past year of commit activity
    Python 120 Apache-2.0 58 83 (4 issues need help) 18 Updated Oct 8, 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 757 Apache-2.0 323 329 (24 issues need help) 15 Updated Oct 7, 2026
  • agentic-files Public

    Share useful skills, agents, etc

    nipreps/agentic-files's past year of commit activity
    Shell 0 Apache-2.0 0 24 0 Updated Oct 7, 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 47 67 16 Updated Oct 6, 2026