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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 705 308

  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 73 25

  3. smriprep smriprep Public

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

    Python 157 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 341 134

  5. petprep petprep Public

    PETPrep: A Robust Preprocessing Pipeline for PET Data

    Jupyter Notebook 18 13

Repositories

Showing 10 of 60 repositories
  • niquery Public

    A principled tool to query open neuroimaging datasets, extract relevant information and create new datasets for research

    nipreps/niquery’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Dec 6, 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 6 39 (1 issue needs help) 21 Updated Dec 6, 2025
  • niworkflows Public

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

    nipreps/niworkflows’s past year of commit activity
    Python 106 Apache-2.0 54 78 (4 issues need help) 11 Updated Dec 6, 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 36 (1 issue needs help) 11 Updated Dec 6, 2025
  • petprep Public

    PETPrep: A Robust Preprocessing Pipeline for PET Data

    nipreps/petprep’s past year of commit activity
    Jupyter Notebook 18 Apache-2.0 13 18 10 Updated Dec 4, 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 705 Apache-2.0 308 307 (24 issues need help) 8 Updated Dec 3, 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 20 (1 issue needs help) 5 Updated Dec 2, 2025
  • smriprep Public

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

    nipreps/smriprep’s past year of commit activity
    Python 157 Apache-2.0 47 63 (1 issue needs help) 7 Updated Dec 1, 2025
  • fmripost-template Public template

    A generic fMRIPost workflow

    nipreps/fmripost-template’s past year of commit activity
    Python 0 Apache-2.0 4 6 3 Updated Dec 1, 2025
  • fmripost-phase Public

    An attempt at an fMRIPost workflow for handling phase data

    nipreps/fmripost-phase’s past year of commit activity
    Python 3 Apache-2.0 1 10 3 Updated Dec 1, 2025

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