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@bids-apps

BIDS Apps

A collection of containerized neuroimaging workflows and pipelines that accept datasets organized according to the Brain Imaging Data Structure (BIDS).
README.md

👋 Welcome to the BIDS Apps github organization 👋

Click the following link if you want to view the BIDS Apps website.

If you want to learn more about BIDS in general, have a look at the bids-standard GitHub organization.

For generic BIDS related question use the NeuroStars Discourse Forum, under the bids tag.

Otherwise, feel free to open an issue on any of those repositories if you have specific questions or requests, or register more BIDS Apps by adding them to apps.yml.

As a reminder, all contributors have to adhere to our Code of Conduct.

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  1. dockerfile-templates dockerfile-templates Public

    Dockerfile templates commonly used in BIDS Apps

    Dockerfile 11 6

  2. example example Public template

    This an example app that can serve as a template.

    Python 17 33

Repositories

Showing 10 of 43 repositories
  • rsHRF Public

    Resting state HRF estimation from BOLD-fMRI signal

    bids-apps/rsHRF’s past year of commit activity
    Python 40 MIT 13 4 2 Updated Apr 22, 2026
  • cat12 Public

    BIDS app version of the CAT12 toolbox

    bids-apps/cat12’s past year of commit activity
    Python 1 MIT 0 7 1 Updated Apr 20, 2026
  • maintenance-tools Public
    bids-apps/maintenance-tools’s past year of commit activity
    Shell 0 0 7 0 Updated Apr 7, 2026
  • giga_connectome Public

    generate connectome from fMRIPrep outputs

    bids-apps/giga_connectome’s past year of commit activity
    Python 12 MIT 9 21 0 Updated Apr 7, 2026
  • matlab-compiler-runtime Public

    Base image with Matlab Compiler Runtime (MCR)

    bids-apps/matlab-compiler-runtime’s past year of commit activity
    Python 2 1 1 1 Updated Apr 6, 2026
  • example Public template

    This an example app that can serve as a template.

    bids-apps/example’s past year of commit activity
    Python 17 Apache-2.0 33 3 1 Updated Apr 6, 2026
  • MRtrix3_connectome Public

    Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.

    bids-apps/MRtrix3_connectome’s past year of commit activity
    Python 54 Apache-2.0 28 44 4 Updated Mar 18, 2026
  • SPM Public

    BIDS App containing an instance of the SPM software.

    bids-apps/SPM’s past year of commit activity
    MATLAB 15 Apache-2.0 11 4 6 Updated Mar 17, 2026
  • afni_proc Public

    prototype AFNI bids app implmenting participant level preprocessing with afni_proc.py

    bids-apps/afni_proc’s past year of commit activity
    HTML 2 Apache-2.0 4 4 1 Updated Mar 16, 2026
  • MAGeTbrain Public
    bids-apps/MAGeTbrain’s past year of commit activity
    Python 3 5 3 0 Updated Mar 16, 2026
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