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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 7

  2. example example Public template

    This an example app that can serve as a template.

    Python 17 32

Repositories

Showing 10 of 43 repositories
  • giga_connectome Public

    generate connectome from fMRIPrep outputs

    bids-apps/giga_connectome’s past year of commit activity
    Python 10 MIT 9 19 5 Updated Oct 1, 2025
  • cat12 Public

    BIDS app version of the CAT12 toolbox

    bids-apps/cat12’s past year of commit activity
    Python 1 MIT 0 6 5 Updated Oct 1, 2025
  • BRAINSAutoworkup Public
    bids-apps/BRAINSAutoworkup’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Sep 22, 2025
  • maintenance-tools Public
    bids-apps/maintenance-tools’s past year of commit activity
    Shell 0 0 7 0 Updated Sep 22, 2025
  • dockerfile-templates Public

    Dockerfile templates commonly used in BIDS Apps

    bids-apps/dockerfile-templates’s past year of commit activity
    Dockerfile 11 Apache-2.0 7 2 1 Updated Sep 22, 2025
  • tracula Public

    implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.

    bids-apps/tracula’s past year of commit activity
    Python 3 Apache-2.0 4 1 2 Updated Sep 22, 2025
  • rs_signal_extract Public

    BIDS App for resting state signal extraction using nilearn.

    bids-apps/rs_signal_extract’s past year of commit activity
    Python 6 Apache-2.0 6 1 2 Updated Sep 22, 2025
  • oppni Public

    runs fast optimization of preprocessing pipelines for BOLD fMRI

    bids-apps/oppni’s past year of commit activity
    Shell 5 Apache-2.0 3 7 1 Updated Sep 22, 2025
  • ndmg Public

    BIDS app for NeuroData's MRI to Graphs pipeline

    bids-apps/ndmg’s past year of commit activity
    Dockerfile 5 Apache-2.0 8 2 1 Updated Sep 22, 2025
  • matlab-compiler-runtime Public

    Base image with Matlab Compiler Runtime (MCR)

    bids-apps/matlab-compiler-runtime’s past year of commit activity
    Python 2 2 1 1 Updated Sep 22, 2025
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