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@bids-apps BIDS Apps

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    43 repositories

    • MRtrix3_connectome

      Public
      Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
      mribidsdiffusion-mribidsapp
      Python
      •
      Apache License 2.0
      •27•54•42•4•Updated Jan 6, 2026Jan 6, 2026

    • giga_connectome

      Public
      generate connectome from fMRIPrep outputs
      Python
      •
      MIT License
      •9•12•22•1•Updated Jan 5, 2026Jan 5, 2026

    • cat12

      Public
      BIDS app version of the CAT12 toolbox
      Python
      •
      MIT License
      •0•1•7•3•Updated Jan 1, 2026Jan 1, 2026

    • matlab-compiler-runtime

      Public
      Base image with Matlab Compiler Runtime (MCR)
      Python
      •2•2•1•0•Updated Dec 15, 2025Dec 15, 2025

    • BROCCOLI

      Public
      BIDS App for BROCCOLI
      mribidsbidsapp
      Dockerfile
      •
      Apache License 2.0
      •1•7•5•0•Updated Dec 15, 2025Dec 15, 2025

    • BrainSuite

      Public
      BrainSuite's structural, diffusion, and functional MRI processing pipelines with QC functionalities.
      mribidsbidsappmri-analysis
      Python
      •
      Other
      •4•12•1•0•Updated Dec 15, 2025Dec 15, 2025

    • CPAC

      Public
      BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)
      mripreprocessingbidsbidsapp
      Python
      •
      Apache License 2.0
      •18•14•10•1•Updated Dec 15, 2025Dec 15, 2025

    • MAGeTbrain

      Public
      Python
      •5•3•3•0•Updated Dec 15, 2025Dec 15, 2025

    • QAP

      Public
      PCP Quality Assessment Protocol
      quality-controlbidsbidsapp
      Python
      •
      Apache License 2.0
      •4•7•6•3•Updated Dec 15, 2025Dec 15, 2025

    • SPM

      Public
      BIDS App containing an instance of the SPM software.
      spmbidsbidsapp
      MATLAB
      •
      Apache License 2.0
      •12•14•4•7•Updated Dec 15, 2025Dec 15, 2025

    • SnPM

      Public
      BIDS App containing an instance of the SnPM software.
      spmbidsbidsapp
      MATLAB
      •
      Apache License 2.0
      •0•0•1•0•Updated Dec 15, 2025Dec 15, 2025

    • DPARSF

      Public
      Docker version of DPARSF, also deployed at OpenNeuro.org
      MATLAB
      •4•3•2•0•Updated Dec 15, 2025Dec 15, 2025

    • SyntheticDiffusion

      Public
      Python
      •0•1•1•0•Updated Dec 15, 2025Dec 15, 2025

    • afni_proc

      Public
      prototype AFNI bids app implmenting participant level preprocessing with afni_proc.py
      mripreprocessingbidsbidsap
      HTML
      •
      Apache License 2.0
      •4•2•4•1•Updated Dec 15, 2025Dec 15, 2025

    • antsCorticalThickness

      Public
      BIDS App for calculating cortical thickness using ANTs
      bidsbidsapp
      Python
      •
      Apache License 2.0
      •2•0•0•1•Updated Dec 15, 2025Dec 15, 2025

    • base_fsl

      Public
      Dockerfile
      •
      Apache License 2.0
      •1•2•1•0•Updated Dec 15, 2025Dec 15, 2025

    • brainiak-srm

      Public
      This is the BIDS-app version of the Shared Response Model (SRM) of BrainIAK
      bidsbidsapp
      Python
      •
      Apache License 2.0
      •3•1•0•0•Updated Dec 15, 2025Dec 15, 2025

    • baracus

      Public
      Predicts brain age, based on data from Freesurfer 5.3
      bidsbidsapp
      Python
      •
      Apache License 2.0
      •9•9•5•1•Updated Dec 15, 2025Dec 15, 2025

    • dockerfile-templates

      Public
      Dockerfile templates commonly used in BIDS Apps
      Dockerfile
      •
      Apache License 2.0
      •7•11•2•0•Updated Dec 15, 2025Dec 15, 2025

    • hyperalignment

      Public
      Hyperalignment is a functional alignment method that aligns subjects' brain data in a high-dimensional space of voxels/features.
      bidsbidsapp
      Python
      •
      Apache License 2.0
      •6•17•1•0•Updated Dec 15, 2025Dec 15, 2025

    • mindboggle

      Public
      Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data
      mribidsbidsapp
      Python
      •
      Apache License 2.0
      •4•5•9•1•Updated Dec 15, 2025Dec 15, 2025

    • freesurfer

      Public
      BIDS app wrapping recon-all from FreeSurfer
      mripreprocessingbidsanatomical-mribidsapp
      Python
      •
      Apache License 2.0
      •35•44•13•1•Updated Dec 15, 2025Dec 15, 2025

    • example

      Public template
      This an example app that can serve as a template.
      bidsbids-apps
      Python
      •
      Apache License 2.0
      •32•17•3•0•Updated Dec 15, 2025Dec 15, 2025

    • base_validator

      Public
      bids
      Dockerfile
      •
      Apache License 2.0
      •3•0•1•0•Updated Dec 15, 2025Dec 15, 2025

    • rs_signal_extract

      Public
      BIDS App for resting state signal extraction using nilearn.
      bidsresting-state-fmribidsapp
      Python
      •
      Apache License 2.0
      •6•6•1•1•Updated Dec 15, 2025Dec 15, 2025

    • oppni

      Public
      runs fast optimization of preprocessing pipelines for BOLD fMRI
      mribidsbidsappfunctional-mri
      Shell
      •
      Apache License 2.0
      •3•6•7•0•Updated Dec 15, 2025Dec 15, 2025

    • tracula

      Public
      implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.
      bidsdiffusion-mribidsapp
      Python
      •
      Apache License 2.0
      •4•3•1•1•Updated Dec 15, 2025Dec 15, 2025

    • ndmg

      Public
      BIDS app for NeuroData's MRI to Graphs pipeline
      docker-containerbidssingularity-containerconnectomicsdiffusion-mribidsapp
      Dockerfile
      •
      Apache License 2.0
      •8•5•2•0•Updated Dec 15, 2025Dec 15, 2025

    • HCPPipelines

      Public
      A BIDS App for minimal preprocessing using the HCP Pipelines
      mripreprocessingbidsanatomical-mribidsappfunctional-mri
      Python
      •31•37•16•5•Updated Dec 15, 2025Dec 15, 2025

    • maintenance-tools

      Public
      Shell
      •0•0•7•0•Updated Dec 15, 2025Dec 15, 2025