Repositories list

• cat12

  Public

  bids-apps/cat12’s past year of commit activity
  BIDS app version of the CAT12 toolbox

  Python

  •

  MIT License

  •0•1•7•2•Updated Mar 1, 2026Mar 1, 2026

• example

  Public template
  This an example app that can serve as a template.

  bidsbids-apps

  Python

  •

  Apache License 2.0

  •33•17•3•0•Updated Feb 27, 2026Feb 27, 2026

• giga_connectome

  Public
  generate connectome from fMRIPrep outputs

  Python

  •

  MIT License

  •9•12•23•1•Updated Feb 27, 2026Feb 27, 2026

• maintenance-tools

  Public
  Shell

  •0•0•7•0•Updated Feb 27, 2026Feb 27, 2026

• rsHRF

  Public
  Resting state HRF estimation from BOLD-fMRI signal

  timeseriesfmribids+ 2fmri-data-analysisbidsapp

  Python

  •

  MIT License

  •12•39•4•2•Updated Feb 13, 2026Feb 13, 2026

• matlab-compiler-runtime

  Public
  Base image with Matlab Compiler Runtime (MCR)

  Python

  •2•2•1•1•Updated Jan 19, 2026Jan 19, 2026

• MRtrix3_connectome

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

  mribidsdiffusion-mri+ 1bidsapp

  Python

  •

  Apache License 2.0

  •27•54•42•4•Updated Jan 6, 2026Jan 6, 2026

• 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.

  mribidsbidsapp+ 1mri-analysis

  Python

  •

  Other

  •4•13•1•0•Updated Dec 15, 2025Dec 15, 2025

• CPAC

  Public

  bids-apps/CPAC’s past year of commit activity
  BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)

  mripreprocessingbids+ 1bidsapp

  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•15•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

  mripreprocessingbids+ 1bidsap

  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•10•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

  mripreprocessingbids+ 2anatomical-mribidsapp

  Python

  •

  Apache License 2.0

  •36•44•13•1•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

  mribidsbidsapp+ 1functional-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-container+ 3connectomicsdiffusion-mribidsapp

  Dockerfile

  •

  Apache License 2.0

  •8•5•2•0•Updated Dec 15, 2025Dec 15, 2025