Repositories list

• cat12

  Public
  BIDS app version of the CAT12 toolbox

  Python

  •

  MIT License

  •0•1•7•1•Updated Mar 23, 2026Mar 23, 2026

• giga_connectome

  Public
  generate connectome from fMRIPrep outputs

  Python

  •

  MIT License

  •9•12•22•1•Updated Mar 23, 2026Mar 23, 2026

• MRtrix3_connectome

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

  mribidsdiffusion-mri+ 1

  mribidsdiffusion-mribidsapp

  Python

  •

  Apache License 2.0

  •28•54•42•4•Updated Mar 18, 2026Mar 18, 2026

• SPM

  Public
  BIDS App containing an instance of the SPM software.

  spmbidsbidsapp

  spmbidsbidsapp

  MATLAB

  •

  Apache License 2.0

  •11•15•4•6•Updated Mar 17, 2026Mar 17, 2026

• example

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

  bidsbids-apps

  bidsbids-apps

  Python

  •

  Apache License 2.0

  •33•17•3•0•Updated Mar 16, 2026Mar 16, 2026

• afni_proc

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

  mripreprocessingbids+ 1

  mripreprocessingbidsbidsap

  HTML

  •

  Apache License 2.0

  •4•2•4•1•Updated Mar 16, 2026Mar 16, 2026

• MAGeTbrain

  Public
  Python

  •5•3•3•0•Updated Mar 16, 2026Mar 16, 2026

• mindboggle

  Public
  Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data

  mribidsbidsapp

  mribidsbidsapp

  Python

  •

  Apache License 2.0

  •4•5•9•1•Updated Mar 16, 2026Mar 16, 2026

• freesurfer

  Public
  BIDS app wrapping recon-all from FreeSurfer

  mripreprocessingbids+ 2

  mripreprocessingbidsanatomical-mribidsapp

  Python

  •

  Apache License 2.0

  •35•45•13•3•Updated Mar 16, 2026Mar 16, 2026

• CPAC

  Public
  BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)

  mripreprocessingbids+ 1

  mripreprocessingbidsbidsapp

  Python

  •

  Apache License 2.0

  •18•14•10•1•Updated Mar 16, 2026Mar 16, 2026

• oppni

  Public
  runs fast optimization of preprocessing pipelines for BOLD fMRI

  mribidsbidsapp+ 1

  mribidsbidsappfunctional-mri

  Shell

  •

  Apache License 2.0

  •3•6•7•0•Updated Mar 16, 2026Mar 16, 2026

• brainiak-srm

  Public
  This is the BIDS-app version of the Shared Response Model (SRM) of BrainIAK

  bidsbidsapp

  bidsbidsapp

  Python

  •

  Apache License 2.0

  •3•1•0•0•Updated Mar 16, 2026Mar 16, 2026

• rs_signal_extract

  Public
  BIDS App for resting state signal extraction using nilearn.

  bidsresting-state-fmribidsapp

  bidsresting-state-fmribidsapp

  Python

  •

  Apache License 2.0

  •6•6•1•1•Updated Mar 16, 2026Mar 16, 2026

• matlab-compiler-runtime

  Public
  Base image with Matlab Compiler Runtime (MCR)

  Python

  •1•2•1•0•Updated Mar 16, 2026Mar 16, 2026

• DPARSF

  Public
  Docker version of DPARSF, also deployed at OpenNeuro.org

  MATLAB

  •4•3•2•0•Updated Mar 16, 2026Mar 16, 2026

• SnPM

  Public
  BIDS App containing an instance of the SnPM software.

  spmbidsbidsapp

  spmbidsbidsapp

  MATLAB

  •

  Apache License 2.0

  •0•0•1•0•Updated Mar 16, 2026Mar 16, 2026

• antsCorticalThickness

  Public
  BIDS App for calculating cortical thickness using ANTs

  bidsbidsapp

  bidsbidsapp

  Python

  •

  Apache License 2.0

  •2•0•0•1•Updated Mar 16, 2026Mar 16, 2026

• baracus

  Public
  Predicts brain age, based on data from Freesurfer 5.3

  bidsbidsapp

  bidsbidsapp

  Python

  •

  Apache License 2.0

  •9•10•5•1•Updated Mar 16, 2026Mar 16, 2026

• QAP

  Public
  PCP Quality Assessment Protocol

  quality-controlbidsbidsapp

  quality-controlbidsbidsapp

  Python

  •

  Apache License 2.0

  •4•7•6•3•Updated Mar 16, 2026Mar 16, 2026

• BRAINSAutoworkup

  Public
  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 16, 2026Mar 16, 2026

• SyntheticDiffusion

  Public
  Python

  •0•1•1•0•Updated Mar 16, 2026Mar 16, 2026

• ndmg

  Public
  BIDS app for NeuroData's MRI to Graphs pipeline

  docker-containerbidssingularity-container+ 3

  docker-containerbidssingularity-containerconnectomicsdiffusion-mribidsapp

  Dockerfile

  •

  Apache License 2.0

  •8•5•2•0•Updated Mar 16, 2026Mar 16, 2026

• hyperalignment

  Public
  Hyperalignment is a functional alignment method that aligns subjects' brain data in a high-dimensional space of voxels/features.

  bidsbidsapp

  bidsbidsapp

  Python

  •

  Apache License 2.0

  •6•18•1•0•Updated Mar 16, 2026Mar 16, 2026

• dockerfile-templates

  Public
  Dockerfile templates commonly used in BIDS Apps

  Dockerfile

  •

  Apache License 2.0

  •6•11•2•0•Updated Mar 16, 2026Mar 16, 2026

• BROCCOLI

  Public
  BIDS App for BROCCOLI

  mribidsbidsapp

  mribidsbidsapp

  Dockerfile

  •

  Apache License 2.0

  •1•7•5•0•Updated Mar 16, 2026Mar 16, 2026

• 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

  bidsdiffusion-mribidsapp

  Python

  •

  Apache License 2.0

  •3•3•1•1•Updated Mar 16, 2026Mar 16, 2026

• base_fsl

  Public
  Dockerfile

  •

  Apache License 2.0

  •1•2•1•0•Updated Mar 16, 2026Mar 16, 2026

• HCPPipelines

  Public
  A BIDS App for minimal preprocessing using the HCP Pipelines

  mripreprocessingbids+ 3

  mripreprocessingbidsanatomical-mribidsappfunctional-mri

  Python

  •31•37•16•5•Updated Mar 16, 2026Mar 16, 2026

• BrainSuite

  Public
  BrainSuite's structural, diffusion, and functional MRI processing pipelines with QC functionalities.

  mribidsbidsapp+ 1

  mribidsbidsappmri-analysis

  Python

  •

  Other

  •3•14•1•0•Updated Mar 16, 2026Mar 16, 2026

• base_validator

  Public
  bids

  bids

  Dockerfile

  •

  Apache License 2.0

  •2•0•1•0•Updated Mar 16, 2026Mar 16, 2026