Repositories list

• rsHRF

  Public
  Resting state HRF estimation from BOLD-fMRI signal

  timeseriesfmribids+ 2fmri-data-analysisbidsapp

  Python

  •

  MIT License

  •12•37•4•2•Updated Jul 30, 2025Jul 30, 2025

• cat12

  Public
  BIDS app version of the CAT12 toolbox

  Python

  •

  MIT License

  •0•1•6•1•Updated Jul 28, 2025Jul 28, 2025

• giga_connectome

  Public
  generate connectome from fMRIPrep outputs

  Python

  •

  MIT License

  •9•9•19•1•Updated Jul 22, 2025Jul 22, 2025

• matlab-compiler-runtime

  Public
  Base image with Matlab Compiler Runtime (MCR)

  Python

  •2•2•1•1•Updated Jun 23, 2025Jun 23, 2025

• maintenance-tools

  Public
  Shell

  •0•0•7•1•Updated Jun 23, 2025Jun 23, 2025

• 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•52•41•3•Updated Jun 19, 2025Jun 19, 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 Mar 4, 2025Mar 4, 2025

• bids-apps.github.io

  Public
  This BIDS Apps website has now been integrated to the BIDS website: https://github.com/bids-standard/bids-website.git

  neuroimagingbids

  CSS

  •

  Other

  •14•3•0•0•Updated Feb 22, 2025Feb 22, 2025

• .github

  Public
  0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• base_validator

  Public
  bids

  Dockerfile

  •

  Apache License 2.0

  •3•0•1•0•Updated Nov 10, 2024Nov 10, 2024

• 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 Nov 4, 2024Nov 4, 2024

• 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 Nov 4, 2024Nov 4, 2024

• 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 Nov 4, 2024Nov 4, 2024

• 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 Nov 4, 2024Nov 4, 2024

• oppni

  Public
  runs fast optimization of preprocessing pipelines for BOLD fMRI

  mribidsbidsapp+ 1functional-mri

  Shell

  •

  Apache License 2.0

  •3•5•7•0•Updated Nov 4, 2024Nov 4, 2024

• 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 Nov 4, 2024Nov 4, 2024

• dockerfile-templates

  Public
  Dockerfile templates commonly used in BIDS Apps

  Dockerfile

  •

  Apache License 2.0

  •8•11•2•0•Updated Nov 4, 2024Nov 4, 2024

• freesurfer

  Public
  BIDS app wrapping recon-all from FreeSurfer

  mripreprocessingbids+ 2anatomical-mribidsapp

  Python

  •

  Apache License 2.0

  •35•42•13•1•Updated Nov 4, 2024Nov 4, 2024

• 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 Nov 4, 2024Nov 4, 2024

• 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 Nov 4, 2024Nov 4, 2024

• base_fsl

  Public
  Dockerfile

  •

  Apache License 2.0

  •1•2•1•0•Updated Nov 4, 2024Nov 4, 2024

• SyntheticDiffusion

  Public
  Python

  •0•1•1•0•Updated Nov 4, 2024Nov 4, 2024

• baracus

  Public
  Predicts brain age, based on data from Freesurfer 5.3

  bidsbidsapp

  Python

  •

  Apache License 2.0

  •9•9•5•1•Updated Nov 4, 2024Nov 4, 2024

• antsCorticalThickness

  Public
  BIDS App for calculating cortical thickness using ANTs

  bidsbidsapp

  Python

  •

  Apache License 2.0

  •2•0•0•1•Updated Nov 4, 2024Nov 4, 2024

• QAP

  Public
  PCP Quality Assessment Protocol

  quality-controlbidsbidsapp

  Python

  •

  Apache License 2.0

  •4•5•6•3•Updated Nov 4, 2024Nov 4, 2024

• BROCCOLI

  Public
  BIDS App for BROCCOLI

  mribidsbidsapp

  Dockerfile

  •

  Apache License 2.0

  •1•6•5•0•Updated Nov 4, 2024Nov 4, 2024

• SPM

  Public
  BIDS App containing an instance of the SPM software.

  spmbidsbidsapp

  MATLAB

  •

  Apache License 2.0

  •12•14•4•7•Updated Nov 4, 2024Nov 4, 2024

• SnPM

  Public
  BIDS App containing an instance of the SnPM software.

  spmbidsbidsapp

  MATLAB

  •

  Apache License 2.0

  •0•0•1•0•Updated Nov 4, 2024Nov 4, 2024

• BRAINSAutoworkup

  Public
  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• CPAC

  Public
  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 Nov 4, 2024Nov 4, 2024