bids-apps repositories

43 repositories

cat12
Public
BIDS app version of the CAT12 toolbox
Python
•
MIT License
•0•1•7•0•Updated Oct 6, 2026Oct 6, 2026
giga_connectome
Public
generate connectome from fMRIPrep outputs
Python
•
MIT License
•12•14•21•0•Updated Oct 5, 2026Oct 5, 2026
rs_signal_extract
Public
BIDS App for resting state signal extraction using nilearn.
bids resting-state-fmri bidsapp
bids resting-state-fmri bidsapp
Python
•
Apache License 2.0
•6•6•1•2•Updated Oct 5, 2026Oct 5, 2026
tracula
Public
implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.
bids diffusion-mri bidsapp
bids diffusion-mri bidsapp
Python
•
Apache License 2.0
•4•4•1•2•Updated Oct 5, 2026Oct 5, 2026
rsHRF
Public
Resting state HRF estimation from BOLD-fMRI signal
timeseries fmri bids
timeseries fmri bids fmri-data-analysis bidsapp
Python
•
MIT License
•15•42•5•3•Updated Oct 5, 2026Oct 5, 2026
oppni
Public
runs fast optimization of preprocessing pipelines for BOLD fMRI
mri bids bidsapp
mri bids bidsapp functional-mri
Shell
•
Apache License 2.0
•3•6•7•1•Updated Oct 5, 2026Oct 5, 2026
ndmg
Public
BIDS app for NeuroData's MRI to Graphs pipeline
docker-container bids singularity-container
docker-container bids singularity-container connectomics diffusion-mri bidsapp
Dockerfile
•
Apache License 2.0
•8•5•2•1•Updated Oct 5, 2026Oct 5, 2026
mindboggle
Public
Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data
mri bids bidsapp
mri bids bidsapp
Python
•
Apache License 2.0
•4•5•9•2•Updated Oct 5, 2026Oct 5, 2026
matlab-compiler-runtime
Public
Base image with Matlab Compiler Runtime (MCR)
Python
•1•2•1•1•Updated Oct 5, 2026Oct 5, 2026
maintenance-tools
Public
Shell
•0•0•7•1•Updated Oct 5, 2026Oct 5, 2026
hyperalignment
Public
Hyperalignment is a functional alignment method that aligns subjects' brain data in a high-dimensional space of voxels/features.
bids bidsapp
bids bidsapp
Python
•
Apache License 2.0
•6•18•1•1•Updated Oct 5, 2026Oct 5, 2026
freesurfer
Public
BIDS app wrapping recon-all from FreeSurfer
mri preprocessing bids
mri preprocessing bids anatomical-mri bidsapp
Python
•
Apache License 2.0
•36•47•16•4•Updated Oct 5, 2026Oct 5, 2026
dockerfile-templates
Public
Dockerfile templates commonly used in BIDS Apps
Dockerfile
•
Apache License 2.0
•6•11•2•1•Updated Oct 5, 2026Oct 5, 2026
example
Public template
This an example app that can serve as a template.
bids bids-apps
bids bids-apps
Python
•
Apache License 2.0
•34•17•3•2•Updated Oct 5, 2026Oct 5, 2026
brainiak-srm
Public
This is the BIDS-app version of the Shared Response Model (SRM) of BrainIAK
bids bidsapp
bids bidsapp
Python
•
Apache License 2.0
•3•1•0•1•Updated Oct 5, 2026Oct 5, 2026
base_fsl
Public
Dockerfile
•
Apache License 2.0
•1•2•1•1•Updated Oct 5, 2026Oct 5, 2026
SyntheticDiffusion
Public
Python
•0•1•1•1•Updated Oct 5, 2026Oct 5, 2026
base_validator
Public
bids
bids
Dockerfile
•
Apache License 2.0
•2•0•1•1•Updated Oct 5, 2026Oct 5, 2026
baracus
Public
Predicts brain age, based on data from Freesurfer 5.3
bids bidsapp
bids bidsapp
Python
•
Apache License 2.0
•9•11•5•2•Updated Oct 5, 2026Oct 5, 2026
antsCorticalThickness
Public
BIDS App for calculating cortical thickness using ANTs
bids bidsapp
bids bidsapp
Python
•
Apache License 2.0
•2•1•0•2•Updated Oct 5, 2026Oct 5, 2026
SnPM
Public
BIDS App containing an instance of the SnPM software.
spm bids bidsapp
spm bids bidsapp
MATLAB
•
Apache License 2.0
•0•0•1•1•Updated Oct 5, 2026Oct 5, 2026
afni_proc
Public
prototype AFNI bids app implmenting participant level preprocessing with afni_proc.py
mri preprocessing bids
mri preprocessing bids bidsap
HTML
•
Apache License 2.0
•4•2•4•2•Updated Oct 5, 2026Oct 5, 2026
QAP
Public
PCP Quality Assessment Protocol
quality-control bids bidsapp
quality-control bids bidsapp
Python
•
Apache License 2.0
•4•7•6•4•Updated Oct 5, 2026Oct 5, 2026
SPM
Public
BIDS App containing an instance of the SPM software.
spm bids bidsapp
spm bids bidsapp
MATLAB
•
Apache License 2.0
•11•15•4•7•Updated Oct 5, 2026Oct 5, 2026
MAGeTbrain
Public
Python
•5•3•3•1•Updated Oct 5, 2026Oct 5, 2026
DPARSF
Public
Docker version of DPARSF, also deployed at OpenNeuro.org
MATLAB
•4•3•2•1•Updated Oct 5, 2026Oct 5, 2026
HCPPipelines
Public
A BIDS App for minimal preprocessing using the HCP Pipelines
mri preprocessing bids
mri preprocessing bids anatomical-mri bidsapp functional-mri
Python
•32•38•16•6•Updated Oct 5, 2026Oct 5, 2026
CPAC
Public
BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)
mri preprocessing bids
mri preprocessing bids bidsapp
Python
•
Apache License 2.0
•18•15•10•2•Updated Oct 5, 2026Oct 5, 2026
BrainSuite
Public
BrainSuite's structural, diffusion, and functional MRI processing pipelines with QC functionalities.
mri bids bidsapp
mri bids bidsapp mri-analysis
Python
•
Other
•3•16•1•1•Updated Oct 5, 2026Oct 5, 2026
BRAINSAutoworkup
Public
Python
•
Apache License 2.0
•1•0•0•1•Updated Oct 5, 2026Oct 5, 2026

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BIDS Apps

All

43 repositories

cat12

giga_connectome

rs_signal_extract

tracula

rsHRF

oppni

ndmg

mindboggle

matlab-compiler-runtime

maintenance-tools

hyperalignment

freesurfer

dockerfile-templates

example

brainiak-srm

base_fsl

SyntheticDiffusion

base_validator

baracus

antsCorticalThickness

SnPM

afni_proc

QAP

SPM

MAGeTbrain

DPARSF

HCPPipelines

CPAC

BrainSuite

BRAINSAutoworkup

Repositories list

43 repositories