BIDS Apps

All

43 repositories

giga_connectome
Public
generate connectome from fMRIPrep outputs
Python
•
MIT License
•9•9•19•1•Updated Jul 22, 2025Jul 22, 2025
cat12
Public
BIDS app version of the CAT12 toolbox
Python
•
MIT License
•0•1•6•1•Updated Jul 21, 2025Jul 21, 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.
mri bids diffusion-mri bidsapp
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.
bids bids-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
neuroimaging bids
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.
bids diffusion-mri bidsapp
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
mri bids bidsapp
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.
bids bidsapp
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.
bids resting-state-fmri bidsapp
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
mri bids bidsapp functional-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-container bids singularity-container connectomics diffusion-mri bidsapp
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
mri preprocessing bids anatomical-mri bidsapp
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
mri preprocessing bids bidsap
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
bids bidsapp
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
bids bidsapp
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
bids bidsapp
Python
•
Apache License 2.0
•2•0•0•1•Updated Nov 4, 2024Nov 4, 2024
QAP
Public
PCP Quality Assessment Protocol
quality-control bids bidsapp
Python
•
Apache License 2.0
•4•5•6•3•Updated Nov 4, 2024Nov 4, 2024
BROCCOLI
Public
BIDS App for BROCCOLI
mri bids bidsapp
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.
spm bids bidsapp
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.
spm bids bidsapp
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)
mri preprocessing bids bidsapp
Python
•
Apache License 2.0
•18•14•10•1•Updated Nov 4, 2024Nov 4, 2024
MAGeTbrain
Public
Python
•5•2•3•0•Updated Nov 4, 2024Nov 4, 2024