BIDS Apps
A collection of containerized neuroimaging workflows and pipelines that accept datasets organized according to the Brain Imaging Data Structure (BIDS).
Pinned Repositories
bids-apps.github.io
This BIDS Apps website has now been integrated to the BIDS website: https://github.com/bids-standard/bids-website.git
dockerfile-templates
Dockerfile templates commonly used in BIDS Apps
example
This an example app that can serve as a template.
freesurfer
BIDS app wrapping recon-all from FreeSurfer
HCPPipelines
A BIDS App for minimal preprocessing using the HCP Pipelines
hyperalignment
Hyperalignment is a functional alignment method that aligns subjects' brain data in a high-dimensional space of voxels/features.
maintenance-tools
MRtrix3_connectome
Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
rsHRF
Resting state HRF estimation from BOLD-fMRI signal
SPM
BIDS App containing an instance of the SPM software.
BIDS Apps's Repositories
bids-apps/freesurfer
BIDS app wrapping recon-all from FreeSurfer
bids-apps/example
This an example app that can serve as a template.
bids-apps/CPAC
BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)
bids-apps/hyperalignment
Hyperalignment is a functional alignment method that aligns subjects' brain data in a high-dimensional space of voxels/features.
bids-apps/SPM
BIDS App containing an instance of the SPM software.
bids-apps/dockerfile-templates
Dockerfile templates commonly used in BIDS Apps
bids-apps/BrainSuite
BrainSuite's structural, diffusion, and functional MRI processing pipelines with QC functionalities.
bids-apps/baracus
Predicts brain age, based on data from Freesurfer 5.3
bids-apps/PyMVPA
runs MVPA and RSA analysis BIDS bold derivative data
bids-apps/BROCCOLI
BIDS App for BROCCOLI
bids-apps/rs_signal_extract
BIDS App for resting state signal extraction using nilearn.
bids-apps/ndmg
BIDS app for NeuroData's MRI to Graphs pipeline
bids-apps/oppni
runs fast optimization of preprocessing pipelines for BOLD fMRI
bids-apps/QAP
PCP Quality Assessment Protocol
bids-apps/giga_connectome
generate connectome from fMRIPrep outputs
bids-apps/mindboggle
Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data
bids-apps/bids-apps.github.io
This BIDS Apps website has now been integrated to the BIDS website: https://github.com/bids-standard/bids-website.git
bids-apps/DPARSF
Docker version of DPARSF, also deployed at OpenNeuro.org
bids-apps/tracula
implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.
bids-apps/afni_proc
prototype AFNI bids app implmenting participant level preprocessing with afni_proc.py
bids-apps/base_fsl
bids-apps/MAGeTbrain
bids-apps/matlab-compiler-runtime
Base image with Matlab Compiler Runtime (MCR)
bids-apps/brainiak-srm
This is the BIDS-app version of the Shared Response Model (SRM) of BrainIAK
bids-apps/SyntheticDiffusion
bids-apps/maintenance-tools
bids-apps/antsCorticalThickness
BIDS App for calculating cortical thickness using ANTs
bids-apps/base_validator
bids-apps/BRAINSAutoworkup
bids-apps/SnPM
BIDS App containing an instance of the SnPM software.