BIDS Apps

bids-apps

A collection of containerized neuroimaging workflows and pipelines that accept datasets organized according to the Brain Imaging Data Structure (BIDS).

http://bids-apps.neuroimaging.io

BIDS Apps's repositories

MRtrix3_connectome

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

Language:PythonApache-2.048 5 91

freesurfer

BIDS app wrapping recon-all from FreeSurfer

Language:PythonApache-2.040 7 40

HCPPipelines

A BIDS App for minimal preprocessing using the HCP Pipelines

Language:Python33 12 43

example

This an example app that can serve as a template.

Language:PythonApache-2.016 3 15

CPAC

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

Language:PythonApache-2.014 6 25

hyperalignment

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

Language:PythonApache-2.014 6 1

SPM

BIDS App containing an instance of the SPM software.

Language:MATLABApache-2.014 8 14

dockerfile-templates

Dockerfile templates commonly used in BIDS Apps

Language:DockerfileApache-2.010 4 2

baracus

Predicts brain age, based on data from Freesurfer 5.3

Language:PythonApache-2.09 6 12

BrainSuite

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

Language:PythonNOASSERTION9 3 2

BROCCOLI

BIDS App for BROCCOLI

Language:DockerfileApache-2.06 5 6

rs_signal_extract

BIDS App for resting state signal extraction using nilearn.

Language:PythonApache-2.06 6 4

ndmg

BIDS app for NeuroData's MRI to Graphs pipeline

Language:DockerfileApache-2.05 4 12

oppni

runs fast optimization of preprocessing pipelines for BOLD fMRI

Language:ShellApache-2.05 7 19

QAP

PCP Quality Assessment Protocol

Language:PythonApache-2.05 6 6

mindboggle

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

Language:PythonApache-2.04 5 11

niak

Pipeline for preprocessing of fMRI and structural MRI scans

Language:MATLABNOASSERTION4 3 13

DPARSF

Docker version of DPARSF, also deployed at OpenNeuro.org

Language:MATLAB3 6 10

tracula

implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.

Language:PythonApache-2.03 5 18

afni_proc

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

Language:HTMLApache-2.02 4 8

base_fsl

Language:DockerfileApache-2.02 3 7

FibreDensityAndCrosssection

Language:PythonApache-2.02 7 6

MAGeTbrain

Language:Python2 6 6

matlab-compiler-runtime

Base image with Matlab Compiler Runtime (MCR)

Language:Python2 3 2

brainiak-srm

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

Language:PythonApache-2.01 7 7

maintenance-tools

Language:Shell05 7

aa

BIDS App containing an instance of the Automatic Analysis

Language:DockerfileNOASSERTION06 9

antsCorticalThickness

BIDS App for calculating cortical thickness using ANTs

Language:PythonApache-2.005 2

base_validator

Language:DockerfileApache-2.005 4

BRAINSAutoworkup

Language:PythonApache-2.0050