BIDS Apps

freesurfer

BIDS app wrapping recon-all from FreeSurfer

example

This an example app that can serve as a template.

CPAC

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

SPM

BIDS App containing an instance of the SPM software.

hyperalignment

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

dockerfile-templates

Dockerfile templates commonly used in BIDS Apps

baracus

Predicts brain age, based on data from Freesurfer 5.3

BrainSuite

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

PyMVPA

runs MVPA and RSA analysis BIDS bold derivative data

rs_signal_extract

BIDS App for resting state signal extraction using nilearn.

BROCCOLI

BIDS App for BROCCOLI

ndmg

BIDS app for NeuroData's MRI to Graphs pipeline

oppni

runs fast optimization of preprocessing pipelines for BOLD fMRI

QAP

PCP Quality Assessment Protocol

bids-apps.github.io

Portable neuroimaging pipelines that understand BIDS datasets

DPARSF

Docker version of DPARSF, also deployed at OpenNeuro.org

giga_connectome

generate connectome from fMRIPrep outputs

mindboggle

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

tracula

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

afni_proc

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

base_fsl

MAGeTbrain

matlab-compiler-runtime

Base image with Matlab Compiler Runtime (MCR)

brainiak-srm

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

SyntheticDiffusion

maintenance-tools

antsCorticalThickness

BIDS App for calculating cortical thickness using ANTs

base_validator

BRAINSAutoworkup

SnPM

BIDS App containing an instance of the SnPM software.