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BIDS Apps (@bids-apps)

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MRtrix3_connectome

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

freesurfer

BIDS app wrapping recon-all from FreeSurfer

HCPPipelines

A BIDS App for minimal preprocessing using the HCP Pipelines

rsHRF

Resting state HRF estimation from BOLD-fMRI signal

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

BrainSuite

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

baracus

Predicts brain age, based on data from Freesurfer 5.3

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

nipypelines

Preprocess functional tasks in a BIDS dataset.

ndmg

BIDS app for NeuroData's MRI to Graphs pipeline

QAP

PCP Quality Assessment Protocol

oppni

runs fast optimization of preprocessing pipelines for BOLD fMRI

fmriprep

This repository has moved to https://github.com/poldracklab/fmriprep

niak

Pipeline for preprocessing of fMRI and structural MRI scans

mindboggle

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

giga_connectome

generate connectome from fMRIPrep outputs

bids-apps.github.io

Portable neuroimaging pipelines that understand BIDS datasets

tracula

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

DPARSF

Docker version of DPARSF, also deployed at OpenNeuro.org

base_fsl

MAGeTbrain

matlab-compiler-runtime

Base image with Matlab Compiler Runtime (MCR)

afni_proc

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

FibreDensityAndCrosssection

SyntheticDiffusion

brainiak-srm

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