MNE-BIDS — Peer-reviewed • Rank 21.0 • Science 100%

MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis - Published in JOSS (2019)

PyBIDS — Peer-reviewed • Rank 21.5 • Science 95%

PyBIDS: Python tools for BIDS datasets - Published in JOSS (2019)

PET2BIDS — Peer-reviewed • Rank 12.4 • Science 100%

PET2BIDS: a library for converting Positron Emission Tomography data to BIDS - Published in JOSS (2024)

Reducing the efforts to create reproducible analysis code with FieldTrip — Peer-reviewed • Rank 12.3 • Science 95%

Reducing the efforts to create reproducible analysis code with FieldTrip - Published in JOSS (2024)

Connectome Mapper 3 — Peer-reviewed • Rank 11.1 • Science 95%

Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping - Published in JOSS (2022)

bidsschematools • Rank 23.1 • Science 77%

Brain Imaging Data Structure (BIDS) Specification

COSplay — Peer-reviewed • Rank 4.3 • Science 95%

COSplay: Contrast Optimized Stimulation Player - Published in JOSS (2019)

bids-validator • Rank 21.1 • Science 77%

Validator for the Brain Imaging Data Structure

Bidsme — Peer-reviewed • Rank 4.8 • Science 93%

Bidsme: expandable BIDS-ifier of brain imagery datasets - Published in JOSS (2023)

qsiprep • Rank 15.4 • Science 77%

Preprocessing of diffusion MRI

brkraw • Rank 11.1 • Science 77%

BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data

mne-hfo • Rank 8.6 • Science 77%

Estimate/compute high-frequency oscillations (HFOs) from iEEG data that are BIDS and MNE compatible using a scikit-learn-style API.

dcm2bids • Rank 8.4 • Science 77%

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

dataset-phenotypes • Rank 4.9 • Science 72%

Preparatory scripts for BIDS tabular phenotypic data in large neuroimaging datasets.

phys2bids • Rank 14.1 • Science 59%

Python3 library to format physiological files in BIDS. At the moment, it supports Acqknowledge and Labchart. BrainHack participants, check the issues with the BrainHack labels!

bidsmreye • Rank 5.1 • Science 67%

BIDS app using deepMReye to decode eye motion for fMRI time series data.

dmriprep • Rank 11.8 • Science 59%

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

pymialsrtk • Rank 9.5 • Science 59%

The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.

fmriprep • Rank 19.1 • Science 49%

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

bids-nirs-tapping • Rank 2.6 • Science 54%

Example fNIRS BIDS dataset

https://github.com/openneuroorg/openneuro • Rank 17.9 • Science 36%

A free and open platform for analyzing and sharing neuroimaging data

sdc-bids-fmri • Rank 6.2 • Science 44%

fMRI Imaging Analysis

sdc-bids-intromri • Rank 5.6 • Science 44%

Introduction to MRI and BIDS

bidsgnostic • Rank 2.3 • Science 44%

BIDS app to view a dataset content and the events file content

https://github.com/bids-apps/freesurfer • Rank 6.8 • Science 33%

BIDS app wrapping recon-all from FreeSurfer

remodnav • Rank 13.6 • Science 23%

Robust Eye Movement Detection for Natural Viewing

https://github.com/bids-apps/rshrf • Rank 11.4 • Science 20%

Resting state HRF estimation from BOLD-fMRI signal

https://github.com/bids-apps/mrtrix3_connectome • Rank 5.6 • Science 23%

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

https://github.com/aramis-lab/pydra-bids • Rank 9.0 • Science 10%

Pydra tasks for BIDS I/O

https://github.com/aramis-lab/pydra-dcm2bids • Rank 4.5 • Science 10%

Pydra tasks for dcm2bids

datahipy • Science 36%

Containerized tool written in Python to manage neuroimaging data in the Human Intracranial EEG Platform (HIP)

bidspm • Science 67%

an SPM centric BIDS app

sdc-bids-dmri • Science 44%

Introduction to dMRI

bids-matlab • Science 67%

MATLAB / Octave tools for BIDS datasets

https://github.com/bids-apps/qap • Science 36%

PCP Quality Assessment Protocol

cpp_ptb • Science 67%

a set of function to make it easier to create behavioral, EEG, fMRI experiment with psychtoolbox

bids-bep016 • Science 67%

BEP016: diffusion derivatives

https://github.com/bids-apps/brainiak-srm • Science 26%

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

spm_2_bids • Science 67%

convert SPM output to BIDS derivatives

https://github.com/bids-apps/hcppipelines • Science 36%

A BIDS App for minimal preprocessing using the HCP Pipelines

https://github.com/bids-apps/spm • Science 13%

BIDS App containing an instance of the SPM software.

https://github.com/bids-apps/ndmg • Science 13%

BIDS app for NeuroData's MRI to Graphs pipeline

https://github.com/bids-apps/hyperalignment • Science 26%

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

https://github.com/bids-standard/pybids-reports • Science 36%

A subpackage of pyBIDS, implementing automatic report generation from BIDS datasets.

https://github.com/bids-standard/bids-website • Science 26%

Website for the Brain Imaging Data Structure standard.

https://github.com/bids-standard/awesome-bids • Science 26%

A curated list of awesome BIDS projects, proposals, apps and resources

https://github.com/bids-standard/bids-elections • Science 13%

Data and code related to the BIDS elections

https://github.com/bids-apps/base_validator • Science 13%

https://github.com/bids-apps/rs_signal_extract • Science 26%

BIDS App for resting state signal extraction using nilearn.

https://github.com/bids-standard/bids-examples • Science 49%

A set of BIDS compatible datasets with empty raw data files that can be used for writing lightweight software tests.

snirf2bids • Science 36%

Python package for generating BIDS-fNIRS files from SNIRF files

halfpipe • Science 49%

ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data

UnfoldBIDS • Science 44%

qsirecon • Science 67%

Reconstruction of preprocessed q-space images (dMRI)

https://github.com/bids-standard/bids-2-devel • Science 26%

Discussions and suggestions of backwards incompatible changes to BIDS

sdc-bids-eeg-eeglab • Science 44%

Working with EEGLAB and BIDS-EEG

sdc-bids-smri • Science 26%

Structural Neuroimaging Analysis in Python

fmriflows • Science 26%

fmriflows is a consortium of many (dependent) fMRI analysis pipelines, including anatomical and functional pre-processing, univariate 1st and 2nd-level analysis, as well as multivariate pattern analysis.

execution-spec • Science 44%

BIDS app execution specification

cpp_roi • Science 67%

Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to play nice with BIDS datasets. Mostly volume-based and SPM centric.

https://github.com/aramis-lab/idhm2022-bids-primer • Science 26%

https://github.com/bids-apps/brainsuite • Science 26%

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

https://github.com/bids-apps/oppni • Science 13%

runs fast optimization of preprocessing pipelines for BOLD fMRI

https://github.com/bids-apps/pymvpa • Science 36%

runs MVPA and RSA analysis BIDS bold derivative data

https://github.com/bids-apps/mindboggle • Science 26%

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

https://github.com/bids-apps/aa • Science 13%

BIDS App containing an instance of the Automatic Analysis

https://github.com/bids-apps/bids-apps.github.io • Science 13%

This BIDS Apps website has now been integrated to the BIDS website: https://github.com/bids-standard/bids-website.git

https://github.com/bids-apps/snpm • Science 13%

BIDS App containing an instance of the SnPM software.

https://github.com/bids-standard/legacy-validator • Science 26%

Validator for the Brain Imaging Data Structure

https://github.com/bids-apps/example • Science 13%

This an example app that can serve as a template.

https://github.com/bids-apps/cpac • Science 36%

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

https://github.com/bids-apps/baracus • Science 36%

Predicts brain age, based on data from Freesurfer 5.3

https://github.com/bids-apps/tracula • Science 36%

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

https://github.com/bids-apps/broccoli • Science 36%

BIDS App for BROCCOLI

https://github.com/bids-apps/afni_proc • Science 13%

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

bids-specification-pdf-releases • Science 67%

Releases of the BIDS specification PDF version

cpp_bids • Science 67%

a set of matlab / octave function to create BIDS comptible folder structure and filenames

https://github.com/bids-apps/antscorticalthickness • Science 13%

BIDS App for calculating cortical thickness using ANTs