Projects in Awesome Lists tagged with bids

https://github.com/fieldtrip/fieldtrip

The MATLAB toolbox for MEG, EEG and iEEG analysis

analysis beamformer bids brain connectivity dipole donders ecog eeg fieldtrip ieeg matlab meg neuroimaging neuroscience seeg statistics time-frequency

Last synced: 14 May 2025

https://github.com/nipreps/fmriprep

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 brain-imaging fmri fmri-preprocessing image-processing neuroimaging

Last synced: 28 Jan 2026

https://github.com/bids-standard/bids-specification

Brain Imaging Data Structure (BIDS) Specification

bids data-standards neuroimaging standards

Last synced: 04 Feb 2026

https://github.com/bids-standard/bids-starter-kit

The Starter-kit has moved to the new BIDS website.

bids tutorials

Last synced: 04 Oct 2025

https://bids-standard.github.io/bids-starter-kit/

Collection of tutorials, wikis, and templates to get you started with creating BIDS compliant datasets

bids closember tutorials

Last synced: 29 Apr 2025

https://github.com/bids-standard/pybids

Python tools for querying and manipulating BIDS datasets.

api bids python

Last synced: 04 Oct 2025

https://github.com/bids-standard/bids-examples

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

bids data-standards dataset neuroimaging standards

Last synced: 04 Oct 2025

https://bids-standard.github.io/bids-examples/

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

bids data-standards dataset neuroimaging standards

Last synced: 29 Apr 2025

https://github.com/bids-standard/legacy-validator

Validator for the Brain Imaging Data Structure

bids data-validation neuroimaging

Last synced: 04 Oct 2025

https://unfmontreal.github.io/Dcm2Bids/

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

bids neuroimaging neuroscience

Last synced: 29 Apr 2025

https://github.com/mne-tools/mne-bids-pipeline

Automatically process entire electrophysiological datasets using MNE-Python.

bids group-analysis mne-python neuroscience pipeline python

Last synced: 14 Jun 2026

https://github.com/mne-tools/mne-bids

MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.

bids eeg electroencephalography ieeg magnetoencephalography meg mne neuroimaging neuroscience

Last synced: 21 Oct 2025

https://github.com/PennLINC/qsiprep

Preprocessing of diffusion MRI

bids denoising-images diffusion-mri distortion-correction motion-correction pipelines

Last synced: 29 Apr 2025

https://github.com/openneuroorg/openneuro

A free and open platform for analyzing and sharing neuroimaging data

bids datasets graphql neuroimaging neuroscience react

Last synced: 02 Apr 2026

https://github.com/MICA-MNI/micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

awesome bids connectome diffusion-mri imageprocessing microstructure mri multimodal neuroimaging resting-state

Last synced: 29 Apr 2025

https://github.com/mica-mni/micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

awesome bids connectome diffusion-mri imageprocessing microstructure mri multimodal neuroimaging resting-state

Last synced: 24 Jul 2025

https://github.com/wiheto/teneto

Temporal Network Tools

bids community-detection dynamics fmri network-theory networks neuroscience python temporal-network-theory temporal-networks time-varying-connectivity

Last synced: 30 Dec 2025

https://github.com/connectomicslab/connectomemapper3

Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.

bids bids-apps bidsapp brain chuv connectome dmri docker eeg fmri parcellation pipelines python singularity

Last synced: 14 Jan 2026

https://github.com/HALFpipe/HALFpipe

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

bids fmri meta-analysis neuroimaging pipeline reproducibility

Last synced: 01 May 2025

https://github.com/nipreps/dmriprep

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.

bids bids-apps diffusion-mri magnetic-resonance-imaging preprocessing

Last synced: 06 May 2025

https://github.com/physiopy/phys2bids

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!

acqknowledge bids brainweb closember ge hacktoberfest labchart physiological-recordings physiological-signals physiology python3-library spike2

Last synced: 16 Jan 2026

https://github.com/psychoinformatics-de/remodnav

Robust Eye Movement Detection for Natural Viewing

bids eye-tracking

Last synced: 13 Jun 2025

https://github.com/miykael/fmriflows

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.

bids fmri neuroimaging python

Last synced: 01 May 2025

https://github.com/bids-standard/bids-matlab

MATLAB / Octave tools for BIDS datasets

bids closember eeg ieeg matlab meg mri neuroimaging octave pet

Last synced: 03 Oct 2025

https://github.com/bids-apps/MRtrix3_connectome

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

bids bidsapp diffusion-mri mri

Last synced: 29 Apr 2025

https://github.com/BrkRaw/brkraw

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

bids bruker converter dataloader nibabel simpleitk

Last synced: 29 Apr 2025

https://github.com/bids-apps/freesurfer

BIDS app wrapping recon-all from FreeSurfer

anatomical-mri bids bidsapp mri preprocessing

Last synced: 29 May 2026

https://github.com/carpentries-incubator/sdc-bids-fmri

fMRI Imaging Analysis

bids binder carpentries-incubator english fmri fmri-analysis fmri-data-analysis lesson neuroimaging nilearn pre-alpha programming python

Last synced: 07 Apr 2025

https://github.com/bids-apps/rshrf

Resting state HRF estimation from BOLD-fMRI signal

bids bidsapp fmri fmri-data-analysis timeseries

Last synced: 29 May 2026

https://github.com/bids-apps/rsHRF

Resting state HRF estimation from BOLD-fMRI signal

bids bidsapp fmri fmri-data-analysis timeseries

Last synced: 29 Apr 2025

https://github.com/brainlife/ezbids

A web service for semi-automated conversion of raw imaging data to BIDS

bids bids-converter brain-imaging data-curation dicom interoperability mri neuroimaging nifti web

Last synced: 22 Apr 2026

https://github.com/bids-apps/HCPPipelines

A BIDS App for minimal preprocessing using the HCP Pipelines

anatomical-mri bids bidsapp functional-mri mri preprocessing

Last synced: 29 Apr 2025

https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit

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.

bids bids-apps fetal itk mri nipype super-resolution workflow

Last synced: 29 Apr 2025

https://github.com/robertoostenveld/bids-tools

Tools for dealing with neuroimaging data in the BIDS structure

afni bids fieldtrip fmri fsl meg mri neuroimaging spm

Last synced: 12 Jun 2025

https://github.com/carpentries-incubator/sdc-bids-smri

Structural Neuroimaging Analysis in Python

bids carpentries-incubator english lesson mri neuroimaging pre-alpha python

Last synced: 02 Sep 2025

https://github.com/openneuropet/PET2BIDS

PET2BIDS helps you convert your PET data into BIDS! raw PET scanner files (e.g. ecat, dicom) and additional side files like .e.g excel sheets -- paper @JOSS https://doi.org/10.21105/joss.06067

bids converter json metadata

Last synced: 29 Apr 2025

https://github.com/carpentries-incubator/sdc-bids-intromri

Introduction to MRI and BIDS

alpha bids binder carpentries-incubator english helpwanted-list lesson mri neuroimaging python

Last synced: 24 Jul 2025

https://github.com/carpentries-incubator/sdc-bids-dmri

Introduction to dMRI

ants bids carpentries-incubator diffusion-mri dipy dmri dwi fsl lesson neuroimaging pre-alpha programming python tractography

Last synced: 02 Sep 2025

https://github.com/bids-standard/bids-validator

Validator for the Brain Imaging Data Structure

bids data-standards neuroimaging-data validation

Last synced: 16 Jan 2026

https://github.com/childmindresearch/bids2table

Index BIDS datasets fast, locally or in the cloud

arrow bids neuroimaging

Last synced: 16 Jan 2026

https://github.com/bids-apps/example

This an example app that can serve as a template.

bids bids-apps

Last synced: 29 May 2026

https://github.com/bids-apps/hyperalignment

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

bids bidsapp

Last synced: 29 May 2026

https://github.com/nidea1/e-auction

A Django(backend) & React(frontend) based full-stack real time auction application

auction auction-apps auction-website bidding bids bids-apps bidsapp django drf drf-jwt e-commerce ecommerce full-stack online react

Last synced: 23 Apr 2025

https://github.com/bids-apps/CPAC

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

bids bidsapp mri preprocessing

Last synced: 29 Apr 2025

https://github.com/mne-tools/mne-hfo

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

bids hfo-detection ieeg ieeg-data mne-hfo mne-python

Last synced: 14 Jan 2026

https://github.com/bids-apps/SPM

BIDS App containing an instance of the SPM software.

bids bidsapp spm

Last synced: 29 Apr 2025

https://github.com/benoitberanger/niix2bids

Automatic BIDS architecture

bids bids-converter mri

Last synced: 22 Apr 2025

https://github.com/rob-luke/bids-nirs-tapping

Example fNIRS BIDS dataset

bids bids-format fnirs neuroimaging neuroscience

Last synced: 28 Jan 2026

https://github.com/bids-standard/bids-2-devel

Discussions and suggestions of backwards incompatible changes to BIDS

bids

Last synced: 14 Feb 2026

https://bids-standard.github.io/bids-validator/

Validator for the Brain Imaging Data Structure

bids data-standards neuroimaging-data validation

Last synced: 29 Apr 2025

https://github.com/bids-apps/BrainSuite

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

bids bidsapp mri mri-analysis

Last synced: 29 Apr 2025

https://github.com/neurodatascience/ukbm

Data management helper code for the UK Biobank.

bids data-management ukb ukbiobank

Last synced: 09 Apr 2025

https://github.com/bids-apps/baracus

Predicts brain age, based on data from Freesurfer 5.3

bids bidsapp

Last synced: 29 May 2026

https://github.com/nimh-dsst/dataset-phenotypes

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

abcd abcd-study abide abide-data bids data-dictionary dataset datasets hbn hcp nki phenotype phenotypic pnc tabular tabular-data ukb ukbb ukbiobank

Last synced: 22 Jan 2026

https://github.com/bids-apps/pymvpa

runs MVPA and RSA analysis BIDS bold derivative data

bids bidsapp multivariate-pattern-analysis mvpa similarity-analysis

Last synced: 29 May 2026

https://github.com/remi-gau/bids_cookbook

A simple recipe to convert your neuroimaging data into a BIDS dataset.

bids data eeg fmri matlab meg spm12 tutorial

Last synced: 23 Apr 2025

https://github.com/cpp-lln-lab/bidspm

an SPM centric BIDS app

automated-analysis bids bidsapp closember fmri pipeline spm12

Last synced: 29 Apr 2025

https://github.com/bids-apps/PyMVPA

runs MVPA and RSA analysis BIDS bold derivative data

bids bidsapp multivariate-pattern-analysis mvpa similarity-analysis

Last synced: 29 Apr 2025

https://github.com/triimaging/bidstools.jl

Tools for working with Brain Imaging Data Structure from Julia

bids brain-imaging julia

Last synced: 28 Aug 2025

https://macquarie-meg-research.github.io/Biscuit/

GUI for easy MEG to BIDS conversion

bids magnetoencephalography meg neuroimaging

Last synced: 29 Apr 2025

https://github.com/cpp-lln-lab/bidsMReye

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

bids bidsapp closember eye-tracking

Last synced: 29 Apr 2025

https://github.com/bids-apps/rs_signal_extract

BIDS App for resting state signal extraction using nilearn.

bids bidsapp resting-state-fmri

Last synced: 29 May 2026

https://github.com/bids-apps/BROCCOLI

BIDS App for BROCCOLI

bids bidsapp mri

Last synced: 29 Apr 2025

https://github.com/bids-standard/bids-bep016

BEP016: diffusion derivatives

bids

Last synced: 04 Oct 2025

https://github.com/bids-apps/oppni

runs fast optimization of preprocessing pipelines for BOLD fMRI

bids bidsapp functional-mri mri

Last synced: 29 May 2026

https://github.com/bids-apps/ndmg

BIDS app for NeuroData's MRI to Graphs pipeline

bids bidsapp connectomics diffusion-mri docker-container singularity-container

Last synced: 29 May 2026

https://github.com/bids-apps/QAP

PCP Quality Assessment Protocol

bids bidsapp quality-control

Last synced: 29 Apr 2025

https://github.com/bids-standard/bep021

Organizing and coordinating the BIDS Extension Proposal 21: Common Electrophysiology Derivatives

bids eeg ieeg meg

Last synced: 04 Oct 2025

https://github.com/bids-apps/mindboggle

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

bids bidsapp mri

Last synced: 29 May 2026

https://github.com/bids-apps/nipypelines

Preprocess functional tasks in a BIDS dataset.

bids bidsapp

Last synced: 29 May 2026

https://github.com/carobellum/data-sharing-tools

Tools created for sharing of MRI and behavioural data as part of my work with Professor Kate Watkins in the Speech & Brain Lab at the University of Oxford.

bids bids-format data-sharing deface deidentify open-data open-science science

Last synced: 07 May 2026

https://github.com/ellisdg/hcplifespan2bids

Convert HCP Lifespan, Aging, and Development data to BIDS format

bids bids-format hcp

Last synced: 22 Sep 2025

https://github.com/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 bidsapp diffusion-mri

Last synced: 29 May 2026

https://github.com/dissagaliyeva/sim2bids

App to load, transform & download BIDS compliant data

bids computational-neuroscience conversion neuroscience

Last synced: 16 Jan 2026

https://github.com/sccn/nemar-citations

Insights on how NEMAR datasets are being used in the academic context

bids fair-data open-data

Last synced: 18 Jan 2026

https://github.com/bids-apps/afni_proc

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

bids bidsap mri preprocessing

Last synced: 29 May 2026

https://github.com/khanlab/funcmasker-flex

BIDS App for U-net brain masking of fetal bold MRI

bids bold masking mri unet

Last synced: 05 Feb 2026

https://github.com/jbkordass/lightweight-pipeline

A Python package to write data processing pipelines with. Initially designed for eeg/meg analysis using MNE-Python with MNE-BIDS.

bids eeg meg mne neuroscience

Last synced: 11 Mar 2026

https://github.com/marcelzwiers/mriqc_sub

mriqc_sub.py is a wrapper around mriqc that queries the bids directory for new participants and then runs participant-level mriqc jobs on the compute cluster. If the participant-level jobs have all finished, you can run the group-level "mriqc bidsdir outputdir group" command to generate group level results (the group level report and the features CSV table)

bids mriqc

Last synced: 30 Dec 2025

https://github.com/martinkalema/purchases-extended

Creating a customization such that one RFQ can be assigned to mulitple vendors at the model level.

bids odoo procurement purchase-module request-for-quotation vendors

Last synced: 16 Jun 2026

https://github.com/bids-standard/bids-specification-pdf-releases

Releases of the BIDS specification PDF version

bids

Last synced: 17 Feb 2026

https://github.com/arasgungore/orderbook-reconstruction

A C++ project which implements two orderbooks that sorts and outputs the best bids and asks.

asks bid-ask bids hft hft-simulation hft-trading high-frequency-trading high-performance high-performance-computing network network-programming orderbook orderbook-snapshots quant quant-trading quantitative-trading sorting tcp-ip trading-algorithms udp

Last synced: 30 Jun 2025

https://github.com/carpentries-incubator/sdc-bids-eeg-eeglab

Working with EEGLAB and BIDS-EEG

bids bids-eeg carpentries-incubator eeg eeg-analysis eeg-data eeg-signals eeglab english lesson matlab neuroimaging pre-alpha programming

Last synced: 02 Sep 2025

https://github.com/adelavega/bids_test

A bids test dataset with stimuli, with all files in tracked by a git annex remote

bids

Last synced: 14 Feb 2026

https://github.com/robertoostenveld/brainvision

Python implementation to read and write EEG data in the BrainVision Core data format

bids brainvision eeg python

Last synced: 22 Jun 2025

https://github.com/remi-gau/bids_workshop

bids mri neuroimaging workshop

Last synced: 02 Feb 2026

https://github.com/bids-standard/pybids-reports

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

bids brain methods

Last synced: 04 Oct 2025

https://github.com/bids-apps/brainiak-srm

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

bids bidsapp

Last synced: 29 May 2026

https://github.com/vanandrew/neurosplitter

A collection of tools for neuroimaging data formatting for deep learning applications

bids deep-learning machine-learning neuroimaging neuroscience

Last synced: 28 Apr 2026

https://github.com/aaronearlerichardson/server_gui_client

A user interface for cloud based medical image storage

bids bids-apps database eeg-data flask flask-restful gui ieeg image-viewer mne-bids-pipeline mne-python python qt5-gui tkinter-gui

Last synced: 29 Apr 2026

https://github.com/sebastientourbier/synapsy-eeg-meeting-04-2021

Synapsy-DMP-Meeting Presentation about standardization of EEG data

bids eeg-data nccr-synapsy slides

Last synced: 19 Jun 2025

https://github.com/sebastientourbier/synapsy-annual-meeting-04-21

Presentation about the standardization of neuroimaging data management inside Synapsy project

bids datalad nccr-synapsy slides

Last synced: 12 Feb 2026

https://github.com/cimcyc/bids-converter-mri-matlab

This repository provides a set of functions and scripts designed to facilitate the creation of BIDS-compliant datasets and the conversion of DICOM files to NIFTI format.

bids matlab mri

Last synced: 28 Jun 2026