bids

There are 3 repositories under bids topic.

• fieldtrip / fieldtrip

  The MATLAB toolbox for MEG, EEG and iEEG analysis

  analysisbeamformerbidsbrainconnectivitydipoledondersecogeegfieldtripieegmatlabmegneuroimagingneuroscienceseegstatisticstime-frequency
  Language:MATLAB 809

• 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.

  fmrifmri-preprocessingbrain-imagingneuroimagingbidsimage-processing
  Language:HTML 607

• bids-standard / bids-specification

  Brain Imaging Data Structure (BIDS) Specification

  bidsdata-standardsneuroimagingstandards
  Language:Python 255

• bids-standard / bids-starter-kit

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

  bidsclosembertutorials
  Language:MATLAB 251

• bids-standard / pybids

  Python tools for querying and manipulating BIDS datasets.

  apibidspython
  Language:Python 211

• bids-standard / bids-validator

  Validator for the Brain Imaging Data Structure

  bidsneuroimagingdata-validation
  Language:JavaScript 176

• bids-standard / bids-examples

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

  bidsdatasetdata-standardsstandardsneuroimaging
  Language:MATLAB 156

• UNFmontreal / Dcm2Bids

  Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

  neuroscienceneuroimagingbids
  Language:Python 151

• mne-tools / mne-bids-pipeline

  Automatically process entire electrophysiological datasets using MNE-Python.

  bidsgroup-analysismne-pythonneurosciencepipelinepython
  Language:Python 128
• bidscoin

  Donders-Institute / bidscoin

  BIDScoin converts your source-level neuroimaging data to BIDS

  bidsmrineuroimagingdicompetimagingdata-sharingmulti-echomulti-echo-combinebrain-imagingdata-standardsdefacedefacingparrecnibabeldcm2niixspec2niimrshpcbids-apps
  Language:Python 124
• mne-bids

  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.

  bidsmnemagnetoencephalographyelectroencephalographyieegeegmegneuroscienceneuroimaging
  Language:Python 121

• OpenNeuroOrg / openneuro

  A free and open platform for analyzing and sharing neuroimaging data

  neuroimagingneurosciencereactgraphqldatasetsbids
  Language:JavaScript 97

• BIDeveloperExtensions / bideveloperextensions

  A Visual Studio extension that enhances development functionality in Business Intelligence Development Studio (BIDS) and SQL Server Data Tools (SSDT).

  ssdtbids-helpersql-server-bissasssrsssisanalysis-servicesreporting-servicesintegration-servicesvisual-studio-extensionbibusiness-intelligencesql-server-data-toolsbi-development-studiobids
  Language:C# 87

• wiheto / teneto

  Temporal Network Tools

  bidscommunity-detectiondynamicsfmrinetwork-theorynetworksneurosciencepythontemporal-network-theorytemporal-networkstime-varying-connectivity
  Language:Python 83

• 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

  awesomebidsconnectomediffusion-mriimageprocessingmicrostructuremrimultimodalneuroimagingresting-state
  Language:Shell 76
• connectomemapper3

  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.

  bidsbids-appsbidsappbrainchuvconnectomedmridockereegfmriparcellationpipelinespythonsingularity
  Language:HTML 63

• 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.

  magnetic-resonance-imagingdiffusion-mripreprocessingbidsbids-apps
  Language:Python 63

• HALFpipe / HALFpipe

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

  neuroimagingreproducibilitypipelinemeta-analysisbidsfmri
  Language:Python 61

• 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.

  bidsfmrineuroimagingpython
  Language:MATLAB 59
• phys2bids

  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!

  acqknowledgebidsbrainwebclosemberhacktoberfestlabchartphysiological-recordingsphysiological-signalsphysiologypython3-library
  Language:Python 56

• psychoinformatics-de / remodnav

  Robust Eye Movement Detection for Natural Viewing

  eye-trackingbids
  Language:Python 54

• bids-standard / bids-matlab

  MATLAB / Octave tools for BIDS datasets

  bidsmatlaboctaveneuroimagingeegmegieegpetmriclosember
  Language:MATLAB 47

• bids-apps / MRtrix3_connectome

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

  bidsbidsappdiffusion-mrimri
  Language:Python 46

• BrkRaw / brkraw

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

  bidsbrukerdataloaderconvertersimpleitknibabel
  Language:Python 42

• IBT-FMI / SAMRI

  Small Animal Magnetic Resonance Imaging via Python.

  biomedicalfmrifunctional-connectivitydwibidsfslneuroimagingsmall-animalsrodentregistration
  Language:Python 42

• bids-apps / freesurfer

  BIDS app wrapping recon-all from FreeSurfer

  bidsbidsappanatomical-mrimripreprocessing
  Language:Python 40

• carpentries-incubator / SDC-BIDS-fMRI

  fMRI Imaging Analysis

  carpentries-incubatorpythonneuroimagingprogrammingenglishpre-alphalessonbinderfmrifmri-analysisfmri-data-analysisbidsnilearn
  Language:Jupyter Notebook 38

• bids-apps / HCPPipelines

  A BIDS App for minimal preprocessing using the HCP Pipelines

  anatomical-mribidsbidsappfunctional-mrimripreprocessing
  Language:Python 31

• bids-apps / rsHRF

  Resting state HRF estimation from BOLD-fMRI signal

  timeseriesfmri-data-analysisfmribidsbidsapp
  Language:Python 28

• bids-standard / bids-website

  Website for the Brain Imaging Data Structure standard.

  bidsbids-specificationbids-websiteneuroimaging
  Language:HTML 26

• carpentries-incubator / SDC-BIDS-sMRI

  Structural Neuroimaging Analysis in Python

  lessonenglishpre-alphacarpentries-incubatorpythonmribidsneuroimaging
  Language:Jupyter Notebook 26

• robertoostenveld / bids-tools

  Tools for dealing with neuroimaging data in the BIDS structure

  bidsneuroimagingmegmrifmrifieldtripspmfslafni
  Language:Python 26
• mialsuperresolutiontoolkit

  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.

  fetalmrisuper-resolutionworkflowbidsbids-appsitknipype
  Language:C++ 24

• carpentries-incubator / SDC-BIDS-IntroMRI

  Introduction to MRI and BIDS

  alphabidsbindercarpentries-incubatorenglishlessonmrineuroimagingpython
  Language:Jupyter Notebook 23

• carpentries-incubator / SDC-BIDS-dMRI

  Introduction to dMRI

  carpentries-incubatorneuroimagingpre-alphalessonbidspythonprogrammingdwidmridiffusion-mridipytractographyfslants
  Language:Jupyter Notebook 20

• openneuropet / PET2BIDS

  PET2BIDS helps you convert your PET data into BIDS! raw PET scanner files (e.g. ecat, dicom) and additional side file like .e.g excel sheets

  metadataconverterjsonbids
  Language:Python 19