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awesome-bids

A curated list of awesome BIDS projects, proposals, apps and resources
https://github.com/bids-standard/awesome-bids

Last synced: 4 days ago
JSON representation

Converters
- MRI
  - SAMRI
  - BIDScoin - level (raw) neuroimaging data sets to BIDS without needing to code anything. It features automatic data discovery based on header as well as filesystem information, and comes with a user-friendly GUI to add missing information and tweak the results. BIDScoin supports multiple source data formats with plugins (e.g. employing dcm2niix, spec2nii or nibabel) and allows customization of the prior knowledge about your data (allowing for fully automatic CLI data conversion if you like).
  - ![Last commit
  - BIDSconvertR - friendly workflow with graphical user interfaces. It consists of the following steps: (i) convert DICOM data to NIfTI data using dcm2niix (ii) structure this data according to the BIDS specification (iii) provide the papayaWidget viewer for inspecting the images
  - ![Last commit - 3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
  - ![Last commit - UvA/bidsify)[![PyPI version](https://badge.fury.io/py/bidsify.svg)](https://pypi.org/project/bidsify)[![Docker version](https://img.shields.io/docker/pulls/lukassnoek/bidsify.svg?style=plastic)](https://hub.docker.com/r/lukassnoek/bidsify)
  - bidskit
  - ![Last commit - MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
  - ![Last commit - dcm2niix.svg?style=plastic)](https://hub.docker.com/r/colinvdb/bmat-dcm2niix)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
  - ![Last commit - 3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
  - Clinica
  - ![Last commit - lab/clinica)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
  - ![Last commit
  - ![Last commit - MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
  - ![Last commit - 3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
  - Explore ASL - BIDS format.
  - ![Last commit
  - ezBIDS - based BIDS conversion tool with four unique features: (1) No installation or programming requirements. (2) Handling of both imaging and task events data and metadata. (3) Semi-automated inference and guidance for adherence to BIDS. (4) Multiple data management options, including download BIDS data to local system, or transfer to OpenNeuro.org or to brainlife.io.
  - HeuDiConv
  - ![Last commit - Apache_2.0-blue.svg?style=plastic)](https://opensource.org/licenses/Apache-2.0)
  - ![Last commit - bids-output)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
  - ![Last commit - imaging/mercure-dcm2bids)[![Docker version](https://img.shields.io/docker/pulls/mercureimaging/mercure-dcm2bids.svg?style=plastic)](https://hub.docker.com/r/mercureimaging/mercure-dcm2bids)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
  - ![Last commit - 3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
  - ![Last commit - standard/openfmri2bids)
  - ![Last commit - MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
  - ReproIn - based turnkey solution: a setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners.
  - ![Last commit - MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
  - SAMRI
  - Autobids
  - bidsify - compatible datasets.
  - BMAT
  - BrkRaw
  - dac2bids
  - Data2Bids
  - Dcm2Bids
  - Horos (Osirix) export plugin
  - mercure-dcm2bids - source DICOM orchestration platform that can integrate containerized apps into clinical workflows. It has a graphical user interface making it easy to setup and manage BIDS configurations for multiple protocols. The Dcm2Bids tool is used for conversion.
  - niix2bids
  - OpenfMRI2BIDS
  - PET2BIDS
  - XNAT2BIDS - compatible output (nii+json).
  - - commit/kamillipi/2bids?style=plastic)](https://github.com/kamillipi/2bids)
  - ![Last commit - Institute/bidscoin)[![PyPI version](https://badge.fury.io/py/bidscoin.svg)](https://pypi.org/project/bidscoin)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
- MEEG
  - ![Last commit - MEG-Research/Biscuit)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
  - EEGLAB - MATLAB-tools'>See plugins</a>
  - ![Last commit
  - ![Last commit - 3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
  - MNE-BIDS - BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.
  - sovabids
  - ![Last commit
  - ![Last commit - 2.0](https://img.shields.io/badge/License-GPLv2-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-2.0)
  - Biscuit
  - - commit/aces/EEG2BIDS?style=plastic)](https://github.com/aces/EEG2BIDS)
  - BIDSme
  - FieldTrip - data2bids
- physiological
- others
  - ![Last commit - eprime)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
  - ![Last commit
  - ![Last commit
  - ![Last commit - MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
  - convert-eprime - Prime files to CSVs. Not currently being developed.
  - DCM2NIIx
  - DICM2NII
  - sim2bids
BIDS Extension Proposals (BEP)
- raw
  - BEP042
  - BEP004
  - BEP020
  - BEP022
  - BEP024
  - BEP026
  - BEP032
  - BEP033
  - BEP036
  - BEP037 - Invasive Brain Stimulation
  - BEP038
  - BEP039 - based networks
  - BEP040
- others
  - documentation regarding the BIDS extension proposal process
- derivative
  - BEP011
  - BEP012
  - BEP014
  - BEP016
  - BEP017
  - BEP021
  - BEP023
  - BEP034
  - BEP035 - analyses with non-compliant derivatives
  - BEP041
BIDS Apps
- others
  - ![Docker version
  - BIDS Apps website
  - ![Docker version
  - ![Docker version
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  - ![Docker version
  - ![Docker version - srm)
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  - ![Docker version
  - ![Docker version
  - ![Docker version - bidsapp)
  - ![Docker version
  - ![Docker version
  - ![Docker version
  - ![Docker version - flex)
  - ![Docker version
  - ![Docker version
  - ![Docker version
  - ![Docker version
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  - ![Docker version
  - ![Docker version
  - ![Docker version - bids)
  - afni_proc
  - antsCorticalThickness
  - baracus
  - brainiak-srm - app version of the Shared Response Model (SRM) of BrainIAK
  - BrainSuite
  - BROCCOLI
  - CPAC - PAC)
  - DPARSF
  - freesurfer - all from FreeSurfer
  - giga_connectome - App to extract signal from a parcellation with nilearn, typically useful in a context of resting-state data processing.
  - HCPPipelines
  - hyperalignment - dimensional space of voxels/features.
  - mindboggle
  - MRtrix3_connectome - subject connection density normalisation, using the MRtrix3 software package.
  - ndmg
  - nipypelines
  - oppni
  - PyMVPA
  - QAP
  - rsHRF - fMRI signal
  - SPM
  - tracula - sectional as well as longitudinal (multi session) input data.
  - connectomemapper3 - resolution brain parcellation with corresponding connection matrices.
  - bidsMReye
  - bidspm
  - fmriprep-fake
  - funcmasker-flex - net brain masking of fetal bold MRI
  - hippunfold
  - mialsuperresolutiontoolkit - 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.
  - micapipe - mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
  - dmriprep - to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
  - fmriprep - to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
  - mriqc
  - nibabies
  - nirodents
  - smriprep
  - BIDSonym - anonymization of neuroimaging data
  - aslprep
  - qsiprep
  - xcp_d - processing of fMRIPrep, nibabies, HCP, and DCAN BOLD derivatives for functional connectivity analysis
  - fitlins
  - multiscalebrainparcellator - Scale Brain Parcellator, part of the Connectome Mapping Toolkit (CMTK), is a BIDS App that implements a full anatomical MRI processing pipeline, from raw T1w data to structural brain parcellation at five different scales.
  - gift-bids
Documentation
Social media
- YouTube
- Twitter / X
- Mastodon
- Bluesky
- anchor
Community
Datasets
- OpenNeuro
- BIDS examples
Tools
- others
  - babs
  - ![Last commit
  - bids stats model - standard.github.io/stats-models/index.html)
  - ![PyPI version
  - bids-cfood
  - ![Last commit - standard/bids-matlab)
  - ![Last commit - standard-phantoms/bids-pydantic) [![PyPI version](https://badge.fury.io/py/BIDS-pydantic.svg)](https://pypi.org/project/BIDS-pydantic/)
  - ![Last commit - Gau/bids2cite)
  - ![Last commit
  - ![Last commit - MEG-Research/BIDSHandler)
  - clpipe
  - ![Last commit
  - cuBIDS
  - ![Last commit
  - ![Last commit - Labs/file-mapper)
  - ![Last commit - g/BIDS)
  - Hierarchical Event Descriptors (HED) python tools
  - ![Last commit - standard/hed-python) [![PyPI version](https://badge.fury.io/py/hedtools.svg)](https://pypi.org/project/hedtools/)
  - Lead-DBS
  - mne-bids
  - neurobagel annotate
  - neurobagel query - demographic and imaging parameters.
  - nipopy
  - ![Last commit
  - PRFmodel
  - ![Last commit
  - ![Last commit - standard/pybids) [![PyPI version](https://badge.fury.io/py/pybids.svg)](https://pypi.org/project/pybids/)
  - ![Last commit
  - spm_2_bids
  - ![Last commit - lln-lab/spm_2_bids)
  - ![Last commit - tools/mne-bids)
  - bids-matlab
  - BIDS-pydantic - pydantic-models](https://pypi.org/project/BIDS-pydantic-models/).
  - bids2cite
  - bidser
  - BIDSHandler
  - File mapper
  - ![Last commit - standard/hed-Python) [![PyPI version](https://badge.fury.io/py/hedtools.svg)](https://pypi.org/project/hedtools/)
  - rbids
  - psychopy-bids
  - Brainstorm
Code
- others
Publications
- derivative
  - our zotero group
Validation
- others
  - use it in a browser
  - install the package

Programming Languages

Python 44 MATLAB 7 HTML 5 Shell 5 R 2 Dockerfile 2 JavaScript 2 C++ 2 Jupyter Notebook 2 Objective-C 1

Ecosyste.ms: Awesome

awesome-bids

Converters

MRI

MEEG

physiological

others

BIDS Extension Proposals (BEP)

raw

others

derivative

BIDS Apps

others

Documentation

Social media

Community

Datasets

Tools

others

Code

others

Publications

derivative

Validation

others