{"id":18143857,"url":"https://github.com/remi-gau/bids_workshop","last_synced_at":"2026-02-02T06:03:13.768Z","repository":{"id":60262305,"uuid":"535352805","full_name":"Remi-Gau/bids_workshop","owner":"Remi-Gau","description":null,"archived":false,"fork":false,"pushed_at":"2024-10-08T08:15:20.000Z","size":2243,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-06T19:39:57.168Z","etag":null,"topics":["bids","mri","neuroimaging","workshop"],"latest_commit_sha":null,"homepage":"https://remi-gau.github.io/bids_workshop/","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Remi-Gau.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-09-11T16:12:59.000Z","updated_at":"2024-10-08T08:15:22.000Z","dependencies_parsed_at":"2024-04-09T07:33:57.191Z","dependency_job_id":"97321fd6-3141-406f-ab88-3a202eabb9e3","html_url":"https://github.com/Remi-Gau/bids_workshop","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/Remi-Gau/bids_workshop","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Remi-Gau%2Fbids_workshop","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Remi-Gau%2Fbids_workshop/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Remi-Gau%2Fbids_workshop/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Remi-Gau%2Fbids_workshop/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Remi-Gau","download_url":"https://codeload.github.com/Remi-Gau/bids_workshop/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Remi-Gau%2Fbids_workshop/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261789229,"owners_count":23209774,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bids","mri","neuroimaging","workshop"],"created_at":"2024-11-01T19:09:01.360Z","updated_at":"2026-02-02T06:03:08.725Z","avatar_url":"https://github.com/Remi-Gau.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7110398.svg)](https://doi.org/10.5281/zenodo.7110398)\n[![License: CC BY 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)\n\n\u003ch2 id=\"TOC\"\u003e Table of content \u003c/h2\u003e\n\n- [Content](#content)\n  - [\"Theory\": The BIDS data management principles](#theory-the-bids-data-management-principles)\n  - [BIDS conversion by hand](#bids-conversion-by-hand)\n  - [Automated BIDS conversion](#automated-bids-conversion)\n  - [Using BIDS apps](#using-bids-apps)\n- [Notes](#notes)\n- [Not covered](#not-covered)\n- [Pre-requisites](#pre-requisites)\n- [Softwares to install](#softwares-to-install)\n  - [Visual studio code](#visual-studio-code)\n  - [Python](#python)\n  - [Dcm2niix](#dcm2niix)\n  - [BIDScoin](#bidscoin)\n  - [Docker](#docker)\n  - [Optional: VSCode extensions](#optional-vscode-extensions)\n\n\u003cbr\u003e\n\nThe\n[brain imaging data structure (BIDS)](https://bids-specification.readthedocs.io/en/latest/)\nis fast becoming the main standard to organize raw neuroimaging data.\n\nHaving your data in BIDS offers many downstream advantages to users: use of\nstandardized pipelines, facilitate data sharing and reuse…\n\nBut getting your data to be BIDS compliant and using can also be source of much\nfrustration. Especially when it is the first time you are dealing with\nneuroimaging data.\n\nThis workshop aims to lessen the frustration level you will experience when\ncurating and using your data.\n\n## Content\n\nThis workshop is divided in 4 parts.\n\n### \"Theory\": The BIDS data management principles\n\nRemembering and following a rule is always easier when you understand why the\nrule was put in place: this first part explains some of the reasons why BIDS is\nstructured the way it is.\n\nSlides are available [here](https://osf.io/zxp9e).\n\n### BIDS conversion by hand\n\nUsing automated BIDS converters is recommended, but using them too early can\nturn BIDS into a black box. So doing the conversion of one small dataset by hand\nhelps better understand \"what data/information goes where\".\n\nTo do this part you can follow along the [\"cookbook\" page](./cookbook.md).\n\n### Automated BIDS conversion\n\nConverting large numbers files quickly becomes impractical and error prone when\nby hand. So learning to use a bids converters should be the next logical step.\n\nHere are a few [intro slides](https://osf.io/zcfne).\n\nTo do this part you can follow along the\n[\"bids_conversion\" page](./bids_conversion.md).\n\n### Using BIDS apps\n\nTo wrap up it is good use BIDS applications on the dataset we have created.\n\nTo do this part you can follow along the [\"bids_app\" page](./bids_apps.md).\n\n## Notes\n\nThis workshop is mostly geared for the MRI part of BIDS but many principles of\nBIDS apply to all imaging modalities.\n\nWe will finish the workshop with a \"ask me anything about BIDS\" session where\nyou can come with more specific questions as they relate to your use case.\n\n## Not covered\n\nThe follow issues are be covered in this workshop:\n\n- Where to store data\n- Ethical issues around data sharing (notably GDPR)\n- Data version control (for example with Datalad)\n\n## Pre-requisites\n\n- Coding experience: `none`\n- Prior experience with neuroimaging data: `none`\n- Data: feel free to bring your own dataset to work on but if you do not have\n  data, some data is provided.\n- Data type\n  - fMRI and resting state\n  - Anat\n  - DTI\n  - Physio / eyetracking\n\n## Softwares to install\n\nBelow is a list of softwares, you will need to install to follow the workshop.\n\nIf you have troubles when installing any of these, please contact me before the\nworkshop and come to the \"open-office\" that will happen before the workshop`\nstarts.\n\nFor more details and trouble shooting eventual installation problems, check the\npage dedicated to your operating system:\n\n- [Windows](./troubleshooting_install/win.md)\n- [MacOs](./troubleshooting_install/macos.md)\n- [Linux](./troubleshooting_install/linux.md)\n\n### Visual studio code\n\nInstall [Visual studio code](https://code.visualstudio.com/) as your code\neditor.\n\n### Python\n\nIf you have never used Python before, install it with the installer adapted to\nyour system (32 vs 64 bit, Apple M1 vs Intel...)\n[miniconda](https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links).\n\n- For Windows, you should only have to run the `.exe` installer.\n- For MacOs, you can try to simply use the `.pkg` installer adapted for your\n  computer. If that does not work try the method described\n  [here](./troubleshooting_install/macos.md#python).\n- For Linux, you should use the bash installer as described\n  [here](./troubleshooting_install/linux.md#python).\n\n### Dcm2niix\n\nInstall the DICOM to Nifti converter:\n[Dcm2niix](https://github.com/rordenlab/dcm2niix#install)\n\nIf installing with\n[the correct installer for your operating system](https://github.com/rordenlab/dcm2niix/releases)\ndoes not work, try installing\n[MRIcroGL](https://www.nitrc.org/frs/?group_id=889) that should ship with\n`Dcm2niix`.\n\n### BIDScoin\n\nInstall the [BIDScoin converter](https://bidscoin.readthedocs.io/en/stable/)\n\nIf you have installed Miniconda properly, you should only need to open a\nTerminal (for Linux and MacOS) or an Anaconda Powershell Prompt (for Windows)\nand type:\n\n```bash\npip install bidscoin\n```\n\nBIDScoin will need to be able to find the `dcm2niix` executable that you\ninstalled on your computer.\n\nTo test this you can run the following command in a terminal:\n\n```bash\nbidseditor .\n```\n\nThis will ask you to open a `bidsmap.yml` file, you can click `cancel` to load\nthe default values. You can then go to the `Options` tab where there is a\n`dcm2niix2bids - plugin` section.\n\n\u003cimg  src=\"./images/bidscoin_dcm2nii.png\"\n      alt=\"bidscoin_dcm2nii\"\n      width=\"80%\"\n      style=\"padding-left: 10%; border-color: black \"/\u003e\n\nThe `command` part of this section refers to what command bidscoin must run to\nuse `dcm2niix`.\n\nThis should be the path to the `dcm2niix` executable on your computer.\n\n- For example on Windows: `\"C:\\Program Files\\dcm2niix\\bin\\dcm2niix.exe\"`\n- For Linux or Mac: `/usr/local/bin/dcm2niix`\n\nOn Mac or Linux, you can check the path to `dcm2niix` by running the following:\n\n```bash\nwhich dcm2niix\n```\n\nMore details on the\n[bidscoin documentation](https://bidscoin.readthedocs.io/en/stable/options.html#dcm2niix2bids-plugin).\n\n### Docker\n\nInstall [Docker Desktop](https://www.docker.com/)\n\nTo check that things are properly installed, open a Terminal (for Linux and\nMacOS) or an Anaconda Powershell Prompt (for Windows) and type the following to\nmake sure everything works:\n\n```bash\ndocker run hello-world\n```\n\nA brief introductory message should then be printed to the screen.\n\nOnce you have done this, you can download the \"images\" of 2 bids app: be careful\nthat they may take quite a bit of space on your hard drive (about 12 Go each),\nso make sure you have enough free space.\n\n- download the latest version of the\n  [MRIQC](https://mriqc.readthedocs.io/en/latest/) docker image for quality\n  control.\n\n```bash\ndocker pull nipreps/mriqc:latest\n```\n\n- download the latest version of the [fmriprep](https://fmriprep.org/en/stable/)\n  docker image for preprocessing.\n\n```bash\ndocker pull nipreps/fmriprep:latest\n```\n\nNote that to run fmriprep, you will also need a license for Freesurfer that you\ncan get for free here: https://surfer.nmr.mgh.harvard.edu/registration.html.\n\n### Optional: VSCode extensions\n\nThose extensions are not needed but may help you when dealing with python code\nor json files in general.\n\n\u003e ars. 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