{"id":13676377,"url":"https://github.com/bids-apps/giga_connectome","last_synced_at":"2026-05-29T00:03:41.384Z","repository":{"id":82584320,"uuid":"575450568","full_name":"bids-apps/giga_connectome","owner":"bids-apps","description":"generate connectome from fMRIPrep outputs","archived":false,"fork":false,"pushed_at":"2025-04-21T06:37:02.000Z","size":926,"stargazers_count":7,"open_issues_count":26,"forks_count":6,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-21T07:42:56.721Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://giga-connectome.readthedocs.io/en/stable/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bids-apps.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-12-07T14:42:00.000Z","updated_at":"2025-04-21T06:37:04.000Z","dependencies_parsed_at":"2025-04-11T15:13:26.524Z","dependency_job_id":"2c95363f-04ab-40ff-8bfb-5a2f1f519a3b","html_url":"https://github.com/bids-apps/giga_connectome","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fgiga_connectome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fgiga_connectome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fgiga_connectome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fgiga_connectome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bids-apps","download_url":"https://codeload.github.com/bids-apps/giga_connectome/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251455888,"owners_count":21592256,"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":[],"created_at":"2024-08-02T13:00:24.383Z","updated_at":"2026-05-29T00:03:41.378Z","avatar_url":"https://github.com/bids-apps.png","language":"Python","funding_links":[],"categories":["BIDS Apps","Python"],"sub_categories":["others"],"readme":"[![DOI](https://joss.theoj.org/papers/10.21105/joss.07061/status.svg)](https://doi.org/10.21105/joss.07061)\n[![All Contributors](https://img.shields.io/github/all-contributors/bids-apps/giga_connectome?color=ee8449\u0026style=flat)](#contributors)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![codecov](https://codecov.io/gh/bids-apps/giga_connectome/branch/main/graph/badge.svg?token=P4EGV7NKZ8)](https://codecov.io/gh/bids-apps/giga_connectome)\n[![.github/workflows/test.yml](https://github.com/bids-apps/giga_connectome/actions/workflows/test.yml/badge.svg)](https://github.com/bids-apps/giga_connectome/actions/workflows/test.yml)\n[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/bids-apps/giga_connectome/main.svg)](https://results.pre-commit.ci/latest/github/bids-apps/giga_connectome/main)\n[![Documentation Status](https://readthedocs.org/projects/giga-connectome/badge/?version=stable)](https://giga-connectome.readthedocs.io/en/latest/?badge=stable)\n![https://github.com/psf/black](https://img.shields.io/badge/code%20style-black-000000.svg)\n[![Docker pulls](https://img.shields.io/docker/pulls/bids/giga_connectome)](https://hub.docker.com/r/bids/giga_connectome/tags)\n\n# giga-connectome\n\nThis is a BIDS-App to extract signal from a parcellation with `nilearn`,\ntypically useful in a context of resting-state data processing.\n\nYou can read our [JOSS paper](https://doi.org/10.21105/joss.07061) for the background of the project and the details of implementations.\n\n## Description\n\nFunctional connectivity is a common approach in analysing resting state fMRI data.\nThe Python tool `Nilearn` provides utilities to extract and denoise time-series on a parcellation.\n`Nilearn` also has methods to compute functional connectivity.\nWhile `Nilearn` provides useful methods to generate connectomes,\nthere is no standalone one stop solution to generate connectomes from `fMRIPrep` outputs.\n`giga-connectome` (a BIDS-app!) combines `Nilearn` and `TemplateFlow` to denoise the data, generate timeseries,\nand most critically `giga-connectome` generates functional connectomes directly from `fMRIPrep` outputs.\nThe workflow comes with several built-in denoising strategies and\nthere are several choices of atlases (MIST, Schaefer 7 networks, DiFuMo, Harvard-Oxford).\nUsers can customise their own strategies and atlases using the configuration json files.\n\n\n## Supported `fMRIPrep` versions\n\n`giga-connectome` fully supports outputs of fMRIPrep LTS (long-term support) 20.2.x.\n\nFor `fMRIPrep` 23.1.0 and later, `giga-connectome` does not support ICA-AROMA denoising,\nas the strategy is removed from the `fMRIPrep` workflow.\n\n## Quick start\n\nPull from `Dockerhub` (Recommended)\n\n```bash\ndocker pull bids/giga_connectome:latest\ndocker run -ti --rm bids/giga_connectome --help\n```\n\nIf you want to get the bleeding-edge version of the app,\npull the `unstable` version.\n\n```bash\ndocker pull bids/giga_connectome:unstable\n```\n\n## How to report errors\n\nPlease use the [GitHub issue](https://github.com/bids-apps/giga_connectome/issues) to report errors.\nCheck out the open issues first to see if we're already working on it.\nIf not, [open up a new issue](https://github.com/bids-apps/giga_connectome/issues/new)!\n\n## How to contribute\n\nYou can review open [issues]((https://github.com/bids-apps/giga_connectome/issues)) that we are looking for help with.\nIf you submit a new pull request please be as detailed as possible in your comments.\nIf you have any question related how to create a pull request, you can check our [documentation for contributors](https://giga-connectome.readthedocs.io/en/latest/contributing.html).\n\n## Contributors\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --\u003e\n\u003c!-- prettier-ignore-start --\u003e\n\u003c!-- markdownlint-disable --\u003e\n\u003ctable\u003e\n  \u003ctbody\u003e\n    \u003ctr\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://wanghaoting.com/\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/13743617?v=4?s=100\" width=\"100px;\" alt=\"Hao-Ting Wang\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eHao-Ting Wang\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#ideas-htwangtw\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"#research-htwangtw\" title=\"Research\"\u003e🔬\u003c/a\u003e \u003ca href=\"#code-htwangtw\" title=\"Code\"\u003e💻\u003c/a\u003e \u003ca href=\"#test-htwangtw\" title=\"Tests\"\u003e⚠️\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/Hyedryn\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/5383293?v=4?s=100\" width=\"100px;\" alt=\"Quentin Dessain\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eQuentin Dessain\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#userTesting-Hyedryn\" title=\"User Testing\"\u003e📓\u003c/a\u003e \u003ca href=\"#platform-Hyedryn\" title=\"Packaging/porting to new platform\"\u003e📦\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/clarkenj\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/57987005?v=4?s=100\" width=\"100px;\" alt=\"Natasha Clarke\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eNatasha Clarke\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#userTesting-clarkenj\" title=\"User Testing\"\u003e📓\u003c/a\u003e \u003ca href=\"#example-clarkenj\" title=\"Examples\"\u003e💡\u003c/a\u003e \u003ca href=\"#bug-clarkenj\" title=\"Bug reports\"\u003e🐛\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://remi-gau.github.io/\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/6961185?v=4?s=100\" width=\"100px;\" alt=\"Remi Gau\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eRemi Gau\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#infra-Remi-Gau\" title=\"Infrastructure (Hosting, Build-Tools, etc)\"\u003e🚇\u003c/a\u003e \u003ca href=\"#maintenance-Remi-Gau\" title=\"Maintenance\"\u003e🚧\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"http://simexp.github.io\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/1670887?v=4?s=100\" width=\"100px;\" alt=\"Lune Bellec\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eLune Bellec\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#ideas-pbellec\" title=\"Ideas, Planning, \u0026 Feedback\"\u003e🤔\u003c/a\u003e \u003ca href=\"#financial-pbellec\" title=\"Financial\"\u003e💵\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/shnizzedy\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/5974438?v=4?s=100\" width=\"100px;\" alt=\"Jon Cluce\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eJon Cluce\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#bug-shnizzedy\" title=\"Bug reports\"\u003e🐛\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/emullier\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/43587002?v=4?s=100\" width=\"100px;\" alt=\"Emeline Mullier\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eEmeline Mullier\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#bug-emullier\" title=\"Bug reports\"\u003e🐛\u003c/a\u003e\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://jdkent.github.io/\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/12564882?v=4?s=100\" width=\"100px;\" alt=\"James Kent\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eJames Kent\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#bug-jdkent\" title=\"Bug reports\"\u003e🐛\u003c/a\u003e \u003ca href=\"#doc-jdkent\" title=\"Documentation\"\u003e📖\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://marcel.stimberg.info\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/1381982?v=4?s=100\" width=\"100px;\" alt=\"Marcel Stimberg\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eMarcel Stimberg\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"#userTesting-mstimberg\" title=\"User Testing\"\u003e📓\u003c/a\u003e \u003ca href=\"#doc-mstimberg\" title=\"Documentation\"\u003e📖\u003c/a\u003e \u003ca href=\"#bug-mstimberg\" title=\"Bug reports\"\u003e🐛\u003c/a\u003e\u003c/td\u003e\n    \u003c/tr\u003e\n  \u003c/tbody\u003e\n\u003c/table\u003e\n\n\u003c!-- markdownlint-restore --\u003e\n\u003c!-- prettier-ignore-end --\u003e\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:END --\u003e\n\n## Acknowledgements\n\nPlease cite the following paper if you are using `giga-connectome` in your work:\n```bibtex\n@article{Wang2025,\n    doi = {10.21105/joss.07061},\n    url = {https://doi.org/10.21105/joss.07061},\n    year = {2025}, publisher = {The Open Journal},\n    volume = {10},\n    number = {110},\n    pages = {7061},\n    author = {Hao-Ting Wang and Rémi Gau and Natasha Clarke and Quentin Dessain and Lune Bellec},\n    title = {Giga Connectome: a BIDS-app for time series and functional connectome extraction},\n    journal = {Journal of Open Source Software}\n}\n```\n\n`giga-connectome` uses `nilearn` under the hood,\nhence please consider cite `nilearn` using the Zenodo DOI:\n\n```bibtex\n@software{Nilearn,\n    author = {Nilearn contributors},\n    license = {BSD-4-Clause},\n    title = {{nilearn}},\n    url = {https://github.com/nilearn/nilearn},\n    doi = {https://doi.org/10.5281/zenodo.8397156}\n}\n```\nNilearn’s Research Resource Identifier (RRID) is: [RRID:SCR_001362][]\n\nWe acknowledge all the [nilearn developers][]\nas well as the [BIDS-Apps team][]\n\nThis is a Python project packaged according to [Contemporary Python Packaging - 2023][].\n\n[Contemporary Python Packaging - 2023]: https://effigies.gitlab.io/posts/python-packaging-2023/\n[RRID:SCR_001362]: https://rrid.site/data/record/nlx_144509-1/SCR_001362/resolver?q=nilearn\u0026l=nilearn\u0026i=rrid:scr_001362\n[nilearn developers]: https://github.com/nilearn/nilearn/graphs/contributors\n[BIDS-Apps team]:https://github.com/orgs/BIDS-Apps/people\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2Fgiga_connectome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbids-apps%2Fgiga_connectome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2Fgiga_connectome/lists"}