{"id":50316399,"url":"https://github.com/bids-apps/example","last_synced_at":"2026-05-29T00:03:13.953Z","repository":{"id":61668413,"uuid":"64416917","full_name":"bids-apps/example","owner":"bids-apps","description":"This an example app that can serve as a template.","archived":false,"fork":false,"pushed_at":"2026-03-16T10:01:39.000Z","size":131,"stargazers_count":17,"open_issues_count":3,"forks_count":33,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-04-03T17:32:48.651Z","etag":null,"topics":["bids","bids-apps"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1371/journal.pcbi.1005209","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","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":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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2016-07-28T17:58:07.000Z","updated_at":"2026-03-16T10:01:37.000Z","dependencies_parsed_at":"2024-04-09T07:35:07.342Z","dependency_job_id":"46fe0c49-0edd-475d-b018-f85ce62493d1","html_url":"https://github.com/bids-apps/example","commit_stats":null,"previous_names":[],"tags_count":7,"template":true,"template_full_name":null,"purl":"pkg:github/bids-apps/example","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fexample","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fexample/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fexample/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fexample/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bids-apps","download_url":"https://codeload.github.com/bids-apps/example/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fexample/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33631002,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-05-28T02:00:06.440Z","response_time":99,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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","bids-apps"],"created_at":"2026-05-29T00:03:10.821Z","updated_at":"2026-05-29T00:03:13.944Z","avatar_url":"https://github.com/bids-apps.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## An example BIDS App (template repository)\nEvery BIDS App needs to follow a minimal set of command arguments common across\nall of the Apps. This allows users and developers to easily use and integrate\nBIDS Apps with their environment.\n\nThis is a minimalist example of a BIDS App consisting of a Dockerfile and a simple\nentry point script (written in this case in Python) accepting the standard BIDS\nApps command line arguments. This repository can be used as a template for new BIDS Apps.\n\nFor more information about the specification of BIDS Apps see [here](https://docs.google.com/document/d/1E1Wi5ONvOVVnGhj21S1bmJJ4kyHFT7tkxnV3C23sjIE/).\n\n### Description\nThis is a placeholder for a short description explaining to the user what your App will doing.\n\n### Documentation\nProvide a link to the documentation of your pipeline.\n\n### How to report errors\nProvide instructions for users on how to get help and report errors.\n\n### Acknowledgments\nDescribe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)\n\n### Usage\nThis App has the following command line arguments:\n\n\tusage: run.py [-h] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--skip_bids_validator] [-v]\n\t\t\t\tbids_dir output_dir {participant,group}\n\n\tExample BIDS App entrypoint script.\n\n\tpositional arguments:\n\tbids_dir              The directory with the input dataset formatted according to the BIDS standard.\n\toutput_dir            The directory where the output files should be stored. If you are running group level analysis this folder should\n\t\t\t\t\t\t\tbe prepopulated with the results of theparticipant level analysis.\n\t{participant,group}   Level of the analysis that will be performed. Multiple participant level analyses can be run independently (in\n\t\t\t\t\t\t\tparallel) using the same output_dir.\n\n\toptions:\n\t-h, --help            show this help message and exit\n\t--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]\n\t\t\t\t\t\t\tThe label(s) of the participant(s) that should be analyzed. The label corresponds to sub-\u003cparticipant_label\u003e from\n\t\t\t\t\t\t\tthe BIDS spec (so it does not include \"sub-\"). If this parameter is not provided all subjects should be analyzed.\n\t\t\t\t\t\t\tMultiple participants can be specified with a space separated list.\n\t--skip_bids_validator\n\t\t\t\t\t\t\tWhether or not to perform BIDS dataset validation\n\t-v, --version         show program's version number and exit\n\nTo run it in participant level mode (for one participant):\n\n    docker run -i --rm \\\n\t\t-v /Users/filo/data/ds005:/bids_dataset:ro \\\n\t\t-v /Users/filo/outputs:/outputs \\\n\t\tbids/example \\\n\t\t/bids_dataset /outputs participant --participant_label 01\n\nAfter doing this for all subjects (potentially in parallel), the group level analysis\ncan be run:\n\n    docker run -i --rm \\\n\t\t-v /Users/filo/data/ds005:/bids_dataset:ro \\\n\t\t-v /Users/filo/outputs:/outputs \\\n\t\tbids/example \\\n\t\t/bids_dataset /outputs group\n\n### Special considerations\nDescribe whether your app has any special requirements. For example:\n\n- Multiple map reduce steps (participant, group, participant2, group2 etc.)\n- Unusual memory requirements\n- etc.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2Fexample","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbids-apps%2Fexample","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2Fexample/lists"}