{"id":13676318,"url":"https://github.com/bids-apps/afni_proc","last_synced_at":"2026-05-29T00:03:32.540Z","repository":{"id":73504498,"uuid":"113127138","full_name":"bids-apps/afni_proc","owner":"bids-apps","description":"prototype AFNI bids app implmenting participant level preprocessing with afni_proc.py","archived":false,"fork":false,"pushed_at":"2026-03-16T10:01:00.000Z","size":83,"stargazers_count":2,"open_issues_count":5,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-03-16T20:52:13.064Z","etag":null,"topics":["bids","bidsap","mri","preprocessing"],"latest_commit_sha":null,"homepage":"","language":"HTML","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":"2017-12-05T03:27:34.000Z","updated_at":"2026-03-16T10:00:57.000Z","dependencies_parsed_at":null,"dependency_job_id":"6f1330e7-b1e0-4584-b0a5-d27049cdd0d9","html_url":"https://github.com/bids-apps/afni_proc","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/bids-apps/afni_proc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fafni_proc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fafni_proc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fafni_proc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fafni_proc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bids-apps","download_url":"https://codeload.github.com/bids-apps/afni_proc/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fafni_proc/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","bidsap","mri","preprocessing"],"created_at":"2024-08-02T13:00:22.718Z","updated_at":"2026-05-29T00:03:32.515Z","avatar_url":"https://github.com/bids-apps.png","language":"HTML","funding_links":[],"categories":["BIDS Apps"],"sub_categories":["others"],"readme":"## Prototype AFNI preprocessing app\n\n### Description\n\nThis is a prototype AFNI bids app implmenting participant level preprocessing\nwith afni_proc.py. This pipeline is currently doing temporal alignment,\nnonlinear registration to standard space, bluring of 4 mm, masking, and scaling\nfor all epis in the input bids dataset using the following afni proc command:\n\n```bash\nafni_proc.py -subj_id {subj_id} \\\n  -script proc.bids -scr_overwrite -out_dir {out_dir} \\\n  -blocks tshift align tlrc volreg blur mask scale \\\n  -copy_anat {anat_path} -tcat_remove_first_trs 0 \\\n  -dsets {epi_paths} -align_opts_aea -cost lpc+ZZ -giant_move \\\n  -tlrc_base MNI152_T1_2009c+tlrc -tlrc_NL_warp \\\n  -volreg_align_to MIN_OUTLIER \\\n  -volreg_align_e2a -volreg_tlrc_warp -blur_size 4.0 -bash\n```\n\n### Documentation\n\nDocumenation for afni_proc.py is available\n[here](https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html).\n\n### How to report errors\n\nSpecific issues with this BIDS App should be reported on its\n[issues page](https://github.com/nih-fmrif/afni_proc_BIDS_app/issues). AFNI\nissues should be posted to the\n[AFNI Message Board](https://afni.nimh.nih.gov/afni/community/board/list.php?1)\n\n### Acknowledgements\n\nPlease cite the 1996 paper if you use AFNI: Cox RW (1996) AFNI: Software for\nanalysis and visualization of functional magnetic resonance neuroimages. Comput\nBiomed Res 29(3):162–173\n\n### Usage\n\nThis App has the following command line arguments:\n\n    \tusage: run.py [-h]\n    \t              [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]\n    \t              bids_dir output_dir\n\n    \tExample BIDS App entry point script.\n\n    \tpositional arguments:\n    \t  bids_dir              The directory with the input dataset formatted\n    \t                        according to the BIDS standard.\n    \t  output_dir            The directory where the output files should be stored.\n    \t                        If you are running a group level analysis, this folder\n    \t                        should be prepopulated with the results of\n    \t                        the participant level analysis.\n    \t  {participant}         Level of the analysis that will be performed. Multiple\n                                participant level analyses can be run independently\n                                (in parallel). Only \"participant\" is currently supported.\n\n    \toptional arguments:\n    \t  -h, --help            show this help message and exit\n    \t  --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]\n    \t                        The label(s) of the participant(s) that should be\n    \t                        analyzed. The label corresponds to\n    \t                        sub-\u003cparticipant_label\u003e from the BIDS spec (so it does\n    \t                        not include \"sub-\"). If this parameter is not provided\n    \t                        all subjects will be analyzed. Multiple participants\n    \t                        can be specified with a space separated list.\n    \t  --afni_proc AFNI_PROC\n                                Optional: command string for afni proc. Parameters\n                                that vary by subject should be encapsulated in curly\n                                braces and must all be included {subj_id},\n                                {out_dir}, {anat_path}, or {epi_paths}.-script option\n                                is added automatically so don't add it to the command. The first\n                                _T1w for each subject will currently be used as the\n                                anat.All of the _bold will be used as the\n                                functionals.Example:--afni_proc=\"-subj_id {subj_id} -scr_overwrite -out_dir {out_dir} -blocks tshift align tlrc volreg blur mask scale -copy_anat {anat_path} -tcat_remove_first_trs 0 -dsets {epi_paths} -align_opts_aea -cost lpc+ZZ -giant_move -tlrc_base MNI152_T1_2009c+tlrc -tlrc_NL_warp -volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -blur_size 4.0 -bash\"\n\nTo run it in participant level mode (for one participant):\n\n```bash\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```\n\n### Special considerations\n\nThis is a very early prototype. More functionality is likely coming. Expect\nbreaking changes.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2Fafni_proc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbids-apps%2Fafni_proc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2Fafni_proc/lists"}