{"id":13676338,"url":"https://github.com/bids-apps/brainiak-srm","last_synced_at":"2026-05-29T00:03:14.420Z","repository":{"id":73504502,"uuid":"64772444","full_name":"bids-apps/brainiak-srm","owner":"bids-apps","description":"This is the BIDS-app version of the Shared Response Model (SRM) of BrainIAK","archived":false,"fork":false,"pushed_at":"2026-03-09T11:26:35.000Z","size":50,"stargazers_count":1,"open_issues_count":0,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2026-03-09T16:17:52.562Z","etag":null,"topics":["bids","bidsapp"],"latest_commit_sha":null,"homepage":"","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":"2016-08-02T16:12:49.000Z","updated_at":"2026-03-09T11:26:39.000Z","dependencies_parsed_at":"2023-11-14T11:28:37.693Z","dependency_job_id":"c22ab6b7-8ea5-4fa1-918e-1b74b6165a7e","html_url":"https://github.com/bids-apps/brainiak-srm","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/bids-apps/brainiak-srm","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fbrainiak-srm","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fbrainiak-srm/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fbrainiak-srm/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fbrainiak-srm/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bids-apps","download_url":"https://codeload.github.com/bids-apps/brainiak-srm/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2Fbrainiak-srm/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","bidsapp"],"created_at":"2024-08-02T13:00:23.201Z","updated_at":"2026-05-29T00:03:14.404Z","avatar_url":"https://github.com/bids-apps.png","language":"Python","funding_links":[],"categories":["BIDS Apps"],"sub_categories":["others"],"readme":"## BrainIAK-SRM BIDS app\n\nShared Response Model (SRM) from the\n[Brain Imaging Analysis Kit (BrainIAK)](https://github.com/brainiak/brainiak).\n\n### Description\n\nThe Shared Response Model (SRM) is a method for aligning fMRI scans from several\nsubjects by assuming similar functional behavior in the brain. The voxels of\neach subject are mapped to voxels of other subjects by projecting the\ninformation from each subject into a low-dimensional space.\n\n### Documentation\n\nhttp://brainiak.org/docs/brainiak.funcalign.html\n\n### How to report errors\n\nOpen a GitHub issue in [BrainIAK](https://github.com/brainiak/brainiak) (if the\nissue is about SRM) or here (if the issue is about this wrapper app). We also\nwelcome all kinds of\n[contributions to BrainIAK](http://brainiak.org/docs/contributing.html).\n\n### Acknowledgements\n\nPlease cite the following papers based on which SRM is implemented.\n\n\"A Reduced-Dimension fMRI Shared Response Model\", P.-H. Chen, J. Chen, Y.\nYeshurun-Dishon, U. Hasson, J. Haxby, P. Ramadge, Advances in Neural Information\nProcessing Systems (NIPS), 2015.\nhttp://papers.nips.cc/paper/5855-a-reduced-dimension-fmri-shared-response-model\n\n\"Enabling Factor Analysis on Thousand-Subject Neuroimaging Datasets\", Michael J.\nAnderson, Mihai Capotă, Javier S. Turek, Xia Zhu, Theodore L. Willke, Yida Wang,\nPo-Hsuan Chen, Jeremy R. Manning, Peter J. Ramadge, Kenneth A. Norman, IEEE Big\nData, 2016. https://doi.org/10.1109/BigData.2016.7840719\n\n### Usage\n\nThis App has the following command line arguments:\n\n    usage: run.py [-h]\n                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]\n                  [--run RUN] [--task TASK] [--preproc PREPROC] [--mask MASK]\n                  [--iterations ITERATIONS] [--features FEATURES]\n                  bids_dir output_dir {participant,group}\n\n    Shared Response Model runner\n\n    positional arguments:\n      bids_dir              Input directory\n      output_dir            Output directory\n      {group}   Level of the analysis that will be performed\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]\n                            Labels for participants to be analyzed (default: None)\n      --run RUN             Run to be analyzed (default: 01)\n      --task TASK           Task to be analyzed, default is any (default: *)\n      --preproc PREPROC     Preprocessing tag, default is any (default: *)\n      --mask MASK           Mask tag (default: bmask)\n      --iterations ITERATIONS\n                            Number of iterations, default is SRM default (default:\n                            None)\n      --features FEATURES   Number of features, default is SRM default (default:\n                            None)\n\n### Special considerations\n\nThis app requires preprocessed data with all volumes of a subject registered. It\nalso requires masks to be present in the input data; all to-be-analyzed volumes\nof a subject must use the same mask.\n\nSRM works only on group level because it is a method for aligning fMRI scans\nfrom multiple subjects.\n\nThe data must be time-synchronized, i.e., all subjects must be presented with\nthe same stimuli with the same duration in the same order.\n\nMultiple runs and tasks can be given (\"\\*\") if the number of voxels is the same\nwithin subject (the number of voxels can differ across subjects).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2Fbrainiak-srm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbids-apps%2Fbrainiak-srm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2Fbrainiak-srm/lists"}