{"id":13676476,"url":"https://github.com/khanlab/hippunfold","last_synced_at":"2025-12-14T11:01:09.403Z","repository":{"id":37233847,"uuid":"282100834","full_name":"khanlab/hippunfold","owner":"khanlab","description":"BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)","archived":false,"fork":false,"pushed_at":"2025-12-11T04:06:42.000Z","size":513769,"stargazers_count":63,"open_issues_count":33,"forks_count":21,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-12-11T18:14:28.911Z","etag":null,"topics":["deep-learning","hippocampus","mri","python","segmentation"],"latest_commit_sha":null,"homepage":"https://hippunfold.readthedocs.io","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/khanlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"docs/contributing/contributing.md","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":"2020-07-24T02:14:54.000Z","updated_at":"2025-12-03T09:07:15.000Z","dependencies_parsed_at":"2025-12-11T07:01:01.356Z","dependency_job_id":null,"html_url":"https://github.com/khanlab/hippunfold","commit_stats":{"total_commits":751,"total_committers":11,"mean_commits":68.27272727272727,"dds":0.59254327563249,"last_synced_commit":"cc9b57ae3880353c4f57e40783810e01049f574b"},"previous_names":[],"tags_count":25,"template":false,"template_full_name":null,"purl":"pkg:github/khanlab/hippunfold","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanlab%2Fhippunfold","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanlab%2Fhippunfold/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanlab%2Fhippunfold/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanlab%2Fhippunfold/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/khanlab","download_url":"https://codeload.github.com/khanlab/hippunfold/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanlab%2Fhippunfold/sbom","scorecard":{"id":114277,"data":{"date":"2025-08-11","repo":{"name":"github.com/khanlab/hippunfold","commit":"f37db70a99179dbc106679d7797cac1d999459cc"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":4.1,"checks":[{"name":"Code-Review","score":2,"reason":"Found 3/14 approved changesets -- score normalized to 2","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Maintained","score":10,"reason":"0 commit(s) and 22 issue activity found in the last 90 days -- score normalized to 10","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/bump_version.yml:1","Warn: no topLevel permission defined: .github/workflows/dags.yml:1","Warn: no topLevel permission defined: .github/workflows/deploy.yml:1","Warn: no topLevel permission defined: .github/workflows/manual_release_drafter.yml:1","Warn: no topLevel permission defined: .github/workflows/push_container.yml:1","Warn: no topLevel permission defined: .github/workflows/python-testing.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: MIT License: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":-1,"reason":"internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration","details":null,"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/bump_version.yml:13: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/bump_version.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/bump_version.yml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/bump_version.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/bump_version.yml:45: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/bump_version.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/bump_version.yml:52: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/bump_version.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/bump_version.yml:59: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/bump_version.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/bump_version.yml:74: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/bump_version.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/dags.yml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/dags.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/dags.yml:28: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/dags.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/dags.yml:57: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/dags.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/deploy.yml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/deploy.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/deploy.yml:28: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/deploy.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/deploy.yml:49: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/deploy.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/deploy.yml:56: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/deploy.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/deploy.yml:63: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/deploy.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/deploy.yml:78: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/deploy.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/deploy.yml:83: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/deploy.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/manual_release_drafter.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/manual_release_drafter.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/manual_release_drafter.yml:22: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/manual_release_drafter.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/push_container.yml:15: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/push_container.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/python-testing.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/python-testing.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/python-testing.yml:46: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/python-testing.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/python-testing.yml:51: update your workflow using https://app.stepsecurity.io/secureworkflow/khanlab/hippunfold/python-testing.yml/master?enable=pin","Warn: containerImage not pinned by hash: Dockerfile:1: pin your Docker image by updating khanlab/hippunfold_deps:v0.5.1 to khanlab/hippunfold_deps:v0.5.1@sha256:50b27ea2a4e16067de306b123a132be39debe4d6ab4320bb956ca6a5622016fc","Warn: pipCommand not pinned by hash: Dockerfile:12-15","Warn: pipCommand not pinned by hash: .github/workflows/dags.yml:38","Warn: pipCommand not pinned by hash: .github/workflows/dags.yml:39","Info:   0 out of   6 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of  16 third-party GitHubAction dependencies pinned","Info:   0 out of   1 containerImage dependencies pinned","Info:   0 out of   3 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Vulnerabilities","score":1,"reason":"9 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2024-48 / GHSA-fj7x-q9j7-g6q6","Warn: Project is vulnerable to: GHSA-cpwx-vrp4-4pq7","Warn: Project is vulnerable to: GHSA-gmj6-6f8f-6699","Warn: Project is vulnerable to: GHSA-q2x7-8rv6-6q7h","Warn: Project is vulnerable to: GHSA-33p9-3p43-82vq","Warn: Project is vulnerable to: PYSEC-2022-42969","Warn: Project is vulnerable to: GHSA-9hjg-9r4m-mvj7","Warn: Project is vulnerable to: GHSA-48p4-8xcf-vxj5","Warn: Project is vulnerable to: GHSA-pq67-6m6q-mj2v"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 29 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}}]},"last_synced_at":"2025-08-15T23:44:57.488Z","repository_id":37233847,"created_at":"2025-08-15T23:44:57.488Z","updated_at":"2025-08-15T23:44:57.488Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":27726929,"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","status":"online","status_checked_at":"2025-12-14T02:00:11.348Z","response_time":56,"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":["deep-learning","hippocampus","mri","python","segmentation"],"created_at":"2024-08-02T13:00:28.063Z","updated_at":"2025-12-14T11:01:09.398Z","avatar_url":"https://github.com/khanlab.png","language":"Python","funding_links":[],"categories":["BIDS Apps"],"sub_categories":["others"],"readme":"[![Documentation Status](https://readthedocs.org/projects/hippunfold/badge/?version=latest)](https://hippunfold.readthedocs.io/en/latest/?badge=latest)\n![Docker Pulls](https://img.shields.io/docker/pulls/khanlab/hippunfold)\n![Version](https://img.shields.io/github/v/tag/khanlab/hippunfold?label=version)\n\u003cimg align=\"right\" width=\"200\" src=\"https://github.com/khanlab/hippunfold/assets/25106300/0c16d33e-893a-4ac3-b127-21fa843823d5\"\u003e\n\n**Full Documentation:**  [here](https://hippunfold.readthedocs.io/en/latest/?badge=latest)\n\n# Hippunfold\n\nThis tool aims to automatically model the topological folding structure\nof the human hippocampus, and computationally unfold it.\n![Hippo Fold Unfold](https://raw.githubusercontent.com//khanlab/hippunfold/master/docs/images/subfields_foldunfold.png)\n\nThis is especially useful for:\n- Visualization\n- Topologically-constrained intersubject registration\n- Parcellation (ie. registration to an unfolded atlas)\n- Morphometry (eg. thickness, surface area, curvature, and gyrification measures)\n- Quantitative mapping (eg. map your qT1 MRI data to a midthickness surface; extract laminar profiles perpendicular to this surface)\n\n## NEW: Version 1.3.x release \n\nMajor changes include the addition of unfolded space registration to a reference atlas harmonized across seven ground-truth histology samples. This method allows shifting in unfolded space, providing even better intersubject alignment. \n\n*Note: this replaces the default workflow, however you can revert to the legacy workflow, disabling unfolded space registration, by setting `--atlas bigbrain` or `--no-unfolded-reg`*\n\nRead more in our [ manuscript](https://doi.org/10.7554/eLife.88404.3)\n\nAlso the ability to specify a new **experimental** UNet model that is contrast-agnostic using [synthseg](https://github.com/BBillot/SynthSeg) and trained using more detailed segmentations. This generally produces more detailed results but has not been extensively tested yet. \n\nNote: Docker containers for version 1.3.x and above do not come pre-shipped with nnU-net models (and are accordingly more lightweight!) - models are downloaded automatically when running, but please see the FAQ for more information!\n\n## Workflow\n\nThe overall workflow can be summarized in the following steps:\n\n![Pipeline Overview](https://raw.githubusercontent.com//khanlab/hippunfold/master/docs/images/hippunfold_overview_unfoldreg.png)\n\nFor more information, see\n**Full Documentation:**  [here](https://hippunfold.readthedocs.io/en/latest/?badge=latest)\n\n## Additional tools\n\nFor plotting, mapping fMRI, DWI or other data, and manipulating surfaces, see [here](https://github.com/jordandekraker/hippunfold_toolbox)\n\nFor statistical testing (spin tests) in unfolded space, see [here](https://github.com/Bradley-Karat/Hippo_Spin_Testing)\n\n## Publications\n\n### HippUnfold methods paper\n\n- DeKraker, J., Haast, R. A., Yousif, M. D., Karat, B., Lau, J. C., Köhler, S., \u0026 Khan, A. R. (2022). Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold. Elife, 11, e77945. [link](https://doi.org/10.7554/eLife.77945)\n  -  **Please cite this if you use any version of HippUnfold)**\n  \n### Unfolded space registration and multihist7 atlas\n- DeKraker Jordan, Palomero-Gallagher Nicola, Kedo Olga, Ladbon-Bernasconi Neda, Muenzing Sascha E.A., Axer Markus, Amunts Katrin, Khan Ali R., Bernhardt Boris, Evans Alan C. (2023) Evaluation of surface-based hippocampal registration using ground-truth subfield definitions eLife 12:RP88404 [link](https://doi.org/10.7554/eLife.88404.3)\n  -  **Please cite this if you use HippUnfold version \u003e= 1.3.0)**\n\n### Commentary on surface-based hippocampal segmentation\n- DeKraker J, Köhler S, Khan AR. Surface-based hippocampal subfield segmentation. Trends Neurosci. 2021 Nov;44(11):856-863. doi: 10.1016/j.tins.2021.06.005. Epub 2021 Jul 22. PMID: 34304910. [link](https://pubmed.ncbi.nlm.nih.gov/34304910/)\n\n### Related papers\n\n- DeKraker J, Ferko KM, Lau JC, Köhler S, Khan AR. Unfolding the hippocampus: An intrinsic coordinate system for subfield segmentations and quantitative mapping. Neuroimage. 2018 Feb 15;167:408-418. doi: 10.1016/j.neuroimage.2017.11.054. Epub 2017 Nov 23. PMID: 29175494. [link](https://pubmed.ncbi.nlm.nih.gov/29175494/)\n- DeKraker J, Lau JC, Ferko KM, Khan AR, Köhler S. Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain. Neuroimage. 2020 Feb 1;206:116328. doi: 10.1016/j.neuroimage.2019.116328. Epub 2019 Nov 1. PMID: 31682982. [link](https://pubmed.ncbi.nlm.nih.gov/31682982/)\n- Karat BG, DeKraker J, Hussain U, Köhler S, Khan AR. Mapping the macrostructure and microstructure of the in vivo human hippocampus using diffusion MRI. Hum Brain Mapp. 2023 Nov;44(16):5485-5503. Epub 2023 Aug 24. PMID: 37615057; PMCID: PMC10543110.[link](https://doi.org/10.1002/hbm.26461)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkhanlab%2Fhippunfold","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkhanlab%2Fhippunfold","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkhanlab%2Fhippunfold/lists"}