{"id":44215372,"url":"https://github.com/samuelstjean/autodmri","last_synced_at":"2026-02-10T01:35:52.657Z","repository":{"id":54096554,"uuid":"193885318","full_name":"samuelstjean/autodmri","owner":"samuelstjean","description":"Automated characterization of noise distributions in diffusion MRI data","archived":false,"fork":false,"pushed_at":"2025-08-05T19:28:33.000Z","size":29394,"stargazers_count":7,"open_issues_count":1,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-09-25T16:42:54.335Z","etag":null,"topics":["diffusion-mri","python"],"latest_commit_sha":null,"homepage":null,"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/samuelstjean.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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}},"created_at":"2019-06-26T10:44:22.000Z","updated_at":"2025-08-05T19:28:36.000Z","dependencies_parsed_at":"2025-08-05T21:19:19.242Z","dependency_job_id":null,"html_url":"https://github.com/samuelstjean/autodmri","commit_stats":{"total_commits":79,"total_committers":5,"mean_commits":15.8,"dds":0.6075949367088608,"last_synced_commit":"95593402e6697e11d9fd13d81c5a123c767e69c3"},"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"purl":"pkg:github/samuelstjean/autodmri","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samuelstjean%2Fautodmri","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samuelstjean%2Fautodmri/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samuelstjean%2Fautodmri/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samuelstjean%2Fautodmri/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/samuelstjean","download_url":"https://codeload.github.com/samuelstjean/autodmri/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samuelstjean%2Fautodmri/sbom","scorecard":{"id":798542,"data":{"date":"2025-08-11","repo":{"name":"github.com/samuelstjean/autodmri","commit":"92bbea4aa06df664ec6e06ae9bcfef4b1d9d2ad1"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":3.1,"checks":[{"name":"Maintained","score":0,"reason":"1 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"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":"Code-Review","score":0,"reason":"Found 0/20 approved changesets -- score normalized to 0","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":"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/python-package.yml:1","Warn: no topLevel permission defined: .github/workflows/pythonpublish.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":"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":"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":"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":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"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":0,"reason":"Project has not signed or included provenance with any releases.","details":["Warn: release artifact v0.2.7 not signed: https://api.github.com/repos/samuelstjean/autodmri/releases/138022472","Warn: release artifact v0.2.6 not signed: https://api.github.com/repos/samuelstjean/autodmri/releases/82084875","Warn: release artifact v0.2.5 not signed: https://api.github.com/repos/samuelstjean/autodmri/releases/39571250","Warn: release artifact v0.2.4 not signed: https://api.github.com/repos/samuelstjean/autodmri/releases/39503239","Warn: release artifact v0.2.3 not signed: https://api.github.com/repos/samuelstjean/autodmri/releases/27797349","Warn: release artifact v0.2.7 does not have provenance: https://api.github.com/repos/samuelstjean/autodmri/releases/138022472","Warn: release artifact v0.2.6 does not have provenance: https://api.github.com/repos/samuelstjean/autodmri/releases/82084875","Warn: release artifact v0.2.5 does not have provenance: https://api.github.com/repos/samuelstjean/autodmri/releases/39571250","Warn: release artifact v0.2.4 does not have provenance: https://api.github.com/repos/samuelstjean/autodmri/releases/39503239","Warn: release artifact v0.2.3 does not have provenance: https://api.github.com/repos/samuelstjean/autodmri/releases/27797349"],"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"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/python-package.yml:21: update your workflow using https://app.stepsecurity.io/secureworkflow/samuelstjean/autodmri/python-package.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/python-package.yml:24: update your workflow using https://app.stepsecurity.io/secureworkflow/samuelstjean/autodmri/python-package.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pythonpublish.yml:14: update your workflow using https://app.stepsecurity.io/secureworkflow/samuelstjean/autodmri/pythonpublish.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pythonpublish.yml:17: update your workflow using https://app.stepsecurity.io/secureworkflow/samuelstjean/autodmri/pythonpublish.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pythonpublish.yml:31: update your workflow using https://app.stepsecurity.io/secureworkflow/samuelstjean/autodmri/pythonpublish.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pythonpublish.yml:34: update your workflow using https://app.stepsecurity.io/secureworkflow/samuelstjean/autodmri/pythonpublish.yml/master?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/python-package.yml:30","Warn: pipCommand not pinned by hash: .github/workflows/python-package.yml:31","Warn: pipCommand not pinned by hash: .github/workflows/pythonpublish.yml:23","Warn: pipCommand not pinned by hash: .github/workflows/pythonpublish.yml:24","Info:   0 out of   4 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   2 third-party GitHubAction dependencies pinned","Info:   0 out of   4 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":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"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":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 19 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":"2025-08-23T09:44:11.987Z","repository_id":54096554,"created_at":"2025-08-23T09:44:11.987Z","updated_at":"2025-08-23T09:44:11.987Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29288576,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-09T21:57:15.303Z","status":"ssl_error","status_checked_at":"2026-02-09T21:57:11.537Z","response_time":56,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["diffusion-mri","python"],"created_at":"2026-02-10T01:35:52.578Z","updated_at":"2026-02-10T01:35:52.649Z","avatar_url":"https://github.com/samuelstjean.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Automated characterization of noise distributions in diffusion MRI data\n\n[miccai]: https://arxiv.org/abs/1805.12071\n[miccai_publisher]: https://link.springer.com/chapter/10.1007%2F978-3-030-00928-1_35\n[media]: https://www.sciencedirect.com/science/article/pii/S1361841520301225\n\n###  The example and documentation\n\nThe latest version can be installed with\n~~~\npip install autodmri\n~~~\n\nYou can find a quick example and datasets over [here](example) and the full documentation at http://autodmri.rtfd.io/.\n\nAn example, super basic call to the script would be\n\n~~~bash\nautodmri_get_distribution dwi.nii.gz sigma.nii.gz N.nii.gz mask.nii.gz\n~~~\n\nBe sure to check the options by passing `--help` to the script.\n\n###  The manuscript and references\n\nYou can read the [journal version][media] in Medical Image Analysis and the datasets are available here https://zenodo.org/record/2483105.\n\nThe conference version of the manuscript (as published in MICCAI 2018) is available [here][miccai] for free\nand from the [publisher][miccai_publisher].\n\nHere is a bibtex entry for the journal version\n\n~~~\n@article{St-jean2020_media,\nauthor = {St-Jean, Samuel and {De Luca}, Alberto and Tax, Chantal M.W. and Viergever, Max A. and Leemans, Alexander},\ndoi = {10.1016/j.media.2020.101758},\neprint = {1906.12121},\nissn = {13618415},\njournal = {Medical Image Analysis},\nmonth = {jun},\npages = {101758},\ntitle = {{Automated characterization of noise distributions in diffusion MRI data}},\nurl = {https://linkinghub.elsevier.com/retrieve/pii/S1361841520301225},\nyear = {2020}\n}\n~~~\n\nand for the conference manuscript in MICCAI\n\n~~~\n@InProceedings{St-jean2018_miccai,\nauthor=\"St-Jean, Samuel\nand De Luca, Alberto\nand Viergever, Max A.\nand Leemans, Alexander\",\neditor=\"Frangi, Alejandro F.\nand Schnabel, Julia A.\nand Davatzikos, Christos\nand Alberola-L{\\'o}pez, Carlos\nand Fichtinger, Gabor\",\ntitle=\"Automatic, Fast and Robust Characterization of Noise Distributions for Diffusion MRI\",\nbooktitle=\"Medical Image Computing and Computer Assisted Intervention -- MICCAI 2018\",\nyear=\"2018\",\npublisher=\"Springer International Publishing\",\naddress=\"Cham\",\npages=\"304--312\",\nisbn=\"978-3-030-00928-1\"\n}\n~~~\n\n###  Referencing the code itself\n\nThe code is also autoarchived on zenodo for those wanting to refer to a specific version over here\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3339157.svg)](https://doi.org/10.5281/zenodo.3339157)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsamuelstjean%2Fautodmri","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsamuelstjean%2Fautodmri","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsamuelstjean%2Fautodmri/lists"}