{"id":13812767,"url":"https://github.com/Sikerdebaard/dcmrtstruct2nii","last_synced_at":"2025-05-14T22:31:07.699Z","repository":{"id":34115459,"uuid":"166835376","full_name":"Sikerdebaard/dcmrtstruct2nii","owner":"Sikerdebaard","description":"DICOM RT-Struct to mask","archived":false,"fork":false,"pushed_at":"2024-02-28T18:12:45.000Z","size":4290,"stargazers_count":101,"open_issues_count":8,"forks_count":27,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-20T02:16:38.386Z","etag":null,"topics":[],"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/Sikerdebaard.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}},"created_at":"2019-01-21T15:19:54.000Z","updated_at":"2025-03-02T23:07:04.000Z","dependencies_parsed_at":"2023-02-18T16:31:23.107Z","dependency_job_id":"296c65e4-9717-4b02-9d9b-37f0e08d255c","html_url":"https://github.com/Sikerdebaard/dcmrtstruct2nii","commit_stats":{"total_commits":90,"total_committers":7,"mean_commits":"12.857142857142858","dds":0.5555555555555556,"last_synced_commit":"9a6669bf73454f1cb2550664d42faabf58776f7d"},"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sikerdebaard%2Fdcmrtstruct2nii","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sikerdebaard%2Fdcmrtstruct2nii/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sikerdebaard%2Fdcmrtstruct2nii/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sikerdebaard%2Fdcmrtstruct2nii/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Sikerdebaard","download_url":"https://codeload.github.com/Sikerdebaard/dcmrtstruct2nii/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254239493,"owners_count":22037715,"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","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":[],"created_at":"2024-08-04T04:00:55.254Z","updated_at":"2025-05-14T22:31:02.590Z","avatar_url":"https://github.com/Sikerdebaard.png","language":"Python","funding_links":[],"categories":["Libraries"],"sub_categories":["Python"],"readme":"[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4037864.svg)](https://doi.org/10.5281/zenodo.4037864)\n![unit tests](https://github.com/Sikerdebaard/dcmrtstruct2nii/workflows/Unit%20Tests/badge.svg)\n  \n\n# dcmrtstruct2nii\nDICOM RT-Struct to nii-mask. This is a naïve approach to rasterizing rt-struct to masks in nii format. If there's holes in your RT-Struct then this approach will most likely not work. The RT-Struct needs to be within the bounds of the slices of the original DICOM. Rasterization is done on a slice-by-slice basis, interpolation between slices is currently unsupported.\n\n# Interpolation\nInterpolation of the mask between slices is currently unsupported. Send us an algorithm or a pull requests and we'll happly add it.\n\n# Input file format\nThe DICOM and RT-Struct inputs need to be unzipped in a directory. Currently this is the only way to read the input files.\n\n# CLI Tool\n```\n# install using pip and show tool help\npip install dcmrtstruct2nii\ndcmrtstruct2nii --help\n\n# list structures in DICOM RT Struct\ndcmrtstruct2nii ls -r /path/to/rtstruct/file\n\n# convert help output\ndcmrtstruct2nii convert --help\n\n# convert DICOM RT Structs to .nii.gz masks\ndcmrtstruct2nii convert -r /path/to/rtstruct/file.dcm -d /path/to/original/extracted/dicom -o /output/path\n```\n\n# Python API\n```\n# install using pip and show tool help\npip install dcmrtstruct2nii\n```\n\n```\n# lets test it\nfrom dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs\n\nprint(list_rt_structs('/path/to/dicom/rtstruct/file.dcm'))\n\ndcmrtstruct2nii('/path/to/dicom/rtstruct/file.dcm', '/path/to/original/extracted/dicom/files', '/output/path')\n```\n\n# License and academic use\n\nThe software is licensed [MIT License](https://github.com/Sikerdebaard/dcmrtstruct2nii/blob/master/LICENSE).\n\nFor academic use, use a presistent copy from [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4037864.svg)](https://doi.org/10.5281/zenodo.4037864). \n\nPlease cite:\n\n```Thomas Phil, Thomas Albrecht, Skylar Gay, \u0026 Mathis Ersted Rasmussen. (2023). Sikerdebaard/dcmrtstruct2nii: dcmrtstruct2nii v5 (Version v5). Zenodo. https://doi.org/10.5281/zenodo.4037864```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSikerdebaard%2Fdcmrtstruct2nii","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FSikerdebaard%2Fdcmrtstruct2nii","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSikerdebaard%2Fdcmrtstruct2nii/lists"}