{"id":20361131,"url":"https://github.com/reubendo/skinsegmentator","last_synced_at":"2026-06-07T11:32:09.502Z","repository":{"id":227541947,"uuid":"771706087","full_name":"ReubenDo/SkinSegmentator","owner":"ReubenDo","description":"Skin Segmentator ","archived":false,"fork":false,"pushed_at":"2024-03-28T18:55:37.000Z","size":53,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-15T03:06:48.158Z","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/ReubenDo.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}},"created_at":"2024-03-13T19:48:46.000Z","updated_at":"2024-03-13T20:33:07.000Z","dependencies_parsed_at":"2024-11-14T23:46:45.754Z","dependency_job_id":"6a6fe27c-ab10-4b3c-ab67-b444e98a8181","html_url":"https://github.com/ReubenDo/SkinSegmentator","commit_stats":null,"previous_names":["reubendo/skinsegmentator"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FSkinSegmentator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FSkinSegmentator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FSkinSegmentator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReubenDo%2FSkinSegmentator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ReubenDo","download_url":"https://codeload.github.com/ReubenDo/SkinSegmentator/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241903978,"owners_count":20040011,"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":"2024-11-14T23:46:37.516Z","updated_at":"2025-03-04T18:40:48.424Z","avatar_url":"https://github.com/ReubenDo.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SkinSegmentator\n\nThis repository is adapted from [TotalSegmentator](https://github.com/wasserth/TotalSegmentator/)\n\n### Installation\n\nSkinSegmentator works on Ubuntu, Mac, and Windows and on CPU and GPU.\n\nInstall dependencies:\n* Python \u003e= 3.9\n* [Pytorch](http://pytorch.org/) \u003e= 2.0.0\n\nInstall SkinSegmentator\n```\npip install skinsegmentator\n```\n\n\n### Usage\n```\nSkinSegmentator -i mr.nii.gz -o segmentations\n```\n\u003e Note: A Nifti file or a folder with all DICOM slices of one patient is allowed as input\n\n\u003e Note: If you run on CPU use the option `--fast` to greatly improve runtime.\n\n\u003e Note: This is not a medical device and is not intended for clinical usage.\n\n\n\n### Python API\nYou can run SkinSegmentator via Python:\n```python\nimport nibabel as nib\nfrom skinsegmentator.python_api import skinsegmentator\n\nif __name__ == \"__main__\":\n    input_path = 'test/Validation_T1_001_0000.nii.gz'\n    output_path = 'test/skin.nii.gz'\n    # option 1: provide input and output as file paths\n    skinsegmentator(input_path, output_path) \n\n    input_path = 'test/Validation_T1_001_0000.nii.gz'\n    output_dir = 'test/'\n    # option 2: provide input file path and output dir\n    skinsegmentator(input_path, output_dir) \n\n    # option 3: provide input and output nifti image objects\n    input_img = nib.load(input_path)\n    output_img = skinsegmentator(input_img)\n    nib.save(output_img, output_path)\n```\nYou can see all available arguments [here](https://github.com/reubendo/SkinSegmentator/blob/master/SkinSegmentator/python_api.py). Running from within the main environment should avoid some multiprocessing issues.\n\n### Install latest master branch (contains latest bug fixes)\n```\npip install git+https://github.com/reubendo/SkinSegmentator.git\n```\n\n### Typical problems\n\n**ITK loading Error**\nWhen you get the following error message\n```\nITK ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition was found!\n```\nyou should do\n```\npip install SimpleITK==2.0.2\n```\n\nAlternatively you can try\n```\nfslorient -copysform2qform input_file\nfslreorient2std input_file output_file\n```\n\n\n### Reference\nTODO\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freubendo%2Fskinsegmentator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Freubendo%2Fskinsegmentator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freubendo%2Fskinsegmentator/lists"}