{
 "schema_version": 1,
 "generated": "2026-10-31",
 "id": "wasserth-totalsegmentator--segment-anatomy-in-a-ct-scan-with-totalsegmentator",
 "repo": "wasserth/TotalSegmentator",
 "repo_url": "https://github.com/wasserth/TotalSegmentator",
 "repo_slug": "wasserth-totalsegmentator",
 "title": "Get organ masks from a CT or MR scan in one command",
 "page_title": "How to get organ masks from a CT or MR scan in one command with Total Segmentator",
 "summary": "Run the default task to write one segmentation file per anatomical class.",
 "who": "A researcher starting an imaging study who needs structures labeled.",
 "problem": "Manual contouring of organs takes hours per scan.",
 "outcome": "A folder of segmentation files, one per class, for your scan.",
 "steps": [
  "Install it with `pip install TotalSegmentator`",
  "For CT run `TotalSegmentator -i ct.nii.gz -o segmentations`",
  "For MR run `TotalSegmentator -i mri.nii.gz -o segmentations --task total_mr`",
  "On CPU add `--fast` or `--roi_subset`, and on an M series Mac use `--device mps`"
 ],
 "agent_prompt": "Using wasserth/TotalSegmentator, install it with `pip install TotalSegmentator`, run `TotalSegmentator -i ct.nii.gz -o segmentations` on <my scan>, and summarize which classes came out nonempty.",
 "agents": [
  "claude-code",
  "codex",
  "cursor",
  "gemini-cli"
 ],
 "difficulty": "Intermediate",
 "time": "1 hour",
 "basis": "readme",
 "caveat": "Weights download automatically on the first run, so the first scan is slower.",
 "category": "Security and science",
 "tags": [
  "Security and science"
 ],
 "lang": "",
 "requirements": [
  "Python 3.10 or newer and PyTorch 2.0.0 or newer",
  "A Nifti file, or a folder or zip of all DICOM slices of one patient, as input",
  "A GPU for reasonable runtime; CPU works with the --fast or --roi_subset options",
  "A free non-commercial license number for the non-open tasks and for totalseg_get_body_stats"
 ],
 "risk": "none",
 "seen_in_the_wild": false,
 "mentioned_publicly": false,
 "risks": [
  {
   "tag": "health",
   "notice": "The README states this is not a medical device and is not intended for clinical usage."
  }
 ],
 "best": true,
 "score": 1.0,
 "evidence": [],
 "url": "https://dedupedai.com/use-cases/wasserth-totalsegmentator/segment-anatomy-in-a-ct-scan-with-totalsegmentator/",
 "md": "https://dedupedai.com/use-cases/wasserth-totalsegmentator/segment-anatomy-in-a-ct-scan-with-totalsegmentator/index.md",
 "disclaimer": "Deduped lists open-source repositories that belong to other people. We do not own, maintain, audit, or vouch for any of them, and a repo appearing here is not an endorsement or a safety check. The use cases, steps, and prompts are written by AI and may be incomplete, outdated, or just wrong. Where a use case is marked \"Seen in the wild\", we link to public posts where someone described something similar, but we have not verified those posts and the use case itself is still our AI's own write-up. Use all of this at your own risk. Only run code, commands, or agents on systems and accounts you are authorized to use, and read the code and every command before you run it, especially anything that touches credentials, files, or the network. Nothing here is professional, security, legal, or financial advice. All trademarks and project names belong to their respective owners, and their use here does not imply affiliation. Content is provided as is, without warranties of any kind. Found a mistake, a safety problem, or something you want removed? Email hello@dedupedai.com and we will look at it promptly.",
 "api": "https://dedupedai.com/api/v1/usecases/wasserth-totalsegmentator--segment-anatomy-in-a-ct-scan-with-totalsegmentator.json",
 "api_version": "v1"
}