{
 "schema_version": 1,
 "generated": "2026-10-31",
 "id": "wasserth-totalsegmentator--measure-organ-volumes-with-totalsegmentator-statistics",
 "repo": "wasserth/TotalSegmentator",
 "repo_url": "https://github.com/wasserth/TotalSegmentator",
 "repo_slug": "wasserth-totalsegmentator",
 "title": "Measure organ volumes and intensities automatically",
 "page_title": "How to measure organ volumes and intensities automatically with Total Segmentator",
 "summary": "Add the statistics flag so each segmented class comes with its volume and mean intensity.",
 "who": "A team building a cohort study that needs numbers, not just masks.",
 "problem": "Reading volumes off masks by hand does not scale across a cohort.",
 "outcome": "A statistics.json with volume in cubic millimetres and mean intensity per class.",
 "steps": [
  "Install it with `pip install TotalSegmentator`",
  "Run Total Segmentator with the `--statistics` option to write statistics.json next to the segmentations",
  "If structures that touch the image border report zero, rerun with `TotalSegmentator -i ct.nii.gz -o seg --statistics --stats_include_incomplete`",
  "Use `--statistics_extra` when you also want n_voxels, intensity std, min and max, centroid_vox and bbox_vox"
 ],
 "agent_prompt": "With wasserth/TotalSegmentator, run the total task on every scan in <my folder> with `--statistics`, then build one CSV of per organ volumes across the cohort.",
 "agents": [
  "claude-code",
  "codex",
  "cursor",
  "gemini-cli"
 ],
 "difficulty": "Intermediate",
 "time": "1 hour",
 "basis": "readme",
 "caveat": "By default a structure whose mask reaches the image border is treated as incomplete and reported as zero.",
 "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": "Not a medical device and not intended for clinical usage, as the README says."
  }
 ],
 "best": false,
 "score": 0.9,
 "evidence": [],
 "url": "https://dedupedai.com/use-cases/wasserth-totalsegmentator/measure-organ-volumes-with-totalsegmentator-statistics/",
 "md": "https://dedupedai.com/use-cases/wasserth-totalsegmentator/measure-organ-volumes-with-totalsegmentator-statistics/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--measure-organ-volumes-with-totalsegmentator-statistics.json",
 "api_version": "v1"
}