How to get organ masks from a CT or MR scan in one command with Total Segmentator

health. The README states this is not a medical device and is not intended for clinical usage.

What you need first

• 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

Steps

1. Install it with pip install TotalSegmentator
2. For CT run TotalSegmentator -i ct.nii.gz -o segmentations
3. For MR run TotalSegmentator -i mri.nii.gz -o segmentations --task total_mr
4. On CPU add --fast or --roi_subset, and on an M series Mac use --device mps

Prompt for your agent

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.

Caveat. Weights download automatically on the first run, so the first scan is slower.

Using the Deduped MCP, get the setup steps for wasserth/TotalSegmentator and "Get organ masks from a CT or MR scan in one command"

claude mcp add --transport http deduped https://dedupedai.com/mcp

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