| name | totalsegmentator |
| description | Use for requests involving medical-image files or image-based analysis, especially CT or MR, including anatomy or pathology detection, segmentation, mask creation, modality detection, contrast-phase estimation, quantitative measurements, and body-statistics estimation. Check TotalSegmentator capabilities before using custom code, shell commands, or general imaging tools. |
TotalSegmentator imaging workflow
Use the TotalSegmentator MCP tools for supported medical-image analysis. Segmentation may be the final output or an intermediate step for quantitative or higher-level analysis.
Capability-first rule
For any request involving medical-image files or image-based analysis, first check whether TotalSegmentator provides a relevant task, class, or analysis tool.
Do this before using shell commands, custom Python, general imaging libraries, or manual voxel inspection.
Choose the operation
Use the smallest operation that satisfies the request:
get_modality: determine CT versus MR for NIfTI input.detect_contrast_phase: estimate CT contrast phase.estimate_body_statistics: estimate weight, height, age, sex, BMI, and body-surface area.run_segmentation: create anatomical or pathological masks, localize structures, or obtain quantitative measurements.
Do not run segmentation when another tool directly answers the request.
Capability discovery
When the relevant class or task is uncertain:
- Call
list_all_classes.
- Select plausible exact class names.
- Call
get_class_options.
- Call
get_task_details for candidate tasks.
Use list_all_tasks when exploring tasks directly.
Never invent task names, classes, modalities, speeds, licensing requirements, or other options.
Segmentation workflow
- Locate the NIfTI file, DICOM directory, or DICOM ZIP.
- Determine the modality.
- Determine the requested anatomy or pathology and downstream purpose.
- Prefer a specialized task when available.
- For focused requests using compatible
total* tasks, use an exact roi_subset.
- Select device and speed deliberately.
- Statistics are enabled by default.
- Immediately before calling
run_segmentation, state the selected task, modality, device, speed, ROI subset, and statistics setting in one or two lines.
- Report the output location, generated masks, and statistics path. Preferable output directory location is in same directory as input file.
Execution choices
Device
Use the preferred server device unless the user requests another supported device. Ask only when the device remains unclear, and reuse previously stated preferences.
Speed
standard: boundaries, small structures, morphology, or precise measurements matter.fast: rapid localization, exploratory analysis, or approximate measurements.fastest: maximum throughput matters more than resolution.
Ask about runtime versus quality only when the request does not make the choice clear.
ROI subset
Use roi_subset only with compatible total* tasks and exact supported class names. Apply it automatically for focused requests. Prefer a specialized task when available.
Statistics
Statistics are enabled by default and provide structure volume and mean image intensity or HU.
Keep them enabled for focused tasks and quantitative requests. Before running a broad task with many classes, especially total* without a focused roi_subset, ask whether the user wants the additional CPU, memory, and runtime cost.
Statistics may include structures cut off by the scan boundaries, and the output does not identify which structures are incomplete. Do not assume every reported volume represents the complete structure.
Interpretation
Contrast phase, body statistics, and pathology-specific outputs are model estimates, not definitive clinical findings.
A detected pathology mask may support a finding. An empty mask must not be treated as reliably excluding it.
