Guilherme_Augusto
Fri, 27 Jun 2025 13:21:17 +0000
Support

TotalSegmentator Licensed Tasks Not Appearing in 3D Slicer Interface

Problem Description

I have TotalSegmentator v2.10.0 installed and working via Python API in 3D Slicer 5.7.0, but licensed tasks like thigh_shoulder_muscles and thigh_shoulder_muscles_mr do not appear in the module interface dropdown, even though I have a valid academic license configured.

System Information

3D Slicer Version: 5.7.0-2024-11-06

Operating System: Windows 10 (22631)

TotalSegmentator Version: 2.10.0 (confirmed via pip)

Python Environment: PythonSlicer.exe

GPU: NVIDIA RTX 4060 Laptop (CUDA 12.9)

What I’ve Tried

1. License Configuration:

Successfully configured academic license (aca_65EL3LSCMMNB9J) via config.json

License verification works in Python API

File location: ~/.totalsegmentator/config.json

2. Module Reinstallation:

Uninstalled and reinstalled TotalSegmentator extension via Slicer

Confirmed v2.10.0 is installed

Restarted Slicer multiple times

3. Python API Testing:

Basic tasks work perfectly (total, total_mr)

Licensed tasks fail with license validation hanging

Non-licensed tasks execute successfully

Current Behavior

Interface: Only shows non-licensed tasks in dropdown (see screenshot)

Python API: Licensed tasks start but hang during license validation

Error Message: No explicit errors, just license validation prompt

Expected Behavior

Licensed tasks like thigh_shoulder_muscles and thigh_shoulder_muscles_mr should appear in the task dropdown when a valid academic license is configured.

Questions

1. License Integration: How does the Slicer extension read the TotalSegmentator license configuration? Does it use the same ~/.totalsegmentator/config.json file?

2. Task Discovery: Is there a way to force the extension to re-scan available tasks after license configuration?

3. Alternative Configuration: Is there a Slicer-specific way to configure the TotalSegmentator license within the extension interface?

4. Version Compatibility: Could there be a version mismatch between the Slicer extension and the installed TotalSegmentator Python package?

Minimal Reproduction

# This works (non-licensed)
from totalsegmentator.python_api import totalsegmentator
result = totalsegmentator(input="test.nii.gz", output="output/", task="total_mr")

# This hangs during license validation (licensed)
result = totalsegmentator(input="test.nii.gz", output="output/", task="thigh_shoulder_muscles_mr")

Additional Context

I’m working on a research project for automatic rotator cuff muscle segmentation and specifically need access to the thigh_shoulder_muscles_mr task for MR images. The task exists and is documented in TotalSegmentator v2.10.0, but the Slicer integration seems to have issues with licensed task discovery.

Any help would be greatly appreciated! Is this a known issue with the current TotalSegmentator extension, or am I missing a configuration step?

3 posts - 3 participants