TotalSegmentator: Failed to install required packages

gsmattay
Tue, 17 Sep 2024 01:46:50 +0000
Support

Operating system: MacOS Big Sur 11.4
Slicer version: 5.6.2
Hello,

I have installed Slicer, installed Pytorch version 2.2.2 via the Pytorch utils module, installed the 3d segmentator module, and restarted Slicer. When attempting to run segmentation on test CT Chest data, I get the following error.

Failed to install required packages.

Command ‘[’/Applications/Slicer.app/Contents/bin/…/bin/PythonSlicer’, ‘-m’, ‘pip’, ‘install’, ‘rt-utils’]’ returned non-zero exit status 1.

Here are the more detailed logs:

TotalSegmentator Python package is required. Installing it from https://github.com/wasserth/TotalSegmentator/archive/7274faac4673298d17b63a5a8335006f02e6d426.zip… (it may take several minutes)

Installing numpy<2…

Installing nibabel>=2.3.0…

Installing tqdm>=4.45.0…

Installing p-tqdm…

Installing xvfbwrapper…

Installing rt-utils…

Failed to install Python dependencies:

Command ‘[’/Applications/Slicer.app/Contents/bin/…/bin/PythonSlicer’, ‘-m’, ‘pip’, ‘install’, ‘rt-utils’]’ returned non-zero exit status 1.

I have also attempted a force reinstall Total Segmentator Python package under advanced settings and this did not work. Would appreciate your help. Thank you.

15 posts - 5 participants