Total Segmentator not working

Support
1

Hi, Total Segmentator worked just fine in my laptop but suddenly it stopped working

|Processor|13th Gen Intel(R) Core™ i9-13980HX 2.20 GHz|
|Installed RAM|64.0 GB |
NVIDIA RTX 4080 12GB

Traceback (most recent call last):
  File "C:\Users\Manjula Herath\AppData\Local\slicer.org\Slicer 5.8.1\bin\Python\slicer\util.py", line 3303, in tryWithErrorDisplay
    yield
  File "C:/Users/Manjula Herath/AppData/Local/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py", line 309, in onApplyButton
    self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
  File "C:/Users/Manjula Herath/AppData/Local/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py", line 1054, in process
    self.processVolume(inputFile, inputVolume,
  File "C:/Users/Manjula Herath/AppData/Local/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py", line 1119, in processVolume
    self.log(_("Total Segmentator arguments: {options}").format(options))
KeyError: 'options'

image
image1404×866 56 KB

I have Cuda compilation tools, release 12.8, V12.8.61
Build cuda_12.8.r12.8/compiler.35404655_0

I have tried uninstalling and deleting and fresh install and pretty much everything mentioned on the forum.

Thank you

2

Appears to be a result of some recent changes in the following commit:

I have asked the developer of the commit to address the issue:

1 Like
3

thank you so much James… :smiley:

2 Likes
4

Hi everyone, we have committed a fix. Probably in the next nightly build (if you installed using the Extension Manager), the extension will run without errors.

1 Like
5

Hello

Hello, where can one download the new version [c2aaf8f] (COMP: Fix recently introduced syntax errors · lassoan/SlicerTotalSegmentator@c2aaf8f · GitHub) mentionned ? The plugin from Slicer’s extension manager is still 2baf4d4.

In short, the problem is still the same for me than the one presented above, with the KeyError ‘options’

Thanks for your help

6

So in the meatime I’ve made the changes suggested by the latest fix directly in the TotalSegmentator.py file (Contents/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/).

Then I got the following line in the error traceback:
pkg_resources.DistributionNotFound: The ‘pyarrow’ distribution was not found and is required by TotalSegmentator

Solved it by adding the package directly into Slicer’s Python (sudo /Applications/Slicer.app/Contents/bin/PythonSlicer -m pip install pyarrow xvfbwrapper)

Works fine now !

7

Works out of the box with Slicer 5.9.0 revision 33722 built 2025-06-27 .Thank you @DouSam and @jamesobutler