manjula
(Manjula Herath)
June 26, 2025, 5:41pm
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'
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
Appears to be a result of some recent changes in the following commit:
committed 03:46AM - 25 Jun 25 UTC
I have asked the developer of the commit to address the issue:
There appears to be some string formatting issues due to changes in this PR. See… https://discourse.slicer.org/t/total-segmentator-not-working/43506.
@LuskasHusty Can you take a look and resolve?
1 Like
DouSam
(Douglas Samuel Gonçalves)
June 26, 2025, 8:56pm
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
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
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 !
manjula
(Manjula Herath)
June 27, 2025, 7:39pm
7
Works out of the box with Slicer 5.9.0 revision 33722 built 2025-06-27 .Thank you @DouSam and @jamesobutler