Hi ! I have a question, do the previous version works with Slicer 5.4? because I’m not been able to run it on my pc. I will appreciate an answer, best regards.
Yes, TotalSegmentator extension still works well in Slicer-5.4. It uses the TotalSegmentator v1 model. There are constant updates in Python packages and so we had to make some fixes recently. If you experience any problems then I would recommend to reinstall Slicer (remove the existing application installation folder completely; or reinstall Slicer in a completely new folder) and then install TotalSegmentator extension.
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Hello,
I tried TotalSegmentator v2 within Slicer 5.6.1.
The limbs are missing (below the knee / humerus) on all CTs I tried (5).
Version 5.5 is mentioned there:
but not available in the collection of older slicer packages on Kitware’s site (5.4->5.6).
Did anyone have luck with the limbs?
Using which version of slicer?
Thanks
Philippe
PS: i’ll post on github too and update if I have a response
TotalSegmentator v2 began to work with Slicer Preview 5.5 which ultimately became Slicer Stable 5.6.x. So using Slicer 5.6.1 is sufficient for your case and going back to Slicer 5.5 won’t get you anything more.
Are the segment tasks that you are expecting in the list of the ones available in v2? Do you have a license for the ones that require a license? See below:
Maybe you can get a free academic license if you contact Jakob Wasserthal from TotalSegmentator.
Dummy me. I did not realize that they called the extremities “appendicular bones”.
Thanks for the pointer. I’ll ask a license
Sorry to post again.
I got a license but there is an error installing it:
Failed to set TotalSegmentator license.
Command '['C:/Users/-------/AppData/Local/slicer.org/Slicer 5.6.1/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\-------\\AppData\\Local\\slicer.org\\Slicer 5.6.1\\lib\\Python\\Scripts\\totalseg_set_license.exe', '-l', '
Traceback (most recent call last):
File "C:\\Users\\-------\\AppData\\Local\\slicer.org\\Slicer 5.6.1\\bin\\Python\\slicer\\util.py", line 3255, in tryWithErrorDisplay
yield
File "C:/Users/-------/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 318, in onSetLicense
self.logic.setlicense(self.ui.licenseLineEdit.text)
File "C:/Users/-------/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 831, in setlicense
licenseToolOutput = self.logProcessOutput(proc, returnOutput=True)
File "C:/Users/-------/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 779, in logProcessOutput
if not line:
UnboundLocalError: local variable \'line\' referenced before assignment']' returned non-zero exit status 1.
The error is related to line 779:
try:
line = proc.stdout.readline()
except UnicodeDecodeError as e:
# Code page conversion happens because `universal_newlines=True` sets process output to text mode,
# and it fails because probably system locale is not UTF8. We just ignore the error and discard the string,
# as we only guarantee correct behavior if an UTF8 locale is used.
My PC is in french. Slicer is set in english.
There are no special characters in the license key;
Total segmentator works fine otherwise.
Any idea on how to solve it?
Thanks
Philippe
@lassoan could you please check this? Thank you
Thank you, I’ve pushed a fix that will be available in the extensions manager from tomorrow. Please update the extension tomorrow and try again.
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Thanks a lot.
I confirm the license is working now.
Philippe
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Awesome, thanks for testing.
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Hello,my slicer is 3.6.1.The following error occurs when using TotalSegmentator.
Restart is unuseful.
Application is required to complete installation of required Python packages.
Press OK to restart.