Problems with path

[weemscreekstudios]

I am trying to use the Cervical Vertebra Tools extension on 5.03 r30893/7ea0f43 and am getting a “setup local paths variables” error. Searching has not found a good link.

Ubuntu 20.04

I get the following errors:

VisSimCommonLogic: initializing global variables:

Defaults paths:

  VisSimTools folder: /home/xyx/VisSimTools

  Output folder     : /home/xyz/VisSimTools/outputs

  elastix binaries are found in /home/matt/Downloads/Slicer-5.0.3-linux-amd64/NA-MIC/Extensions-30893/SlicerElastix/lib/Slicer-5.0/elastix

  Spine Extension is selected

  Models or contents are wrong, trying to download ...

  Downloading VisSim Tools  ... 

  Downloading VisSimTools others ...

 Extracting to user home 

  Error: can not download and extract VisSimTools ...

"There is no item named '/home/xyz/' in the archive"

setup local paths variables.........................

removeOtputsFolderContents ........................

STOPPED: error in input or during the segmentation

unsupported operand type(s) for >>: 'builtin_function_or_method' and 'PythonQtStdOutRedirect'. Did you mean "print(, file=)"?

Thanks

[idhamari]

Thanks for reporting, tge extension is not updated. Please use Slicer 4.10.2.

[weemscreekstudios]

Thank you for responding.

Unfortunately, I am getting a similar error message with Slicer 4.10.2 running in windows and running on Ubuntu. Previously it was on 5.03 on linux.

The Ubuntu version produces a 1.2MB .nrrd file in /home/VisSimTools/ but I cannot get anything to display.

4.10.2 Windows error message

=======================================================
   VisSim Cervical Vertebra Tools               
=======================================================
VisSimCommonLogic: initializing global variables:
 Defaults paths: 
      VisSimTools folder: C:\Users\Parents\VisSimTools
      Output folder     : C:\Users\Parents\VisSimTools\outputs
      elastix binaries are found in C:\Users\abc\AppData\Roaming\NA-MIC\Extensions-28257\SlicerElastix\lib\Slicer-4.10/elastix.exe
      Spine Extension is selected
      sha256computedCheckSum: 9a2ee6a67a190e438a18be811310cbf4eb26b6ad3e00243affa44cc0b26c4393
      Model folder is found...
      Parameter file: C:\Users\abc\VisSimTools\pars\parSpiSeg.txt
      Cropping Length: [ 80 , 80 , 50 ]
point changed,  4 is selected
 ..... getting vertebra location in the input image
Fiducial adding event!
0
<type 'vtkSlicerMarkupsModuleMRMLPython.vtkMRMLMarkupsFiducialNode'>
point changed,  4 is selected
 ..... location RAS: [-18.552085876464844, -150.97610504134425, 140.48018800337093]
 ..... location in the input image set to: [214 209  25]
time:1662328940.65
Processing started
VisSimCommonLogic: initializing global variables:
 Defaults paths: 
      VisSimTools folder: C:\Users\abc\VisSimTools
      Output folder     : C:\Users\abc\VisSimTools\outputs
      elastix binaries are found in C:\Users\abc\AppData\Roaming\NA-MIC\Extensions-28257\SlicerElastix\lib\Slicer-4.10/elastix.exe
      Spine Extension is selected
      sha256computedCheckSum: 9a2ee6a67a190e438a18be811310cbf4eb26b6ad3e00243affa44cc0b26c4393
      Model folder is found...
      Parameter file: C:\Users\abc\VisSimTools\pars\parSpiSeg.txt
      Cropping Length: [ 80 , 80 , 50 ]
setup local paths variables.........................
STOPPED: error in input or during the segmentation
'NoneType' object has no attribute 'GetFileName'

[idhamari]

I will try to update the code next weekend. For now, please move the folder VisSimTools to your home folder. This should fix the path issue. Please notice that deep learning produces better spine segmentation.

[weemscreekstudios]

Do you have a recommendation for a deep learning module for spine segmentation?

[idhamari]

Not sure as I used this some years ago, I think you may need to train the model yourself. You can check here https://deep-spine.de/