HD_BET does not work in latest Slicer Preview Release

Development
1

While the code below works without any errors in the stable version, it gives an error in the preview version.

import HDBrainExtractionTool             
        
HDBetLogic = HDBrainExtractionTool.HDBrainExtractionToolLogic()                            
        
brainNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLScalarVolumeNode')        
brainSegNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
HDBetLogic.process(masterVolumeNode,brainNode ,brainSegNode ,0)
slicer.util.setSliceViewerLayers(background=brainNode)

image

  File "C:/ProgramData/slicer.org/Slicer5.3.0/slicer.org/Extensions-31866/HDBrainExtraction/lib/Slicer-5.3/qt-scripted-modules/HDBrainExtractionTool.py", line 346, in process
    from HD_BET.run import run_hd_bet
ModuleNotFoundError: No module named 'HD_BET'
2

Please post the exact error.

Also, it could help to post a fully reproducible example that someone can easily paste into the python console to reproduce what you are seeing. E.g. us the sample data methods to load data, etc.

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3

@Muhammed_Fatih_Talu You need to install prerequisite packages (pytorch and hd_bet). You can do that by running the module once using the GUI. If you install and run the module from script, make sure you call HDBetLogic.setupPythonRequirements() before HDBetLogic.process(...).

4

Hi,
I am running into similar issue:

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image1242×536 94.5 KB

Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/bin/Python/slicer/util.py”, line 3255, in tryWithErrorDisplay
yield
File “/Applications/Slicer.app/Contents/Extensions-32448/HDBrainExtraction/lib/Slicer-5.6/qt-scripted-modules/HDBrainExtractionTool.py”, line 237, in onApplyButton
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputVolumeSelector.currentNode(),
File “/Applications/Slicer.app/Contents/Extensions-32448/HDBrainExtraction/lib/Slicer-5.6/qt-scripted-modules/HDBrainExtractionTool.py”, line 346, in process
from HD_BET.run import run_hd_bet
ModuleNotFoundError: No module named ‘HD_BET.run’

Now, PyTorch is installed, but how do I do add the suggested hd_bet package?

Help is appreciated…

5

The Slicer HDBrainExtension currently specifies to use the latest code of the HD_BET Python package, but the developer has refactored the code resulting in API compatibility issues. I have written up the following GitHub issue to track the work associated with updating the Slicer extension to use an older version of HD_BET that would be compatible.

cc: @lassoan

1 Like