Radiomics problem for VUE images

Support
1

Operating system: macOS Catalina
Slicer version: 4.10.2
Expected behavior: extract radiomics features from a label map created from a virtual unenhanced CT (dual energy)
Actual behavior: No features extracted, following errors returned

Python 2.7.13 (default, May 16 2019, 14:32:14)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)] on darwin

Loading with imageIOName: GDCM
Generating customization file
Feature extraction started
Initializing output table
Feature calculation failed.
Feature calculation failed.
Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 407, in onApplyButton
self.onFinished)
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 743, in runCLI
self.runCLIWithParameterFile(imageNode, maskNode, tableNode, parameterFile, callback)
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 782, in runCLIWithParameterFile
self._startCLI(firstRun=True)
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 537, in _startCLI
labelName, labelNode, label_idx, imageNode = next(self._labelGenerators)
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 494, in _getLabelGeneratorFromLabelMap
combinedLabelImage = sitk.ReadImage(sitkUtils.GetSlicerITKReadWriteAddress(labelNode.GetName()))
File “/Applications/Slicer.app/Contents/bin/Python/sitkUtils.py”, line 44, in GetSlicerITKReadWriteAddress
myNode = nodeObjectOrName if isinstance(nodeObjectOrName, slicer.vtkMRMLNode) else slicer.util.getNode(nodeObjectOrName)
File “/Applications/Slicer.app/Contents/bin/Python/slicer/util.py”, line 710, in getNode
raise MRMLNodeNotFoundException(“could not find nodes in the scene by name or id ‘%s’” % (pattern if (type(pattern) == str) else “”))
MRMLNodeNotFoundException: could not find nodes in the scene by name or id ‘304: VNC [HU*] , VNC, Spectral (3)-label’

2

Can you try if removing the * character from the node name fixes the issue?

3

I have removed the * in the hierarchy details, however I still get these error messages

Python 2.7.13 (default, May 16 2019, 14:32:14)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)] on darwin

Loading with imageIOName: GDCM
Irregular volume geometry detected, but maximum error non-zero but is within tolerance (maximum error of 1.2207e-05 mm, tolerance threshold is 0.001 mm).
Generating customization file
Feature extraction started
Initializing output table
Feature calculation failed.
Feature calculation failed.
Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 407, in onApplyButton
self.onFinished)
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 743, in runCLI
self.runCLIWithParameterFile(imageNode, maskNode, tableNode, parameterFile, callback)
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 782, in runCLIWithParameterFile
self._startCLI(firstRun=True)
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 537, in _startCLI
labelName, labelNode, label_idx, imageNode = next(self._labelGenerators)
File “/Applications/Slicer.app/Contents/Extensions-28257/SlicerRadiomics/lib/Slicer-4.10/qt-scripted-modules/SlicerRadiomics.py”, line 494, in _getLabelGeneratorFromLabelMap
combinedLabelImage = sitk.ReadImage(sitkUtils.GetSlicerITKReadWriteAddress(labelNode.GetName()))
File “/Applications/Slicer.app/Contents/bin/Python/sitkUtils.py”, line 44, in GetSlicerITKReadWriteAddress
myNode = nodeObjectOrName if isinstance(nodeObjectOrName, slicer.vtkMRMLNode) else slicer.util.getNode(nodeObjectOrName)
File “/Applications/Slicer.app/Contents/bin/Python/slicer/util.py”, line 710, in getNode
raise MRMLNodeNotFoundException(“could not find nodes in the scene by name or id ‘%s’” % (pattern if (type(pattern) == str) else “”))
MRMLNodeNotFoundException: could not find nodes in the scene by name or id ‘304: VNC [HU] , VNC, Spectral (3)-label’

4

The square brackets around HU are also a problem for that method. Try taking those out too and let us know.

Thanks for reporting this - it looks like one small change should fix the problem.

5

works perfectly now, thanks so much :pray: