# Radiomics problem for VUE images

**URL:** <https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207>\
**Category:** Support\
**Tags:** radiomics\
**Created:** [April 20, 2020, 3:15pm UTC](https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207 "2020-04-20T15:15:39Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![aileeno](https://avatars.discourse-cdn.com/v4/letter/a/3e96dc/32.png) [@aileeno](https://discourse.slicer.org/u/aileeno)\
**Post date:** [April 20, 2020, 3:15pm UTC](https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207/1 "2020-04-20T15:15:39Z")

</div>

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’

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [April 20, 2020, 3:16pm UTC](https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207/2 "2020-04-20T15:16:29Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![aileeno](https://avatars.discourse-cdn.com/v4/letter/a/3e96dc/32.png) [@aileeno](https://discourse.slicer.org/u/aileeno)\
**Post date:** [April 20, 2020, 4:26pm UTC](https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207/3 "2020-04-20T16:26:15Z")

</div>

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’

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [April 20, 2020, 5:01pm UTC](https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207/4 "2020-04-20T17:01:48Z")

</div>

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](https://github.com/Radiomics/SlicerRadiomics/pull/60) should fix the problem.

---

<div class="post-metadata">

**Author:** ![aileeno](https://avatars.discourse-cdn.com/v4/letter/a/3e96dc/32.png) [@aileeno](https://discourse.slicer.org/u/aileeno)\
**Post date:** [April 20, 2020, 6:28pm UTC](https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207/5 "2020-04-20T18:28:54Z")

</div>

works perfectly now, thanks so much 🙏