We aren't getting the filtering options to display while using parenchyma analysis package on a few chest CTs.

Support
,
1

Operating system: Windows & MAC
Slicer version: 4-10-2
Expected behavior:

  1. Filtering on and off should display options.

  2. output for attenuation areas should be generated as numbers
    Actual behavior:
    We are facing below 2 key issues below and hope we can connect again to troubleshoot.

  3. We aren’t getting the filtering options to display. There is an error message that pops up that makes us think there might be an issue with the code for displaying these. Here is the error message:

Traceback (most recent call last):
File "C:\Users\bryant.england\OneDrive - University of Nebraska Medical Center\Documents\SlicerCIP4-10-2\SlicerCIP4-10-2-Extensions\Chest_Imaging_Platform\lib\Slicer-4.10\qt-scripted-modules\CIP\ui\PreProcessingWidget.py", line 198, in hideFilterParams
self.showFilterOptions(False)
File "C:\Users\bryant.england\OneDrive - University of Nebraska Medical Center\Documents\SlicerCIP4-10-2\SlicerCIP4-10-2-Extensions\Chest_Imaging_Platform\lib\Slicer-4.10\qt-scripted-modules\CIP\ui\PreProcessingWidget.py", line 216, in showFilterOptions
self.filterOptionsFrame.setShown(show)
AttributeError: QFrame has no attribute named 'setShown'
Traceback (most recent call last):
File "C:\Users\bryant.england\OneDrive - University of Nebraska Medical Center\Documents\SlicerCIP4-10-2\SlicerCIP4-10-2-Extensions\Chest_Imaging_Platform\lib\Slicer-4.10\qt-scripted-modules\CIP\ui\PreProcessingWidget.py", line 195, in showFilterParams
self.showFilterOptions(True)
File "C:\Users\bryant.england\OneDrive - University of Nebraska Medical Center\Documents\SlicerCIP4-10-2\SlicerCIP4-10-2-Extensions\Chest_Imaging_Platform\lib\Slicer-4.10\qt-scripted-modules\CIP\ui\PreProcessingWidget.py", line 216, in showFilterOptions
self.filterOptionsFrame.setShown(show)
AttributeError: QFrame has no attribute named 'setShown'
  1. If we try to create a lung label map despite the above error, it seems to create a map and segment the lungs. However, no output for attenuation areas is generated. Attached is a screenshot of the result:
    CIP_Issue
    CIP_Issue1911×1039 139 KB

Several Debug, Error, Info, and Critical messages appear. The last of these which we wonder if it might be the most serious is the following:

Traceback (most recent call last):
File "C:/Users/bryant.england/OneDrive - University of Nebraska Medical Center/Documents/SlicerCIP4-10-2/bin/../SlicerCIP4-10-2-Extensions/Chest_Imaging_Platform/lib/Slicer-4.10/qt-scripted-modules/CIP_ParenchymaAnalysis.py", line 434, in onApply
if not self.inputVolumesAreValid():
File "C:/Users/bryant.england/OneDrive - University of Nebraska Medical Center/Documents/SlicerCIP4-10-2/bin/../SlicerCIP4-10-2-Extensions/Chest_Imaging_Platform/lib/Slicer-4.10/qt-scripted-modules/CIP_ParenchymaAnalysis.py", line 362, in inputVolumesAreValid
self.createLungLabelMap()
File "C:/Users/bryant.england/OneDrive - University of Nebraska Medical Center/Documents/SlicerCIP4-10-2/bin/../SlicerCIP4-10-2-Extensions/Chest_Imaging_Platform/lib/Slicer-4.10/qt-scripted-modules/CIP_ParenchymaAnalysis.py", line 408, in createLungLabelMap
input_array = vtk.util.numpy_support.vtk_to_numpy(label_image.GetPointData().GetScalars())
AttributeError: 'module' object has no attribute 'util'
2

Please fully install the latest version of 3D Slicer and try again. Would be great if you could report back.

image
image1397×691 163 KB

3

Thank you, Rudolf, for your response !

We installed the version from:
cip.bwh.harvard.edu

Is that the latest version you are suggesting?

Punyasha

4

You should install the chest imaging platform from 3D Slicers installation manager.