Different Volume Calculation Results

Support
1

I have a binary mask, I loaded it in 3D slicer as a segmentation file, and in Data module, I used “export visible segments to model”. Then in Models module, I can see the model volume is 55349.06 mm^3 (none smooth).

image
image1329×457 114 KB

Then, I used my own vtk codes to calculate its volume:

mask = vtk.vtkNIFTIImageReader()
mask.SetFileName('origCT_nodule_0.nii.gz')
mask.Update()
nodule = vtk.vtkDiscreteMarchingCubes()
nodule.SetInputData(mask.GetOutput())
nodule.Update()

massProperties = vtk.vtkMassProperties()
massProperties.SetInputData(nodule.GetOutput())
massProperties.Update()
volume = massProperties.GetVolume()
print(volume)

However, the volume is 47789.92 mm^3. I visualized it to check what happened:

image
image1290×720 67.4 KB

Oh, it seems this is an unclosed surface representation. I know 3D Slicer will close it first and then calculate its volume (as in the first screenshot). Then, I used vtkFillHolesFilter() to close the surface first:

fill_holes_filter = vtk.vtkFillHolesFilter()
fill_holes_filter.SetInputData(nodule.GetOutput())
fill_holes_filter.SetHoleSize(100.0)
fill_holes_filter.Update()

image
image1290×720 48.2 KB

This time, the volume is 40265.35 mm^3. What happened???

2

The topic was posted on the 3D Slicer forum, too:

@dzzhang in general, avoid posting the same question at the same time to multiple forums, because it may lead to several people spending time with providing the same answers. Very rarely, in some exceptional cases (e.g., the question is really urgent for you) you might decide to cross-post anyway, but then at least add a link to all other locations where you posted.

3

Thanks for the reminder, I will avoid this in future. Just would like more answers from two forums.