Creating 3D model from large (90GB) segmentation (NRRD volume)

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21

I don’t have acccess to commercial cloud, but will add 1TB swap and see if this replicates.

23

Actually I tried with the new surface nets/smoothing option enabled, and everything worked fine, up to a point. Model is supposedly generated and saved into the scene, I can look up it is properties. It is over 600M polygons.

image
image517×663 49.9 KB

But no model is being displayed in 3D viewer. There is an error about display properties:

Switch to module:  "ImageStacks"
Switch to module:  "Data"
GetItemName: Failed to find subject hierarchy item by ID 27


Switch to module:  "SegmentEditor"
ctkSliderWidget::setSingleStep()  0 is out of bounds. 0 10 1
void qMRMLSegmentationGeometryWidget::setReferenceImageGeometryForSegmentationNode() : Reference image geometry of Affenschaedel_0000_Segmentation is set to ' -0.0086287;0;0;0.01294305;0;-0.0086287;0;0.01294305;0;0;0.0086287;-0.01294305;0;0;0;1;176;3655;600;3671;312;5811; '
Switch to module:  "Segmentations"
Warning: In vtkMRMLSegmentationDisplayNode.cxx, line 302
vtkMRMLSegmentationDisplayNode (0x5f51020): vtkMRMLSegmentationDisplayNode::GetSegmentDisplayProperties: no display properties are found for segment ID=2.25.166211090335523915802933448538484626475, return default


void qMRMLSegmentationDisplayNodeWidget::updateSelectedSegmentSection() : No display properties found for segment ID  "2.25.166211090335523915802933448538484626475"
Warning: In vtkMRMLSegmentationDisplayNode.cxx, line 302
vtkMRMLSegmentationDisplayNode (0x5f51020): vtkMRMLSegmentationDisplayNode::GetSegmentDisplayProperties: no display properties are found for segment ID=2.25.166211090335523915802933448538484626475, return default


void qMRMLSegmentationDisplayNodeWidget::updateSelectedSegmentSection() : No display properties found for segment ID  "2.25.166211090335523915802933448538484626475"
virtual double qSlicerSubjectHierarchyFolderPlugin::canOwnSubjectHierarchyItem(vtkIdType) const : Input item is invalid
Warning: In vtkMRMLSubjectHierarchyNode.cxx, line 2156
vtkMRMLSubjectHierarchyNode (0xb85a3c0): GetItemDataNode: Invalid item ID given


Switch to module:  "Data"

Right now I am saving it as PLY, it has been over 30GB and still going on.

@Tyler so things are working, but the resultant model will be so big am not sure what you can do with it.

24

Ill try that, I assumed the new surface nets option is less accurate though?

25

I have not noticed any issues with it to make me thing it is any less accurate.

26

ill make a comparison then with the halved part too

27

tried with the surface nets option (not smoothing) and same error.