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Hi Nicole. It might be a large dataset issue but so far I have yet to kill it strictly speaking with that (at least for volumes and volume labels). The mac pro has 12 core, 128gb of ram and dual ati FirePro D700 6144mb. With dynamic addition of swap as needed it doesn't seem to run out of memory (though in this case I believe I hadn't even run out of physical memory yet). The reason I was wondering on GPU rendering was that when one does this for volume rendering I quite often run out of graphics memory and crash vs cpu rendering which can take advantage of the much larger ram size on the computer works just fine.
In case it was more of a corruption issue, here is the text from that log file as well if that help:
[DEBUG][Qt] 19.04.2016 16:01:24 [] (unknown:0) - Session start time .......: 2016-04-19 16:01:24
[DEBUG][Qt] 19.04.2016 16:01:24 [] (unknown:0) - Slicer version ...........: 4.5.0-2016-04-17 (revision 25012) macosx-amd64 - installed
[DEBUG][Qt] 19.04.2016 16:01:25 [] (unknown:0) - Operating system .........: Mac OS X / 10.11.4 / 15E65 - 64-bit
[DEBUG][Qt] 19.04.2016 16:01:25 [] (unknown:0) - Memory ...................: 131072 MB physical, 1024 MB virtual
[DEBUG][Qt] 19.04.2016 16:01:25 [] (unknown:0) - CPU ......................: GenuineIntel 2.700 MHz, 12 cores
[DEBUG][Qt] 19.04.2016 16:01:25 [] (unknown:0) - Developer mode enabled ...: no
[DEBUG][Qt] 19.04.2016 16:01:25 [] (unknown:0) - Prefer executable CLI ....: yes
[DEBUG][Qt] 19.04.2016 16:01:25 [] (unknown:0) - Additional module paths ..: (none)
[CRITICAL][Qt] 19.04.2016 16:01:28 [] (unknown:0) - Error(s):
Cannot load library /Applications/slicer_4-18-2016/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libPerformMetricTestLib.dylib: (dlopen(/Applications/slicer_4-18-2016/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libPerformMetricTestLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib
Referenced from: /Applications/slicer_4-18-2016/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libPerformMetricTestLib.dylib
Reason: image not found)
[CRITICAL][Qt] 19.04.2016 16:01:29 [] (unknown:0) - Error(s):
Cannot load library /Applications/slicer_4-18-2016/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libVBRAINSDemonWarpLib.dylib: (dlopen(/Applications/slicer_4-18-2016/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libVBRAINSDemonWarpLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4-build/lib/libITKIOBMP-4.10.1.dylib
Referenced from: /Applications/slicer_4-18-2016/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libVBRAINSDemonWarpLib.dylib
Reason: image not found)
[DEBUG][Qt] 19.04.2016 16:01:29 [] (unknown:0) - Number of registered modules: 143
[DEBUG][Qt] 19.04.2016 16:01:34 [] (unknown:0) - Number of instantiated modules: 143
[WARNING][Qt] 19.04.2016 16:01:34 [] (unknown:0) - When loading module "CLIEventTest" , the dependency "CLI4Test" failed to be loaded.
[INFO][Stream] 19.04.2016 16:01:34 [] (unknown:0) - Initializing terminology mapping for map file /Applications/slicer_4-18-2016/Slicer.app/Contents/share/Slicer-4.5/ColorFiles/Terminology//GenericAnatomyColors-SNOMED.csv
[INFO][Stream] 19.04.2016 16:01:34 [] (unknown:0) - 288 terms were read for Slicer LUT GenericAnatomyColors
[WARNING][Qt] 19.04.2016 16:01:35 [] (unknown:0) - When loading module "TwoCLIsInARowTest" , the dependency "CLI4Test" failed to be loaded.
[WARNING][Qt] 19.04.2016 16:01:35 [] (unknown:0) - When loading module "TwoCLIsInParallelTest" , the dependency "CLI4Test" failed to be loaded.
[DEBUG][Qt] 19.04.2016 16:01:35 [] (unknown:0) - Number of loaded modules: 140
[DEBUG][Qt] 19.04.2016 16:01:35 [] (unknown:0) - Switch to module: "Welcome"
[CRITICAL][FD] 19.04.2016 16:05:39 [] (unknown:0) - 2016-04-19 16:05:39.719 Slicer[8290:981178] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[CRITICAL][FD] 19.04.2016 16:06:07 [] (unknown:0) - 2016-04-19 16:06:07.260 Slicer[8290:981178] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[CRITICAL][FD] 19.04.2016 16:06:16 [] (unknown:0) - 2016-04-19 16:06:16.586 Slicer[8290:981178] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[INFO][VTK] 19.04.2016 16:08:10 [vtkMRMLVolumeArchetypeStorageNode (0x13e0da940)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:455) - Loaded volume from file: /Volumes/Sammy_Tank/CT_Scan_Place/MK84/korbin_segmented/mk84_segmented-label_2.nrrd. Dimensions: 1500x1500x7540. Number of components: 1. Pixel type: short.
[DEBUG][Qt] 19.04.2016 16:08:11 [] (unknown:0) - "Volume" Reader has successfully read the file "/Volumes/Sammy_Tank/CT_Scan_Place/MK84/korbin_segmented/mk84_segmented-label_2.nrrd"
[WARNING][Qt] 19.04.2016 16:08:25 [] (unknown:0) - libpng warning: iCCP: known incorrect sRGB profile
[WARNING][Qt] 19.04.2016 16:08:25 [] (unknown:0) - libpng warning: iCCP: known incorrect sRGB profile
[DEBUG][Qt] 19.04.2016 16:08:26 [] (unknown:0) - Switch to module: "ModelMaker"
[CRITICAL][FD] 19.04.2016 16:08:35 [] (unknown:0) - 2016-04-19 16:08:35.626 Slicer[8290:981178] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[DEBUG][Qt] 19.04.2016 16:10:04 [] (unknown:0) - Found CommandLine Module, target is /Applications/slicer_4-18-2016/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/ModelMaker
[DEBUG][Qt] 19.04.2016 16:10:04 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 19.04.2016 16:11:00 [] (unknown:0) - Model Maker command line:
/Applications/slicer_4-18-2016/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/ModelMaker --color /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_vtkMRMLColorTableNodeFileGenericColors.txt.ctbl --modelSceneFile /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_AxBGIBIfFGA.mrml#vtkMRMLModelHierarchyNode1 --name whatevs --generateAll --start -1 --end -1 --skipUnNamed --smooth 5 --filtertype Laplacian --decimate 0.25 --splitnormals --pointnormals --pad --debug /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_vtkMRMLLabelMapVolumeNodeB.nrrd
[DEBUG][Qt] 19.04.2016 16:56:29 [] (unknown:0) - Model Maker standard output:
The input volume is: /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_vtkMRMLLabelMapVolumeNodeB.nrrd
The labels are:
The starting label is: -1
The ending label is: -1
The model name is: whatevs
Do joint smoothing flag is: 0
Generate all flag is: 1
Number of smoothing iterations: 5
Number of decimate iterations: 0.25
Split normals? 1
Calculate point normals? 1
Pad? 1
Filter type: Laplacian
Input color hierarchy scene file: None
Output model scene file: /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_AxBGIBIfFGA.mrml#vtkMRMLModelHierarchyNode1
Color table file : /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_vtkMRMLColorTableNodeFileGenericColors.txt.ctbl
Save intermediate models: 0
Debug: 1
Starting...
Models file: /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_AxBGIBIfFGA.mrml
Model Hierarchy ID: vtkMRMLModelHierarchyNode1
Imported model scene file /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_AxBGIBIfFGA.mrml
Got model hierarchy node vtkMRMLModelHierarchyNode1
GenerateAll! set make mult to true
useStartEnd = 0, numModelsToGenerate = 1, numFilterSteps 13
Adding 1 pixel padding around the image, shifting origin.
Colour table file name = /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_vtkMRMLColorTableNodeFileGenericColors.txt.ctbl
Setting the colour node's storage node id to vtkMRMLColorTableStorageNode1, it's file name = /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_vtkMRMLColorTableNodeFileGenericColors.txt.ctbl
Read colour file /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_vtkMRMLColorTableNodeFileGenericColors.txt.ctbl
Using color node to get max label
Setting histogram extentMax = 307
Skipping 0
Hist: Min = 1 and max = 4 (image scalar type = 4, max = 32767)
GenerateAll flag is true, resetting the start and end labels from: -1 and -1 to 1 and 4
GenerateAll: there are 0 models to be generated.
Reset numFilterSteps to 4
Marching cubes: Using end label = 4, start label = 1
Image data extents: 0 1499 0 1499 0 7539
Label 4 has 9.1521e+09 voxels.
Got color name, set label name = whatevs_4_4 (color name w/o spaces = 4)
Number of polygons = 267487428
After decimation, number of polygons = 200615570
Writing model whatevs_4_4 to file /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/whatevs_4_4.vtk
Adding model whatevs_4_4 to the output scene, with filename /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/whatevs_4_4.vtk
Got colour: 0.435294 0.721569 0.823529 1
Added display node: id = vtkMRMLModelDisplayNode2
Setting model's storage node: id = vtkMRMLModelStorageNode1
...done adding model to output scene
End of looping over labels
Made models from labels: 4
Skipped making models from labels: 1 2 3
Writing to model scene output file: /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_AxBGIBIfFGA.mrml, to url: /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_AxBGIBIfFGA.mrml
Models saved to scene file /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/ICJA_AxBGIBIfFGA.mrml
Cleaning up
Deleting cubes
Deleting hist
Deleting smoother poly
Deleting decimator
Deleting mcubes
Deleting image threshold
... done deleting image threshold
Deleting image to structured points
Deleting transform ijk to ras
Deleting transformer
Deleting normals
Deleting stripper
Deleting ici, no set input null
Deleting reader
Deleting model scene
[DEBUG][Qt] 19.04.2016 16:56:29 [] (unknown:0) - Model Maker completed without errors |
