Can't export segmentation to binary labelmap in 4.11 Ubuntu 25.05.2020 version

Hi,

As in the title, I can’t export my segmentation to binary labelmap in 4.11 Ubuntu. It works perfectly in Windows & Mac, not in Ubuntu.

Please help.
Thanks in advance.

Lukasz

[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Session start time …: 2020-10-22 06:21:35
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Slicer version …: 4.11.0-2020-05-25 (revision 29077 / fb87a55) linux-amd64 - installed release
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Operating system …: Linux / 5.4.0-52-generic / #57-Ubuntu SMP Thu Oct 15 10:57:00 UTC 2020 - 64-bit
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Memory …: 32121 MB physical, 2047 MB virtual
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - CPU …: AuthenticAMD AMD Ryzen 9 3900X 12-Core Processor, 12 cores, 24 logical processors
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - VTK configuration …: OpenGL2 rendering, Sequential threading
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Qt configuration …: version 5.11.2, with SSL, requested OpenGL 3.2 (core profile)
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Developer mode enabled …: no
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Prefer executable CLI …: yes
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Application path …: /home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/bin
[DEBUG][Qt] 22.10.2020 06:21:35 [] (unknown:0) - Additional module paths …: /home/dugi/.config/NA-MIC/Extensions-29077/SegmentEditorExtraEffects/lib/Slicer-4.11/qt-scripted-modules, /home/dugi/.config/NA-MIC/Extensions-29077/MarkupsToModel/lib/Slicer-4.11/qt-loadable-modules, /home/dugi/.config/NA-MIC/Extensions-29077/VolumeClip/lib/Slicer-4.11/qt-scripted-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerHeart/lib/Slicer-4.11/cli-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerHeart/lib/Slicer-4.11/qt-loadable-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerHeart/lib/Slicer-4.11/qt-scripted-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerIGT/lib/Slicer-4.11/qt-loadable-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerIGT/lib/Slicer-4.11/qt-scripted-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerRT/lib/Slicer-4.11/cli-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerRT/lib/Slicer-4.11/qt-loadable-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerRT/lib/Slicer-4.11/qt-scripted-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerVMTK/lib/Slicer-4.11/qt-loadable-modules, /home/dugi/.config/NA-MIC/Extensions-29077/SlicerVMTK/lib/Slicer-4.11/qt-scripted-modules
[CRITICAL][Qt] 22.10.2020 06:21:37 [] (unknown:0) - Error(s):
CLI executable: /home/dugi/.config/NA-MIC/Extensions-29077/SlicerVMTK/lib/Slicer-4.11/qt-loadable-modules/vtkvmtk.py
The process failed to start. Either the invoked program is missing, or you may have insufficient permissions to invoke the program.
[CRITICAL][Qt] 22.10.2020 06:21:37 [] (unknown:0) - Fail to instantiate module “vtkvmtk”
[CRITICAL][Qt] 22.10.2020 06:21:37 [] (unknown:0) - The following modules failed to be instantiated:
[CRITICAL][Qt] 22.10.2020 06:21:37 [] (unknown:0) - vtkvmtk
[DEBUG][Python] 22.10.2020 06:21:40 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/lib/Slicer-4.11/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations
[DEBUG][Python] 22.10.2020 06:21:42 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/lib/Slicer-4.11/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 22.10.2020 06:21:42 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/lib/Slicer-4.11/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 22.10.2020 06:21:42 [] (unknown:0) - Switch to module: “Welcome”
[INFO][VTK] 22.10.2020 06:21:43 [vtkMRMLVolumeArchetypeStorageNode (0x6ace820)] (/work/Preview/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:471) - Loaded volume from file: /home/dugi/.config/NA-MIC/Extensions-29077/SlicerVMTK/lib/Slicer-4.11/qt-scripted-modules/Resources/Vesselness.png. Dimensions: 65x50x1. Number of components: 3. Pixel type: unsigned char.
[DEBUG][Qt] 22.10.2020 06:21:46 [] (unknown:0) - Switch to module: “DICOM”
[ERROR][Python] 22.10.2020 06:21:51 [Python] (/home/dugi/.config/NA-MIC/Extensions-29077/SlicerHeart/lib/Slicer-4.11/qt-scripted-modules/DicomUltrasoundPlugin.py:134) - sopClassUID 1.2.840.10008.5.1.4.1.1.2 != supportedSOPClassUID 1.2.840.10008.5.1.4.1.1.3.1
[CRITICAL][Stream] 22.10.2020 06:21:51 [] (unknown:0) - sopClassUID 1.2.840.10008.5.1.4.1.1.2 != supportedSOPClassUID 1.2.840.10008.5.1.4.1.1.3.1
[DEBUG][Python] 22.10.2020 06:21:51 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/bin/…/lib/Slicer-4.11/qt-scripted-modules/MultiVolumeImporterPlugin.py:456) - MultiVolumeImportPlugin::examine
[DEBUG][Python] 22.10.2020 06:21:52 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/bin/…/lib/Slicer-4.11/qt-scripted-modules/MultiVolumeImporterPlugin.py:496) - DICOMMultiVolumePlugin found 1 multivolumes!
[DEBUG][Python] 22.10.2020 06:21:52 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/bin/…/lib/Slicer-4.11/qt-scripted-modules/MultiVolumeImporterPlugin.py:168) - MultiVolumeImportPlugin:examineMultiseries
[DEBUG][Python] 22.10.2020 06:21:52 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/bin/…/lib/Slicer-4.11/qt-scripted-modules/MultiVolumeImporterPlugin.py:173) - DICOMMultiVolumePlugin found 0 multivolumes!
[INFO][Python] 22.10.2020 06:21:52 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/bin/…/lib/Slicer-4.11/qt-scripted-modules/DICOMScalarVolumePlugin.py:336) - Loading with imageIOName: GDCM
[INFO][Python] 22.10.2020 06:21:54 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/bin/…/lib/Slicer-4.11/qt-scripted-modules/DICOMScalarVolumePlugin.py:408) - Window/level found in DICOM tags (center=100.0, width=600.0) has been applied to volume 2: Std
[DEBUG][Python] 22.10.2020 06:21:54 [Python] (/home/dugi/Dokumenty/Slicer-4.11.0-2020-05-25-linux-amd64/bin/…/lib/Slicer-4.11/qt-scripted-modules/DICOMScalarVolumePlugin.py:741) - Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 2.96484e-06 mm, tolerance threshold is 0.001 mm).
[INFO][Stream] 22.10.2020 06:21:52 [] (unknown:0) - Loading with imageIOName: GDCM
[INFO][Stream] 22.10.2020 06:21:54 [] (unknown:0) - Window/level found in DICOM tags (center=100.0, width=600.0) has been applied to volume 2: Std
[DEBUG][Qt] 22.10.2020 06:22:00 [] (unknown:0) - Switch to module: “SegmentEditor”
[WARNING][Qt] 22.10.2020 06:22:00 [] (unknown:0) - QLayout::addChildLayout: layout “” already has a parent
[WARNING][Qt] 22.10.2020 06:22:00 [] (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1
[DEBUG][Qt] 22.10.2020 06:22:10 [] (unknown:0) - Switch to module: “Data”
[ERROR][VTK] 22.10.2020 06:22:13 [vtkMRMLSegmentationNode (0x9641dc0)] (/work/Preview/Slicer-0/Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.cxx:1016) - ExportSegmentsToLabelmapNode: Failed to generate shared labelmap
[CRITICAL][Qt] 22.10.2020 06:22:13 [] (unknown:0) - void qSlicerSubjectHierarchySegmentationsPlugin::exportToBinaryLabelmap() : “Failed to export segments from segmentation Segmentation to labelmap node!\n\nMost probably the segment cannot be converted into binary labelmap representation”
[DEBUG][Qt] 22.10.2020 06:28:01 [] (unknown:0) - Switch to module: “SegmentEditor”
[DEBUG][Qt] 22.10.2020 06:28:01 [] (unknown:0) - Switch to module: “Segmentations”
[ERROR][VTK] 22.10.2020 06:28:27 [vtkMRMLSegmentationNode (0x9641dc0)] (/work/Preview/Slicer-0/Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.cxx:1016) - ExportSegmentsToLabelmapNode: Failed to generate shared labelmap
[CRITICAL][Qt] 22.10.2020 06:28:27 [] (unknown:0) - bool qSlicerSegmentationsModuleWidget::exportFromCurrentSegmentation() : “Failed to export segments from segmentation Segmentation to labelmap node Segmentation-Segment_1-label_1!\n\nMost probably the segment cannot be converted into binary labelmap representation.”

I get a lot of lines of this:
[ERROR][Python] 22.10.2020 06:21:51 [Python] (/home/dugi/.config/NA-MIC/Extensions-29077/SlicerHeart/lib/Slicer-4.11/qt-scripted-modules/DicomUltrasoundPlugin.py:134) - sopClassUID 1.2.840.10008.5.1.4.1.1.2 != supportedSOPClassUID 1.2.840.10008.5.1.4.1.1.3.1

and this:
[CRITICAL][Stream] 22.10.2020 06:21:51 [] (unknown:0) - sopClassUID 1.2.840.10008.5.1.4.1.1.2 != supportedSOPClassUID 1.2.840.10008.5.1.4.1.1.3.1

Just erased them, so I could fit the log in here.

Regards,
Lukasz

Please try with latest Slicer Stable Release and let us know if you run into any problems.

4.11 from 25.05 is the latest stable that works under Ubuntu. 4.11 from 5.10.2020 and 4.13 just don’t start.

Many people uses latest version of Slicer (4.11.20200930) on Ubuntu without any problems. What CPU, Graphics, and Ubuntu version do you have?

Ryzen 3900x, amd r5 230 gpu, ubuntu 20.4

Radeon R5 230 was launched in April 2014. Do you have this one? We try to balance between compatibility and performance/simplicity of our code base. As a result, we aim for keeping compatibility with hardware that is released in the past 5 years. Can you try with a newer card or at least latest drivers?

Does latest ParaView version work on your computer?

Paraview runs OK, I just installed it, the program opens and windows respond.

I have this R5 230 that you mention. Will update drivers and let you know.

Regards,
Lukasz

Updated AMD drivers to the latest version, didn’t help. Still can’t export segmentation to binary labelmap. Your help would be very much appreciated.

Regards,
Łukasz

ParaView uses similar Qt and VTK versions as Slicer, so it it probably just some trivial configuration option that causes you problems.

What do you see when you start Slicer? Are any windows displayed? Do you see any error messages? Can you get a stack trace?

Does Slicer start if you remove Slicer.ini (or the entire Slicer settings folder)?

When I start 25.05 4.11 version - all is OK, until I try to export to binary - then it is not possible.
Version 4.11 form 30.09 - just does not start, for a millisecond a initial logo appers and instantly disappears.

Shame on me, but I can’t locate Slicer.ini. I have extracted Slicer folders into documents folder, can’t find .ini file.

OK, just found Slicer.ini. Will experiment.

I just remember now that there is a problem with recent Qt versions on linux - this may solve your problem:

Super. The problem was solved by reinstalling xinerama:

sudo apt-get install --reinstall libxcb-xinerama0

Now latest 4.11 works, and export to binary works as well.

Thank you!
Best regards,

Lukasz

1 Like

Awesome. I’ll add this to the linux install instructions.

1 Like