Error when using segmentmesher

Support
1

Hello all,
I got the following error when I want to mesh my segmentations in segmentmesher:

./config/NA-MIC/Extensions-28797/SegmentMesher/lib/Slicer-4.11/qt-scripted-modules/SegmentMesher.py", line 296, in onApplyButton
self.cleaverPaddingPercentSpinBox.value * 0.01)

./config/NA-MIC/Extensions-28797/SegmentMesher/lib/Slicer-4.11/qt-scripted-modules/SegmentMesher.py", line 569, in createMeshFromSegmentationCleaver
self.logProcessOutput(ep, self.cleaverFilename)

./config/NA-MIC/Extensions-28797/SegmentMesher/lib/Slicer-4.11/qt-scripted-modules/SegmentMesher.py", line 472, in logProcessOutput
raise subprocess.CalledProcessError(return_code, processName)
subprocess.CalledProcessError: Command ‘cleaver-cli’ died with <Signals.SIGKILL: 9>.

Does any body know what are these errors related to?

2

It means that the kernel killed your process, most likely because you have run out of memory. Increase the swap space or lower your memory usage (by reducing the size of input volume or resolution of the output mesh).

3

Thank you very much for your answer. You are correct I monitored my memory and found that the memory limit is causing this error. How can I reduce the size of input volume? Should I do the segmentations again?
Thanks

4

No need to segment again. You can tune meshing parameters as described here: https://github.com/lassoan/SlicerSegmentMesher#mesh-generation-parameters. If the description is not clear enough then just try to change the parameters and see how it impacts the output. You may learn it on a smaller, simpler mesh, and once you are confident you can switch to your large mesh.

You can also increase swap space to prevent running out of memory (but execution may become much slower).

1 Like
5

Thank you very much for your help.