Segmenting a bottle in a CT scan is slow

Support
1

Hello,
I would like to segment a bottle geometry from the DICOM file and save it as a vtk file. I started with “Segment Editor” and “Crop Volume” but the 3D slicer works super slow. Can you please help me to find the best way/modules for this purpose?
Many thanks

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2

The image size is 512 x 512 x 692, so it is not very large. If you have something like 4GB free RAM then all operations should be quite fast. On my 3-year-old computer (8th-gen Intel Core i7, 32GB RAM) segmentation takes a couple of seconds in Segment Editor module.

Please provide detailed description of the steps you perform (include every click you make) and how long they take.

3

Hi Lassoan,
Thank you for your prompt respond.
I’ve tried to clean up my system and I believe it works faster now (3D Slicer 5.0.3). However, I like to describe the steps I did:

  • Volumes: click on “Center Volume”/magnifying all views
  • Volume Rendering: changing the ROI/ click on “Display ROI”
  • Crop Volume: click on “Apply”
  • Segment Editor: “Add”/ on segment_1 I tring to segment the object using “Paint”/“Level Tracing”
  • click on “Show 3D”
  • since I made mistaks and the bottle should be hollow, here I clicked on “Fill Between Slices” first that took time to act.
  • Then I clicked on “Erase” but didn’t work.
  • I tried to use undo but nothings can change anymore.

Thanks in adnavce!

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Comments on the performed steps:

  • Volumes: click on “Center Volume”/magnifying all views → OK
  • Volume Rendering: changing the ROI/ click on “Display ROI” → do not use volume rendering, because it will occlude your segmentation; if you want to show volume rendering to get an idea of what is in the image, make sure you hide the volume rendering before you proceed with the next steps
  • Crop Volume: click on “Apply” → no need for cropping the volume; it is small enough that you should not run out ot memory if you have at least 8GB RAM in your computer
  • Segment Editor: “Add”/ on segment_1 I tring to segment the object using “Paint”/“Level Tracing” → it is easier to use Threshold effect to segment the bottle in 3D in a few seconds
  • click on “Show 3D” → OK
  • since I made mistaks and the bottle should be hollow, here I clicked on “Fill Between Slices” first that took time to act. → no need to use “Fill between slices” (Threshold effect is sufficient)
  • Then I clicked on “Erase” but didn’t work. → no need to use Erase
  • I tried to use undo but nothings can change anymore. → no need for Undo
1 Like
5

sounds perfect… the bottle has been segmented in a few seconds as you said byThreshold effect.
I appreciate your support.

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A post was split to a new topic: Segmenting 3D printed heartseg