# Segmenting a bottle in a CT scan is slow

**URL:** <https://discourse.slicer.org/t/segmenting-a-bottle-in-a-ct-scan-is-slow/30128>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [June 19, 2023, 7:01pm UTC](https://discourse.slicer.org/t/segmenting-a-bottle-in-a-ct-scan-is-slow/30128 "2023-06-19T19:01:19Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Raha\_Sep](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/raha_sep/32/15684_2.png) [@Raha\_Sep](https://discourse.slicer.org/u/Raha_Sep)\
**Post date:** [June 19, 2023, 7:01pm UTC](https://discourse.slicer.org/t/segmenting-a-bottle-in-a-ct-scan-is-slow/30128/1 "2023-06-19T19:01:19Z")

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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

_(download link removed on request of the original poster)_

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 19, 2023, 7:12pm UTC](https://discourse.slicer.org/t/segmenting-a-bottle-in-a-ct-scan-is-slow/30128/2 "2023-06-19T19:12:52Z")

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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.

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**Author:** ![Raha\_Sep](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/raha_sep/32/15684_2.png) [@Raha\_Sep](https://discourse.slicer.org/u/Raha_Sep)\
**Post date:** [June 20, 2023, 1:58pm UTC](https://discourse.slicer.org/t/segmenting-a-bottle-in-a-ct-scan-is-slow/30128/3 "2023-06-20T13:58:14Z")

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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!

 ![0](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/e/ee67ef72632bc5eac38714301a6e289e64f81efb.jpeg)  
 ![1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/3/03fd7706b7eefafbe30c82a3540eaa164aa0762c.jpeg)  
 ![2](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/6/667280d9d19c8797397a2fb1ef7bd31a8a5798cd.jpeg)  
 ![3](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/d/2d2ec17d67d77773238b39c7ae21f816b22fd201.jpeg)

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 20, 2023, 3:16pm UTC](https://discourse.slicer.org/t/segmenting-a-bottle-in-a-ct-scan-is-slow/30128/4 "2023-06-20T15:16:05Z")

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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

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<div class="post-metadata">

**Author:** ![Raha\_Sep](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/raha_sep/32/15684_2.png) [@Raha\_Sep](https://discourse.slicer.org/u/Raha_Sep)\
**Post date:** [June 20, 2023, 4:23pm UTC](https://discourse.slicer.org/t/segmenting-a-bottle-in-a-ct-scan-is-slow/30128/5 "2023-06-20T16:23:15Z")

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

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [September 8, 2023, 1:03pm UTC](https://discourse.slicer.org/t/segmenting-a-bottle-in-a-ct-scan-is-slow/30128/6 "2023-09-08T13:03:28Z")

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A post was split to a new topic: [Segmenting 3D printed heartseg](https://discourse.slicer.org/t/segmenting-3d-printed-heartseg/31617)