Paint Bucket tool in the editor?

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Paint Bucket tool in the editor?

_-_-_
This post was updated on .
Hello everybody

Is there a paint bucket tool in the editor to fill enclosed areas?
Independent of the background value of the enclosed pixels.



Thank you
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Re: Paint Bucket tool in the editor?

Andras Lasso-2

Paint bucket tool would not work for creating solid models from bone CT. The issue is that simple thresholding can only segment thick cortical bone. Filling “holes” manually would be too tedious, especially because the contour is often not closed.

 

Try the following:

·       Before thresholding, apply a noise filter (for example, Anisotropic anomalous diffusion filter, in AnomalousFiltersExtension works very well)

·       After thresholding, fill small holes using Smoothing effect, with Closing (fill holes) method

·       Fill large holes manually, using Paint effect or LevelTracing effect (no need to be very accurate, just make large holes a bit smaller)

·       Repeat the last two steps until all holes are gone

 

If the contrast in the image is very low then you may manually segment on a few slices and interpolate between them using “Auto-complete” effect, “Fill between parallel slices” method.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of _-_-_
Sent: December 23, 2016 4:13
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Paint Bucket tool in the editor?

 

Hello everybody Is there something like a paint bucket tool in the editor to fill enclosed areas.? I've attached a picture. Thank you


View this message in context: Paint Bucket tool in the editor?
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Re: Paint Bucket tool in the editor?

_-_-_
Thanks for the hints. I will give it a try.

The CT contains heavy metal artifacts radiating from an implant. So the
noise is not homogeneous distributed in the volume.



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Re: Paint Bucket tool in the editor?

_-_-_
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In reply to this post by Andras Lasso-2
Thanks for the hints. I will give it a try.

The CT contains heavy metal artifacts radiating from an implant. So the noise is not homogeneous distributed in the volume.
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Re: Paint Bucket tool in the editor?

Andras Lasso-2
In reply to this post by _-_-_

FYI, I’ve added this tool to the Segment editor. It’s available in “Islands” effect, choose “Add selected island” operation and click in the hollow region to fill it.

 

Most probably it’ll not be very useful for your problem (because cortical bone is rarely creates a watertight enclosure), but it was easy to add this feature and it can be useful for others.

 

I’ve also added the options of keeping largest island, remove all small island (speckles), split islands to segments, and keep or remove clicked island.

 

Andras

 

From: Andras Lasso
Sent: December 23, 2016 14:38
To: '_-_-_' <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: RE: Paint Bucket tool in the editor?

 

Paint bucket tool would not work for creating solid models from bone CT. The issue is that simple thresholding can only segment thick cortical bone. Filling “holes” manually would be too tedious, especially because the contour is often not closed.

 

Try the following:

  • Before thresholding, apply a noise filter (for example, Anisotropic anomalous diffusion filter, in AnomalousFiltersExtension works very well)
  • After thresholding, fill small holes using Smoothing effect, with Closing (fill holes) method
  • Fill large holes manually, using Paint effect or LevelTracing effect (no need to be very accurate, just make large holes a bit smaller)
  • Repeat the last two steps until all holes are gone

 

If the contrast in the image is very low then you may manually segment on a few slices and interpolate between them using “Auto-complete” effect, “Fill between parallel slices” method.

 

Andras

 

From: slicer-users [[hidden email]] On Behalf Of _-_-_
Sent: December 23, 2016 4:13
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Paint Bucket tool in the editor?

 

Hello everybody Is there something like a paint bucket tool in the editor to fill enclosed areas.? I've attached a picture. Thank you


View this message in context: Paint Bucket tool in the editor?
Sent from the slicer-users mailing list archive at Nabble.com.


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[hidden email]
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