Threshold segmentation problem

Provides a system for patient-specific cardiovascular modeling and simulation.
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Justin Tso
Posts: 14
Joined: Thu May 16, 2019 4:23 pm

Threshold segmentation problem

Post by Justin Tso » Sat Jul 20, 2019 8:04 pm

Hi, I'm using the Windows version of SimVascular, and I'm using the threshold tool to make my segmentations, as LevelSet doesn't appear to work. However, for the images that I'm using, whenever I attempt to use the threshold tool, the yellow counter doesn't appear. If I move the preset value to some arbitrary value and then click on the image to perform the threshold, the preset value immediately goes back to zero and doesn't change no matter where I click on the Display. In addition, when I try using batch segmentation, nothing happens. When I use the threshold tool on the various clinical examples, it performs normally, but it doesn't work on these images. Would you happen to know what's happening?

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David Parker
Posts: 225
Joined: Tue Aug 23, 2005 2:43 pm

Re: Threshold segmentation problem

Post by David Parker » Mon Jul 22, 2019 2:30 pm

Hi Justin,

What SV version are you using? There is a new 2019-07-10 version that fixes the level set problem.

When you say yellow counter do you mean the yellow marker used to locate the image center? The path you are using to segment with needs to be visible for the yellow marker to show up.

When Preset is selected you click on Threshold to use the preset value, don't click on the image. When you select Preset what are the max/min values set for the slider? Can you please post a picture?

Cheers,
Dave

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Justin Tso
Posts: 14
Joined: Thu May 16, 2019 4:23 pm

Re: Threshold segmentation problem

Post by Justin Tso » Mon Jul 22, 2019 6:55 pm

Hi, I updated to the 2019-07-10 version and that fixes the LevelSet problem for the examples provided in the documentation. However, with the images I'm using, it produces the same error message as it did before in the previous version: "contour not created and added since it's invalid." The same error message pops up when I select Preset and try to use the threshold, and as stated before, if I try not using the Preset setting, the yellow contour marker (the one that you control with the left mouse button, sliding up and down the image until it matches the counter) doesn't appear at all. The max/min range for the Preset slider does seem unusually high: the minimum value is 0 while the maximum value is 1679.0, but the aortofemoral normal-2 example ranges from -3000 to 3000, so I'm not sure if that's the problem.

Attached is a screenshot of what I'm seeing. Thanks for your help!
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thresholderror.PNG
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David Parker
Posts: 225
Joined: Tue Aug 23, 2005 2:43 pm

Re: Threshold segmentation problem

Post by David Parker » Tue Jul 23, 2019 3:03 pm

Hi Justin,

The Contour not created error you are getting means that no contour can be extracted from the image data for the given Preset value, the max/min of the image data is larger or smaller than the Preset value.

You can examine the image data (Pixel value) by closing the Segmentation panel and moving the cross hairs using the left mouse button over the area you'd like to segment, see what range of values you are getting. The image value at the cross hair is displayed at the bottom left of the SV window. You can then try values within that range. Maybe your image contrast is just not very good in that area.

Cheers,
Dave

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