segmentation by threshold

[Johannes Martens]

Hi everybody,

I am new to SimVascular, using it since last week and following the Modelling Tutorial on the Homepage (http://simvascular.ucsd.edu/docsModelGu ... ngLevelSet) to create a model of cardiac vessels.

In the segmetation-section "using thresholding to define a contour" in the tutorial it is possible to set a Center (X- and Y-coordinate) for the "threshold contour". However, this possibility is somehow missing in the program. Can anybody tell me if this is still possible? Or how do I have to proceed to set the center of the threshold. The program just chooses any of the areas in the the window (presumably the one with the highest graylevel). I attached a screenshot of the problem.

There are a couple of other differences between my installation (newer version than the one in the tutorial?) and the one described in the tutorial, but most of them I got figured out. Just this problem with the missing possibility to choose the center of thresholding, I could not yet figure out.

Can anybody help me with this issue?

Thanks a lot in advance!

Johannes

[Adam Updegrove]

Hi Johannes,

The threshold currently does not use a center value. The largest closed contour generated in the threshold is selected as the 2D segmentation. The center functionality was in a previous version and has since been removed. We are working at putting it back in.

If the current threshold method does not give a good enough representation of the vessel, try using the level set methods or the manual segmentations.

Thanks!

The SimVascular Development Team

[Johannes Martens]

Hi Adam,

thanks a lot for the reply and the information! This saves me a lot of time looking for the feature in different places.

I have been using the level set segmentation method as a work around but in some case the segmentation by threshold (with a center) could have been a better solution before manual segmentation.

Thanks again.

Johannes