Most of the softwares (that I know of) segment based on the intensity. Is there any software that can segment based on thickness? I am trying to segment left ventricle based on thickness from cardiac CT. I have been able to color code based on thickness using Amira but want to create different segments based on thickness of the wall. Your help is much appreciated. Thank you.
You can develop a code to do that for your own purposes. Post a sample image, so I can recommend you an approach for segmentation.
You could use morphological operations to identify segments with different thickness.
So let's say you have your segmentation (i.e. label-field) of the heart. In Amira you could now use the module Opening to remove voxels from the surface of the labelled region. If you set the size in pixels to, let's say, 4, in the new label-field all features with thickness smaller than 8 voxels will be removed. (For the other settings I recommend using "3D", "Ball", and "Precise".)
If you are interested in those regions which had been removed, i.e. those with thickness smaller than 8 voxels, you could use the Arithmetic module to subtract the new label-field from the original one.
Maybe some clean-up of the result is necessary to get rid of edge effects. You could use another Opening operation on it with size equal 1 pixel.
Arash Rabbani Thank you so much. I apologize for my late response. I have attached an image below. The LV endocardium has been segmented(although not perfect). Now I want to further segment the LV myocardium based on thickness.
Andreas Staude Thank you so much for your valuable comments. I apologize for late response. I could not locate the module "Opening" on amira. Is it a new module on latest version? FYI I am using Amira 5.4.3 which is not the latest one. And I am a newbie to the software which does not help. Thank you again.
Saroj Timilsina You are right, the module "Opening" is available in later versions (6.X) of Amira.
However, the functionality (not as versatile as in the later versions) is also available in earlier versions with the "Quantification+" extension, but you have to access it differently (attach a "Quantification" module to the label-field.
Thank you all for your valuable input. I think I have finally solved the problem of segmentation based on thickness.
Using the "measure thickness" or "measure distance" function to color code the 3D object (LV shell in my case) and manually selecting the triangles using pencil and deleting them followed by "extract surface" probably does the trick.
Arash Rabbani, Andreas Staude do you know if there is a way to change the scale to "mm" or a way to convert into mm? I have attached an image for reference. Any help would be much appreciated.
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