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Chan Vese Segmentation mask is not working Properly

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I cropped my DICOM image so the active contour be faster and segment between the black area and soft tissue.
Instead, I got a contour that overlaps the edge of the image and goes beyond this. How can this happen? See attached image.
Let me know if you need the m files.


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Accepted Answer

Anton Semechko
Anton Semechko on 26 Jun 2018
Your image appears to be "padded" on the top and bottom with gray values. The transition between the black background (containing the region of interest; ROI) and these gray regions, has large gradient that will attract the contour during segmentation; because evolution of the contour is guided by the strength of the image intensity gradient. My suggestions to you, (1) remove the padding, (2) initialize contour close to the ROI you want to segment.


Anton Semechko
Anton Semechko on 27 Jun 2018
'FastFCMeans' performs image segmentation by clustering of image intensities and is thus fundamentally different from the level-set segmentation algorithm you were using before. There is no initialization involved and the resulting segmentation depends only on the input parameters 'c' and 'q'; 'c' controls the number of intensity clusters and 'q' is a fuzzification parameter. See 'FastFCMeans' documentation for additional info.
Stelios Fanourakis
Stelios Fanourakis on 31 Aug 2018
Hi Anton.
Thanks for your valuable help so far. What I have not understand yet is how to get what I need. FastFCMeans algorithm indeed segmented the gray soft tissue from the background. What I want now is to get the black area above the soft tissue. Only this region above the tissue. I need to somehow segment it and measure its length, pixel area size, dimensions. Do I have to implement a snake contour like chan vese. How else can I obtain the values of this area? (pixel size, pixels in number, dimensions, length from top of the image to the beginning of the tissue).
Stelios Fanourakis
Stelios Fanourakis on 31 Aug 2018
Moreover, if you notice the soft tissue at the last pic available (untitled.png) you'll notice some black gaps between the soft tissue especially at the lower left side of the image. I need some kind of interpolation method to fill those gaps so the contour will not get messed. So the soft tissue will be a unit of seamless gray or white matter with no black gaps.
I attach an image to see the results so far. See that the contour gets troubled to the points where the soft tissue is not seamless and black gaps occur. Any idea of how to fix it?

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