How to fill the holes in 3D image reconstructed from binary images of CT slides

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I have around 200 CT slides from patients and need to reconstruct them and segment out the eye orbit. I read the original DICOM image, use imbinarize(I,T) to change them to binary image, and then stack them up to form the 3D orbital image (see attached images below).
However, as you can see, there are many holes inside the orbit. To cope with this, I use bwmorph() with 'thicken' and 'bridge', then use imclose() with the 'disk' parameter:
for i = 30 : 160
info = dicominfo(dirOutput(i).name,'UseDictionaryVR',true);
imgTemp = dicomread(info);
imgCropped = imcrop(imgTemp,bboxCrop);
imgCroppedBin = imbinarize(imgCropped,0.51728);
img_thick = bwmorph(imgCroppedBin,'thicken');
img_bridge = bwmorph(img_thick,'bridge',Inf);
se = strel('disk',1);
I(:,:,i) = imclose(img_bridge,se);
I(:,:,i) is the resulting 3D array. Then I use fv = isosurface(I,ISOVALUE) and patch() to reconstruct the 3D array to a 3D image (as attached above).
The resulting 3D image still has many holes unfilled. Increasing the STREL element size or decreasing the ISOVALUE will make the final model thick and coarse (e.g. with stair case inside).
May I ask how can I fill the resulting holes in the 3D model and still preserve the original smoothness of the image? Should I do this in the 3D image or do this in 2D binary image before the reconstruction?

Accepted Answer

Matt J
Matt J on 22 Jan 2018
It might help to look at some of these Examples with alphaShape. Basically, if you tune the alpha radius right, I think you might be able to plug the holes.

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