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I have a stack of medical images which have 2.5 mm slice thickness and 1.5 mm slice spacing. So the slices are overlapping. I intend to create a 3D volume from these slices and I am not sure if I am not scaling in the z direction (where the slice spacing makes it confusing to me). Please let me know how to accurately construct 3D volume from 2D slices which are overlapping.

This is what I did so far

I read the CT slices, slice by slice(in a for loop) into a 3D matrix. 

    for count = 1:totalSlices
      fileName = dirData(count).name;
      dicomImage = dicomread(fileName);
      imageStack(:,:,count) = dicomImage;
    end

And I used the ExportVoxelData function from Matlab central to generate an stl file from the image stack above

I do have an stl model but I do not know if it is scaled correctly in the z direction My pixel dimensions are 0.9766 mm in X and Y dimensions. My slice thickness is 2.5 mm My slice spacing is 1.5 mm

kish
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1 Answers1

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Are they overlapping? Half voxel thickness= 1.25mm. Spacing between image planes is 1.5mm. You have 0.25mm gaps between adjacent voxels in the z-direction.

orangozhang
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  • If the slice thickness is less than the spacing between slices, then there is a gap region between the slices that was not imaged. If the slice thickness is greater than the spacing between slices, then the slices overlap (there exists a region that contributed information to both of the adjacent slices). So the overlap in my slices is 2.5-1.5 = 1 mm. The problem is I dont know how to account for this overlap when I am making a 3D model... – kish Nov 11 '14 at 15:10