Duplicated Segmentation Error


(Pervin Hüseyinova) #1

I am working on dicom files, where i segment vessels on every slice. I crop every volume, apply curvature anisotropic diffusion and oversample the volume to get higher quality segmentation. My problem is that after a while of segmentation i start seeing the same segmentations on consecutive slices, eventough i labelled them differently. For example, as seen in the pictures below. I labeled them differently, but somehow labels ended up being duplicated and i lost the segmentation i did for the second one.
Screenshot_1 Screenshot_2

Thank you in advance.


(Andras Lasso) #2

See the answer in this topic:


(Andras Lasso) #3

Also note that when you iterate through the image slice by slice then the current background volume spacing is used for determining step size. You can enable slice intersections (click on the down-arrow button next to the crosshair button on the toolbar and check “Slice intersections”) to see how much the slice position is offset with each step.


(Pervin Hüseyinova) #4

But i didn’t painted the adjacent slice. I painted them all differently, but somehow some of the labels ended up being exactly same. This is a huge problem for me since I’m losing a lot of my work, what can be causing this? Is it possible that this is happenning because i use oversampling with isotropic spacing?


(Andras Lasso) #5

You can see the brush thickness in the orthogonal slices to verify if you indeed paint only in a single slice.

It may be confusing to edit a segmentation that has higher resolution than the master volume (because arrow keys on keyboard jump by one slice thickness distance but you may not be centered on the slice; slide offset slider above the slice viewer jumps a small amount, which is typically somewhat smaller than the slice thickness, so it may put you somewhere off the center of the slice). It may be simpler to just resample the master volume using Crop&resample module before you start segmenting.