Segmenting a Entire Slice!

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1

The my Micro CT data are reformated with " Fit slice plane to markup fiducials " script. I expected to fill the entire selected slice with Scissor effect by drawing a rectangle. (Same with the paint). However there are areas of unfilled areas which corresponds to the slice below. !

Is this has to do with reformatting ?

2
21176×624 152 KB

1
11906×507 152 KB

And when we do the segment growing etc… the final results in the last two slice are not very good becuase of this.

.

3
31309×1102 234 KB

Is there a way to make a very nice clean cut ? because when we try with segment effects always the changes in this slice will be reflect in the above slice so on…

  1. Why is this happening ?

  2. Is there a better way of obtaining a clean cut segment of predictable height ? ( we want to make sure the segment height is always 2 mm. )

2

This looks normal. See explanation here: https://lassoan.github.io/SlicerSegmentationRecipes/ObliqueSliceSegmentation/

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3

Thank you proffesor @lassoan the oversampling (by 2 ) works well.

I do not understand about oversampling. Does this affect volume calculations ?

What does oversampling actually does ?

What are the advantage/ disadvantages of this ?

4

It should not significantly affect volume calculations, probably the difference is well below 1%.

Subdivides the original voxels to smaller ones.

Advantage is that you can represent finer details. Disadvantage is that it increases memory usage and computation time.

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