Changing the voxel size after segmentation

Support
1

I have done multiple segmentations. The problem is I now realized that the voxel size is to big. Can I still change them and if so in what module?

2

See detailed instructions here. Let us know if something is not clear.

1 Like
3

@lassoan I had a student who performed segmentations on several specimens but didn’t use the correct spacing (should have been 0.005 rather than 1 mm) - and now I’m getting this error.

image
image539Ă—387 34.7 KB
. I don’t think there’s any way I’ve run out of RAM. Suggestions to fix this, please?
image
image570Ă—150 6.49 KB

4

If the physical size of the segmentation remains the same but the resolution is increased 1 / 0.005 = 200 times along each axis then the segmentation would become enormous (a 100MB segmentation size would grow to 100MB * 200 * 200 * 200 = 781 GB). Instead, you need to scale down both the physical size and the resolution of the image and the segmentation.

You can scale the segmentation and the corresponding image by creating a scaling transform in Transforms module (write 0.005 into the first 3 elements of the transformation matrix diagonal) and then apply and harden it on the volume and segmentation.

@muratmaga Is there a SlicerMorph tutorial for this?

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5

No, but I guess I should do an FAQ for this. To mitigate suggest exporting the segmentation as a labelmap and then entering correct image spacing both for source volume and labelmap, and then reimporting the labelmap as a segmentation to continue the work.

It is a bit simpler for people not to mess with transforms.

1 Like
6

Thanks! I will try it!

7

Thanks! If you do a FAQ on it, can you please send/tag me in it if you remember? Thank you.