Segmentation issue - "invisible" labels

Support
1

Hi all,

sorry for semi-reposting (I initially thought this was a pyradiomics issue and therefore posted there, but now figured that it is a segmentation issue):

I am having a problem with importing CNN generated segmentations of two brain structures (bilaterally, so 4 segmentations / VOIs in total) on MRI.

When I load the MRI volume and the segmentation file, it looks good, only the light blue VOI isn’t fully recognized as a segmentation/label it seems:

Screen1
Screen11603×693 199 KB

But when I add it in the Segmentations module it looks fine:

Screen2
Screen21642×941 243 KB

However, out of the four segmentations, I can only edit a single one (the brown one, seg 4), although all four are visible - any segmentation tool that I try on the other three will result in nothing - as if they were not there at all.

How can that be?

The volume and segmentation file are in the folder below (all deidentified of course):

Link

Many thanks!

2

You can try upgrading to the current Slicer version (5.6.1) and make sure you save the segmentation into an image with integer type (unsigned char, short, etc).

3

Thanks - I tried the new version, but no change, still not editable.

In terms of saving, what option would that be (i.e. file extension)?

4

To fix the loading issue, you can convert your numpy array to uint8 before writing to file. Like this: