label_image in view function does not show the segmented tumor!

[ManooshSamiei]

Hello,
I have tried all the notebooks in this repo, but i noticed in the new itk versions, i cant visualize the segmented tumor in the 3d visulization. Can you please help me find the issue?

[kirbyju]

I had some trouble installing itk stuff after upgrading to python 3.12. Here's the issue I submitted and their reply: InsightSoftwareConsortium/ITK#4451. After downgrading to Python 3.11 things worked again with itk 3.5.0. Not sure if this is your problem or if it's something else. I'd need more details. Also cc'ing @aylward as I've noticed that when I run through the MONAI notebook it only shows the prostate images and not the labels/segmentations. Maybe that's also what @ManooshSamiei was trying to say?

[aylward]

For fastest attention, this should be posted to the itkWidgets issue tracker.
https://github.com/InsightSoftwareConsortium/itkwidgets/issues

What version of jupyter lab/notebook are your running, what os, version of itkwidgets, etc.

[ManooshSamiei]

Also cc'ing @aylward as I've noticed that when I run through the MONAI notebook it only shows the prostate images and not the labels/segmentations. Maybe that's also what @ManooshSamiei was trying to say?

Yes exactly the segmentation is not shown. A clear example is MONAI notebook I also attach a screen shot of what should be shown in pink but is not shown... The python version in colab is 3.10.12, and the itk version is 5.3.0.

[kirbyju]

@ManooshSamiei Thanks for creating InsightSoftwareConsortium/itkwidgets#737. I'll keep an eye on their reply in case I need to update the notebooks here.

[kirbyju]

I've inquired in InsightSoftwareConsortium/itkwidgets#737 to see if there's anything I can do, but I think we're still waiting on the itkWidgets team.