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kirbyju / TCIA_Notebooks

Notebooks for working with The Cancer Imaging Archive datasets. Have you written one? Submit a PR!
https://cancerimagingarchive.net
Apache License 2.0
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label_image in view function does not show the segmented tumor! #26

Open ManooshSamiei opened 9 months ago

ManooshSamiei commented 9 months ago

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 commented 9 months ago

I had some trouble installing itk stuff after upgrading to python 3.12. Here's the issue I submitted and their reply: https://github.com/InsightSoftwareConsortium/ITK/issues/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 commented 9 months ago

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 commented 9 months ago

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.

Screenshot 2024-02-11 at 7 38 03 PM
kirbyju commented 9 months ago

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

kirbyju commented 1 month ago

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