Integration of MONAILabel in OHIF Viewer 3.6.1 on XNAT 1.8.10

[JHOAN SEBASTIAN MORA COLORADO]

Hello everyone, i hope you are all doing well

I'm seeking guidance on how to integrate MONAILabel into OHIF Viewer 3.6.1 within XNAT 1.8.10. Currently, we are using the OHIF viewer integrated into our XNAT server, but we would like to transition to MONAILabel for segmentation, as the NVIDIA tool we were using is deprecated. Could anyone provide any advice, tutorials, or resources that might help me make this integration successfully?

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UdeA

[Ahmed Harouni]

Hi Jhoan

I can defiantly help you with that. We created a full DLI workshop at GTC 2023 and GTC 2024 showing this work flow please take a look at this https://www.nvidia.com/en-us/on-demand/session/gtc24-dlit61433/ starting min47 where we show Xnat integration. 

There are multiple scripts that we have setup in to make the DLI simple so please let me know if you get stuck or something is not clear. 

We are working on making this workshop available as self paced 

[Simon Doran]

Hi Ahmed,

  Kudos to you for such a great demonstration! The number of different integrations you showed is very impressive.

  Thanks for putting together all the resources in terms of the Jupyter notebooks. Are you able to post a link here to the notebooks themselves?

  Best wishes,

Simon

[Ahmed Harouni]

Hi Simon 

Glad you liked the content with all the integrations.

We are still not sure where is the best place to post these notebooks. We might create a self paced DLI if there is enough interest for it. We might push it to the monai gibhub repo. I am slowly pushing features to the monai label xnat datastore but it is taking sometime. 

[Ryan Sullivan]

Hi Ahmed,

Anywhere for starters! We have started work integrating MONAI into the Australian Imaging Service, to connect to XNAT-OHIF, 3DSlicer, QuPath, and CVAT viewers (we have a diverse array of research projects needing different ones). The notebooks would be very useful for my development team.

Cheers,
Ryan
Head of the Australian Imaging Service
The University of Sydney

[An ZHAO]

Good work. The video demo around 50 minutes is particularly interesting for me. 

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[Ahmed Hosny]

Indeed - I second that. It would be great to get some documentation on integrating MONAILabel with XNAT-OHIF, especially wrt setting up the dicom listener in XNAT. We have been using MONAILabel with Slicer, and would like to transition to XNAT-OHIF since all our data lives in there. Great video demo!

[DrRadiohead]

Dear Ahmed,

We had same thought, and grateful to @Ahmed Harouni to discuss this. great demo again.

Issue is OHIF segmentations are currently stored as dicom segments, there is no plugin to convert them into nifty.

Maybe you can support the issue I have raised on OHIF xnat plugin.

https://bitbucket.org/icrimaginginformatics/ohif-viewer-xnat-plugin/issues/57/ohif-plugin-to-save-a-nifti-mask-of-the

Warm Regards