Plans to support DICOM Segmentation Storage IOD?

Hi there,

I would like to use Clara to segment scans and view them in the OHIF Viewer (https://github.com/OHIF/Viewers/, http://ohif.org/). We plan to support DICOM Segmentation Storage files in OHIF directly, and I was wondering if this is a planned output of Clara’s DICOM adapter.

I tested the organ segmentation pipeline and it looks like it is producing CT Image Storage DICOM objects with the labelled regions as different label values in the grayscale image. I couldn’t find any configuration for the output in the docs (https://docs.nvidia.com/clara/deploy/ngc/DicomAdapter.html).

I suppose I could write a pipeline operator to convert from the CT Image Storage to a Segmentation Storage file using dcmqi (https://github.com/qiicr/dcmqi), but it feels like this should be built into the adapter.

Thanks,

Erik

Hi

Thanks for reaching out and your interest in Clara.
We would defiantly be interested in integrating with OHIF. Your proposal defiantly makes sense to create a new clara write converting segmentation labels and produce DICOM SEG format that OHIF can automatically read and overlay. Just wondering since OHIF is going through structure changes between 1.x and 2.x. Is Dicom Seg supported for both 1.x and 2.x?

I hope you are part of the hackathon next week to implement this. If not I will respond end of next week with updates.

Thanks

Yes I will be participating!

That is a good question. 1.x OHIF by itself doesn’t support SEG, but the XNAT-OHIF plugin does (which is what the hackathon is about).

Thanks,

Erik

Hi,

As a XNAT user with the OHIF Viewer plugin, I am looking for a solution such as the one you have outlined, Erik. Do you have any news or information about DICOM SEG’s support?

Thanks to both of you,
Sebastien

Hi

Thanks for you interest. Yes we are working on getting SEG support as a Clara Writer format. This would work with OHIF2.x. We are also working on getting it supported for Xnat-OHIF too. We are in prototyping phase so no time lines yet.

Thanks

Hi,

Thanks for your answer.
I am very interested in SEG support in general, for Xnat-OHIF among others.

If I can be useful in performing tests, please do not hesitate to contact me.

Thanks,

Is there any updates to this?

Hi Thanks for your interest - yes, this is currently on the development roadmap and we are working on enhancing our DICOM Writer. Hope to have an update in the fall.

Clara Deploy already has another DICOM Object Writer for reporting segmentation (contours), namely the DICOM RT Structure Set Writer.
The DICOM Segmentation Object Writer is being released to Clara Deploy Early Access, and is definitely the correct “SEG”. The legacy Clara Dicom Writer merely served as a demo piece for wrapping and sending results out in a DICOM series, not intended to fully integrate with imaging workflow.

Regards.