Upload RT Structure to XNAT

[Vesa Alexandru]

Hello,

I'm new to XNAT. I want to know if it's possible to upload a RT Struct for a current patient?

Do i need to convert it into XML? if yes, how?

Thanks,

Alex

[Charlie Moore]

Hi Alex,

The answer to this depends on what you want to do with the RTSTRUCT. If you just want to store it in XNAT along side the other series in a study, there isn't really anything special to do, as the normal upload mechanisms will handle it just fine as long as the based series are also uploaded with the RTSTRUCT. If you're trying to view the RTSTRUCT in the OHIF Viewer Plugin, you'd need to get it into an "ROI Collection" [container for the RTSTRUCT within XNAT] assessor that the viewer expects. I think your options for that are...

1. https://bitbucket.org/icrimaginginformatics/roiuploadassistant/src/master/ I believe this a GUI tool written by the ICR team to create an ROI Collection, although I don't have experience with it.

2. Convert it with a container: I'm not sure if it's still supported, but it looks like there's a container to generate the assessor here https://hub.docker.com/r/xnat/rt-struct-scan-to-assessor .

3. Manually create the ROI Collection with REST, more details here: https://groups.google.com/g/xnat_discussion/c/zrQNtZgLIaw/m/urGwd4YBBgAJ

Thanks,

Charlie

[Vesa Alexandru]

Hi, 

Thanks a lot for your answer.

Have you used any of this method? I need some help tho.

Thanks again,

Alex

[James d'Arcy]

Hi Alex

I have recently updated the README for the ROIUploadAssistant to indicate how to use it. In terms of 3, how to use the REST API to upload an RTSTRUCT is there in the post. You will need to replace SEG with RTSTRUCT for your use case. Documentation for the right command line options to use with curl are easy to find.

James

[loren...@gmail.com]

Hi Alex, 

If you want to see an example using XNATPy as well, you can have a look here: https://github.com/loressa/MyXNATPy/blob/master/upload_ROI.py

Best,

Lorena 

[Ahmed Hosny]

Thanks James for updating the ROIUploadAssistant README. 

I have an issue where valid RTSTRUCT and DICOM SEG files are greyed out for me and hence I am unable to select them for upload. Any ideas there?

The files are valid as I can load them in 3D Slicer.