Best way of handling multi-modality sessions

[angel.m...@gmail.com]

Hi I'm trying to work out the best way to handle data sets where patients have images of multiple modalities that may have been taken in the same session or may not and that may be uploaded together in a single zip or may be uploaded in separate zip files. 

Some context...

We are setting up an XNAT server to manage multiple trials from different centres and ideally we would like the upload process to result in consistently handled image sets regardless of how people group the data during upload. 

For example some trials will have a Pet CT session or a SPECT CT session. There are some constraints we have to consider

• In many centres researchers are not able to install programs locally to help with uploads so would want to use the uploader.
• In some cases these images will be exported to a single folder without anything in the file names to indicate if they belong to the PET or CT for example.
• In other cases the images will be exported separately. 

What we had hoped to do was to use custom DICOM routing to allow us to ensure that it didn't matter whether the images were uploaded together or not but this hasn't been possible. It seems that XNAT is not happy to have multiple image sessions uploaded in a single zip or to add an image uploaded at a later time via the compressed uploader to an existing session. If you manually create a scan in the existing session and upload to it via the file manager the files are not processed in the same way as they would have been if you used the compressed uploader. 

I thought I would test out the PET-MR session to see how it works and whether it was a viable solution to this issue but I haven't been able to get XNAT to use it. I enabled in the project settings (i.e create a single PET-MR rather than separate sessions for PET-MR) but it just made a PET session and stuck both images in it. It would be great if someone could explain what criteria have to be met so that XNAT will create a PET-MR session. The sample data I had didn't include an MR so I just changed the modality type of a PET-CT to be PET and MR instead but perhaps there are other fields that would need to be modified. Alternatively perhaps someone could tell me which loggers to change to a higher level so that I can see messages from XNAT regarding what it's doing when it choses a Session type to create?

any help is much appreciated

Angel

[Moore, Charlie]

Hi Angel,

The first thing to explain is how XNAT assigns session types. Setting aside PET/MR for a second, when XNAT gets a collection of DICOM instances for a session, it looks at the modalities present in the collection and picks the highest one up in this list: https://bitbucket.org/xnatdcm/dicom-xnat/src/master/dicom-xnat-sop/src/main/resources/lead-modalities.txt . PET-MR is different in that it's configurable what it does, but it unfortunately has various problems that you may be running into:

1. DQR being installed at all makes the feature break: https://issues.xnat.org/browse/XNAT-6098
2. Project-level anonymization makes the feature break: https://issues.xnat.org/browse/XNAT-6865
3. The settings for it don't work quite right: https://issues.xnat.org/browse/XNAT-4825

Assuming you're on XNAT 1.8.X, have you seen the setting under Administer > Site Administration > Miscellaneous for "Prevent Cross-Modality Post-Archive Session Merger"? If that setting is off, it may be blocking the merges you're attempting. You can turn it on, but it has some inherent drawbacks I've listed here: https://groups.google.com/g/xnat_discussion/c/RqX87mN_XDI/m/lkAkB156AgAJ . In particular, turning the setting on makes "consistently handled image sets regardless of how people group the data during upload" impossible. If the user uploads the CT part of a PET-CT first, and then merges in the PET part, you will end up with a CT session. Likewise if the user uploads the PET [PT] part first, you'll get a PET Session.

Thanks,

Charlie

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Subject: [XNAT Discussion] Best way of handling multi-modality sessions

 

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[angel.m...@gmail.com]

Thanks Charlie, that's a very helpful response. I will read up on those links and we should be able to use this info to decide how we can best handle multi-modality sessions for our trials.

regards

Angel