Querying and persisting clinical data (Age, MMSE.......) in XNAT

[Reda Fritet]

Hello everyone,

I have a question regarding accessing and modifying clinical or derived data directly via the XNAT PostgreSQL database.

In my XNAT 1.8.9 instance, I noticed that some information displayed in the UI (for example Patient Age shown in the MR Session details) is read from the DICOM files at display time and does not appear to be persisted in PostgreSQL (e.g. dcmpatientbirthdate is NULL, and there is no age column in xnat_subjectdata).

On the other hand, values entered through Custom Field Sets / Form Manager (such as MMSE scores) are stored in PostgreSQL (for example in xnat_experimentdata.custom_fields as JSONB), and can be queried with SQL.

My questions are:

1. Is it recommended or supported to insert or update values directly in PostgreSQL (e.g. updating custom_fields JSONB) for derived or clinical variables like MMSE or Age?

2. For DICOM-derived values such as PatientAge (0010,1010), is there a recommended way to persist them in XNAT so that they become searchable via SQL or XNAT search (e.g. via Subject Variables, Assessors, or custom datatypes)?

3. Are there best practices for making DICOM-derived metadata queryable (without breaking XNAT indexing, permissions, or audit trails)?

The goal is to enable queries such as “all sessions/subjects with age = 55” or “MMSE ≥ 24” in a safe and XNAT-compliant way.

Thank you in advance for your guidance.

Best regards,
Reda

[Timothy Olsen]

Age is a calculated field.  If you have the subject dob (or yob) populated and the date populated in your experiment, then the form should show the age.  The Age column should be available in the Edit Columns option when you list all of your imaging sessions, either on the project page or from Data -> [Modality] Sessions.  Are you seeing it there?

Tim

Timothy R Olsen 

Founder, President

 t...@xnatworks.io

 xnatworks.io | Find us on LinkedIn! 

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[Reda Fritet]

Thanks for the clarification. In my instance, session dates are populated, but the subject DOB/YOB isn’t stored (likely due to anonymization), so Age can’t be calculated. I also don’t see an Age column under Edit Columns when listing sessions. Is Age computed strictly from stored DOB/YOB, or can it also use the DICOM PatientAge (0010,1010) tag?

[Timothy Olsen]

XNAT doesn't currently support populating the Age from the DICOM. I'm not exactly sure why it was never added, but at present it isn't there.  Maybe its because we were more focused on the DOB, which was more complicated.

I know some people have written scripts to pull the YOB and Age from the DICOM, but I don't think any of those have ever been made public.  It would probably be easy to have Claude write a script that does it and then throw it in a container that runs automatically for each session.  It's annoying to have to do that, apologies.  Or you could add it to your Custom Form and manually input it.

Tim

Timothy R Olsen 

Founder, President

 t...@xnatworks.io

 xnatworks.io | Find us on LinkedIn! 

To view this discussion visit https://groups.google.com/d/msgid/xnat_discussion/36cc889e-0eab-4043-8a0d-2559ade0b229n%40googlegroups.com.

[Elena Baumeister]

Hello Reda, 
how did you manage to set the custom_fields. Are you doing it via a Python script? In my case I can set them, but next time I wanna get them from a specific scan they are not existing anymore.
So maybe you can show a code snippet?

Kind regards,

Elena