Question about T1-volume atlas statistics for GM, WM, and CSF

[Aira Fatima]

Dear Clinica team,

I am currently using the T1-volume pipeline for my study cohort, and I would like to clarify one point regarding the outputs.

At present, the pipeline saves atlas statistics for gray matter, which I understand correspond to regional average gray matter intensity/density. I was wondering whether it is also possible to obtain atlas-level statistics for white matter and CSF intensities, as well as ROI-level GM, WM, and CSF volume-related measures.

I ask because I can already see the corresponding segmented GM, WM, and CSF files in normalized space, including both modulated-on and modulated-off images. I would therefore like to know whether these measures can be extracted directly from the outputs already generated?

I would be very grateful for your advice. and yes, thank you very much for this excellent platform.

Best,

Aiira

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[Alice Joubert]

Hello Aiira,

Thanks for reaching out. Indeed, the atlases we currently use in T1-Volume are specifically for GM statistics. Details about them can be found here in the documentation. I think you could apply the t1-volume-parcellation part of the pipeline with another atlas that would describe more WM and CSF to get these statistics. You can add your own atlases to use with the pipeline, which is described here in the documentation.

Hope this helps !

Tell me if you need more details,

Alice