[Freesurfer] Flipped Hemisphere longitudinal analysis

Dear Freesurfers,

Has anyone accomplished analysis of longitudinal cortex changes in a dataset with "flipped" hemispheres?

I am currently struggling with data from stroke patients, half of them with lesions on the right, half of them on the left side of the brain.

What I am planning: flip all healthy hemispheres to left and perform longitud. analysis of cortical thickness change on that (helthy) hemisphere.

I have read the notes on Surface-based Interhemispheric Registration (xhemi) and most of the comments here. It seems to me that this would allow me to compare both hemisph. sides at ONE timepoint. (but not actually analyzing ONE (flipped) hemisphere over time).

Any help to point me in the right direction is greatly appreciated!

Bastian