[Freesurfer] Freesurfer vs. CAT12

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Hi,

Recently, I ran an analysis on Freesurfer and found increased cortical thickness on the patients compared to controls.

Then, I heard about CAT12 and wanted to see if my results would be robust enough and be replicated using this other software. When I ran the analysis on CAT12, the results look completely different (both increased and decreases). I was not able to see the same clusters on the CAT12 results. I used the same subjects and covariates.

I ran recon-all using both T1 and T2 images, whereas in CAT12 you can only use T1 images.

Has anyone experimented with both software before?

Best, Omar