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Dear Free Surfer team,
Sorry for double posting but I would like to explain well so it will be easier to understand what I am looking for.
1. I have run recon-all -all in a participant 2. The skull stripped image has skull and dura behind. 3. I can manual edit or I can do -autorecon1 and then supply the brainmask.nii.gz generated from my betted image. 4. Questions:
a) If I run -autorecon1 and make the substitution of the brainmask: I am afraid this is not going to improve the grey matter and white matter segmentation. So, if this first step is not well solved, I think that then, no matter if I change my brainmask for a better one, that I will have the same problems with -autorecon2 and -autorecon3, is that correct?
b) If I do manual edition, then I will have to run -autorecon1 again...not sure if this would be the best solution.
As I am new to this, I would greatly appreciate your experience.
Best wishes, Rosalia