Hi Rosalia
yes, editing and rerunning recon-all should work. Or update the brainmask.mgz with your own version if you want. We should detect that and retain it.
cheers Bruce
On Wed, 14 Nov 2018, Rosalia Dacosta Aguayo wrote:
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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.
- I have run recon-all -all in a participant
- The skull stripped image has skull and dura behind.
- 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