Re: [Freesurfer] recon-all after n4 correction

Hi Katie

I think that should be ok, but of course the only way to know for sure is to try!

cheers Bruce

On Mon, 26 Nov 2018, Kathryn Fitzgerald wrote:

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Dear FS experts,

I was wondering if it is possible to run recon-all (e.g. autorecon2, autorecon3) on skull-stripped i mages which have gone through N4 correction.

Would it be okay to run?

recon-all -i sub1.nii.gz -subjid s1 -autorecon1 -sd . -noskullstrip

I saw the work around for already skull-stripped images, but I wasn't sure if this would be appropri ate for images which have also been corrected by N4. Or is there another way I should approach this?

Thank you for the help in advance!

Kind regards, Katie