Hi Michele,

For now the best work-around is to just re-run recon-all -normalization -subjid <subjid>

this will regenerate a T1 that has the skull and you can use this to fix your skull strip. I might suggest you rename your current T1.mgz volume before running this, otherwise you will write over it.

Jenni

On Tue, 15 Nov 2005, Bruce Fischl wrote:

Hi Michele,

this is the way that the dev version currently works - the T1 gets recreated in a 2nd pass that rerun the intensity normalization. We're going to change this in the upcoming official release because it's too confusing.

Bruce

On Tue, 15 Nov 2005, Michele Perry wrote:

...

Hi, I am having problems with the dev version of Freesurfer. I realized after viewing the aseg that there was a skullstrip problem that I hadn't noticed when I checked the brain volume between -autorecon1 and -autorecon2. When I open brain.mgz and T1.mgz in tkmedit, they look identical (i.e. I can't see skull in the T1). Any idea what went wrong? Michele _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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