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
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--
Jenni Pacheco, M.A.
Massachusetts General Hospital
Athinoula A. Martinos Center for Biomedical Imaging
Bldg. 149, 13th Street, CNY 2301
Charlestown, MA 02129
[EMAIL PROTECTED]
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