Hi Bruce,
It doesn't look good; actually, I can't see anything when I load it in tkmedit.
If I re-run the alignment with mritotal as described in the manual (Final objective function value = 0.38553751), I do get an image, although it appears shrunken. Not sure what might cause this, or how to fix.
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2 & 3, Alan Gilbert Building
161 Barry St
Carlton South Vic 3053 Australia
Ph: +61 3 8344 1624
Fax: +61 3 9348 0469
email: alexander.fornito@wh.org.au
-----Original Message-----
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: Fri 4/28/2006 1:35 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] 3T problems
did you check the talairach?
On Fri, 28 Apr 2006, Fornito, Alexander wrote:
Hi,
I'm trying to segment some Siemens 3T images (200x200x256; 1mm3) and have encountered some problems at autorecon1 - the normalization seems to label some of the background as white matter. Needless to say, the skullstrip fails spectacularly. I've attached a snapshot of the T1 image showing the problem.Any ideas as to why this might occur?
I'm running recon-all version 1.104
Thanks,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2 & 3, Alan Gilbert Building
161 Barry St
Carlton South Vic 3053 Australia
Ph: +61 3 8344 1624
Fax: +61 3 9348 0469
email: alexander.fornito@wh.org.au
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