Hi Alex,

You can follow the instructions on the wiki, here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to fix the talairach using tkregister2. Since you have not run far enough to get surfaces yet, you will not need the last argument "-surf orig" nor will you see the green surface outline.

Jenni

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Fornito, Alexander Sent: Friday, April 28, 2006 1:54 AM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] 3T problems

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

As a 3T, the corpus callosum tends to be brighter than other wm, but the images that fail don't seem to be all that different to the ones that succeed, by eye.

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: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sat 4/29/2006 1:59 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3T problems

Did you look at the raw data to make sure there were no artifacts?

Fornito, Alexander wrote:

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer