Re: [Freesurfer] Talairach xform problem

That probably means that the registration is way off. As an experiment, try running it with --regheader to see if it looks more reasonable (eg, something that looks like a brain regardless of how far off the registration is). Can you send the talairach.xfm?

doug

On 8/13/10 12:55 AM, Tricia Merkley wrote:

Hi Bruce,

Yes, I can get tkregister2 to run properly, but the "moveable" image is just a single bright line. When I try to scale, translate, rotate, etc., the line will move a little bit. But it is still just a single line, instead of a volume to compare with the target image.

Have you seen anything like this before?

Thanks, Tricia

--- On *Thu, 8/12/10, Bruce Fischl /fischl@nmr.mgh.harvard.edu/* wrote:

From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Talairach xform problem
To: "Tricia Merkley" <tmerkle22@yahoo.com>
Cc: freesurfer@nmr.mgh.harvard.edu
Date: Thursday, August 12, 2010, 6:34 PM

Hi Tricia,

when you say "to no avail" what do you mean? Have you been able to
get
tkregister2 to run properly?

cheers
Bruce
On Thu, 12 Aug 2010, Tricia Merkley wrote:

> Hi Freesurfers,
>
> Is there a solution for fixing a bad talairach transform as
shown in the attached figures?  Recon-all completed without error
(with the -notal-check included, v4.5.0), and the output looks
pretty good.  However I'm concerned that the 'IntraCranialVol'
value will be off since it is based on the tal xform.
>
> I've tried to fix it as described at
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, but
to no avail.  I'd appreciate any suggestions.
>
> Thanks,
> Tricia
>
>
>
>


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