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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

sounds like the talairach.xfm is degenerate. Can you start with the identity matrix instead?

cheers Bruce On Thu, 12 Aug 2010, 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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.