Hi Martin,

Thanks for the input, but I think you got me wrong. The talairach registration and talairach check during -autorecon1 is fine. I think the -careg stage during -autorecon2 might fail, which "generates a multi-dimensinal talairach transform" (mri_ca_register). And I was looking for something like the tutorials you mentioned, however not for the talairach registration during -autorecon1, but for mri_ca_register.

Regards, Falk

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Kavec Sent: Thursday, May 28, 2009 1:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting

Hi Falk,

On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote:

Hello,

I’m having trouble to generate a correct aseg.mgz for one volume of mine. The nu_noneck.mgz is also incorrect and therefore I think the -careg stage of autorecon2 might fail. Is there a way to do some kind quality check, like the tal-check during autorecon1, to see whether the talairach.m3z is incorrect? Are there some kind of instructions like fixing the bad output from the talairach registration?

For this you can follow instruction on

http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction

and more specifically

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

Hope some of that may lead you to successful reconstruction.

Best,

Martin

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