Hi Kelli,

2 reasons. One is if you use the talairach to average functional data for whole-brain analysis. The other is for reporting purposes. We do use it a bit in the intensity normalization, but if the cortical labels look fine then it's not a problem.

cheers, Bruce On Tue, 2 Jan 2007, Dominick, Kelli, Ray Carpenter wrote:

Thanks so much for your response. Is it necessary for the talairach transform to be corrected for the freesurfer cortical and subcortical segmentation to work properly? Our labels look good. What is the reason/purpose behind fixing the transform? Looking at the ReconAllDevTable it doesn't look like the transform is used.

Thanks again for your help, Kelli

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, December 27, 2006 7:36 PM To: Dominick, Kelli, Ray Carpenter Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] talairach questions

Hi Kelli,

the official talairach xform is in mri/transforms/talairach.xfm and it uses the MNI tools to transform into the MNI space. The talairach.lta is

something that is used as part of the subcortical segmentation, and we believe could work as a tal xform, but we don't use it as such as it hasn't been validated to be a true talairach space. We may do some internal verification one of these days and use it instead, but not yet.

cheers, Bruce

On Wed, 27 Dec 2006, Dominick, Kelli, Ray Carpenter wrote:

...

Hi All, We have had a number of brains with very bad talairach transforms however aparc+aseg looks fine. In addition, while the talairach.xfm transform is very bad talairach.Ita is not. Is the bad xfm transform still a problem even though it is not affecting the labels. And if so which transform should I attempt to correct in tkregister2 in order to fix the problem? (I ask because it looks like that some of the

tutorials

...

still refer to old file names that have changed in the stable

versions).

...

I am using v3.03. Thanks in advance for your help! Kelli