Hi Bruce,

so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation

Hi Maria

you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.

cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:

Hi Bruce,

thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and

DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.

Thanks again, Maria

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation

Hi Maria

as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.

cheers Bruce

p.s. not sure why it would be smaller

On Fri, 9 Sep 2011, Maria Felber wrote:

...

Dear all,

sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.

Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.

However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.

Thanks for the help, Maria

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