Hi Jon, it is not supposed to be horizontal. The anatomy in the target is just supposed to match that in the moveable. doug ps. please respond to the list. thanks!

On 03/26/2013 02:35 PM, Jon Wieser wrote:

HI doug, i viewed it with tkregister2. the transform looks poor, the ac-pc line is not horizontal. i have attached a pic Jon

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, March 26, 2013 11:28:01 AM Subject: Re: [Freesurfer] recon-all bad talairach

Hi Jon, the data are not reoriented or resliced into talairach space. It is just the transform that is computed. To inspect whether this was done right, use

tkregister2 --s subject --fstal

doug

On 03/26/2013 12:20 PM, Jon Wieser wrote:

...

Hello I ran recon-all auto_recon1. and the resulting brainmask file, has a poor talairazation. the ac-pc line is not horizontal, it's tilted, and the interhemisphere fissure is tilted too. how do I fix this? I have attached a picture of the brain

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