Hi Bruce,

I'm using freesurfer version 5.1.0. I currently try to process quantitative T1 (R1) maps derived from 4 and 18 deg. FLASH images and FA maps. Interestingly, transformation appears to fail less often when using single (16 deg.) FLASH images, only. SPM segmentation routine on the other hand works pretty well on both T1 and FLASH images (probably because of using header origin information - which was set to the anterior commissure- as first guess in the registration).

Thanks Simon ________________________________________ Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 9. Juli 2012 20:03 Bis: Baudrexel, Simon Cc: freesurfer@nmr.mgh.harvard.edu; Avi Snyder Betreff: Re: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi

Hi Simon

what version are you using? Avi Snyder (ccd) has been tracking down some interactions between his talairach code and our intensity normalization that seem to have made it more fragilie, particularly in 5.1. He has some suggested fixes that may improve things for you.

cheers Bruce

On Mon, 9 Jul 2012, Baudrexel, Simon wrote:

Hello,

since I experienced a high rate of registration errors using talairach_avi in the conventional recon-all processing stream (more than 50% misregistration), I would like to incorporate SPM affine registration parameters (as provided in the seg_inv_sn.mat file obtained from the segmentation routine) as initial guess "to help" talairach-avi. Is there a possibility to do this? How do I have to adjust the transformation matrix that it can be handled by freesurfer?

I also tried to circumvent the registration-problem using skull-stripped images, which unfortunately also did not improve the results (I think a template made from skull-stripped images has to be used in that case)

Any help would be much appreciated

Regards, Simon

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