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