Hi,

I believe this is repairable with some shifting in tkregister2, after all. I will contact again if this doesn't work, but no need to reply for now.

Thank you! Caroline

On Wed, 19 Dec 2007, Caroline Chapman wrote:

Hi Freesurfers,

Happy Holidays! I have a subject failing at Intensity Normalization, and upon checking the talairach, I found that it is very bad. When loaded in tkregister2, the talairach is off the screen, and the orientation is off--coronal is matched to saggital).

According to the wiki instructions, I will need to correct the transform. Is it possible to fix this bad talairach in tkregister2?

If it is helpful, I have the error message from the Intensity Normalization error printed below.

Thank you! Caroline

mri_normalize -g 1 nu.mgz T1.mgz

using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.484 1.141 -0.183 -61.600; -1.154 0.466 -0.149 -62.214; -0.067 0.226 1.231 276.948; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux node0072 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 athlon i386 GNU/Linux

recon-all exited with ERRORS at Tue Dec 11 15:16:05 EST 2007