Dear FreeSurfers,

In the course of checking my skull-strips I discovered that one of my subjects does not have a T1.mgz because they did not pass the automatic Talairach failure detection. I checked the transformation with tkregister2 and –fstal, and it actually looks quite good; the brain is tilted, but the Talairach brain follows the tilt nicely. Nonetheless, to move things forward I made a few small edits and saved the registration. I then re-ran autorecon1 using the –notalairach option (at the end of the command line) in order to make use of my edits. However, I got the exact same error back—Talairach transformation ***FAILED***--and consequently there’s no T1.mgz.

I thought that by specifying –notalairach at the end of the command line while running autorecon1, I would be bypassing the Talairach detector and thus would be able to avoid this problem, but I’m obviously wrong. How do I make use of my edited Talairach and get autorecon1 to continue?

Thanks in advance,

Dan Dillon, Ph.D.

Post-doctoral Fellow

Affective Neuroscience Lab

Dept. of Psychology, Harvard University

Phone: (617) 495-1889

E-mail: dillon@wjh.harvard.edu