addendum: i mistakenly said that talairach.xfm is used in the
skull-strip stage... it is not. so beyond really bad talairach
failures, the only critical reason to redo the talairach.xfm is if the
ICV calculation (which itself is pretty rough) is valuable to you (for
correcting volume stats by hea
Andy,
I'll answer the last first: that error message (the one in ALL CAPS)
can be ignored. It originates in the bowels of some fortran code in the
VNL library we use. A real error detected at the level of our code
would exit if there was a problem with the minimization.
Per the talairach.xfm,
Hello Freesurfer Experts-
We recently reran several subjects from scratch through the stable
Freesurfer 5.0 pipeline who had previously been processed with the stable
4.5 pipeline. We used tkregister2 for QA of the 5.0 data and noticed that
the talairach transform was off (misaligned) for th
