Maybe I am confused about what the various threads were discussing. There are separate issues:
+ having alignment troubles---how to fix alignment.
+ after good alignment, deciding which affine+nonlinear files to use to apply the transformation to other datasets or for other calculations.
+ calculating a Jacobian from from an existing (good) alignment.
It would probably be best to have separate threads about separate issues.
--pt
Edited 1 time(s). Last edit at 11/01/2021 09:18AM by ptaylor.
