Yes, it is quite confusing, and like most confusing things it is
historical in nature. When tkregister was originally written by
Anders/Marty, they set it up to map from the targ RAS to the mov RAS.
From an internal standpoint, it makes sense, but it is backards when
you think about "moveable" and "target". Believe me, I feel your pain. I
got tired of figuring it out myself, so I just added the --fstal flag.
doug
Michael Harms wrote:
Hello,
I've become confused about the direction of the transformation specified
in the talairach.xfm file.
It seems that if you "manually" specify the --targ and --mov volumes in
conjunction with the --xfm option, that the "target" must be the
talairach average to get proper alignment:
e.g.,
tkregister2 --targ $FREESURFER_HOME/subjects/fsaverage/mri/T1.mgz --mov
orig.mgz --xfm transforms/talairach.xfm --reg tmp.dat
(The same targ/mov definition appears to be the case if you want to use
--lta to view a .lta transform instead).
However, the resulting output to the terminal for "Input registration
matrix" does not match the talairach.xfm file -- is there a matrix
inversion somewhere??
But, if you use the --fstal option
e.g.,
tkregister2 --s 020819_43 --fstal
then orig.mgz is now the "target" and the talairach average is now the
"movable" volume, and the output to the terminal for "Input registration
matrix" now exactly matches the values in the talairach.xfm file. Based
on this, it seems that .xfm maps from mov to target (with orig.mgz being
the target). However that doesn't seem consistent with the required mov
and targ specifications with using the --xfm flag directly...
thanks for clarifying,
Mike H.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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