Hi,
I'm a little confused, so please correct me if I've made the wrong
assumptions. It sounds like your problem is becuase your orig volume is
in the wrong orientation when you view it in tkmedit (ie., the coronal
view in tkmedit does not show a coronal view, but shows the sagital view).
It seems, also, that this was not always the case - until you fixed the
talairach transform. Can you give me the exact mri_convert command that
you used to fix the talaraich?
What type of scans are these? Siemens, GE? what format were they in
before they were in mgz? It may be the case that you need to re-convert
them to correct the orientation. To do this, though, you'd need to be
sure you could identify the right side from the left side. You can use
some switched in mri_convert - I'd be glad to help you figure that command
out if this ends up to be the problem.
Jenni
On Mon, 30 Apr 2007 [EMAIL PROTECTED] wrote:
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final
objective funciton value is fine, ca.0.06)
So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and
it looked pretty fine with tkregister2.
Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed
it with tkmedit and tkreigister2.
Under tkregister2 the talairach transform looks pretty good but not the
target.(the oreientations of the target are totally mixed up,
those of the moveble volume are correct).
I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal
becomes horizontal, etc.
Any suggestions about this ?
Thanks.
Jackie
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