Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the
mri/transforms dir.
When you say "after this step, the orientation of the target volume is
mixed up" do you mean after applying the tal transform? The orientation of
all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz) should be identical.
cheers,
Bruce
On Mon, 30 Apr 2007, Jackie_rwth wrote:
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with tikmedit.
But after I fixed the Talairach transform by using mri_convert T1.mgz T1.mnc
, mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it in tkregister2,
which looks quite fine), then I ran recon-all -subjid xxxx -autorecon1
-notalairach .
But after this step, the orientation of the target volume is mixed up, same
as the orig.mgz volume.(before fixing Talairach the orig voulme are correct)
p.s the orientation of the moveble volumes are correct after fixing
They are nifti files and acquired by Siemens Sonata.
(We already used the avwswapdim to reorient them before running, and we also
put mark on the brain so that we could tell L and R)
Thank you for your help!
Jackie
Jenni Pacheco schrieb:
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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