Hi Jenni,
all the mgz. are all in the wrong orientaions both in tkregister2 and
tkmedit.
except the talairach volume which I fixed, they are in the correct
orientation.
Jackie
Jenni Pacheco schrieb:
Hi Jackie,
So that command will bring up your subject and the talairach subject
and allow you to try and register them - it is not something before
and after talairach.
Going back to the problem of things oriented the wrong way. All the
volumes (orig.mgz, brainmask.mgz, T1.mgz etc) should be oriented the
same as each other - is this true?
Are you seeing them oriented correctly in tkmedit but incorrectly in
tkregister2?
Jenni
On Tue, 1 May 2007, Jackie_rwth wrote:
Hi Jenni,
This is the command line I used for checking talairach transform.
tkregister2 --mgz --s xxxxx --fstal.
cheers,
Jackie
Jenni Pacheco schrieb:
Hi Jackie,
What command line are you using to open tkregister2 to check your
talairach
transform? I'm not sure that the moveable volume is really the one
after
talairach transform - likely (depending on the command you used) the
moveable volume is the talairach subject, the target volume that you
want
your subject to match.
Can you send your command line.
Thanks,
Jenni
-----Original Message-----
From: Jackie_rwth [mailto:[EMAIL PROTECTED] Sent:
Tuesday, May 01, 2007 3:02 AM
To: Bruce Fischl
Cc: Jenni Pacheco; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach transform
Hi Bruce,
Yes, I have renamed the T1.xfm to talairach.xfm and put it in
mri/transforms dir, and also when I ran autorecon1 and put the -
notalairach flag after fixing.
Yes, I mean after fixing the tal transform.
The orientation of the orig.mgz , T1.mgz, and brain.mgz are in
another orietation as the "movebel volume"(the one after tal
transform).
eg. when I used tkregister2 the COMPARE button to check the tal
transfrom, the orietations of two images ( one is after tal
transform, the other is T1.mgz)
are not identical, (when I pressed "coronal" button, the movble
voulme is in coronal direction but the target volume is in
horozontal direction, ...etc.)
And then I used tkmedit to check the orig-, T1-, and brain.mgz, they
are all in the same situation but the wrong one.(coronal view became
horozontal view, horozontal view become sagittal view , etc...)
Any sugguestion will be helpful!
cheers,
Jackie
Bruce Fischl schrieb:
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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