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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