I mean to just load the orig.mgz into tkmedit and see if it is oriented correctly. Assuming that it is oriented correctly, then it sounds like the talairach transform is messed up pretty badly. When you run tkregister2, try adding --regheader. This will ignore the info in the talairaach.xfm file and force it to use the geometry info. it will likely be very far off, but the basic orientation should be ok.

Chacko Cherian wrote:

It has the problem in tkmedit,after I load the
transform..i checked brainmask.img and T1.img after
loading the transform and they had this problem..The
header and geometry info look fine..


--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:

That means that the geometry info in the file is
messed up. Where did 
the data come from? Are the dicoms messed up too?

Chacko Cherian wrote:

No, It has the same problem in tkmedit too.


--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:

Does it view correctly in tkmedit?

Chacko Cherian wrote:

Hello ALL,

Has anybody had trouble with tkregister2..I

loaded

     

          

the

transform and the coronal and horizontal views

are

mixed up.Coronal view of the subject is coupled

with

the horizontal view of the talairach volume.

Thanks in advance
Regards,

Chacko.

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Douglas N. Greve, Ph.D.
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greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the
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Fax: 617-726-7422

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