Thank you very much for your quick reply, Dr. Greve. I asked our institutional MRI center for correct information on qform and sform since the header of nifti files are created by their scripts. But I do not know what they can do to fix this problem. I will appreciate if you have any further suggestion on how to do the registration without the information on qform and sform in case I can not get them. Does convert to ANALYZE format or manually correct in tkregister2 work?

Thank you again,

Xin 


-----Original Message-----
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:09 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed

Hi Xin, the problem is that neither the sform nor the qform are valid.
Did the message below not appear when you ran tkmedit?

WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented

Fix that, and everything will work fine.

doug


Wang, Xin wrote:

> Hello, Freesurfer group,
> I am registering the fMRI results to surface using reg-feat2anat (v
> 1.26.2.1 2007/08/15) and tkregister2. The automatic registration
> catastrophically failed in the subject space, but worked fine in the
> standard space. The orientations of example_func.nii.gz in the subject
> space are flipped in any view. I use the tkmedit to view the
> example_func, and found the orientation is wrong. It seems Freesurfer
> can not read nifti header correctly. I attach the reg-feat2anat log
> file and an example_func.nii.gz. 
> I found the following message from Freesurfer email list.
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
> Does Freesurfer have a solution for this type of problems by now?
>
> Thank you in advance,
>
> Xin
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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