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:

reg-feat2anat failed
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting