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