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:gr...@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 > >------------------------------------------------------------------------ > >_______________________________________________ >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 gr...@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
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