hello, Freesurfer group,
I try to use registration.mat files of FSL/FEAT routines, instead of anat2example_func.bat, to register the orig.mgz and example_func.nii.gz with the thinking that using initial_highres in FEAT may improve the reg. However, tkregister2 catastrophically failed to register two brains when I use --fsl flag. Modifying header of example_func with mri_convert does not solve the problem. I will appreciate any suggestion on using .mat file for registration.
second question: what is the best registration of example_func and orig.mgz? In another word, what should I check besides things in the FS tutorial when I check/modify the registration in tkregister2? Is there golden reference points I can use?
Thank you in advance for any suggestion.
Xin wang
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 12/15/2008 1:26 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed
There is a flag in the nifti header saying whether the qform or sform are valid, and it looks like your scripts do not set this flag. You can use mri_convert (the freesurfer program). This will create valid files that can be read into any program.
doug
Wang, Xin wrote:
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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