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