Hi Xin, I'm not sure what's going wrong here, I think I need more info.
Can you follow the steps in surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?
doug
Wang, Xin wrote:
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
--
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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