Hello, Nick,

Which version of orient_mri you are using?
I read this from FreeSurfer Wiki "First, load up a volume either by passing one on the command line or by using the File menu command or toolbar button. You will see the volume in four views."

However when I call orient_mri, I only saw one view, not four. My version of orient_mri is 1.0.


Thanks a lot!
Guang

> From: nicks@nmr.mgh.harvard.edu
> To: freesurfer_zg@hotmail.com
> Date: Mon, 21 Sep 2009 10:58:15 -0400
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] tkregister2 question
>
> Guang,
>
> You could use the freesurfer utility 'orient_mri'.
>
> First open case_1:
>
> orient_mri --volume case_1.img
>
> then case_2:
>
> orient_mri --volume case_2.nii
>
> Then use the rotate icons to rotate case_1 so that its oriented the same
> as case_2, and save the case_1 volume (you can save as 'case_1.nii').
> Then you can use tkregister2.
>
> Again, without fudicial markers, its difficult to tell left from right,
> so there is no guarantee that your l-r orientation is correct.
>
> Nick
>
>
>
> On Sun, 2009-09-20 at 12:31 -0500, Guang Zeng wrote:
> >
> > Hello, Nick,
> >
> > Thanks a lot for your help. The bad thing is case_1&2 are not oriented
> > the same way.
> > Anything else I can do?
> >
> >
> >
> >
> > Guang
> >
> > > Subject: Re: [Freesurfer] tkregister2 question
> > > From: nicks@nmr.mgh.harvard.edu
> > > To: freesurfer_zg@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Date: Sat, 19 Sep 2009 11:51:28 -0400
> > >
> > > Guang,
> > >
> > > If you're 100% certain that case_2 is oriented the same way as
> > case_1,
> > > for instance if they were from the same scanner, then you can do
> > this:
> > >
> > > mri_convert case_2.nii case_2.img
> > >
> > > (this outputs case_2.mat)
> > >
> > > cp case_2.mat case_1.mat
> > >
> > > now tkregister2 should work. Keep in mind this is a hack accounting
> > for
> > > the missing case_1 data. If the data is from different scanners,
> > then
> > > there is a risk of L-R reversal, because the orientation info may
> > not be
> > > the same.
> > >
> > > Nick
> > >
> > >
> > > On Fri, 2009-09-18 at 17:33 -0500, Guang Zeng wrote:
> > > > Hi, there,
> > > >
> > > > I have a case_1.hdr file and case_1.img file, but no the
> > > > corresponding .mat file which contains the necessary direction
> > cosine
> > > > info.
> > > > So everytime when I try to register another nifti file case_2.nii
> > to
> > > > it using tkregister2 or mri_vol2vol, it always complains that
> > > >
> > > > "INFO: could not find ../../case_1.mat file for direction cosine
> > info.
> > > > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse
> > unflipped
> > > > (default).
> > > > INFO: if not valid, please provide the information
> > in ../../case_1.mat
> > > > file"
> > > >
> > > > Just want to know if there are other methods I can use to register
> > > > case_1 and case_2? Any kinds of method!
> > > >
> > > > Thanks a lot!
> > > >
> > > > Guang
> > > >
> > > >
> > > >
> > > >
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