Hi, Doug,
Thanks a lot, at first I think it may because I use recon-all command which
will call mri_convert ...... --conform at the motion correction step. I did a
simple test, I ran mri_convert A.nii test_data2_orig.mgz, it gave ne something
like,
$ mri_convert A.nii test_data2_orig.mgz
mri_convert A.nii test_data2_orig.mgz
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from A.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.993271, 0.0255268, 0.112962)
j_ras = (0.00635944, 0.961911, -0.273288)
k_ras = (-0.115635, 0.272168, 0.955276)
writing to test_data2_orig.mgz...
I opened A.nii using fsl view and test_data2_orig.mgz using tkmedit, I input
the same volume index and I got the
two different views. Is it because of i_ras, j_ras and k_ras?
Sorry, I am new to FreeSurfer. Your help are highly appreciated!
Guang
> Date: Fri, 7 Aug 2009 18:31:56 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert question
>
> Guang,
>
> mri_convert does NOT automatically convert to 256^3, but it will with
> the -conform option. I have to have your command line to tell for sure.
> This is why you should ALWAYS include a command line with your post. In
> fact, you should see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for
> all the things that will make it easy for us to help you.
>
> thanks!
>
> doug
>
> Guang Zeng wrote:
> > Hi, there,
> >
> > I am new to FreeSurfer, just got a question about the mri_convert command.
> > I have a 169x256x256 binary volume, the format is .nii.
> > I called the mri_convert command to convert it to .mgz format.
> > I open the .mgz volume using tkmedit, and then open the .nii volume
> > using fsl view,
> > I got to a problem, I input the same volume index in tkmedit and fsl
> > view, I got the
> > two different views.
> >
> > I think that is because mri_convert will automatically convert the
> > input volume to a 256x256x256 volume, am I right?
> > If I am right, how can I convert the 256x256x256 volume to the
> > original size when I call mri_convert again to convert the .mgz back
> > to .nii.
> >
> > Thanks a lot!
> >
> > Guang
> >
> > ------------------------------------------------------------------------
> > Windows Live™: Keep your life in sync. Check it out.
> > <http://windowslive.com/explore?ocid=PID23384::T:WLMTAGL:ON:WL:en-US:NF_BR_sync:082009>
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> 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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