I tried using mri_convert without conform, same thing.

Basically, I think if I set -ns = 1 when I use mri_convert, it will not rescale the image. But when I open it using tkmedit, I still
can not see the intensity contrast.

So I think my question is why the same volume (with the same max intensity and minimum intensity) looks different in fslview and
tkmedit?

Thanks!

Guang
 

> Date: Fri, 21 Aug 2009 13:05:25 -0400
> From: greve@nmr.mgh.harvard.edu
> To: freesurfer_zg@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FW: a question about mri_convert
>
> why do you want to conform it?
>
> Guang Zeng wrote:
> > Actually, I also noticed that when mri_convert runs, it says something
> > like "changing data type from 3 to 0 "
> > The data type of the nii file is float32, while the converted .mgz id
> > uchar, is it the problem?
> >
> >
> > Thanks
> > Guang
> >
> > ------------------------------------------------------------------------
> > From: freesurfer_zg@hotmail.com
> > To: freesurfer@nmr.mgh.harvard.edu
> > Date: Fri, 21 Aug 2009 11:37:18 -0500
> > Subject: [Freesurfer] a question about mri_convert
> >
> > Hi, there,
> >
> > I got a question about mri_convert.
> > I have a brainmask.nii file, (max intensity value is 64, and minimum
> > intensity is 0), it shows good intensity contrast.
> > Now I want to use mri_convert to convert it to mgz file, my command
> > line is
> >
> > mri_convert A.nii --conform A.mgz
> >
> > Now, I open A.mgz using Tkmedit, I can not see those significant
> > intensity contrast now, and the max intensity value is 255, and
> > minimum intensity is 0
> > It looks like mri_convert do something like histogram equalization or
> > normalization.
> >
> > Will mri_convert actually change the intensity value of each voxel?
> > Can I keep my original intensity value for each voxel? Use the
> > mri_convert -sc?
> >
> > Thanks a lot!
> >
> > Guang
> >
> >
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