If you just want to convert it to mgz , then run
mri_convert brainmask.nii brainmask.mgz
the voxel values will not change. Conforming it will cause it to be resampled to 256^3, 1mm^3. Is that what you wnat?
Guang Zeng wrote:
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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