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: greve@nmr.mgh.harvard.edu To: freesurfer_zg@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

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