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Sir, I ran the following commands.

mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg

mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o aparc+aseg_native.mgz --regheader aparc+aseg.mgz. I ran without any error, but when I visualize it, I cannot see the volume files in the native space.  I am attaching the screenshot of the same . When I select  show existing labels, there is no parcellation file in it.

I am mot sure what I am doing wrong. 

Looking forward to hearing from you

Regards

Amal 

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Sent: Monday, June 3, 2024 6:39 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to get the parcellations to the initial space as before running recon all

 

Does this web site https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat cover what you need to do?

On 6/3/2024 10:58 AM, Reji, A. (Amal, Student M-EE) wrote:

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Hi,

    I was trying to get the mesh files for cortical parcellations after running recon all. I used the Ernie data set which is the example dataset given by SimNIBS. I did recon all to the Ernie dataset and I got the parcellations. Now I want to get these parcellations to the same space as the space of Ernie. How can I convert the parcellations in the initial space?

Looing forward to hearing from you

Regards

Amal Reji

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