hmm, not sure what is going on. I just confirmed that your command line
works for me. Can you go into $FREESURFER/subject/bert/mri and run that
command?
On 6/3/2024 5:47 PM, Reji, A. (Amal, Student M-EE) wrote:
External Email - Use Caution
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
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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
<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:
* External Email - Use Caution *
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.
<https://simnibs.github.io/simnibs/build/html/dataset.html> 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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