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
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:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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: 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Reji, A. (Amal, Student M-EE)