Adding ROIs in fsaverage will not cause them to appear in the aseg.mgz volume; fsaverage is not the atlas. If you have your ROIs in fsaverage space, you can map them to the individual via a linear or nonlinear mapping, but the accuracy will be debatable. You don't need to merge them with the aseg to do the volume calculation

On 5/16/2022 1:59 AM, Ramtilak Gattu wrote:

External Email - Use Caution

Thank you for the response,

Yes editing the aseg.mgz in the fsaverage directory with the custom roi's.

The purpose of doing it on the aseg.mgz in the fsaverage directory is- so that  we can use these roi's once for all for every subsequent subject we process from here on.

Would it be possible to replace certain existing labels with our own custom roi's and do the final volume calculations?

If so how?

Thanks

Regards Tilak

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*From:* Ramtilak Gattu *Sent:* Sunday, May 15, 2022 5:01 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* creating. or replacing a label of choice in aseg atlas Hi,

We are interested in replacing a couple of labels in aseg atlas with our own roi's already in the same space as of "aseg.mgz" atlas in the fsaverage folder.

What would be the best way to do this? Could someone help or guide me if anyone has done something similar to this query?

Can I just add the regions (in the form of 3d masks) to the aseg atlas and create aseg_modified.mgz and later replace the aseg.mgz with aseg_modified.gz and rename the aseg_modified.mgz back to aseg.mgz.

If I follow this procedure and run "recon-all" will the aseg_stats will give me volumes based on the new volumes?

-- Regards Tilak

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

If you look in recon-all.log, you will see the command that computes the aseg.stats file, something like: mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/7.2.0/ASegStatsLUT.txt --subject subject

Change the name of the --seg argument to point to the new aseg file that you created, change the name of --sum file to indicate the new input seg. You will also need to create a new ctab with the new segmentation names/numbers. Copy ASegStatsLUT.txt and edit it.

On 6/7/2022 12:20 AM, Ramtilak Gattu wrote:

External Email - Use Caution

Hi,

Basically, we have created the CC mask segmented into three regions Genu, body and Splenium.  It is showing as one yellow color as the values are close. But there are 3 segments in it.

What is the best way to replace the existing 3 out of 5 CC segments (CC_anterior, CC_central, and CC_posterior) in the Aseg stats calculations with our above-created CC segments so that whenever we run "recon-all" the seg output should have the volume calculations based on the above newly created mask for these specific regions without altering the other subcortical volumes?

If I add this mask to the aseg atlas with the corresponding label values and replace the original aseg atlas in the fsaverage folder would that suffice?

So from now on, every time I run a subject I get the volumes for CC_genu, splenium and body as part of the aseg_stats.txt along with the other existing subcortical volumes.

Thanks

Regards Tilak

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*From:* Ramtilak Gattu rgatt@med.wayne.edu *Sent:* Monday, May 16, 2022 1:59 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: creating. or replacing a label of choice in aseg atlas Thank you for the response,

Yes editing the aseg.mgz in the fsaverage directory with the custom roi's.

The purpose of doing it on the aseg.mgz in the fsaverage directory is- so that  we can use these roi's once for all for every subsequent subject we process from here on.

Would it be possible to replace certain existing labels with our own custom roi's and do the final volume calculations?

If so how?

Thanks

Regards Tilak

---

*From:* Ramtilak Gattu *Sent:* Sunday, May 15, 2022 5:01 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* creating. or replacing a label of choice in aseg atlas Hi,

We are interested in replacing a couple of labels in aseg atlas with our own roi's already in the same space as of "aseg.mgz" atlas in the fsaverage folder.

What would be the best way to do this? Could someone help or guide me if anyone has done something similar to this query?

Can I just add the regions (in the form of 3d masks) to the aseg atlas and create aseg_modified.mgz and later replace the aseg.mgz with aseg_modified.gz and rename the aseg_modified.mgz back to aseg.mgz.

If I follow this procedure and run "recon-all" will the aseg_stats will give me volumes based on the new volumes?

-- Regards Tilak

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer