Dear Doug,

 

Here is the emails:

 

Message: 6
Date: Fri, 2 Aug 2019 01:55:34 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] How to Create Cortex Parcellation Using
   "mri_aparc2aseg"?
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <183e8a60-1cc2-1680-26a7-bce8a1d03315@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

If you look in the recon-all.log file for any subject, you will see a mri_aparc2aseg command line. YOu can use that specifying your annot and the new output name.

On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote:

        External Email - Use Caution

Dear experts,

I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a parcellation file based on the segmentation and annotation files using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal and extract the parcels:
mri_aparc2aseg --s subject name --annot annotation name --o output name

and I used the segmentation file as the "aseg.mgz" for the above command. Now, I am wondered that do I select the right aseg file or not??
Any help would be appreciated.

Regards,
Mahshid