By the way, My parcels have not been extracted from Freesurfer by using "recon-all". While, the command "mri_vol2surf" needs registration file as input. Still, is it possible to use the mentioned command?? If yes, so what about the registration information? I think that registration file extracted from tkregister or etc, is for registering the output of the recon-all between the native space and Freesurfer template space. However, my parcels are not from Freesurfer. I don't know maybe I think wrong! I would be grateful by receiving your help.

Date: Fri, 10 May 2019 18:58:40 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] A Question about How to Map Parcels of the
Cortex on the surface of the Brain Cortex
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <d2312cef-2e80-2690-501e-83895bd26dad@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Are the parcels in the volume or on the surface? If in the volume, then use mri_vol2surf to map them (as a "segmentation") onto the surface, then use mris_seg2annot to create an annotation file. Run either with --help to get docs and examples

On 5/10/2019 2:26 PM, Bruce Fischl wrote:
Hi Mahsid

matlab is probably the easiest way, but without knowing what format you have them in it isn't easy for us to say. In matlab you can use write_annotation or write_ascii_curv or something to get it into a format we can handle

cheers
Bruce

cheers
Bruce
On Fri, 10 May 2019, mahshid fouladivand wrote:

External Email - Use Caution

Hello Dear Freesurfer Experts,

I have a high resolution brain cortex parcellation that is not extracted from Freesurfer. Now I
want to display the nodes(each parcels) on the pial and inflated surfaces. Both pial and inflated
surfaces have been extracted from T1mprage image of the corresponding subject using recon-all.
Also, the parcels and the T1 image are in the same space. Now, I am wondering is it possible to map
these parcels on the Freesurfer pial/inflated surface?
By the way, How can I create an .annot file for my parcels?
If you could help me with this, I really appreciate your help.

Regards,
Mahshid