Thank you Doug,

As you suggested, I tried to use that command

(mris_seg2annot --seg lh.surf_combined-magn_CL_fwhm1.mgh --s MS072_R01_04 --hemi lh --ctab MS072_R01_04.txt --o lh.cortical_les.annot)

but I got this error on tksurfer:

Successfully parsed tksurfer.tcl
reading white matter vertex locations...
% reading colortable from annotation file...
colortable with 7 entries read (originally MS072_R01_04.txt)
Found embedded color table in annotation.
131940 vertices did not have an annotation!
surfer: WARNING: no labels imported; annotation was empty

I attach my color table file...

Thanks for your help,

Vale

_______________________________________________________________________________________________________

>Greve, Douglas N.,Ph.D. DGREVE at mgh.harvard.edu 
>Tue Feb 19 16:33:32 EST 2019

>You can create an annotation with mris_seg2annot (you basically have a 
>surface-based segmentation). Run it with --help to get more info 
>including examples. You will need to create your own color table

On 2/19/19 3:21 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I have a 3D volume mask of cortical lesions with 8 different clusters 
> (8 cortical lesions).
>
> I projected this mask to the cortex and obtained a .mgh file with the 
> command vol2surf:
>
> mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out 
> $path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" 
> --projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj
>
>
> Now I need to extract label files from this surface file, one 
> label for each cluster, and then an annotation file summarizing all 
> the label files.
>
> How can I do this?
>
> Thanks,
>
> Vale

From: Barletta, Valeria
Sent: Tuesday, February 19, 2019 3:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: clusters annotation file in surface

Dear Freesurfers,

I have a 3D volume mask of cortical lesions with 8 different clusters (8 cortical lesions).

I projected this mask to the cortex and obtained a .mgh file with the command vol2surf:

mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out $path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" --projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj

Now I need to extract label files from this surface file, one label for each cluster, and then an annotation file summarizing all the label files.

How can I do this?

Thanks,

Vale