Hi Fatima - mri_aparc2aseg is the right command, but you should specify the name of your annotation instead of aparc.a2009s (which is one of the standard freesurfer annotations). So if your annotation is lh.mine.annot and rh.mine.annot, then you need "--annot mine².
Anastasia.
On 6/14/17, 3:42 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Almarshad F." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of F.Almarshad@soton.ac.uk> wrote:
Dear FreeSurfer expert
is it possible to create "aparc.a2009s+aseg.mgz" from custom parcellation i have..
i used label2annot to create the 2.annot files from my none overlapping labels.. ! i think mri_aparc2aseghttps://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg --s <subjid> --ribbon --annot aparc.a2009s would create the file .. however i could not understand how the command works, in terms of my two (label/lh.aparc.annot and label/rh.aparc.annot).. if you please can clarify what are the steps i need to make to get the aparc.a2009s+aseg.mgz based on my parcellation
many thinks
fatima
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