brainstem is not part of cortex. Use mri_cor2label with the aseg. get the id from $FREESURFER_HOME/FreeSurferColorLUT.txt
doug

On 6/3/13 6:17 AM, LAOUCHEDI MAKHLOUF wrote:

Hi
i used mri_annotation2label to extract the cortical labels. for this command we must specify which hemisphere (--hemi ?h) and i want to extract the brainstem which is not a lateralized structure, is there any command like mri_annotation2label to extract the brainstem ?

thanks
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