Re: [Freesurfer] use of anot_2_label

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

[Freesurfer] use of anot_2_label

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