you can

mri_binarize --match 1006 --i aparc+aseg.mgz --o left.entorhinal.mgz

(use 2006 for right).

These values you can get from $FREESURFER_HOME/FreeSurferColorLUT.txt

Dear Freesurfer Developers, 

I want to extract the entorhinal cortex from the original T1 image of my subect's MRI scans. Is there a way to do it; I used the the commands below to extract the CA1 subfield of the hippocampus. Is there a similar way to do the same for the entorhinal cortex? 

mri_extract_label lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 leftCA1.mgz
mri_extract_label rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 rightCA1.mgz

mri_mask orig.mgz leftCA1.mgz orig_left_CA1.mgz
mri_mask orig.mgz rightCA1.mgz orig_right_CA1.mgz

Many thanks,  

Stephanos 

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