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
On 5/24/17 9:57 AM, Stephanos Leandrou wrote:
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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