cd $SUBJECTS_DIR/subject/surf mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this generates a surface with jagged edges mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # smooths surface 10 smoothing steps is just a guess

# Visusalize the surface tksurfer subject lh hippocampus.sm10 # See the surface overlaid on the volume tkmedit subject orig.mgz lh.hippocampus.sm10 -aseg

Not that when you run the tkmedit/tksurfer commands, they will complain that the surface does not match. This is not a problem for this application.

doug

Jie Shi wrote:

Hi, thank you very much. Actually we do want to know how to get the surfaces in order to compare with ours.

Jie

On Wed, Nov 9, 2011 at 4:59 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

You can extract a binary mask for any structure with
mri_binarize --i aseg.mgz --match XX --o yourmask.mgh
where XX is a number from $FREESURFER_HOME/FreeSurferColorLUT.txt
(eg, 17 = left hippo)
It is possible to generate hippo surfaces, but we cannot guarantee
accuracy. Let me know if you want to know how.
doug

Jie Shi wrote:

    Hi, experts. We need to use FreeSurfer to process some analyze
    image data. More specifically, we want to extract the
    hippocampus surfaces. We know that FreeSurfer has done
    subcortical segmentation during -autorecon2 stage in
    recon-all. We have checked the resulting aseg.mgz file and
    found that it contains all substructures. So we wonder if
    there is a way to get the separated .mgz files for each
    substructure or could FreeSurfer generate the subcortical
    surfaces? Thanks a lot.

    Best,
    Jie
    ------------------------------------------------------------------------

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MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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<tel:617-726-7422>

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