yes, that has the subcortical segmentation based on the automatic algorithm and any changes that you might have made manually. The "auto" is only the result from the automatic method. doug

Jie Shi wrote:

Thanks a lot. Will try. Basically, is aseg.mgz the resulting file which contains the results of FreeSurfer subcortical segmentation? What role is the aseg.auto.mgz?

Jie

On Wed, Nov 9, 2011 at 5:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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>
    <mailto: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
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