Re: [Freesurfer] Sub-cortical structure

Hi Jie, what do you mean they don't work? I don't know what the difference between mri_mc and mri_tesselate is (another good reason to post to the list so that others who might know can answer the question). doug

Jie Shi wrote:

Sorry I have forgot to describe our surface format.

Vertex 1 x1 y1 z1 Vertex 2 x2 y2 z2 . . . Vertex n xn yn zn Face 1 v1 v2 v3 . . .

On Tue, Nov 29, 2011 at 5:10 PM, Jie Shi <Jie.Shi@asu.edu mailto:Jie.Shi@asu.edu> wrote:

Hi, thanks for your previous help, but I have more questions to
bother you. I have tried mri_tesselete and converted the resulting
surfaces into ascii format. These surfaces work in Matlab but in
our mesh format like the following they don't. If I tesselate the
surface by command mri_mc, the surfaces work in our format. So
what is the difference between mri_tesselate and mri_mc? Since the
resulting surfaces are not good enough (some of them have holes),
I would line to know if FreeSurfer can generate surfaces for
subcortical structures like it does for cortex? Thanks a lot.

Jie



On Wed, Nov 9, 2011 at 5:24 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    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>
        <mailto: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>>
               <mailto: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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