sorry, this thread has gotten too deep. Can someone summarize the question?

On Thu, 11 Sep 2014, _andreia_@sapo.pt wrote:

Ok. Then, I'm not sure if everything is correct with the command lines since
I use 5.0.

Any thought on this Freesurfer team?

Thanks,
Andreia

Citando will brown <willbrown1987@gmail.com>:

      Thanks again, for the record, I'm using freesurfer version 5.3.0
      on Centos 6.

      On 9/09/2014 11:00 PM, <_andreia_@sapo.pt> wrote:

            Hi Will,

            Just to clarify, what version of FS are you using? I
            think it might not be 5.0 and I don't know if
            everything aplies if we are using different
            versions.


            1) Yes, it is only based on the pial surface (and
            these command lines are for the aparc, DK altas).
            The second set provides the surface area for each
            hemisphere without including, for example, the pial
            surface that you see in the hippocampus which is not
            accurate and one should not care about. In the end,
            the second set gives you the sum of the areas in
            aparc, thus, you can just make a sum of that
            parcellation if you want. I just realized that.

            2) No. In the new stats file, the value that you
            want is at the bottom:

            # ColHeaders StructName NumVert SurfArea GrayVol
            ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

            And when running aparcstats2table that's the value
            you should get in the table. I think that # Measure
            Cortex, WhiteSurfArea, White Surface Total Area may
            be including more stuff since it is bigger.


            If what you want is only the total hemisphere
            surface area you only need to run the second set of
            commands. If you want the area of each DK altas
            parcellation then run the first set and then simply
            add them to get total hemisphere surface area.


            Someone from Freesurfer staff will correct me if I'm
            wrong. (Please) I'm Ccing Doug since he was replying
            to your previous emails.

            Let's wait for their feedback.

            Andreia



             

            Citando will brown <willbrown1987@gmail.com>:

                  Thanks Andreia, this does appear to have
                  worked. Please forgive my ignorance but
                  I do just want to double check two
                  things;
                   
1) The first commands you have given provide the stats for
the two hemispheres of the cerebral cortex only based on
the pial surface, whereas the second set of commands
provide the pial boundary stats for the whole brain rather
than just cortex?
 
2) The surface area value that I am looking for (grey
matter surface area at the grey/pial boundary) is listed
in the new stats table next to: # Measure Cortex,
WhiteSurfArea, White Surface Total Area, ?
 
Thanks again,
Will

On Tue, Sep 9, 2014 at 5:36 PM, will brown
<willbrown1987@gmail.com> wrote:
      Thanks very much Andreia, yes this does look
      like what I want. I haven't had a chance to
      test it yet but it does indeed appear to
      answer my question. Thanks to those that have
      offered answers, to clarify, I did indeed mean
      the surface area of the pial surface rather
      than the white/grey boundary.  
Will


On Wed, Sep 3, 2014 at 1:12 AM, <_andreia_@sapo.pt>
wrote:

      Hi Will,

      I use the following commands to get
      surface area from the pial surface:


      In the subject label dir:
       

      mris_anatomical_stats -mgz -cortex
      ../label/lh.cortex.label -f
      ../stats/lh.aparc.pial.stats -b -a
      ../label/lh.aparc.annot -c
      ../label/aparc.annot.ctab SUBJ lh pial

      mris_anatomical_stats -mgz -cortex
      ../label/rh.cortex.label -f
      ../stats/rh.aparc.pial.stats -b -a
      ../label/rh.aparc.annot -c
      ../label/aparc.annot.ctab SUBJ rh pial
       


      Then run aparcstats2table using
      aparc.pial instead of aparc (only
      because I called this new parcellation
      aparc.pial)



      To get the total surface area of each
      hemisphere I use:

      In the subject stats dir:
       

      mris_anatomical_stats -l
      ../label/lh.cortex.label -f
      lh.total_pial.stats -b SUBJ lh pial

      mris_anatomical_stats -l
      ../label/rh.cortex.label -f
      rh.total_pial.stats -b SUBJ rh pial

      Then run aparcstats2table using
      total_pial instead of aparc (again, only
      because I called this new parcellation
      total_pial. You may call it whatever
      you'd like)



      Just remeber to leave the specified dirs
      when creating the tables. If you dont't
      I think they will be created in the
      current dir.

      I use FS 5.0.

      Is this what you want?


      Best,
      Andreia

       

      Citando will brown
      <willbrown1987@gmail.com>:

            Hi all,  
I messed up this question recently so
just want to clarify and try again. We
want to know the cortical gray matter
surface area of our subjects but are
unclear about how to get this info.
 
?.aparc.stats reports:
 
Measure Cortex, WhiteSurfArea, White
Surface Total Area, XXXX, mm^2
 
How about the gray matter?
 
Thanks,
Will
 
 


 

 



 

 



 

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