Re: [Freesurfer] Cortical gray matter surface area

Sure. We'd like to know how to find the surface area of the cortical grey matter from the pial surface. So specifically, what is the surface area of the pial/grey matter boundary of the cortex for each hemisphere?

We're using Freesurfer v5.3 on Centos 6.

Thanks, Will Brown

On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

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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