Re: [Freesurfer] mris_anatomical stats different thickness files

no, that would be 15 "smooth steps". If you want to smooth by 15mm, then use mris_fwhm. doug

krista kelly wrote:

Would the following code give me data smoothed with 15 fwhm kernel?

mris_anatomical_stats -l lh.v1.label -t lh.thickness -nsmooth 15 -b -f BV01/stats/lh.v1_pial.stats BV01 lh pial

Thanks!

On Mon, Oct 24, 2011 at 10:40 AM, krista kelly <krista.kelly16@gmail.com mailto:krista.kelly16@gmail.com> wrote:

Thanks for clearing this up! It makes a lot more sense now.


On Mon, Oct 24, 2011 at 10:35 AM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:



    krista kelly wrote:

        I'm looking at both cortical thickness and surface area
        differences between two groups. I've been using
        mris_anatomical_stats to retrieve values but had a few
        questions:

        1) Do I need to do separate mris_anatomical_stats using
        different thickness files (bolded below) to get cortical
        thickness and surface area measures. For example:

        cortical thickness - mris_anatomical_stats -l lh.v1.label
        -t *lh.thickness* -b -f BV01/stats/lh.v1.stats BV01 lh
        surface area - mris_anatomical_stats -l lh.v1.label -t
        *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh


         Or, since the output files include all of these measures,
        is it fine to just run one of the two?

    Just run the first one.


        2) The output files for both analyses run above (with
        different thickness files) have identical values for
        everything except for tray matter volume. Using
        lh.thickness file - grayvol = 8082; using lh.area file -
        grayvol = 4029. Can anyone clarify why this happens?

    It computes the gray matter volume by thickness*area. If you
    pass it "area" as the "thickness", then you are probably
    getting area*area. Though I'm surprised that the "thickness"
    values are correct.


        3) The default surface area values are for the white
        matter surface. How do I run mri_anatomical_stats to get
        the pial surface? I've tried mris_anatomical_stats -l
        lh.v1.label -t *lh.area.pial *-b -f BV01/stats/lh.v1.stats
        BV01 lh but I get identical values for everything (except
        grayvol).

    Try adding "pial" to the end of the command line (and use
    lh.thickness)
    doug


        Thanks!
        Krista
        ------------------------------------------------------------------------

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    -- 
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
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