Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

I think it depends on how you do the computation. You would probably weight each vertex by the area then sum then divide by the total area and this is probably not much different than just averaging over vertices without taking the area into account. doug

On 5/29/13 9:16 AM, Martijn Steenwijk wrote:

I mean; if you devide the number of vertices by the area per aparc-parcellation, some parcellations have relatively more vertices per mm^2 as others. If you now would compute the average thickness in for example the lobe-parcellation, the thicknesses of some areas (the parcellations with relatively more vertices per mm^2) get a higher weight in the overal average. Is that true?

On Tue, May 28, 2013 at 8:58 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

what do you mean? That the vertices are not uniform? mri_segstats
just computes the mean over the parcellation without reference to
non-uniformity.
doug



On 05/28/2013 02:15 PM, Martijn Steenwijk wrote:

    Sorry, indeed, my reply was too quick. Seems to work, the
    results are similar to mri_anatomical_stats.

    I'm not sure whether this is relevant; but the sampling seems
    to be not equally dense in the different regions. Does
    mri_segstats somehow cope with this?

    Best,
    Martijn

    On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk
    <martijnsteenwijk@gmail.com
    <mailto:martijnsteenwijk@gmail.com>
    <mailto:martijnsteenwijk@gmail.com
    <mailto:martijnsteenwijk@gmail.com>>> wrote:

        Thanks Doug for your quick reply. But mri_segstats
    computes the
        average value inside the cortical region in the volume, right?
        That's not wat I want to have, I want to know the average
    value of
        the data in the volume on the wm/gm surface (i sampled with
        projfrac = 0).

        Any thoughts?



        On Tue, May 28, 2013 at 7:46 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:


            I would use mri_segstats and specify the --annot option
            doug


            On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
            > Dear all,
            >
            > I've created a custom '.mgh' file containing values
    on the
            cortical
            > surface using mri_vol2surf. I would like to compute some
            statistics on
            > this surface in the aparc-areas computed by
    freesurfer. Can
            I then
            > just use  mri_anatomical_stats with option -t
    specifying the
            custom
            > mgh file as 'thickness' input? Or does
    mri_anatomical_stats
            something
            > more complex than just averaging the values inside
    each region?
            >
            > Best,
            > Martijn
            >
            >
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