For subcortical structures, you could consider using a covariate measure that itself includes subcortical gray matter. Not sure if the latest FS version has such a measure automatically constructed or not. In the past, we have used "whole brain volume" as a covariate for analysis of both cortical and subcortical structures, with "whole brain volume" defined as the volume contained within the pial surface (obtained using mris_volume) minus the volume of the lateral ventricles (contained within the aseg).

cheers, -MH

On Tue, 2011-05-17 at 10:19 -0300, Fernanda Palhano wrote:

Thanks, Michael.

I have a follow up question. If I understood, I should use the total cortical gray matter volume to control for a global change in cortical brain volume, so for exemple, if I'm interested in the volume of parahippocampal gyrus, I can normalize this way. And, once I have the measures for both the hemispheres separately, I have to use the total cortical gray matter of each one to normalize? But for other structures like hippocampus or amigdala it makes sense to control using volume of gray matter? Or, I continue using the ICV?

Thanks again,

On Tue, May 17, 2011 at 9:57 AM, Michael Harms mharms@conte.wustl.edu wrote:

    Hi Fernanda,
    The choice between ICV vs a measure of total "brain volume" or
    total
    cortical gray matter volume depends on whether you want to
    control for
    potential overall brain atrophy.  Using ICV will control for
    overall
    "head size", but not for potential overall brain atrophy
    (e.g., with
    age, or related to dementia).  Using total cortical gray
    matter will
    control for overall brain atrophy and thus would allow you to
    say that
    changes in a given structure were "above and beyond" any
    existing global
    atrophy.

    Personally, I find it more informative to control for
    potential global
    atrophy, and thus use total cortical gray matter rather than
    ICV.  After
    all, if a structure is decreased in size, but the overall
    brain is
    decreased as well, you have not established anything regarding
    the
    specificity of that change to the structure of interest if you
    use ICV
    as the covariate.

    cheers,
    -MH


    On Tue, 2011-05-17 at 09:19 -0300, Fernanda Palhano wrote:
    > Hello,
    >
    > I have two questions about volumetric analysis:
    > First: Are the volume measures in the files aseg.stats or ?
    > h.aparc.stats (Gray Matter Volume) already normalized by
    ICV? Or
    > should I divide
    > all the structure volumes which I want to compare between
    subjects by
    > the ICV of each subject?
    > Second: When comparing gray matter volumes the correct is
    use the ICV
    > or the total cortical gray matter volume to normalize? And
    if I have
    > to use the total cortical gray matter volume, how can I
    obtain it? I
    > know that this information is in the aseg.stats file, but I
    was
    > wondering if I can use asegstats2table to extract it.
    >
    >
    > Thank you very much,
    >
    > Fernanda
    >

    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >
    >
    > The information in this e-mail is intended only for the
    person to whom it is
    > addressed. If you believe this e-mail was sent to you in
    error and the e-mail
    > contains patient information, please contact the Partners
    Compliance HelpLine at
    > http://www.partners.org/complianceline . If the e-mail was
    sent to you in error
    > but does not contain patient information, please contact the
    sender and properly
    > dispose of the e-mail.