It seems to me that vertex areas in the native subject space are not meaningful. The orig surfaces should be uniformly tesselated; however, topology correction and final surface finding should introduce complicated and probably uninteresting variation.
But, if a subject's surfaces are resampled to atlas (i.e. make_average_subject with only one subject as input), then the vertex areas should indicate the degree to which squishing or stretching is required to match the atlas (as Bruce said), which could be quite interesting. Or put another way, vertex area represents the relative size of a patch of cortex compared to the collection of subjects that went into the atlas. This measure of vertex area may vary between groups and may be correlated to certain genetic markers.
Since volume depends on both area and thickness, it seems redundant to use all three measures.
> Date: Tue, 17 Feb 2009 23:16:33 -0600
> Subject: Re: [Freesurfer] Qdec area measure
> From: mharms@conte.wustl.edu
> To: fischl@nmr.mgh.harvard.edu
> CC: d.gitelman@gmail.com; freesurfer@nmr.mgh.harvard.edu
>
>
> Here is a question related to this whole discussion (prompted by what
> Darren wrote):
> As a practical matter, have you found the localized (i.e., vertex-based)
> measures of area and volume to be biologically useful and meaningful?
> Have they been used in any published studies? (I don't recall seeing any
> surface maps of "area" or "volume" differences between groups, whereas
> there are obviously many published studies showing surface maps of
> thickness differences).
>
> cheers,
> Mike H.
>
> > Hi Darren
> >
> > the curvature is related to the angles of the edges connected to each
> > vertex (also called the "angle deficit"). The surface area should just be
> > given by how much compression expansion the individual surface undergoes
> > when it aligns to a spot in the atlas. We'll compute it and correct for
> > it sometime soon.
> >
> > cheers,
> > Bruce
> > On Tue, 17 Feb 2009, Darren Gitelman wrote:
> >
> >> Devdutta, Nick, Bruce, Mike
> >>
> >> I'm trying to understand these measures in terms of how they would map
> >> to
> >> the brain physically.
> >>
> >> Would it be correct that the size of the triangles touching a vertex
> >> would
> >> be related to the amount curvature near a particular vertex and
> >> therefore
> >> the amount of unfolding that takes place? Thus surface area would seem
> >> to
> >> relate to both brain size and the foldiness of the brain, and brain size
> >> could relate to a variety of factors including the cortical thickness
> >> but
> >> also the amount of underlying white matter. So overall surface area
> >> seems
> >> to be a complex metric that could reflect changes in underlying white
> >> matter, cortical thickness and foldiness. Is this correct?
> >>
> >> I guess one would have to correct for overall brain size (using TIV or
> >> similar measure as a covariate) when examining surface area because of
> >> the
> >> effect of amount of gray and/or white matter.
> >>
> >> Volume then would be the amount of cortex underlying a vertex and the
> >> triangles connected to it (estimated as an average of the pial and white
> >> matter surface areas).
> >>
> >> Darren
> >>
> >>
> >>
> >>
> >>> I think the area probably should be corrected to preserve the native
> >>> area
> >>>>> of the subject, but as you say we haven't gotten to the correction
> >>>>> yet. On
> >>>>> Tue, 17 Feb 2009, Nick Schmansky wrote:
> >>>>>
> >>>>> Devdutta,
> >>>>>
> >>>>> The 'area' of a vertex on a surface in freesurfer is just the
> >>>>> average
> >>>>> of
> >>>>> the area of the triangles which touch that vertex .
> >>>>>
> >>>>> The volume data associated with a vertex created for a subject is
> >>>>> not
> >>>>> buggy in how it is calculated now. it is the area of the
> >>>>> mid-point
> >>>>> between the white and pial surfaces times the thickness at the
> >>>>> vertex.
> >>>>> The question that has been bandied about internally is whether
> >>>>> this
> >>>>> volume calculation should be corrected when it is mapped to the
> >>>>> fsaverage surface during a group analysis (qdec does this mapping
> >>>>> of
> >>>>> the
> >>>>> volume calcs of each subject to the fsaverage surface, when you
> >>>>> select
> >>>>> 'volume' as one of the measures). At some point we will visit
> >>>>> this
> >>>>> issue (and determine if it is an issue) but other stuff seems to
> >>>>> take
> >>>>> priority. Maybe someone on the list can chime in.
> >>>>>
> >>>>> Nick
> >>>>>
> >>>>> On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
> >>>>>
> >>>>> Hi,
> >>>>> In Qdec, what exactly does the area option measure? As I
> >>>>> understand,
> >>>>> qdec does its calculations vertex by vertex, which makes sense
> >>>>> in
> >>>>> case
> >>>>> of cortical thickness. But if area refers to surface area how
> >>>>> does
> >>>>> that change from vertex to vertex? Or is it calculating the
> >>>>> area
> >>>>> by
> >>>>> ROI? Is my understanding of this correct?
> >>>>>
> >>>>> Also, as regards to the volume option, I was told that it is
> >>>>> not
> >>>>> working. But when I ran it it seems to work fine. Should I
> >>>>> take
> >>>>> that
> >>>>> to mean that the calculation has bugs and that the results it
> >>>>> displays
> >>>>> are incorrect? Or has it been fixed?
> >>>>>
> >>>>> I greatly appreciate any help in this matter.
> >>>>>
> >>>>> Thank you,
> >>>>> Devdutta
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> >>>>>
> >>>>>
> >>>>>
> >>
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