Hello,
Thanks for all the suggestion. Just a few follow-up questions:
1 How should the average thickness be calculated? (The average thickness
measure was defined as a ratio between the sum of product of thickness and
surface area measures in each individual ROI and sum of surface measure each
individual ROI (over 30 ROIs from autorecon3) in the hemisphere?)
2 Since autorecon3 also generates volume and surface measure for each cortical
ROI, any suggestion for covariate for cortical volume and surface?
3 I noticed to calculate the average thickness, the left and right hemisphere
is separated out. But for analyzing results from autorecon2, such as left
putamen volume, the ICV is used as a covariate. Is there is a separate left and
right ICV available?
Thanks
Karl
> From: mha...@conte.wustl.edu
> To: joost.jansse...@gmail.com
> Date: Thu, 8 Apr 2010 07:26:33 -0500
> CC: schn...@gmail.com; freesurfer@nmr.mgh.harvard.edu; remembe...@hotmail.com
> Subject: Re: [Freesurfer] Covariate for results of cortical parcellation
>
>
> Hi Joost,
> If you want to control for possible global differences in thickness,
> then an appropriate covariate of some sort is need. To me, a logical
> covariate for a thickness analysis is the mean cortical thickness, as
> this is more directly related to the measure of interest than something
> like the cube-root of volume (which other studies have used when mean
> cortical thickness was not available as a measure).
>
> It is true that a difference in mean thickness doesn't necessarily imply
> that the difference in thickness is truly equally spread out over the
> entire cortex. But an analogous comment could be applied to volume
> analyses -- a difference in total brain volume between groups doesn't
> necessarily imply that differences in volume are present to an equal
> degree in all structures. Yet, using a volume covariate of some sort is
> a standard part of analyses of regional volumes. As a practical matter,
> I think it is fair to say that you are not going to find differences in
> mean thickness or total volume between groups unless a "substantial"
> portion of the brain is affected.
>
> cheers,
> -Mike H.
>
> On Thu, 2010-04-08 at 10:39 +0200, j janssen wrote:
> > Hi,
> >
> > you could try including average cortical thickness over the
> > entire hemisphere as a covariate. This was Mike Harms'
> > suggestion, and I think a good one.
> >
> > why is it a good one? for cortical thickness: i'm not so sure. my 2
> > cents (and i may be wrong!):
> > - controlling for intracranial volume is done to remove differences
> > due to overall size variability.
> > - the relationship between thickness and size is much less strong than
> > between volume and size (or surface and size).
> > - suppose your groups differ in mean thickness, if you would like to
> > include mean thickness as a covariate in a mapping study (vertex-wise
> > comparisons) of cortical thickness you would have to show that the
> > group-difference in mean thickness is due to an effect that's spread
> > out over the whole cortex (an overall effect, not localized),
> > otherwise the mean thickness covariate is not a good estimator of the
> > overall size factor that you'd like to remove.
> >
> > check Peter Kochunov's recent publications on this.
> >
> > -joost
> >
> >
> >
> >
> >
> > cheers
> > Bruce
> >
> >
> >
> > On Thu, 8 Apr 2010, Liukarl wrote:
> >
> >
> >
> > Hello, Freesurfer experts:
> >
> > I noticed for analyzing the results from autorecon2,
> > the intracranial volume are controlled as covariate in
> > some publications. Is there any corresponding
> > covariate for cortical results from autorecon3,
> > cortical thickness, surface, and volume?
> >
> > In my current study, there are two group: one is a
> > group with less optimal developmental environment and
> > the other is control. I noticed that without any
> > covariate, the r square from cortical measure and
> > group variable was really low, only accounting for 2%.
> > Is any standard way to analyze the cortical data?
> >
> >
> > Thanks!
> >
> > Karl
> >
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