Hi, Michael
Thanks for the guidance. Still I am unclear of how to implement your ideas
1 For the mris_anatomical_stats, should I use -a subjid/label/lh.aparc.annot
or use the �Ct option to check the thickness file (what’s the name of this
file)? If I understand it correctly, I will get a measure of “average cortical
thickness” of each hemisphere for every subject and further I can set this as a
control variable for regional thickness comparison?
2 for each of the cortical regions, there is also a volumetric measure. What
average or overall volume measure I can use as a control variable, the ICV or
something new from autorecon3?
Thanks
Karl
> From: mha...@conte.wustl.edu
> To: remembe...@hotmail.com
> Date: Thu, 16 Dec 2010 12:04:35 -0600
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] How to adjust cortical thickness/area/volume
> measures from autorecon3
>
>
> BTW: You can't "sum" the thicknesses across the various regions in the
> aparc files, as that would be a meaningless measure. You either need to
> compute the average cortical thickness as I suggested, or compute a
> weighted mean from the data in the aparc files, in which you weight each
> region's thickness by its proportion of the total surface area.
>
> cheers,
> -MH
>
> On Thu, 2010-12-16 at 11:57 -0600, Michael Harms wrote:
> > Yes, I think that using average cortical thickness is a reasonable
> > covariate to use in thickness analyses. And total cortical surface area
> > likewise if you are analyzing regional surface areas, although in the
> > case of surface area you need to decide whether to use areas based on
> > the GM or WM surface, or some "mid"-surface in-between.
> >
> > Use mris_anatomical_stats along with the {lh,rh}.cortex.label files to
> > compute these statistics for the overall cortex. If the optional
> > <surface name> at the end of the command is 'pial', then the area will
> > be based on the pial surface. If nothing is specified, it'll be based
> > on the white (default) surface. If you want the area based on the mid-
> > surface, you either need to construct that surface first (if it isn't
> > already computed by recon-all in the most recent FS versions) or run the
> > command separately for the 'pial' and 'white' surfaces and then average
> > the resulting areas].
> >
> > cheers,
> > -MH
> >
> > On Fri, 2010-12-17 at 01:42 +0800, Liukarl wrote:
> > > Hello, Freesurfer experts:
> > >
> > >
> > >
> > > I found to report subcortical volumetric measure, ie, the volume of
> > > amygdale, people tend to use icv as a control variable. Is there any
> > > corresponding measure to correct the cortical thickness/area/volume
> > > results from autorecon3. Because we have priori hypothesis of
> > > hemisphere dichotomy of cortical structures, we need some control
> > > variable for each hemisphere. We want to use an overall measure for
> > > each hemisphere as a control variable. For example, to measure the
> > > group differences on rh_paracentral_thickness, we will use the
> > > rh_whole_thickness as a contral variable (which is the sum of the
> > > thickness measures of all the ROIs in the right hemisphere produced by
> > > Freesurfer). Similarly, to measure the group differences on
> > > rh_paracentral_area and rh_paracentral_volume, we will use the
> > > rh_whole_area and rh_whole_area as a contral variable respectively. Is
> > > this a valid approach to report our results?
> > >
> > >
> > >
> > > Thanks a lot!
> > >
> > >
> > >
> > > Karl
> > >
> > >
> > >
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