You want to use the -l option. Something like:
"mris_anatomical_stats -l lh.cortex.label -f cortexStatsFile.txt
SUBJECTID lh <pial>"
will I think to the trick.
(Use 'pial' at the end if you want the cortical surface area to be that
of the pial surface instead of the white).
For volume, you have to chose what measure you want to use as a control
variable -- eTIV (aka ICV), one of the "new" variables provided in the
aparc.stats files, or one of your own construction. [In the past, I've
used a "brain volume" covariate, derived as the volume enclosed within
the pial surface minus the volume of the lateral and inferior ventricles
(obtained from the aseg.stats)]. The choice depends on exactly what you
want to control for (i.e., controlling for ICV and "brain volume" are
not the same thing in the case of appreciable ventricular atrophy).
cheers,
-MH
On Fri, 2010-12-17 at 05:29 +0800, Liukarl wrote:
>
>
>
>
> 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:
> > &! gt; > 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
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > 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
> &g! t; > > 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.
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> _______________________________________________
> 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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
