I realized that I should use mris_sphere, mris_register and mrisp_paint tools, but I have no idea on how to set the parameters of these commands. May you or somebody else give me some help? Thanks.

Aize

> Date: Fri, 15 Apr 2011 10:47:08 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: caoaize@hotmail.com
> CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Cortical thickness in the template space
>
> Hi Aize,
>
> yes, that should do it.
>
> cheers,
> Bruce
> On Fri, 15 Apr 2011, caoaize wrote:
>
> >
> > Hello there, We have a bunch of files that had freesurfer run already, simply using the command "recon-all -s subjid -all", in order to get the cortical thickness in fs average space, should we have to re-run all of them again using "recon-all -s subjid -qcache -measure thickness", or we may apply some transformation reported already to transform the thickness from subject space to fs average space ? Does anyone have any suggestion on how to do that? Thanks. Aize
> >
> >> Subject: Re: Cortical thickness in the template space
> >> From: nicks@nmr.mgh.harvard.edu
> >> To: caoaize@hotmail.com
> >> CC: freesurfer@nmr.mgh.harvard.edu
> >> Date: Tue, 8 Mar 2011 16:50:41 -0500
> >>
> >> Aize,
> >>
> >> run:
> >>
> >> recon-all -s subjid -qcache -measure thickness
> >>
> >> and this will create files in the /surf dir which sample the thickness
> >> data at different smoothing levels onto the fsaverage subject space.
> >>
> >> n.
> >>
> >> On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote:
> >>>
> >>> Hello,
> >>>
> >>> We try to look at t he two group difference of cortical thickness, but
> >>> I need the lh(or rh).thickness file, which reported in template space
> >>> (FS average space), but after run recon-all -all, what I have is only
> >>> lh.thickness, or rh.thickness, which is in subject's space. Would
> >>> someone point me where or how I can get them? Thanks.
> >>>
> >>> Aize
> >>
> >>
> >>
> >> 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.
> >>
> >