Thanks, Doug.

I'm not planning to use qdec. It's just that I used to generate the
?h.thickness_max10.fwhm10.fsaverage_510.mgh files (which are what we name
the files after running the two commands) before I use mris_preproc and
mri_glmfit. I also generally skip the "smooth" step in freesurfer tutorial
since the files are smoothed in the first place.

Any suggestions?

Cherry

On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:

>
>
> Actually, #2 will not work. I don't think you can use qdec with the
> xhemi stuff anyway. You should use the mris_preproc command followed by
> mri_glmfit.
> doug
>
>
> On 03/28/2013 12:51 PM, Douglas N Greve wrote:
> > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote:
> >> Dear Freesurfer experts,
> >>
> >> I'm trying to investigate lh-to-rh asymmetry, so I register my
> >> subjects to the subject of fsaverage_sym following the instructions on
> >> this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all
> >> the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf.
> >>
> >> In my lab we generally process ?h.thickness files with the next two
> >> commands before statistically analysis:
> >>
> >> "mris_thickness -max 10 subjid ?h thickness_max10"
> >> "recon-all -qcache -measure thickness_max10 -target fsaverage_510
> >> -fwhm 10 -no-isrunning -s subjid -hemi ?h"
> >>
> >> To keep with this protocol, my questions are
> >> 1) how do I use "mris_thickness" properly so that I don't overwrite
> >> the files registered to fsaverage_510?
> > I think it will recreate the basic ?h.thickness file and will not touch
> > registrations.
> >> 2) in "recon-all -qcache", will it do the trick by substituting
> >> "fsaverage_sym" for "fsaverage_510"?
> >>
> > Yes, that should work.
> >> Thank you in advance,
> >> Cherry
> >>
> >>
> >>
> >> _______________________________________________
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> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
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