Re: [Freesurfer] mris_thickness & qcache for xhemi surfaces

Hi Cherry, what I meant was that you cannot use the qcache with xhemi. You'll need to run the mris_preproc command as listed on the web page. doug

On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote:

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 <greve@nmr.mgh.harvard.edu mailto:greve@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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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Fax: 617-726-7422 <tel:617-726-7422>

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