Hi Doug,
As I'm trying to run mris_preproc on this page ( http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I want to know what the --xhemi argument is for. Is it for calculating the difference between lh and rh thickness?
I wanted to calculate a asymmetry index for each vertex, which is (lh-rh)/[(lh+rh)/2] rather than (lh-rh). Can I do that using mris_preproc and how?
Thanks, Cherry
On Thu, Mar 28, 2013 at 1:32 PM, Ejoe Yizhou Ma ym850@nyu.edu wrote:
I see. Then I think I'd better just follow the instructions on the Xhemi page. Thanks!
On Thu, Mar 28, 2013 at 1:06 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
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.**edugreve@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<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 >> >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
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