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
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
- 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.
- 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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