What is your mris_preproc command line? If you run mris_preproc with --xhemi, it should give you two frames (left hemi and right hemi). If you want to compute left-right, then add --paired-diff to the command line. The output will be on the lh of fsaverage_sym. This can be displayed on the white, pial, or inflated of fsaverage_sym. You can use mris_apply_reg to map this back to the subject's native surface if you want to display it there.
doug

On 2/19/16 9:18 AM, Ashkan Faghiri wrote:
Hello,

sorry for asking this again

I want to calculate the difference between the thickness of one subjects different hemispheres and show this on pial (left or right or even fsaverage_sys). so I have ran :

surfreg --s $subject --t fsaverage_sym --lh 
surfreg --s $subject --t fsaverage_sym --lh --xhemi

for my one subject. now I have two .reg files:
shahi/xhemi/surf/lh.fsaverage_sym.sphere.reg
shahi/surf/lh.fsaverage_sym.sphere.reg

If I am understanding this right, these two are the transform matrix for both hemisphere of my one subject to fsaverage_sym (right?)

if I run mris_preproc with xhemi option I will get a vector which have the length equal to number of vertexes. it's values are left-right (or right-left?). how can I convert this vector to pial or inflated surface? and how can I use lh.fsaverage_sym.sphere.reg to register my pial directly to fsaverage_sym?

Regards,
Ashkan
--
-- 
Ashkan Faghiri
MSc student of Bioelectrical Engineering
Department of Electrical Engineering
Sharif University of Technology


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