On 02/20/2016 05:47 AM, Ashkan Faghiri wrote:

Thank you doug for you answer.

So now I have two other question. 1- how can I check the inter hemisphere registration quality? e.g. can I check if the parcellation for the two hemisphere are matched well? or there is other ways?

You can map the curvature (--meas curv) and see how well they align. You can so this with mris_preproc with --meas curv. The output will have two frames, one for each hemi. Load it up in tksurfer or freeview as an overlay and switch between the two.

2- how can I correct for multiple correction for single subject? calculate the p vale for each vertex (to find significant difference between the two hemisphere) and correct these for multiple correction.

I am not aware of a way to do this. You'd have to have a measure of variability. I guess if you had a bunch of "normal" subjects, you could run them through the process and generate a map of means and stddevs, then use that to compute a z-score, then use that to compute a -log10(p), then correct that.

Regards, Ashkan

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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-- 

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

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