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 > > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology
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