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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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