Dear Doug,

Thanks. A regional Laterality Index can be calculated using XHEMI (as described on the wiki) but also in a different way, e.g. using the default FS output from ?h*.stats files and e.g. doing (LH-RH)/((LH+RH)/2) or some other formula. You once mentioned about this latter approach "But the atlas was not created in a symmetrical way, so there might be biases". Could you elaborate on what these biases might be?

I read MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767398/ and it mentions biases when doing registration of a hemisphere to either LH or RH but I am not sure if these are the same biases.

Thanks!

-joost

On Wed, Nov 29, 2023 at 12:02 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Yes, they are. BTW, you should not need to mri_convert the thickness to mgh format

On 11/27/2023 10:01 AM, Joost Janssen wrote:
External Email - Use Caution

Dear Doug,

The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks.

surfreg --s $subject --t fsaverage_sym --lh --no-annot

surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi

mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh

mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh

mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg $subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg $subject/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg

mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg $subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg $subject/xhemi/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg

fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0 $subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o $subject/surf/li.thickness.lh.fsaverage_sym.mgh

mri_segstats --annot fsaverage lh aparc --i $subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum $subject/stats/li.thickness.aparc.stats

-joost
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .