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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 https://secure-web.cisco.com/1TELdMKGVJpKa4ZNA0JT1c2M5j92hscTUXojMSwfCRgHWMi... 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 CautionDear 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
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