External Email - Use Caution 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/1TELdMKGVJpKa4ZNA0JT1c2M5j92hscTUXojMSwfCRgHWMi4h330-7qb3M2OGXIYrgOSZICxTxnpti-05ncWdhR6JaJbIx73FVjtEzOdBqK1bpmrufIS7sOC5rf9sTVNVfUF_2k02iDbUNyl8qoOsQMWS5KZS1t7h7JfI_o3K8yrj9LhxQ2EB54r2L_4CsVC3HXfzZQIQW58QvmALvYxzjqKSlL7ZlrmqwXDwD2yTC98P_wzNSIBNXBRqjKkZWOhCZR0piY0tJiFCGuAw6DMfILX-TiwrTwsyjwWmBqI1d_rxSHX5j2-2gRTFnUWbv9ua4qItxp5KwGEhL5PxfcxxZg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3767398%2F 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 <dgr...@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 > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/173JwiLCCf8LKLMddYHP2EU7Cus-hY6ZJznnIinlohuxt0Foqxiq3fq1kuaiQYCRhPgjbq6Rhe-RKBGECNdsOvyvrmMKI4py4OeFpJPW0y5kGcMjdrhiQ4Mis9WepjU2Rj53v9U2iXwBKt3Wj2fSB333dAVRHMJIVIy8cfvT4jsfgvdlImiIQpWlNmg2mEGb5Nn3svPKck2PIIebNZc0oZsMcgPeDC5xIDKfc6OkUkSJn_tCA5ILej0YDqBjmk7EH_mojv-A6kG3_u6seGK3EQnWdnSUggTIsaiywJo3OUJfvGY8cifhRmFQApEVydSqeyKzsaaCFdGFLgP5Evl86rg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 > https://secure-web.cisco.com/1cB4DTB7HQw_QfQJKMd9vezQQV6KmmdR6zEjg7Dqj_IsdSoxsubiObgElN9cjhoWNoTo7oJbwxB6abX1drJ1pCrtC5bzoyDOp79zAxUf-6mlLyp7MelGEB01F__dy4PM67pfSJ-JxhGWJnwQBvLkPbEkAoHacBIOd0wRYvr0YIiEqR6Di9WBAoLl-8mBGt1AKtFtzkngmN-W6CXbnxW6zOvyITdJNjrsspktv-ANHBzp3zhaCl44N6NfaWfG2uHK0tL7u-PZ6Jt_G0CxkFg6xRro4A_mstsbzcMiKuhFqA3Q30uk6CLqF5f3SEtnOr8Wxj9pk8JJewnQiYG8J9VI3Kg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1cB4DTB7HQw_QfQJKMd9vezQQV6KmmdR6zEjg7Dqj_IsdSoxsubiObgElN9cjhoWNoTo7oJbwxB6abX1drJ1pCrtC5bzoyDOp79zAxUf-6mlLyp7MelGEB01F__dy4PM67pfSJ-JxhGWJnwQBvLkPbEkAoHacBIOd0wRYvr0YIiEqR6Di9WBAoLl-8mBGt1AKtFtzkngmN-W6CXbnxW6zOvyITdJNjrsspktv-ANHBzp3zhaCl44N6NfaWfG2uHK0tL7u-PZ6Jt_G0CxkFg6xRro4A_mstsbzcMiKuhFqA3Q30uk6CLqF5f3SEtnOr8Wxj9pk8JJewnQiYG8J9VI3Kg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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