When creating a laterality-free atlas one needs to make sure to do the same thing to the left and right hemi. Eg, the mni152 is not laterally symmetric, so you will get a different registration when you register your volume directly to the mni152 vs left-right reversing your volume and then registering (and why people will register to a symmetric mni152 when doing such studies). These biases can creep in in other ways. Eg, when manually labeling the brain, the labeler might do the left slightly different than the right, and this might creep into the atlas (though this can be reduced by including left-right reversed labels in the atlas). Our standard labels (eg, aparc) are susceptible to these problems. Any clearer?
On 3/6/2024 10:52 AM, Joost Janssen wrote:
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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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767398/ 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 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 <https://secure-web.cisco.com/173JwiLCCf8LKLMddYHP2EU7Cus-hY6ZJznnIinlohuxt0Foqxiq3fq1kuaiQYCRhPgjbq6Rhe-RKBGECNdsOvyvrmMKI4py4OeFpJPW0y5kGcMjdrhiQ4Mis9WepjU2Rj53v9U2iXwBKt3Wj2fSB333dAVRHMJIVIy8cfvT4jsfgvdlImiIQpWlNmg2mEGb5Nn3svPKck2PIIebNZc0oZsMcgPeDC5xIDKfc6OkUkSJn_tCA5ILej0YDqBjmk7EH_mojv-A6kG3_u6seGK3EQnWdnSUggTIsaiywJo3OUJfvGY8cifhRmFQApEVydSqeyKzsaaCFdGFLgP5Evl86rg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ 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 <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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1cB4DTB7HQw_QfQJKMd9vezQQV6KmmdR6zEjg7Dqj_IsdSoxsubiObgElN9cjhoWNoTo7oJbwxB6abX1drJ1pCrtC5bzoyDOp79zAxUf-6mlLyp7MelGEB01F__dy4PM67pfSJ-JxhGWJnwQBvLkPbEkAoHacBIOd0wRYvr0YIiEqR6Di9WBAoLl-8mBGt1AKtFtzkngmN-W6CXbnxW6zOvyITdJNjrsspktv-ANHBzp3zhaCl44N6NfaWfG2uHK0tL7u-PZ6Jt_G0CxkFg6xRro4A_mstsbzcMiKuhFqA3Q30uk6CLqF5f3SEtnOr8Wxj9pk8JJewnQiYG8J9VI3Kg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <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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