External Email - Use Caution Dear James and FreeSurfer experts, for lobes average cortical thickness we use this solution https://secure-web.cisco.com/12kn5RGwkDP8VJQa9PtCWSWT_3GfJlJYy06k6EpiyBm3DNksk5cBO1m_9Le5zbQFSumsT0NoxwNy2VNIh9LcoRkXkj5UlRW4ZVXK_mdgK-47PUJnpHKrnofShRBd4hn04wUndNIeo9qSFfwRuTCFZskpYzu_dEmSTfNuVH1YD9HszB8ZT58BL0-Oeu3k-_DzqTnsZDIIXHLZvQCrbQ7piw80BQs5FRBpW6WPRUf_ESj7p9BCvwjmzbrdNpfar1S9GUTa01DctAIO9o7810uXB9HXlros3aZXIKNPSevhYnE6HxGRs49xo3zx4Onil9efsTKtHy2JNy2TAmbw8Ze37eg/https%3A%2F%2Fgithub.com%2Fcnnp-lab%2FCorticalFoldingAnalysisTools, hope it helps!
Best, Fernanda Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Doutora em Ciências Médicas | metaBIO (IF-UFRJ) e Instituto D'Or de Pesquisa e Ensino On Wed, Nov 9, 2022 at 11:35 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > I would weight by the number of vertices in each ROI > > On 11/8/2022 12:20 PM, James Brown wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > I would like to know if this procedure is correct. > I have cortical thickness data from aparc+aseg for every ROI in DTK atlas > (i.e. output of recon-all). I need average cortical thickness in frontal, > parietal, temporal, cingulate and occipital lobes. Is it correct to average > thickness measurement of every sub lobe roi (e.g. average thickness in > frontal lobe = average of: > > - Superior Frontal > - Rostral and Caudal Middle Frontal > - Pars Opercularis, Pars Triangularis, and Pars Orbitalis > - Lateral and Medial Orbitofrontal > - Precentral > - Paracentral > - Frontal Pole > > and so on for other lobes... > > Do we need to correct for the number of vertices in every region when we > measure the lobar average thickness? > > Alternatively, do I need to run these commands to generate lobes then > measure thickness in every lobe? > > # mri_annotation2label --subject subject --hemi lh --lobesStrict lobes > # mri_annotation2label --subject subject --hemi rh --lobesStrict lobes > # mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \ > # --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \ > # --annot lobes --base-offset 200 [--base-offset must be last arg] > > > Thank you > James > > _______________________________________________ > 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/1g09wOx4W856aItHj4QzY4FFQdJKxAoTlFtbuLROvtDTsCnjHRmED3ZYPU19GooWKZkBrSmOBIKlZb5WZNIJz4a4VsFIaZ0ngYO2507YB0vLM1ZeiLCVYPE7bt8WbEaBnaE4a_dAbCqohtKS0AT-0FUBF9n5ven3CKjyGmT56NT0ZLU7u9pS_rxHYSXiQYY7QclZi-wF-HWcjZo3XoUZweaTW5NIXp6Uum33gJBJid3odO59BUHGqr_bji5h6puctE2j4Xd8fbtHPZVCumT-2i6tq3WX4kFyjJqY7t91El3sNyELVkl8mp859GXbMT7-W70pTZAkVINi0ZeZRFhVzaA/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/1kdEANE9nCVMm7GA3EzCDzKmUqLLckMOCL-0IYtIcuzPWSPhDxOkpxHBQlQWk597JU6MFs9nOjC8a1IvWHRRs-Wk1AJmNy1mnfBBXgAx_sNp8BLNY-QySLu5r-V09q8H3qDbB0RMdwiHMPMPZ4U_m2CWMe0l5qi53_KRhvM-22FkXbd8_asUzRBt3Q2g-tsawfNpSKx0IsC25vZg0VD6A2MtxGbiFLnSdjvU4K2oS-SX70vJhu5hfL9JIiILRnktAk91Qn-4uAv31IxhJqG-okW7557puyANF1TR2KwC7_WT7WxtQly2O-nzBGNVliucjTiv5fW6hYZDzHzm9nlpKEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1kdEANE9nCVMm7GA3EzCDzKmUqLLckMOCL-0IYtIcuzPWSPhDxOkpxHBQlQWk597JU6MFs9nOjC8a1IvWHRRs-Wk1AJmNy1mnfBBXgAx_sNp8BLNY-QySLu5r-V09q8H3qDbB0RMdwiHMPMPZ4U_m2CWMe0l5qi53_KRhvM-22FkXbd8_asUzRBt3Q2g-tsawfNpSKx0IsC25vZg0VD6A2MtxGbiFLnSdjvU4K2oS-SX70vJhu5hfL9JIiILRnktAk91Qn-4uAv31IxhJqG-okW7557puyANF1TR2KwC7_WT7WxtQly2O-nzBGNVliucjTiv5fW6hYZDzHzm9nlpKEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > -- Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino e metaBIO (IF-UFRJ)
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