External Email - Use Caution Hi Cornelius
I found something that computes the overlap of labels across the same vertex when doing some research about this, not sure if this is what you mean: https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4rsX6beTdCfGCkpiAyjUuMFA31V5ClU95ErPkQPZP8TKRthymZKTmx9z4NZ-1Q_VMNlPzPJ7PZG4H-wntegGfigUm5R6ocjIe4fS6bL4_82SxATBarpW8b6rv_vC1VPBn1ZM4Hj4ld7D7l3hMWkgB8zNZaHVjFrDQM4so73Mk3cuFXo4uZfnmiBKYK9XTJlzfFP24H6-tsGIkT4ka-7BQxMKOmF6bzTYzRo0tE8HTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_label2annot See specifically: --nhits <nhits_file> This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurfer<https://secure-web.cisco.com/1QIgJhgEjv5N9NM6Uh6927wVezy6eduY2p7_2aAiUh0J8fE_QRjLZ5IwPbIC4gnKD6g26N7TVbaIwYLg5BdgQSCFY1LmWY1cDfBL-R49zhRDt-6TzW_S84l6Z-4U3QS-SBlj8HR82qBl0HjcfjS2buz3mtuIQomiilbbafLXzRw1wQSaUnmj1OITA84m-fC1C8HrL430p2kCyyotFmJGKKwiiXBgMYlYljQIFiqINhAJFUVeI9kbMvioqTgmQZvjStJ8ARcmqHgrk_981OzG8NQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeSurfer> 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2). I know there is also a command merge_labels that may help? Best, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Dr. Cornelius Kronlage" <cornelius.kronl...@med.uni-tuebingen.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, February 16, 2021 at 11:19 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] overlap/intersection of labels? External Email - Use Caution Dear freesurfers, is there an elegant way of computing the intersection or overlap of different labels or - which would be even more useful for my application - annotations? I only managed to find labels_intersect (which appears to be from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16WQ5tQQPY74lwcUD6e-u4HAYMeACJcAQ4y9i44WDTIAnwCugW0W6FhO8wM0TL2oLO5bi9fjIhtPrBDzhbCqKzcbupsD5PFcOSeF5Q0Rs_J3sJoI9lWbxxbrYbzUv7-bxMiuXfAqo77oTh3OfNCeUFmsk9uuSK8z0-kYvPRfV89c3qUMvDGvWaz4sAtwVH3FXBf11T46qVKtA6pTCyt2sx-P4ee8nfAHn8Aoz2sdWCcPJLXcMFrrUBot8VS3a2wmrELeIOWXwLg6zxRoTGxpHCw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg11344.html<https://secure-web.cisco.com/12D3ntbm8RDBV366hh41UjEkFWk2mrjQHSMiY8WEom0naUegbdbmI9Bk7UNIwOTDDV40505y4xUMucZzUUWAKig63gNPrAZl0JMYNPDR9rlE4fUcOuQETynMWSKJG67sRNzzZQq8VF7AEsupWpjkrPP17ola-zMVT-3GDtM_dSs0-j76spejYlLevtumd4uKC8BNXwnxiW47uZxy5cBV4IPlI1yL8DP4GKO7QCjCWHuSjiE1xMapPwxOxVnVfHUKM/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg11344.html> ) which is awfully slow. In case this is of use for anyone else, I attached a modified version using 'join' that runs much faster, only has some compatibility issues with Mac. >time labels_intersect precentral.label frontal.label out1.label > /dev/null real 1m41.862s user 0m31.052s sys 0m30.757s >time bash bash_labels_intersect.sh precentral.label frontal.label out2.label real 0m0.193s user 0m0.118s sys 0m0.015s >diff -w out1.label out2.label > Thank you and best wishes Cornelius -- Cornelius Kronlage Assistenzarzt Klinik für Neurologie | Neurologie mit Schwerpunkt Epileptologie Universitätsklinikum Tübingen Hoppe-Seyler-Str. 3 | 72076 Tübingen
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