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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_l7VTkyo4r...

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 FreeSurferhttps://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-bounces@nmr.mgh.harvard.edu on behalf of "Dr. Cornelius Kronlage" Cornelius.Kronlage@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?

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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-u4HAYMeACJcAQ4y9i44WDTIAnwC...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