I don't know of an "elegant" way. You could convert the annotations to labels (mri_annotatoin2label), the binarize the labels (mri_label2label with --mask output), then AND them (fscalc bin1.mgz and bin2.mgz -o and.mgz), then convert that back to a label (mri_cor2label, make sure to use the --surf option)

On 2/16/2021 11:18 AM, Dr. Cornelius Kronlage wrote:

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://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11344.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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer