External Email - Use Caution I have encountered the problem that chrisadamsonmcri<https://secure-web.cisco.com/1xWGWxoOiHrVvr8AONbdJmSDQHTmtv9-28Mk5n8yl42uZZFuoMAQQUxVbuSJ_bnLpivR1APeZnYLRzLCQkUc6mCZX0cTHbqAbV0r9yh3kDijwznIOAGT_7arlILqKT_D2sEQ49W0KZEtX-qcNj7YuA5UUMh948jk1XxvZ-JXzlsxm3Q2EtF5TCtUzC1SWTwmztvvVKBpQx_3pb2AoiyQ3bTDNAGg_FZalY_oAVeeYHo69i4YFRU6c5QEXk7_nDG091L4HqLYatBu_KvBwfK05ZwN44U-JX9BiwAUwGrqcnUv2fHJrR-6eHjO3EBUvkxZt/https%3A%2F%2Fgithub.com%2Fchrisadamsonmcri> describes in issue 898<https://secure-web.cisco.com/1m61bxpBwgxqKDi9Ogsq79O03id3L1GGsM-889UgjAYymOGyG_wpC_8q7kzQFnhZ1oTggchjOJNUAlYSY42udbv0ezecLgcftfdaAcijtQUR1XTns1wUlvhEyo-3b99ocX32VHnJj3JczduO6MJdFQ02B3b50SRl_3jZDHmYz8_xA_0DZGjtUOjOHZ6n4B9GDrABBvQJmfK3r3ycg3TA4lYpwLrAkoSPR_nGOUNIn1cEYwXDCwEA7Rum2-H0TptR45ws3O9H_BEoHvM1s615JMegva0B8sREKTDkkiUl2P1SJXAfL98E0-dca8rB4daCL/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F898>. The last time I used mri_binarize was using FS v6, where it behaves like this:
mri_binarize --replace A B --replace B C Label A would become B in the output. Label B would become C in the output. here's an example: --replace 11 15 # map "4th Ventricle" -> "4th-Ventricle"\ --replace 15 72 # map "5th Ventricle" -> "5th-Ventricle"\ i want to convert a seg where the LUT maps 11 as 4th ventricle and 15 as 5th ventricle. i want to convert these to the FS LUT (using the replacements shown, 15 and 72). But this results in 4th ventricle getting labeled as 5th ventricle! Four years ago i ran a script performing 230 replace functions to map Neuromorphometrics labels to FS, and it worked fine (evidenced by Dice testing and inspection). Today i ran the same script on the same data and get funky results on a half dozen or so structures that follow the example replacement scheme. My current workaround is to use mri_binarize from v6. ---------------------------------------------------------------------- The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately with a copy to lfos...@radnet.com and destroy this message. Please be aware that e-mail communication can be intercepted in transmission or misdirected. Your use of e-mail to communicate protected health information to us indicates that you acknowledge and accept the possible risks associated with such communication. Please consider communicating any sensitive information by telephone, facsimile or regular U.S. mail. If you do not wish to have your information sent by e-mail, please contact the sender immediately.
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