Nick, what happens if you reverse the order (ie, do 15 72 first, then 11
15)?
On 11/28/2023 12:27 PM, Nick Schmansky wrote:
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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.
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