Hi,
‘mri_binarize –replace v1 v2’ performs transitive replacements if multiple ‘–replace’ args are specified. This has been the behavior since May 25, 2021 commit.
Now, new mri_binarize option '--no-transitive-replace' is introduced to turn off the transitive replacements. Let me know if this works for you. The changes should be available in Freesurfer dev version tomorrow.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Lee Tirrell Sent: Tuesday, November 28, 2023 8:19 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Reopen issue 898: mri_binarize --replace misbehavior
External Email - Use Caution That could work in a simple case, but in a more complex case (10+ `--replace X Y` flags, for example) this would be more difficult to do. Also, then the ordering of the flags matter which adds more complication to constructing a command line call.
the workaround now would be to separate out into multiple `mri_binarize` commands if there are any overlap in labels, but the old behavior is preferable
On Wed, Nov 29, 2023 at 7:07 AM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: 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:
External Email - Use Caution
I have encountered the problem that chrisadamsonmcrihttps://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 898https://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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