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harmonzie labels for longitudinal lesions - WIP #1039
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Hello @frheault, Thank you for updating !
Comment last updated at 2024-12-12 19:04:26 UTC |
@Manonedde @ThoumyreStanislas If you have real data (co-registered), this could be tested. If there are corner cases or problems, I will fix them before adding tests. |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1039 +/- ##
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- Coverage 69.46% 69.20% -0.26%
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Files 447 448 +1
Lines 24052 24146 +94
Branches 3291 3310 +19
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+ Hits 16708 16711 +3
- Misses 5946 6037 +91
Partials 1398 1398
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Here are test data from MS myelo-inferno subjects. Lesion masks are coregistered to session 1: sub-004_ms_test_harmonize_lesion.tar.gz The results seem coherent but for the newly labelled lesion 160 (parahip lesion, green-yellow colors), for session 4 it is labelled 169 (in red) whereas it is close to lesion 160 (session 2, 3 and 5). Here are the results: Harmonize_labels.tar.gz Harmonize_labels.tar.gz |
Quick description
This script takes in multiple lesions file (labels) from a single subject (could be scan-rescan, longitudinal, etc.) and relabel the lesions so the overlapping, temporally consistent lesions will have the same labels.
Based on:
https://www.sciencedirect.com/science/article/pii/S2213158218303711?via%3Dihub
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Type of change
Check the relevant options.
Provide data, screenshots, command line to test (if relevant)
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Checklist