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… scatter, updated checkpoints, didn't crash
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…API change (plugin → worker) and Click's automatic underscore-to-hyphen conversion in option names (--metric_dir → --metric-dir).
Codecov Report❌ Patch coverage is ❌ Your patch status has failed because the patch coverage (12.84%) is below the target coverage (80.00%). You can increase the patch coverage or adjust the target coverage. Additional details and impacted files@@ Coverage Diff @@
## main #5 +/- ##
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- Coverage 68.73% 20.93% -47.81%
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Files 12 26 +14
Lines 1206 5115 +3909
Branches 110 730 +620
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+ Hits 829 1071 +242
- Misses 350 4001 +3651
- Partials 27 43 +16 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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…HECK TEMPLATE T1!
Replaces the 5 separate per-metric CSV files (mean/median/std/min/max) per contrast with a single .xlsx file containing one sheet per metric, stored in metrics/xlsx/ instead of metrics/csv/. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…d outputs, figure legends
…) in outer bracket
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The primary contribution of this fork is the addition of a complete DWI preprocessing and QC pipeline integrated as a first-class stage alongside the existing native contrast workflow. This includes automatic DICOM series classification, phase-encoding correction mode selection (rpe_none, rpe_pair, rpe_all, rpe_split), FSL-based DWI preprocessing via dwifslpreproc, tensor fitting to produce ADC and FA maps, and rigid-body T1-to-DWI coregistration using FLIRT — all orchestrated through a new pipeline.py entry point that runs all three stages from a single command. Several refinements were also made to the existing codebase: the ANTs registration check threshold was updated, vial masks are now transformed with nearest-neighbour interpolation to preserve binary values, and the ADC scatter plot was redesigned with open-circle reference markers plotted over the measured values for clearer visual comparison against SPIRIT reference data.