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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 Additional details and impacted files@@ Coverage Diff @@
## main #5 +/- ##
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- Coverage 68.73% 23.17% -45.57%
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Files 12 21 +9
Lines 1206 4566 +3360
Branches 110 658 +548
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+ Hits 829 1058 +229
- Misses 350 3465 +3115
- Partials 27 43 +16 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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…HECK TEMPLATE T1!
Label derivation now finds the first path component that differs between input files by walking inward from the right and identifying the common suffix — surfaces the subject/session directory (e.g. P000009_testing) rather than a shared scan-type directory (native_contrasts_staging). Font sizes increased (axis titles 13→15px, ticks 12→14px, controls 11–12→14px); marker radii increased (session circles 6→9, reference open circles 8→11, group mean squares 8→11); chart height 440→500px. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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.