Single workflow#5
Draft
arkiev wants to merge 80 commits into
Draft
Conversation
… scatter, updated checkpoints, didn't crash
Wiz Scan Summary
To detect these findings earlier in the dev lifecycle, try using Wiz Code VS Code Extension. |
…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 +/- ##
===========================================
- Coverage 68.73% 20.70% -48.04%
===========================================
Files 12 26 +14
Lines 1206 5172 +3966
Branches 110 739 +629
===========================================
+ Hits 829 1071 +242
- Misses 350 4058 +3708
- Partials 27 43 +16 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
…HECK TEMPLATE T1!
…eeds real data testing)
- New `phantomkit plot longitudinal` command (plotting/longitudinal.py) - X-axis: date of scan, Y-axis: ADC/T1/T2, vial selector dropdown - Temperature-adjustable reference line, per-session toggle buttons - scan_date embedded in HTML by pipeline via dcm2niix JSON sidecar - scan_date threaded through phantom_processor → PhantomSessionWf → plot functions - --date CLI option for existing HTML files without embedded scan_date
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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.