Improving T1 Model Selection

[alexdaniel654]

Proposed changes

Pre-processing steps (registration, EPI distortion correction etc) can often cause quite a lot of slightly negative numbers, this then means the T1 mapping code assumes the data has been magnitude corrected. After multiple people have had issues when trying to debug this behaviour we've decided it makes sense to add a flag when instantiating the class to select if the data should be fit to a magnitude corrected model or absolute model.

auto model selection now considers data to have been magnitude corrected if 5% of the voxels of the first inversion are less than -0.05 x the 95th percentile of the signal in the final inversion time i.e. the number of negative voxels required for the signal to be considered magnitude corrected has increased and the threshold at which voxels are considered negative is now based on the dynamic range of the data so floating point errors shouldn't cause voxels with an intensity of -1E-6 to be considered negative any more.

Should close #225

Checklists

• I have read and followed the CONTRIBUTING document
• This pull request is from and to the dev branch
• I have added tests that demonstrate the feature/fix works
• I have added necessary documentation (if appropriate)
• I have updated documentation which becomes obsolete after my changes (if appropriate)
• I have added/updated a notebook to demonstrate the changes (if appropriate)
• Files added follow the repository structure (if appropriate)

[pep8speaks]

Hello @alexdaniel654, thank you for updating!

• In the file ukat/mapping/t1.py:

Line 72:17: E129 visually indented line with same indent as next logical line

Comment last updated at 2024-09-30 12:57:07 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 97.82609% with 1 line in your changes missing coverage. Please review.

Project coverage is 97.96%. Comparing base (9d02642) to head (e11d70e).
Report is 1 commits behind head on dev.

Files with missing lines	Patch %	Lines
ukat/mapping/t1.py	93.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #227      +/-   ##
==========================================
- Coverage   97.97%   97.96%   -0.02%     
==========================================
  Files          48       48              
  Lines        4445     4470      +25     
==========================================
+ Hits         4355     4379      +24     
- Misses         90       91       +1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.