Mdr t1 molli

[plaresmedima]

New mdr keyword in T1 class

• Purpose: introduce a backwards compatible option to perform motion correction.

• Usage: setting mdr=True in T1() performs motion correction prior to computing the parameter maps. The default is False.

map = T1(pixel_array, TI, affine, mdr=True)

• Example: output with and without mdr=True (see below - note the sharper kidney outline when mdr=True). This example is generated by a new module test_mdreg.py, current in /tests. This may not be the appropriate place for it as it is not a proper unit test - more of an illustration.

• New attribute: This PR also introduces a new attribute deformation_field, which has the value None when mdr=False

• New requirement: This brings in mdreg as a requirement, which ships with elastix and skimage.

• Note: There is currently still some inline comments that can be removed or shortened once they are addressed. For instance the current version still includes a hack to avoid the problem of autoselecting the wrong model, which still happened in this eample. This needs another solution but cannot be addressed at the level of mdr. There are also questions that are more an issue of design and the general approach in ukat, e.g. whether we expose coregistration options in the API or not.

• See also Model Driven Registration #164 and MDR #183. The solution here should apply to other classes as well so we should be able to add mdr as an option everywhere with the same API (mdr=True keyword).

[pep8speaks]

Hello @plaresmedima, thank you for updating!

Cheers! There are no PEP8 issues in this Pull Request. 🍻

Comment last updated at 2025-01-13 17:48:59 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 96.49123% with 2 lines in your changes missing coverage. Please review.

Project coverage is 97.94%. Comparing base (7211a80) to head (c89b84a).
Report is 35 commits behind head on dev.

Files with missing lines	Patch %	Lines
ukat/mapping/t1.py	94.28%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #228      +/-   ##
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- Coverage   97.96%   97.94%   -0.02%     
==========================================
  Files          48       48              
  Lines        4466     4520      +54     
==========================================
+ Hits         4375     4427      +52     
- Misses         91       93       +2     

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[alexdaniel654]

TODO Before Merge

In a very rough order

• Merge Improving T1 Model Selection #227 into this branch @alexdaniel654
• Remove np.abs hack so magnitude corrected signals work @alexdaniel654
• Add deformation fields as optional output in to_nifit method @alexdaniel654
• Deal with pep8 issues @alexdaniel654
• Run ukat implementation of MDR on a few example datasets (CBG18, DER110, EDB88, NOT27, TK07 & DER48) and check its giving expected results as before @charlotteebuchanan
• Add automated MDR tests to test_t1.py (based on current test_mdreg.py file) @alexdaniel654
• Add example of MDR to t1_calculation.ipynd @plaresmedima
• Check for any documentation/docstrings that need to be updated @alexdaniel654

Things to check when testing

• Magnitude corrected and abs data
• 2D and 3D images
• Masks
• MOLLI
• 2/3 Parameter fits

[alexdaniel654]

Coverage only decreases a tiny bit.