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ENH: Add flag for multi-step registration to adult templates #415

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merged 8 commits into from
Dec 13, 2024

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@mgxd mgxd commented Dec 6, 2024

This PR adds a flag, --multi-step-reg, that when enabled alters registrations to MNI152NLin6Asym by first registering the anatomical template to MNIInfant:cohort-X, and then concatenating that transform in addition to pre-computed ones (MNIInfant:cohort-X -> MNI152NLin6Asym). If results are promising, other adult templates, such as MNI152NLin2009cAsym will follow.

ATM, this PR fails to include the precomputed transforms, as they are quite a few (11 MNIInfant cohorts) and to/from transforms. I was originally planning on including them in nibabies, but the 3.2GB size is too much.

For the time being, the transforms are hosted at an OSF repository, until they have been finalized and structured for TemplateFlow. We use pooch to fetch the needed transform.

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codecov bot commented Dec 6, 2024

Codecov Report

Attention: Patch coverage is 42.64706% with 78 lines in your changes missing coverage. Please review.

Project coverage is 56.01%. Comparing base (b9efa6f) to head (57c2fcc).

Files with missing lines Patch % Lines
nibabies/workflows/anatomical/registration.py 19.56% 37 Missing ⚠️
nibabies/workflows/anatomical/fit.py 34.00% 31 Missing and 2 partials ⚠️
nibabies/interfaces/patches.py 77.14% 6 Missing and 2 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #415      +/-   ##
==========================================
- Coverage   56.23%   56.01%   -0.22%     
==========================================
  Files          69       69              
  Lines        6553     6675     +122     
  Branches      816      830      +14     
==========================================
+ Hits         3685     3739      +54     
- Misses       2666     2732      +66     
- Partials      202      204       +2     

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@mgxd mgxd marked this pull request as ready for review December 13, 2024 04:57
@mgxd mgxd changed the title ENH: Chain 2-step registration for adult templates ENH: Add flag for multi-step registration to adult templates Dec 13, 2024
@mgxd mgxd merged commit b7e3fcc into nipreps:master Dec 13, 2024
1 check was pending
@mgxd mgxd deleted the enh/mni-reg branch December 13, 2024 05:30
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