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ENH: Add random seed option to ANTs registration #3463

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merged 3 commits into from
May 9, 2022

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ghisvail
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@ghisvail ghisvail commented May 7, 2022

Context

Clinica uses the ANTs registration interfaces for some of its pipelines. Since reproducibility is a major focus for us, it would be desirable to expose and use the random seed option recently introduced to the ANTs registration CLI.

Summary

This PR exposes the corresponding random seed options for antsRegistration and antsRegistrationSynQuick.sh. Both are named differently but expects its value as an integer. If unspecified, the seed value is computed from the system clock internally according to the documentation.

@ghisvail ghisvail mentioned this pull request May 7, 2022
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codecov bot commented May 7, 2022

Codecov Report

Merging #3463 (77b3da1) into master (f662acf) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master    #3463   +/-   ##
=======================================
  Coverage   65.24%   65.24%           
=======================================
  Files         309      309           
  Lines       40838    40840    +2     
  Branches     5377     5377           
=======================================
+ Hits        26645    26647    +2     
  Misses      13118    13118           
  Partials     1075     1075           
Flag Coverage Δ
unittests 65.02% <100.00%> (+<0.01%) ⬆️

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Impacted Files Coverage Δ
nipype/interfaces/ants/registration.py 73.25% <100.00%> (+0.10%) ⬆️

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LGTM. Thanks, I thought I'd actually sent you a request to add min_ver, but it was sitting here in my pending review.

Could you also run make specs?

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ghisvail commented May 9, 2022

Could you also run make specs?

It runs fine on my end.

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ghisvail commented May 9, 2022

It runs fine on my end.

My bad, I thought they were some sorts of additional checks.

Thanks for updating them.

@effigies effigies merged commit b38879d into nipy:master May 9, 2022
@ghisvail ghisvail deleted the ants-reg-seed branch May 9, 2022 14:47
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2 participants