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Disable SCORE/SCRUB for GE/short runs and get GE workflow working #248

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merged 44 commits into from
Apr 3, 2023

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@tsalo tsalo commented Mar 31, 2023

Closes None.

Changes proposed in this pull request

  • Add BIDS-examples datasets as test data.
  • Disable SCORE/SCRUB automatically for GE/short ASL data.
  • Patch in rmsd as a NaN for GE data.
  • Extract the M0 TR in GeReferenceFile.
  • Simplify the code in GeReferenceFile, although I would still like to separate M0 extraction from the reference file generation.
  • Start simplifying the SCORE/SCRUB code. It still needs a lot of work to be readable.
  • Use RepetitionTime for summary interfaces when available, but resort to RepetitionTimePreparation when it's not. This probably won't work with multi-PLD data, but that isn't supported at the moment anyway.
  • I still think slice-timing correction is wonky. The data are actually acquired in a very short perior within the TR, so it's not spaced evenly across the TR like BOLD scans. Additionally, we have control-label pairs where interpolating across volumes doesn't make sense. Even with deltam volumes, the TR is essentially 2X the original, and the slices come from very different times, right?

@tsalo tsalo added the testing Improving testing in the project. label Mar 31, 2023
@tsalo tsalo added bug Something isn't working breaking-change PRs that change results or interfaces. labels Apr 3, 2023
@tsalo tsalo changed the title Add test data from ASL-BIDS examples Disable SCORE/SCRUB for GE/short runs and get GE workflow working Apr 3, 2023
@tsalo tsalo marked this pull request as ready for review April 3, 2023 18:09
@tsalo tsalo merged commit cb178ca into PennLINC:main Apr 3, 2023
@tsalo tsalo deleted the more-test-data branch April 3, 2023 21:21
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