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Support single-PLD Q2TIPS PASL and multi-PLD PCASL #268

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merged 119 commits into from
May 25, 2023
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@tsalo tsalo commented Apr 20, 2023

Closes #250 and closes #251.

To do:

  • Decide between Juttukonda 2021 unweighted average and Dai 2012 weighted average for multi-PLD PCASL CBF calculation.
    • I don't know how to do the weighted average yet.
  • Define T1tissue based on magnet strength.
    • I'm not aware of any papers with formulae, but Manuel Taso pointed me toward Wright et al. (2008). This unfortunately limits us to 1.5, 3, and 7T data.
  • Double-check the code and formulae.

Changes proposed in this pull request

  • Estimate ATT for multi-PLD PCASL data using the Dai 2012 method. Use this to calculate CBF for those data.
  • Use formula from Noguchi 2015 to calculate CBF for single-PLD Q2TIPS data.
  • Add license info for all copied, modified, translated, or otherwise external code.
  • Update test datasets by removing hidden files.
  • Also, fix test_002 dataset:
    • Drop second deltam volume. It's just a duplicate of the first, and was a conversion bug.
    • Add necessary metadata fields, including RepetitionTimePreparation for the M0 scan and LabelingEfficiency, BackgroundSuppression, and BackgroundSuppressionNumberPulses for the asl scan.
  • Add modified version of FSL Split interface that enforces a list output.
  • Modify _select_first_in_list to only return the first item if a list is provided.
  • Rename aslprep.interfaces.cbf_computation to aslprep.interfaces.cbf.

@tsalo tsalo added the enhancement New feature or request label Apr 21, 2023
@tsalo tsalo merged commit 12112e9 into PennLINC:main May 25, 2023
@tsalo tsalo deleted the multi-pld branch May 25, 2023 16:05
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Support Q2TIPS data Re-enable multi-PLD PCASL support
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