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support dcm2niix "Bidsguess" #697

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yarikoptic opened this issue Aug 9, 2023 · 0 comments
Open

support dcm2niix "Bidsguess" #697

yarikoptic opened this issue Aug 9, 2023 · 0 comments

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@yarikoptic
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Tireless @neurolabusc has developed https://github.com/rordenlab/dcm2niix/tree/development/BidsGuess which would populate BidsGuess field in sidecar .json files with dcm2niix's guesses for modality type and entities, e.g.

"BidsGuess": ["anat","_acq-tse2_run-3_PDw"],
"BidsGuess": ["anat","_acq-tse2_run-3_T2w"],

I guess we better make use of this! I see multiple ways

  • We already support some placeholders such as bids_subject_session_prefix and bids_subject_session_dir code. We can add dcm2niix_bids_guess_modality and dcm2niix_bids_guess_entities, so some "lazy" heuristic called dcm2niix_guess could just return {bids_subject_session_dir}/{dcm2niix_bids_guess_modality}/{bids_subject_session_prefix}{dcm2niix_bids_guess_entities} and be done
  • Provide more detailed breakdown of entities, such as dcm2niix_bids_guess_entity_acq, dcm2niix_bids_guess_entity_run, and dcm2niix_bids_guess_suffix (naming might need to be improved) so heuristics like reproin could selectively make use of them.
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