ENH: Runwise bold reference generation #268
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effigies
reviewed
Jan 9, 2023
effigies
reviewed
Jan 9, 2023
nibabies/workflows/bold/base.py
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| # SLICE-TIME CORRECTION (or bypass) ############################################# | ||
| if run_stc: | ||
| bold_stc_wf = init_bold_stc_wf(name="bold_stc_wf", metadata=metadata) | ||
| # fmt:off | ||
| workflow.connect([ | ||
| (inputnode, bold_stc_wf, [('n_dummy_scans', 'inputnode.skip_vols')]), | ||
| (nss_detector, bold_stc_wf, [('n_dummy', 'inputnode.skip_vols')]), |
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At least in fMRIPrep, we allow this to be set manually by setting boldref_wf.inputnode.dummy_scans. Is this not implemented in nibabies?
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Good catch - It is, I guess we should prioritize user input, and default to calculating it with the nonsteadystates detector otherwise.
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Closes #253
This PR reverts bold reference generation to being calculated per run.
Included is a new workflow
init_infant_epi_reference_wfthat uses the following heuristic is used to generate the reference map: