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ENH: Runwise bold reference generation #268
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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_wf
that uses the following heuristic is used to generate the reference map: