ENH: Add flag for STC reference time and set in all cases #2520
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fmriprep/workflows/bold/stc.py
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| @@ -107,7 +107,7 @@ def init_bold_stc_wf(metadata, name='bold_stc_wf'): | |||
| inputnode = pe.Node(niu.IdentityInterface(fields=['bold_file', 'skip_vols']), name='inputnode') | |||
| outputnode = pe.Node(niu.IdentityInterface(fields=['stc_file']), name='outputnode') | |||
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| LOGGER.log(25, 'Slice-timing correction will be included.') | |||
| LOGGER.log(25, f'BOLD series will be slice-timing corrected to an offset of {tzero:.3g}.') | |||
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For the example in lines 69/70 (2s TR, 0-0.9), this would then yield an offset of 0.45, correct? I think that printing/logging this as an output rather than the intended time offset (1s) may be a bit confusing. I'd opt for printing/logging the intended time offset.
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I don't know what you mean by the "intended time offset" here. The default 3dTshift behavior sets tzero to the middle of the acquisition time (0.45), as does the proposed default behavior here. I'm not sure under what circumstances you would expect to see 1s.
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Sorry for not being clearer! The point was that it would perhaps be easier for users to know what the temporal offset is not in terms of percent but in terms of time. Else they might be confused that putting in 0.5 for a TR of 2s returns 0.45 and not 1s. Hope that’s clearer?
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Overall I think this is ready to go. Please let me know if I haven't addressed your concerns, @martinhebart.
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Thanks for adding this @effigies! |
This PR partially address #2477 by providing a flag
--slice-time-refthat can take a float from 0-1 or special values"first"and"middle".This also always sets the
-tzeroflag for 3dTshift (in cases where we run STC) tomin + frac * (max - min), which will generally befrac * max. This should be the same as 3dTshift's default ofmean(SliceTiming), as well asfrac * max, but I update the text to be explicit as well.Millisecond precision is used in reporting.
Closes #2516.