FIX: Do not generate 4D references out of 4D single-band references (SBRefs) #338
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… 4D SBRefs are supplied as input. This patch checks the dimensionality of SBRefs and generates an average if the SBRef is 4D. Fixes nipreps/fmriprep#1579. Intimately related to nipreps#253, although I'm not sure the proposed resampling there is absolutely necessary. It could be detrimental for ``bbregister`` in co-registration. It is very likely necessary for head-motion correction with either ``mcflirt`` or ``3dVolReg``.
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Also fixes nipreps/fmriprep#1463. |
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Have we checked the spec to make sure sbrefs are legal to have as 4d? |
effigies
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Apr 11, 2019
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Have we checked the spec to make sure sbrefs are legal to have as 4d?
I checked. It's never stated explicitly, so I guess this is legal...
This looks fine, overall. One minor code comment,. but TBH we're loading the whole data array anyway so it doesn't make much difference. Are you sure we don't just want the first volume, though, rather than taking the average?
Co-Authored-By: oesteban <[email protected]>
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The averaged should have much higher SNR without a cost in contrast. I think it makes more sense and computationally is not a big deal. |
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EstimateReferenceImagegenerates 4D references if 4D SBRefs are supplied as input. This patch checks the dimensionality of SBRefs and generates an average if the SBRef is 4D.Fixes nipreps/fmriprep#1579.
Intimately related to #253, although I'm not sure the proposed resampling there is absolutely necessary.
It could be detrimental for
bbregisterin co-registration.It is very likely necessary for head-motion correction with either
mcflirtor3dVolReg.