Chris Markiewicz

As to issue 1, it was not a specific goal of mine to copy precomputed files that did not need modification. It's not obvious that that is generally desirable, as...

In general, fMRIPrep should do nothing on the structural side that sMRIPrep doesn't do, so it should be safe to copy from sMRIPrep to fMRIPrep. The most likely cause for...

Thanks! Just to state: fMRIPrep doesn't produce the "correct" number of cosine regressors, it produces those needed for a 128s high-pass cutoff. You are free to use less (or more,...

Would you feel up for opening a PR against the documentation?

The extra dictionary is purely for passing around images in memory. You could write a NIfTI extension to pack anything you want in the header, though: https://github.com/nipy/nibabel/blob/e6ccec4dcda98911f6ad7613ac2069736e25b144/nibabel/nifti1.py#L286-L417 The basic procedure...

~~Yes, for FileTree, where it could be `undefined`. For BIDSFile, since it must always have a parent, typescript complains that it might not be set in the constructor. It's not...

Single-band references will not be used in motion correction, since the contrast may differ strongly from the multiband BOLD. The single-band references are used for coregistration with other images (fieldmaps...

> That's to say, the approach fMRIPrep uses is different from that of the HCP Pipelines. Yes. See https://neurostars.org/t/mcflirt-related-behavour-fmriprep-strange-motion-estimations-in-confounds-timeseries-tsv-lots-of-zeros/18037 for an investigation that led to this divergence. > By the...

Yes, that's right. As a minor clarification, the MNI resampling happens in a single interpolation from the original BOLD data. It's effectively the same as resampling BOLD to T1w and...

What do you mean source space? You mean use targets other than fsLR and MNI152NLin6Asym?