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PennLINC / qsiprep

Preprocessing and reconstruction of diffusion MRI
http://qsiprep.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Documentation sentence ends abruptly #342

Open arokem opened 2 years ago

arokem commented 2 years ago

On this page/section: https://qsiprep.readthedocs.io/en/latest/preprocessing.html#pepolar-topup-distortion-correction, the sentence: "When images with different phase encoding directions are available, either dedicated fieldmaps (in the fmap/ directory) or DWI series (in the dwi/ directory), example b=0 images can be" ends abruptly. What can we do with these b=0 images??

Relatedly, how should I organize a dataset that has one main diffusion MRI measurement (a 103-direction, three b-value sequence, in this case, measured with PA phase encoding) and two additional b=0 measurements: one with AP and the other with PA phase encoding? Is there any use for both of these measurements, or should we only use the additional AP measurement as input to topup? Should the additional measurements be placed in the BIDS dwi folder or in a separate (fmap?) folder? Should there be an "IntendedFor" field in the side-car, in this case?

arokem commented 2 years ago

I think that my latter question is answered in this section of the documentation. Maybe an explanation of all the different pepolar use-cases can be added to the section where that abrupt sentence ending occurs.