I’m currently trying to organize some of my datasets according to BIDS standards* and have a quick question about references to B0 inhomogeneity maps.
Can someone please confirm if having only one Siemens’ GRE_field_mapping image in the fmap folder [saved as *phasediff.nii.gz?] is enough for fmriprep to run field inhomogeneity correction?
Many thanks in advance!
You will need at least one magnitude image in addition to the phasediff image. Have a look at section 8.9.1 of http://bids.neuroimaging.io/bids_spec1.0.2.pdf
The examples in the bids-examples repository do not include binary data. More details at https://github.com/INCF/BIDS-examples
I believe one would need SWIs to derive magnitude images in my case, right? Don’t have it, unfortunately
I’m not sure. The magnitude image is essential to align the fieldmaps to the image you want to apply them to. The standard Siemens fieldmap sequence saves magnitude images (although they might be part of a 4D volume).