BIDS func metadata: PhaseEncodingAxis or PhaseEncodingDirection?

dcm2bids
bids
fmri
neuroimaging
#1

Oh Great BIDS Gurus,

I am trying to figure out whether my func metadata is supposed to have PhaseEncodingAxis or PhaseEncodingDirection as its metadata field name for our BIDS app. The standard currently says this about PhaseEncodingDirection:

RECOMMENDED. Possible values: i , j , k , i- , j- , k- . The letters i , j , k correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless - sign is present (then the order is reversed - starting from the highest index instead of zero). PhaseEncodingDirection is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term InPlanePhaseEncodingDirection which can have ROW or COL values. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction).

source

We use Dcm2Bids (and therefore dcm2niix) and it seems to be outputting PhaseEncodingDirection.

So, which is it? Is PhaseEncodingAxis an artifact of an older standard version maybe?

P.S. I also found this conversation: https://github.com/rordenlab/dcm2niix/issues/258

Thanks,
~Eric Earl, OHSU

#2

Hi Eric,

PhaseEncodingAxis is not part of the BIDS specification. Found via the issue you linked, it appears it was added more recently to account for situations where the axis is known but the polarity is not. BIDS does not address this case, and probably the best place to encode that, if desired, would just be in the phase_dim field of the NIfTI header, with no entry in PhaseEncodingDirection.

Best,
Chris

#3

Thanks @effigies! That helps to know.