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PNL pipeline for NIFTI images
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Fourth parameter in --acqp for FSL eddy #1

Open tashrifbillah opened 5 years ago

tashrifbillah commented 5 years ago

In a BIDS sidecar json file generated by dcm2niix, the fourth parameter is determined as one of the following with descending priority:

  1. TotalReadoutTime
  2. (BandwidthPerPixelPhaseEncode or just BandwidthPerPixel) * (PhaseEncodingSteps - 1)
  3. EffectiveEchoSpacing * (PhaseEncodingSteps - 1)
  4. Least preferred according to our observation of various json files: DwellTime * (PhaseEncodingSteps - 1)

The direction of scan can be determined as one of the following with descending priority:

  1. PhaseEncodingDirectionDisplayed i.e A->P
  2. PhaseEncodingDirection: right-anterior-superior are the positive directions. So if #2 is j, that means P-->A, if it is j- or -j, then it is A-->P. In the former case, we want 0 1 0, in the latter case we want 0 -1 0 as the first three parameters on a line in --acqp file.

Reference: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide

"This file is described here, here and in more detail here."

sbouix commented 5 years ago

For the readout time, I agree and it doesn't really matter for us. For the Phase encoding, it is almost correct except that the 0 -1 0 it has to be expressed in the "slice orientation". For axial acquisitions ((1,0,0),(0,1,0),(0,0,1)) in RAS space. A PA phase encoding direction corresponds to 0 -1 0, but if you have a sagittal acquisition ((0,1,0)(0,0,1)(1,0,0)) than your acq file shoudl be -1 0 0