BIDS fmap phase encoding direction and image orientation - beginner

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Hi @gabeyaw,
(From chatGPT)
To determine whether j- corresponds to AP or PA, you must consider:

  1. Image orientation matrix (qform/sform in NIfTI):
  • This tells how voxel axes map to world (scanner/anatomical) space.
  • For example, j might map to anterior-posterior or left-right depending on the scan orientation.
  1. Scanner coordinate system:
  • For most brain MRI scans:
    • If the image is in RAS (Right-Anterior-Superior) orientation:
      • j often corresponds to the A-P axis.
      • So j- would mean phase encoding from P to A (i.e., “dir-PA”).
    • But in other orientations (e.g., head tilted, oblique FOV), j might correspond to L-R or S-I.
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