What are all those weird images that pop up when a field map is run? Is the scanner broken?
For each slice, the field map generates 4 images: magnitude, phase, real, and imaginary. Only the real and imaginary are used by the processing software. The magnitude images look similar to most MRI images you are probably familar with, while the phase images will generally have stripes through the image. I use EPI with frequency-encode direction set to A/P. Should I set my field map scans to the same frequency-encode direction? Should the view order (e.g. after changing it from from bottom-up to top-down) be reflected when calling ppge? Yes, the frequency-encode direction should be the same for the EPIs and the filed map scans. Note that the unwarp direction is orthogonal to the frequency-encode direction, so that if the frequency direction is set to A/P, the unwarp direction (=phase-encode direction) will be L/R. The unwarp direction can be specified for ppge using option -unwarpdir. Directions are as follows: L/R = x, A/P = y, I/S = z. The change in view order (e.g. from default bo
