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How do I know what phase-encode vectors to put into my acquisition text file?
We are talking about the three first elements of each row of the --datain parameter here. For 99% of you the options are 1 0 0, -1 0 0, 0 1 0 or 0 -1 0. The first two of those options imply that phase-encode is done in the x-direction (left-right) and the two latter that it is done in the y-direction (ant-post). Below you see four examples of EPI images with their associated phase-encode vectors. Simply match up the distortions you see in your image with the appropriate image below and pick that vector.