Dear Taylor,
> Gidday,
I'll leave that one for Mark J
>
> Been refraining from asking but I dont know how to generate the acquisition paramaters or index.txt.
>
> Can you only get it straight of the scanner?
You can't get the file from the scanner, but the information that goes in there should come from the scanner. The "phase-encode vector" (the three first numbers) tell you what direction the phase-encode was in. If you see distortions in the A<->P direction it should be either 0 1 0 or 0 -1 0. To distinguish between those look at the frontal cortex. If it has been stretched out forward it should be [0 1 0], if it has been squashed into the brain it should be [0 -1 0].
The fourth number is the total readout time in seconds (typically ~0.05 to 0.1). It is also the reciprocal of the bandwidth per pixel in the phase encode direction. If you know neither of those numbers just stick something in there. As long as you are consistent between topup and eddy the actual number doesn't really matter for the correction. It only matters if you want to interpret the EC fields, which most people will have no interest in.
Good luck Jesper
>
> Cheers,
>
> Taylor
>
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