I’m following (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup) for how to run TOPUP. I attached a copy of our dsi protocol and also a set of our dsi sequence info. My understanding is that in their example, they had two scans with a positive and negative “blip”. Therefore their ‘my_acq_param.txt’ contained two lines… Ours would only contain one line since it was 1 scan.
Our protocol states “Phase enc. dir. = A>>P” which I believe to mean we go anterior to posterior which is the same as their example, therefor our direction vector is [0 1 0]. I don’t know what a “blip” is so I assume if we only did one scan, it’s probably positive (I also tried negative and got the same error).
The next value is the time (seconds) between the readout of the center of the first echo and last echo, calculated by “dwell time multiplied by # of phase encode steps minus one”. FSL’s manual says “echo spacing” is the same as “dwell time”. I’m not sure how to get my # of echos. According to (http://mriquestions.com/echo-planar-imaging.html), “EPI Factor” is the number of echoes in one ‘shot’. I don’t see a value for how many 'shot’s there are.
I’ve tried [0 1 0 0.09438] which would be using “EPI Factor” as our #phase encode steps and it’s not working.
Help, as always, is greatly appreciated!!!