Thanks Jesper,
I'll keep that in mind going forward. I'm also having an issue with setting up my acqparams.txt file for topup's --datain. I know that the number of rows needs to equal the number of b=0 volumes. With my two DTI scans, the first was collected in the P-A phase encoding direction, and the other one was collected in the A-P phase encoding direction. Therefore, does my txt file only need to look something like this?
0 -1 0 TotalReadOutTime
0 1 0 TotalReadOutTime
Is there a way to determine the number of b=0 volumes?
Also, I realize this question is different from what I initially posted so I can create a new post if need be.
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