Hi-
I'm using two DTI data sets - one acquired in A>>P and one P>>A, each has 6 b0s. We merged the 6b0s from each data set into one and ran topup. Based on the output, topup seemed successful.
We then merged the AP and PA data and ran bet and then eddy. We created an index file assigning the volumes to a b0 (numbered 1-12) based on the b0 location. However, in the output for eddy only some volumes seemed to be adjusted, while others looked the same as they did before eddy was applied. If you have any suggestions on how to combat this, I would greatly appreciate it.
Thanks for your help,
Hailey
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