Hello,
So I have AP and PA diffusion datasets, and for some reason their acqparams.txt files show slightly different readout times (e.g. 0.05953 vs 0.06048). After merging the datasets and applying topup successfully, I'm running into trouble running eddy.
Since eddy reads one row of the acqparams.txt file, I'm not sure which readout time to use in that row. When I use the AP readout time, I get FA maps with a really bad artefact at the occipital pole, while the frontal lobes look like they're missing parts (almost like the images are shifted anteriorly). When I use the PA readout time, I get much better images, but I'm not sure if that's the right thing to do or not.
I hope I explained my problem clearly.
Who ever's reading this, thank you for taking the time!
Shereif
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