Recently I ran into some issues using fsl topup on several oblique EPI datasets. The topup corrected output had what looked like a zipper artifact throughout many of the slices. I found that if I used 3dWarp -deoblique prior to running the topup correction the artifact disappeared (most of the time) but I was not confident that this method did not affect my dataset in other ways. I found that if I used the REL image orientation info from the dicom header (a measure of obliquity in the dataset) in the my_acquisition_parameters file that is fed into the topup commands, the corrected data look great.
Example from dicom header:
REL Image Orientation (Patient)//1\-0\0\-0\0.975766\-0.21881
Example of my_acquisition_parameters file:
0.21881 -0.975766 0 1
0.21881 -0.975766 0 1
-0.21881 0.975766 0 1
-0.21881 0.975766 0 1
Is it appropriate (or necessary) to use measures of obliquity from the dicom header as input for the x and y columns in the my_acquisition_parameters file? Should topup be able to handle oblique datasets without setting the parameters in this way?
Any advice you can offer would be greatly appreciated.
Thanks!
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