I am still encountering this problem with some but not all of my data. It seems as if the issue is with calculating the shift map. It appears that the shift map is shifted with respect to the original field maps. I determined this by displaying
fslview EF_UD_shift+mag.nii.gz and the fmap_mag_brain.nii.gz in the same fslviewer. This shift can easily be seen by comparing
fmap+mag.png and EF_UD_shift+mag.png. I have copied these to the main directory of this link.
https://app.box.com/s/fvcnes91m0v2zigz9fxfdp1206f8zyjk
Any suggestions that anyone may have would be greatly appreciated.
Thank you
Bob
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