Dear Jasper,
I figured out what my mistake was later that day that produced the error! I should have posted the answer here, sorry about forgetting to do so!
The problem was this: I ran topup and created the "my_hifi_b0.nii.gz" image. Then I averaged the volumes of the image across time, skull stripped, binarized, and called the new image "my_hifi_b0_Tcollapsed_brain_mask.nii.gz".
And then when I ran eddy I mistakenly inputed the "my_hifi_b0.nii.gz" in the --mask option instead of the "my_hifi_b0_Tcollapsed_brain_mask.nii.gz". So the "same dimensions" of the error message was probably referring to the fact that the mask image I inputed in eddy had two volumes instead of one.
I hope this is helpful for anyone else that might make the same mistake and get the same error!
(I am running FSL 6.0.1 on macOS Mojave 10.14.3. I am the girl that pointed out in a previous post that since Apple (for the time being) does not support OpenMP and there is no eddy_openmp in the FSL 6.0.1 OSX release but just eddy and eddy_cuda when trying to run eddy from the GUI I get the message that the eddy_openmp file does not exist.(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1903&L=FSL&F=&S=&X=6129380027E12531CE&Y=athanasia.metoki%40temple.edu&P=338311)
So to answer your question I believe "eddy" on my system points to the executable "eddy".)
Best,
Nasia Metoki
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