> Correct me if I'm wrong: looking at the FSL mailing list I've seen that if you acquire an odd number of slice (z axis) you need to remove one slice (top or bottom) in order to use topup.
> There is one other solution which is to modify the Subsampling level 2,2,2,2,2,1,1,1,1 to 1,1,1,1,1,1,1,1,1. It is way slower than removing one slice and I'm not sure the result will be as good as removing one slice.
> My question is: can I consider adding a slice of zeros instead of removing one slice if my FoV is too tight ?
I think your best solution is to do what you suggest with the subsampling levels. If you also change the --lambda values for the first 5 steps you should get just as good results, and all you pay will be execution time.
For getting the --lambda values ~right I suggest you do a test run with 2,2,2,2,2,1,1,1,1 and 1,1,1,1,1,1,1,1,1 for a subject where you have removed one slice and use trial and error to change --lambda so that you get ~the same reduction in SSD for the first five steps in both cases.
> Thank you in advance for your help.
> Arnaud Bore