In my experience, for topup, what I do is I load both images (normal PE and reversed PE) in fslview, and move back and forth between them, noticing the direction along which the distortions happen. Then, I go to the index boxes (labeled 'X', 'Y', 'Z') and increase/decrease the FIRST index. If the crosshair moves in the direction of the distortions, then the topup parameters file should be: +/-1 0 0 (The sign doesn't really matter, since it will produce the same B0 field, but with opposite sign). If not, if the crosshair moves along the distortion direction when you change the SECOND index, then the parameters file should be: 0 +/-1 0.
"the meaning of a "1 0 0" vector is *dependent* on the image orientation -- i.e., "1 0 0" would have a different meaning for a LAS oriented volume vs. an RAS oriented volume."
Yes, "1 0 0" has the opposite meaning for a LAS and a RAS oriented volumes, but it will be in the R/L direction ('x', in NIfTI coordinates). "1 0 0" for PIR, for example, means the A/P direction ('y', in NIfTI coordinates). This is the confusing thing in FSL tools, like fslview and fugue: it shouldn't be 'x', 'y' and 'z', but indices: 'i', 'j', 'k', for example, because they refer to the 3D/4D array of data. 'x', 'y', 'z' are spatial coordinates: 'L>R', 'P>A', 'I>S', and --in principle--, not all the NIfTI files need to be RAS (or LAS) files.
I hope this helps.
-Pablo
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