I used the notation of i, j an k. (which I think it means 1st, 2nd and 3rd dimension of the volume, am I right?)
k are specifically used to refer to image axes, as opposed to “X”, “Y”, “Z”, which would typically be considered to correspond to L-R, A-P, I-S but that may in fact not be the mapping if the acquisition is not approximately axial. The same notation is used in BIDS for the same reason. MRtrix3 goes to the effort of trying to maintain this correspondence automagically in the back-end for you, making the handling of more complicated cases my job.
(One caveat of this is that the input to the
-pe_dir option should be based on how the image looks in
mrview when you do not specify the
-norealign option, and not the actual raw data itself )
How important is to give correct PE direction, because if I give a wrong PE direction of k, the code won’t run for that long time.
Very. The distortion correction assumes the distortions are along that direction only.
Note that this is the case even when using
-rpe_none. Proper modeling of eddy current distortions relies on knowing the direction of phase encoding.
While I was going to say that
topup may well run very quickly if you specify the wrong phase encoding direction (since it’d be essentially unable to find any differences between the images that it was capable of correcting), you’re using
-rpe_none, and so
topup isn’t even being invoked.
Also check your version of
eddy. Some earlier versions of
eddy I personally observed to not engage multi-threading. I don’t know the exact history or reasoning since it’s outside of my control, it’s just something that I remember seeing.