Dwipreproc run for too long time

[jdtournier]

@Yixin_Ma

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?)

Yes, but if you’re in doubt, you can always use the anatomical labels such as AP instead.

@Yixin_Ma

But it takes forever to run the code. (More than 12 hours, does it mean that I miss some parameters and make it unable to converge?)

This might be due to there being lots of b =0 images, which topup takes ages to process – see this recent thread on this issue.

@Yixin_Ma

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. If you correct along the wrong direction, you’ll get the wrong correction.

@Yixin_Ma

Is there any way to not to specify phase encoding direction?

Only if your data contain enough information in the right format for MRtrix3 to figure out the phase-encoding direction by itself. Otherwise, you’ll need to know. But the distortions are typically obvious enough that you figure out by simple looking at the data, right?