Dwipreproc option 2

in option 2 : Reversed phase encode b=0 pair(s), what is the input of blip down

If blip up is the AP full DWI acquisition; is blip down just b0 with PA encoding directions?



Yes. What you’d provide to the se_epi option is a single image consisting of two volumes, by extracting a b=0 volume from your original AP series (dwiextract -bzero might come in handy here), and concatenating that (using mrcat -axis 3) with the corresponding PA b=0.



Small note on that, as described in this blog post: Make sure than when you perform the concatenation, you have the first b=0 AP volume as the first volume in the concatenated SE-EPI series, not the other way around. This will ensure that spatial alignment between the topup and eddy stages is preserved.

There’s also some changes on the way for the next MRtrix3 tag, that will simplify your use case slightly: dwipreproc will deal with this concatenation internally, rather than requiring that you do it beforehand. So in that case you’d just provide your single PA volume via the -se_epi option. Not sure at this stage how far away that change is from being merged to the master branch though.


thank you