hello
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?
thansk
Avner
hello
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?
thansk
Avner
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.
perfect
thanks
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.
perfect
thank you