Dear FSL Experts,
I am concerned about a potential artifact but am hoping that it is something I don't need to worry about after pre-processing. The data come from the following sequence: First, 1 B0 image with P->A phase encoding. Immediately after, 10 B0 images with A->P phase encoding. Immediately after, 60 DWI images with A->P phase encoding at b=1000. There are 70 diffusion directions total. For preprocessing, I use TOPUP (b02b0.cnf) followed by Eddy (w/ TOPUP output, otherwise default settings).
I noticed that in one slice of the DWI, solely in the fourth to last volume, there is a slice that looks very off. Ive uploaded several screenshots showing what it looks like before as well as after preprocessing. They can be found here: http://www.dropbox.com/sh/6pmk7sl94bk8koz/AACx5io2_GZc1mIxf4GBjc2ia?dl=0
As you can see, before preprocessing it appears to be on one single slice. Afterwards, it appears to be on half of each of two slices (still just one volume). The right hemisphere side of the originally affected slice, and the left hemisphere side of one slice superior. The "_Left" files refer to the slice where the left hemisphere appears to be affected after preprocessing whereas "_Right" is the slice where the right hemisphere seems affected.
I apologize for asking such a subjective question, but does this look like an artifact that is a problem even after preprocessing? If so, any advice for how to fix it before I run bedpostX? Would this be something that outlier replacement in Eddy is good for, for example?
Thank you all very much!
-Ben Chernoff
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