Hello,
I am currently working on processing my data with eddy. My data has only been collected in one direction (A>>P; 30 directions run twice, 2 B0s), so running topup is not appropriate in this case. Given I will not be using an output from topup for my mask, what should I use in its place? Would I just run BET and use the mask from that?
Also, I just want to confirm the command I would use for eddy:
eddy --imain=data --mask=[mask from question above] --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --out=eddy_corrected_data
Acqp= 0 -1 0 .095
Index = Sixty-two 1s
Thanks in advance for your time!
Cristina
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