Hi Anna,
1) Regardless of eddy_correct, you need to make sure that the entries in the
bvals/bvecs correspond to the sequence of volumes in the data file. If the
b=0 is the last volume in the data, the b=0 entries should also be at the
end of the bvals/bvecs files.Otherwise, running dtifit or bedpostx will
return wrong estimates. Once you fix that, you can choose any b=0 volume as
a reference for eddy current correction (the first volume is chosen by
default).
2) Yes, unless you have a good reason not to (e.g. very high b value
acquisitions with minimal anatomical contrast).
Cheers,
Stam
----- Original Message -----
From: "Anna Matejko" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Monday, July 11, 2011 7:33 PM
Subject: [FSL] B0 file for Eddy Current Correction
Hello!
I have two quick questions:
1) I am not sure I am selecting the correct reference image for the eddy
current correction. When I look at my bvals file, it looks like my first
volume is the B0 file. However, when I open all volumes in fslview the B0
file appears to be last (64th volume). Do you know why this would be and
which volume I should select as my reference image?
2) Do you recommend the eddy current correction for all datasets?
Best,
Anna
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