Hi Everyone,
I would like to confirm that I have correctly used topup to correct for distortion in my epi data, using fieldmaps, which will be used for subsequent applytopup
Here are the commands I hope to use for the first couple of steps.
#STEP1: merge together fieldmap with phase encoding direction PA and AP to prepare for topup; output boldmerge:
fslmerge -t boldmerge.nii PAfieldmap.nii APfieldmap.nii
#STEP2: runtopup to prepare for applytopup:
topup --imain=boldmerge.nii --datain=/acquisition_parameters_merged.txt --config=b02b0.cnf --out=topupresults
My specific question is about the order of inputs in the file acquisition_parameters_merged.txt. Is what I have shown the correct order, since the input to my merge step was PA then AP (my understanding is that the -1 in 2nd position, row1 is PA and the 1 in second position, row 2 is AP)?
0 -1 0 1
0 1 0 1
I ask because I inherited a script in which they reversed these, which may be an error in that person's script; otherwise perhaps instead my logic is off somewhere. I would like to be sure!
Thanks,
Daniela
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