Dear FSL experts,
I have an 'older' DWI dataset. It comprises 16 3D images: 1 B0 image and 15 diffusion weighted images.
Instead of using the eddy_current script, I realigned the 15 images to the B0 image using FLIRT with 6 dof.
I noticed eddy_current does not specify the number of degrees of freedom, and thus uses 12 dof.
(line from eddy current script= ${FSLDIR}/bin/flirt -in $i -ref ${output}_ref -nosearch -o $i -paddingsize 1 >> ${output}.ecclog)
I also noticed that it is using two options hat I am not sure of what they are doing, or why they are desired:
-nosearch
-paddingsize 1
Could somebody explain:
a) what the two options exactly do (the explanation that comes with flirt -help is not very extensive)
b) if it is better to use the default 12 dof over the 6 dof I am using.
Thanks,
Vincent
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