Dear ladies and gentlemen,
I have a set of three Spin Echo A->P and three Spin Echo P->A images.
Running topup works fine. Now I want to use the output to correct Gradient Echo BOLD images (A->P only).
applytop --imain=fmri_ge.nii.gz --datain=acq_param.txt --inindex=1 --topup=result --method=jac --interp=spline --out=corrected
Is this the right way to correct the GE images with a single encoding direction (using short spin echo scans to calculate a voxel displacement map)?
How is the movpar.txt file relevant for this image?
Does applytopup actually do motion correction? If not at what point in the pipeline would you recommend to do a motion correction?
Would you recommend a coregistration between the spin-echo and the gradient-echo images?
Kind regards,
Niklas Förster
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