Dear FSL users/experts,
I have seen a number of posts related to this, as well as the fnirt webpage, but just wanted to make sure I am doing this correctly.
I have high-resolution structural data, EPI data and field maps, and would like to register the structural image (and associated atlas) to my DTI images, correcting for EPI distortion in the process.
1) Using epi_reg to register the structural image to the EPI image, specifying the fieldmap to distortion-correct the EPI
2) Use invwarp to invert the output warp field from epi_reg
3) Use applywarp as follows:
applywarp -i T1image -r epiImage -w T1_to_epi_invwarp -o T1_regTo_EPI --interp=spline
If I understand this correctly, this will give me the structural image in the original distorted EPI space. There is no need to apply fugue directly to my EPI image, since epi_reg has taken care of the EPI distortion and incorporated it into the inverse warp from T1 to EPI space.
Any advice/suggestions for this approach would be greatly appreciated.
Best,
Mark Wagshul
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