I am attempting to do a linear registration between a neonatal t2w anatomical (1x1x1mm) and diffusion (2x2x4mm). I bet both data sets and run flirt.
flirt -in diff_brain -ref t2w_brain -o test_align -omat lnr_mtrx -dof 6
This gives a nice alignment. I would then like to apply the transformation to the diffusion without changing the voxel size and thus I run
flirt -in diff_brain -ref diff_brain -o diff_brain_lnr -applyxfm -init lnr_mtrx
When I view the output diff_brain_lnr the center of the brain has been dramatically shifted (I think) and the entire brain is crammed in the upper left hand of the fslview viewing gui. Has anyone seen this or experienced it before? I also tried applywarp with no warp and --premat=lnr_mtrx and the results were the same. Is there any way to calculate the center of an image in fsl and add that to the header (that would appear to be the problem).
Any help is greatly appreciated.
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