Hi Matt + FSL Team,
Thanks for your response. If possible, I'd just like to confirm the commands for moving my T2 in b0 space.
flirt -ref my_b0 -in my_t2 -omat my_affine.mat
fnirt --in=my_t2 --aff=my_affine.mat --cout=my_nonlinear_T2toB0 --config=my_b0
applywarp --ref=my_b0 --in=my_t2 --warp=my_nonlinear_transf --out=my_warped_T2
Then, if I eventually want to move a binary lesion mask to my b0 space, I would run the following:
applywarp --ref=my_b0 --in=binary_lesion_mask --warp=my_nonlinear_transf --out=my_warped_lesion_mask
Thanks for your help!
Cristina
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