Hi everybody
I'm trying to register functional data to the anatomical in 20 subjects in a study where both inferior medulla and cortex are involved in the analysis. I first tried the "usual" registration with align_epi_anat.py, the results on the cortex and superior brainstem were good, but I had some problems from the lowest part of the pons dawnwards. I used the suggested procedure on the help page of 3dQwarp and I obtained very good improvements as i set -maxlev 3, while things get worse with higher levels of maxlev. Are there to your knowledge any drowbacks in doing this? Are T2 to T1 nonlinear registrations typical in fmri? Also, should I first invert the contrast in the t2 image?
Thanks for your opinion
Simone