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Dear FSL's experts, I am running linear and non-linear registration to an MPRAGE image as always...but it seems that FNIRT is not working. Is it some change in the command line with fnirt? 1. flirt -ref MNI152_T1_2mm_brain -in ms062_s1_brain -omat ms062_s1.to.MNI.mat -out ms062_s1_brain_flirted 2. fnirt --ref MNI152_T1_2mm_brain--in=ms062_brain_flirted -aff=ms062_s1.to.MNI.mat --config=T1_2_MNI152.cnf --cout=ms062_s1.to.MNI_field --iout=ms062_s1_brain_fnirted Any thougths? Best regards, Rosalia