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I solved it! Thank you, Rosalia 2018-02-20 15:52 GMT+01:00 Rosalia Dacosta Aguayo <[log in to unmask]>: > 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 > > -- Rosalía Dacosta-Aguayo Post-doctoral Fellow, Department of Physical Medicine and Rehabilitation, University of Rutgers, Medical School, Newark, New Jersey. Neuropsychology and Neuroscience Research Kessler Foundation, East Hanover.