Dear FSLexperts,
I am trying to register a b0 MRI volume (extracted from a DTI volume) to the MNI atlas. The performed steps are
1. bet of the b0 volume -> OK
2. flirt registration of the bet result to the MNI atlas (see attached flirt2MNI file) -> OK
3. fnirt registration of the flirt result to the MNI atlas (see attached fnirt2MNI file) -> ERROR.
I cannot figure out why the fnirt step seems to enlarge my b0 image.
The command I used was
fnirt --in=flirt_071_bet2MNI --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz --iout=fnirt_b0MNI_071 --cout=fnirtcout_071 --fout=fnirtfout_071 --jout=fnirtjout_071 --intout=fnirtintout_071 --logout=fnirtlogout_071
Besides, if I add the -aff parameter, the registration fails complitely.
Any suggestion?
Thank you.
Best,
Elisa
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