Dear Fsl experts,

I am sorry to ask so basic question but I am looking for some errors and I am not able to see them.

I have made an alignment with of nodif.nii.gz with flirt command:

flirt -in nodif.nii.gz -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz -omat nodif_to_MNI.mat -out nodif_to_MNI152_2mm   It works!!



After this, I wanted to normalized nodif.nii.gz to MNI template, but it does not work and I do not know why...:

 fnirt --in=nodif.nii.gz --aff=nodif_to_MNI.mat --cout=nodif_to_MNI_warp.nii.gz --config=nodif_to_MNI152_2mm.nii.gz   Have problems!!!. I don't have nodif_to_MNI_warp file....could be this the problem?


Any suggestion would be very appreciate.

Best regards,

Rosalia Dacosta.
Clinical Neuropsychologist
University of Barcelona