Dear Sakura,
> flirt -ref betted_structural -in nodif_brain -dof 6 -omat diff2struct.mat
> flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in betted_structural -omat affine_transf.mat
> fnirt --in=structural --aff=affine_transf.mat --cout=nonlinear_transf --config=T1_2_MNI152_2mm
> applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=nodif_brain --warp=nonlinear_transf --premat=diff2struct.mat --out=warped_diff
>
> When I ran fnirt, I got the following error message for some of the subjects, but all...
> Warning, Jacobian not within prescribed range.
This warning is unlikely to have anything to do with your later problem.
>
> However, even when I did not get the error message, the output image did not look right (the image showed the only part of the brain).
Have you checked if the individual flirts (and fnirt) worked? If not, can I suggest that for one subject where you have problems you complement the flirt calls with something like
-out diff_in_space_of_struct
-out struct_in_standard_space
and the fnirt call with
--iout=struct_fnirted_to_standard
This will allow us to pinpoint where the problem is.
Jesper
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