Dear Suchada,
> Dear FSL expert,
>
> I'm trying to use FNIRT to register FA to T1 on ubuntu operating system.
>
> I type: fnirt --in==fa.nii.gz --ref=t1.nii.gz --aff=fa_t1.mat
>
> It seems to take serveral hours and cannot complete the process.
> I'm wondering how long should this process take usually?
It certainly shouldn't take that long. It appears from your command line that you are attempting to register a T1 image to an FA image. Fnirt is not intended for that. Fnirt is intended for inter-subject-intra-modality registration. For intra-subject-inter-modality registration you should use flirt.
Jesper
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