I have a very simple question. I am trying to co-register my data using flirt command from FSL. My input data is actually 4D where 4th dimension is # of volumes. When I use:

flirt -in Input.nii -ref Source.nii -out New.nii

It co-registers only 1st volume of my input data with Source.nii

Can someone please suggest me how can I use this command to co-register all the volumes of Source.nii ?

Thanks.