afni.nimh.nih.gov

Peter,

I used these commands on a 4D nii file with 515 sub-briks. All the sub-briks were to be registered to the first sub-brik. And finally converted it back to nii if applicable.

afni
3dvolreg -Fourier -prefix outfile -base 0 -dfile matrixfile infile.nii
3dAFNItoNIFTI -prefix niifile outfile+orig

fsl
mcflirt -in infile.nii -out outfile -dof 6 -refvol 0 -mats matrixfile

Thanks
Durai