Thank you both -

My goal is to do spinal cord fMRI motion correction. Specifically, it is a slicewise alignment of each timepoint to a base, so it is a like to like alignment as you mentioned, Daniel. The alignment is limited to just XY translations.

This is an example of the command I am trying to translate:

3dWarpDrive -affine_general \
-parfix 3 0 -parfix 4 0 -parfix 5 0 -parfix 6 0 -parfix 7 1 -parfix 8 1 -parfix 9 1 -parfix 10 0 -parfix 11 0 -parfix 12 0 \
-quintic -final quintic \
-base fmri_slice1_base.nii \
-prefix fmri_slice1_MCnofilt.nii \
-weight fmri_slice1_Gaussian_mask.nii \
-1Dfile fmri_slice1_MC_params.txt \
-1Dmatrix_save fmri_slice1_MC_xform.aff12.1D \
fmri_slice1.nii

And this is what I have tried to run:

3dAllineate -warp affine_general \
-parfix 3 0 -parfix 4 0 -parfix 5 0 -parfix 6 0 -parfix 7 1 -parfix 8 1 -parfix 9 1 -parfix 10 0 -parfix 11 0 -parfix 12 0 \
-interp quintic -final quintic \
-base fmri_slice1_base.nii \
-prefix fmri_slice1_MCnofilt.nii \
-weight fmri_slice1_Gaussian_mask.nii \
-1Dparam_save fmri_slice1_MC \
-1Dmatrix_save fmri_slice1_MC_xform.aff12.1D \
-cost ls -onepass \
fmri_slice1.nii

I have tried the cost function 'ls' and using the -onepass option, which has worked ok so far, but not as well as 3dWarpDrive has worked. If there is no cost function of weighted least squares in the 3dAllineate function, I am gathering that maybe it cannot be used in exactly the same way. The main reason I am looking towards 3dAllineate is because 3dWarpDrive points to using it for future work.

Thanks,
Kim