Is there any way to convert the FSL flirt generated 4x4 matrix to be compatible with that used for 3dwarper -T option? I assume they are similar but it doesn't seem so.

I have A.nii and B.nii as source and target images, respectively.
Using FSL flirt affine registration, the transformation matrix A2B.mat and the resulting image A2B_affine.nii were generated.
Then I used 3dwarper with the A2B.mat for -T option, but the result is much worse that that generated by warping A2B_affine.nii to B.nii without linear transformation.

Did I use the -T option incorrectly, or is there any way the FSL flirt transformation matrix can be combined with the 3dwarper nonlinear transformation directly? Any help is appreciated!

Shengwei