You might experiment with pre-processing your subjects' T2 datasets with 3dUnifize and its '-T2' option.

Also, you can (with the default weighting) use the '-wball' option to add more weight to the region you like the most. My limited experiments on this, focusing on the thalamus, used '-wball 0 14 6 30 40' where '0 14 6' are the xyz coordinates of the ball's center, 30 is its radius, and 40 is the intensification factor for the weight. That factor of 40 might sound large, but since the ball is small in volume relative to the brain, the extra weight doesn't have much effect unless the weight is increased a lot there.

Paul has been urging me to upgrade 3dQwarp to allow alignment using multiple types of images at once -- T1 and T2, for example, or (in his case), diffusion tensor images. Maybe someday. I know HOW to do it in the code, but there are a lot of details that have to been addressed to make it work correctly. Also, such an alignment will take a significant amount of memory!