Hi Bob,
Thanks for the quick reply. I am looking at some brains with very abnormal ventricles while other brain structures within the same brain are normal size. I was trying to figure out how to allow 3dQwarp larger warps in the ventricle areas while restricting the rest to more moderate warps.

(1) As for the -weights option I was trying to figure out it was just a scale or if I needed to estimate the mm shift I would allow certain voxels in the CSF to move. Based on your response, does it seem reasonable to have outside the brain as 0, inside the brain as a moderate value (0.4-0.6) and the CSF voxels as 1 (largest shift). Or should I have the outside of the brain as 0 , inside of the brain as 1 and CSF values as a value larger than 1 (ie 15) to allow for a much larger warp?


(2) As for the -iniwarp it was just a general question. I use 3dQwarp through auto_warp.py and for a few subjects I was considering to run an initial 3dQwarp separately (for the large ventricles with the weights option) and use this as an input into auto_warp.py via the -qw_opts -iniwarp option. I was just curious what the units are for my own knowledge with respects to this step.

Thanks,
Ajay