Hi Babak -

I tried both versions, and the registration doesn't appear to want to give good results with the full sized files.

Here is the script line: 3dwarper -iter 0 -sd 12 -cubicspline -A -trg 3dwarper_only_average_brain_with_header_threshold_512_resampled.nii -sub $file -o $basename""10blur_smooth12_cubicspline_3dwarper.nii"

Thanks,

Matt