Hi Afni Experts,
I wanted to follow up with my original email below to see if anyone had any thoughts/guidance.
Thanks,
Ajay
I am interested in combining subject level corrections using quadratic corrections (3dAllineate -nwarp option with bilinear) with my warps to MNI which are derived from auto_warp.py. In this case, instead of having just the 3dAllineate affine .aff12.1D file, I will have a parameter file instead.
1) If I wanted to combine 3dAllineate parameter file with my 3dQwarp warp field, can I do so similar to the typical case of 3dNwarpApply -nwarp 'warp.nii aff12.1D' ? Will this also combine the bilinear terms or just the affine matrix portion?
2) If this is not possible, is there any other way to get it into one single warp or would I have to first apply the param file and then warp the subsequent file to MNI space?