Hi AFNI Experts,
I had a subject that I ran auto_warp.py once and the outputs had some line/vein artifacts. I took that output and ran auto_warp.py once more and the results came out great. When I concatenated the second set of transforms to apply to the original output of the first auto_warp.py things looked great. (3dNwarpApply -nwarp 'anat.rw.qw_WARP.nii anat.aff.Xat.1D' -source ../anat.aw.nii -prefix anat.final.nii. -interp wsinc5).
The problem comes when I want to concatenate all sets of warps together (3dNwarpApply -nwarp 'anat.rw.qw_WARP.nii anat.aff.Xat.1D ../anat.rw.qw_WARP.nii ../anat.aff.Xat.1D' -source ../anat.nii -prefix anat.final1.nii -interp wsinc5) I still get some line/vein artifact. I would like to combine all transforms so I can apply this warp to other data such as the T2 or BOLD imaging etc.
I also tried to run auto_warp.py (second time) and pass an -iniwarp of the original anat.rw.qw_WARP.nii anat.aff.Xat.1D and then a second time turning affine off so I just get a nonlinear warp and running with iniwarp and in all cases I still get the artifact. The only way this does not occur is if I warp the files once using the original transform and then warping that output again using the newer warp/affine parameters. Could it be a precision error when using a small patch size(minpatch 5) and combining warps? Does 3dNwarpApply use the affine matrix as part of the qform/sform in the same fashion as when writing the file out?
Is there a different way to implement combining warps when using multiple sets of transforms or better way to use iniwarp? I played around with adding IDENT(anat.aw.nii) and different combos of this with no success.
Any suggestions would be much appreciated.
Best,
Ajay
