Hello AFNI experts,
I had a problem when running auto_warp.py and wanted to see if you could help. According to the documentation, for 3dQwarp the smallest patch size accepted is 5mm.

-minpatch mm = Set the minimum patch size for warp searching to 'mm' voxels.
*OR* * The value of mm should be an odd integer.
-patchmin mm * The default value of mm is 25.
* For more accurate results than mm=25, try 19 or 13.
* The smallest allowed value is 5 (which will be VERY slow).
However, you may want stop at a larger patch (say 7 or 9) and use
the -Qfinal option to run that final level with quintic warps,
which might run faster and provide the same degree of warp detail.


I tried using a patch size of 5 by passing it through auto_warp.py -qw_opts -patchmin 5. Unfortunately when it reached a patch of 9x9x9 (Level=11) the algorithm finished (native vox resolution is 1mm isotropic) and output the results. I wanted to see if there is something I am missing such as I wanted to reach a patch size of 5x5x5. Is there another option I have to adjust as well to ensure it will continue to 5x5x5?

Thanks,
Ajay