AFNI Brain Warp

This Flywheel gear warps the warp_target nifti image from standard-space into native-space. The standard and native reference images are nifti files that are inputs to this gear.

The align.csh script comes from the D99 Macaque Atlas AFNI scripts.

next steps

• ensure warp_target processing works for non-atlas data (if it doesn't, tuck segmentation functionality under a flag)
• consider adding a parameter that defines whether warp target is in standard- or native-space (although merely switching the standard and native images suffices to warp a target native-space target to standard-space)
• expose parameters to disable or configure 3dQwarp's -workhard (which makes warping slower and more accurate) and enable -duplo (which makes warping faster and less accurate)
  • parameters like -maxlev and minpatch can also affect speed/accuracy of warping.
• should warped *_aniso* files be copied to output?