alternate reference

source image

variant. applyDeformation/convertDeformationType/Space were assuming voxel
alignment between deformation field and reference image.

field

DefField.deformationType and detectDeformationType. Also fix applyDeformation
where not using altref

nonlinear.DeformationField

is no longer assumed to be aligned with the reference in voxels - it is
only assumed to be aligned to the reference in world coordinates.

can get away with it. Can't be bothered figuring out how to adjust srcToRefMat
in convertDisplacementSpace, so am just not supporting it

used by the DisplacementField class.

logic, instead of re-implementing similar logic, and premat handling is all
in one place.

- CoefficientField can now represent a generic b-spline coefficient
field. Cleaned up fnirt.py, other tweaks and comments

coefficient field to displacement field. Check for TOPUP intent codes

convertDisplacementSpace

nonlinear module. Expand x5 module to handle non-linear. Rename x5 functions
to be more generic.