Transformation order in ANTSpy

This might be related to the issue I raised but I am still having issue getting my head around how the transformation concatenations and orderings are handled in ANTSpy.

So, if I perform a registration in ANTS (the usual SyN), I get the following list as my forward transformations an example:

'/tmp/tmpdddnbjk41Warp.nii.gz', '/tmp/tmpdddnbjk40GenericAffine.mat']

So the first entry is the non linear deformation field and the second one is the initial affine map.

Now, I can use apply_transforms to apply the map. However, what I know about antsApplyTransform, the transforms are applied in the order in which they are encountered on the command line and I think ANTSpy passes them on by simply going through the list.

My question is would this not result in the non linear warp being applied before the affine?

Also, on a related note if I combone two transformation list as:

final = t1 + t2

and use this in apply_transforms would the resulting transformation be t2(t1(x)) where x are the spatial coordinates i.e. t1 first and then t2?

[stnava]

there will be discussions of this in various places here https://github.com/ANTsX/ANTs/wiki and in the papers https://github.com/ANTsX/ANTs#boilerplate-ants as well as in ants*pdf documentation.

the core reasons are mathematical, statistical and practical :

• mathematical: we use Diff_0 which requires fixed boundary conditions. as such, images are mapped to the fixed space by an affine transformation. within the fixed domain, we compute the diffemorphism, member of Diff_0.

• statistical: we want the tail of the deformation fields to be in common (template) space to allow group comparisons

• practical: transformations are only dense under pull back not push forward

[stnava]

edit: 3rd reason