Ordering of tranforms in TransformChain

[oesteban]

In the context of #79, one issue has surfaced. We need to set some convention for the ordering of transforms when concatenating transforms.

At the moment, for individual transforms, we are trying to hold on to the "points" criteria. If we want to keep that for transform chains, then the order of the composed transforms should be reversed to the "image" criteria. In other words, say we have a mapping calculated with ANTs where we have 3 affine registration levels and one final nonlinear layer. Nipype and antsApplyTransforms will expect the ordering to be images (as in, we first apply the 3 affines to the data and finally the nonlinear). But coordinates are mapped the other way around (i.e., the first transform applied would be the nonlinear, and then the three linear).

I would prefer the "points" criteria, although that could fill counter-intuitive w.r.t. the existing software.

EDIT: Actually, I've just found that this problem is present in our preprint (https://osf.io/8aq7b). The last line of column 1 in page 2 says
.

Here, the order of transforms is wrong, it should actually say
.