intra-subject alignment in antsMultivariateTemplateConstruction2

[cauzzo-s5]

Dear experts
I'm using antsMultivariateTemplateConstruction2 to build a template from a dataset of T1 and T2FLAIR images.
Parameters are -d 3 -j 64 -i 8 -n 1 -k 2 -f 6x4x2x1 -r 1 -e 0 -b 1 -v 64gb -s 3x2x1x0 -q 100x100x70x20 -t BSplineSyN -m CC -c 5
I'm getting great results, but I'm struggling in understanding how the program deals with possible misalignment between T2FLAIR and T1 images. I don't see any step performing modality1 to modality2 registration. Plus, I see that the same two transforms (genericAffine + warp) are applied to both modality1 and modality2.
Does antsMultivariateTemplateConstruction2 require aligned inputs across modalities?
Thank you

[cookpa]

Hi,

Yes, the inputs for a particular subject must be aligned ahead of time.

The distortions between modalities can vary widely based on the imaging contrasts and acquisition parameters. Sometimes it's just rigid motion, other times there are complex nonlinear effects that must be dealt with. The template script doesn't attempt to deal with those.