Merge multiple T2w images?

[effigies]

Currently we're just using the first T2w image, which is largely a holdover from FreeSurfer, which takes multiple T1w images and up to 1 T2w image.

Given that we're now building a T1w template and passing a single image to FreeSurfer, does it make sense to run the same procedure on T2w images, when we find multiples of those? I'm inclined to move in that direction, and register the resulting T2w template to the T1w template.

The output would then be:

<output dir>/fmriprep/sub-<subject_label>/
    anat/sub-<subject_label>_T2w_space-T1w_preproc.nii.gz

[oesteban]

I think this can easily be achieved with the generalizations to the T1w workflow we are introducing in NiBabies - WDYT @mgxd ?

[mgxd]

yup, that piece can be brought over to smriprep proper.