Hi Lauren,

1) What was the voxel-size of the raw data?
4) Well this is a tough question. It all depends on how precise registration you need. In general, we want to maximize registration accuracy to maximize the ability to see small differences across people. If however you are looking for big effects, then you could say that you accept some mis-registration due to atrophy. In which of the two categories does your project belong to? About masking out the atrophic brain regions to improve alignment, I don't think DTI-TK does anything like that.

Konstantinos