Providing my script on good faith (despite having been burned doing such of late); anyone looking to make genuine use of it please get in touch.
SIFT2 cannot be used unless the tractogram provided to it encompasses the entire brain white matter. To demonstrate this: Imagine that you perform tractography seeded from a single region. Now imagine two voxels: the first is right in the middle of where the streamlines seeded from that region traverse; another that is traversed by a single erroneous streamline that goes somewhere it shouldn’t have. The FODs in these voxels are expected to be of fairly comparable overall size. Yet because the latter only has a single streamline traversing it, that one streamline will be assigned a very large weight by SIFT2, as that is the only streamline that it has available to it with which to “explain” the FOD amplitude. It’s genuinely erroneous to be applying an algorithm that enforces correspondence between whole-brain FODs and a not-whole-brain tractogram, because they shouldn’t match.