It’s not that simple unfortunately. Once you start using SIFT2, you’ll need to adjust downstream processes to ensure they handle the data correctly, since it’s provided in a different form. With ‘regular’ SIFT, you’d get a (much) smaller tck file, but it was nonetheless just a standalone tck file. With SIFT2, your input tck file remains unmodified, but the command will provide you with an associated weights file (just a text file with one weight per streamline). This additional file needs to be provided alongside your tck file in any command that needs to process it, via the -tck_weights_in option (e.g. for tck2connectome) – otherwise it’ll just process your original tck file unmodified, completely unaware of the existence of the SIFT2 weights.
Also, if you need to filter the streamlines in some way that modifies either the number or order of the streamlines, you’ll need to pass in the weights of the input tck file using the -tck_weights_in option, and produce the corresponding weights for the output file using the -tck_weights_out option (e.g. in tckedit).
We need to spend some time documenting all this properly, there’s admittedly very little information about this in the official docs at the moment…