With the original tcksift command, the output is a new track file , which can subsequently be used as input to any command independently of the fact that SIFT has been applied. SIFT2 is a little trickier: the output of the tcksift2 command is a text file . This text file contains one line for every streamline, and each line contains a number; these are the weights of the individual streamlines. Importantly, the track file that was used as input to the tcksift2 command is unaffected by the execution of that command.
There are therefore two important questions to arise from this:
How do I use the output from SIFT2?
Any MRtrix3 command that receives a track file as input will also have a command-line option, -tck_weights_in . This option is used to pass the weights text file to the command. If this option is omitted, then processing will proceed as normal for the input track file, but without taking the weights into consideration.
Why not just add the weight information to the track data?
The .tck file format was developed quite a long time ago, and doesn’t have the capability of storing such data. Therefore, combining per-streamline weighting data with the track data itself would require either modifying this format (which would break compatibility with MRtrix 0.2, and any other non-MRtrix code that uses this format), using some other existing format for track data (which, given our experiences with image formats, can be ill-devised), or creating a new format (which would need to support a lot more than just per-streamline weights in order to justify the effort, and would likely become a fairly lengthy endeavour).
Furthermore, writing to such a format would require duplicating all of the raw track data from the input file into a new output file. This is expensive in terms of time and HDD space; the original file could be deleted afterwards, but it would then be difficult to perform any operations on the track data where the streamline weight information should be ignored (sure, you could have a command-line option to ignore the weights, but is that any better than having a command-line option to input the weights?)
So, for now, it is best to think of the weights file provided by tcksift2 as accompanying the track file, containing additional data that must be explicitly provided to any commands in order to be used (all commands where this is possible will provide a consistent command-line option “-tck_weights_in”). The track file can also be used without taking into account the streamline weights, simply by not providing the weights.