SIFT- How to record the fibre IDs that are removed/reserved by the filtering?

Dear experts,
Is there any way to record the fibre IDs that are removed/reserved by the SIFT method?


Hi Jinglei,

Not without doing it the exceptionally clumsy way: that is, comparing the tractograms before and after in e.g. Matlab and seeing which remain.

It’s crossed my mind multiple times to have a switch in tcksift whereby instead of writing a new .tck file, the command would instead write a binary vector to a file indicating which streamlines were retained / removed. That could then, for instance, be provided to tckedit as an extraction mask to produce the filtered track file, but could also potentially be used in other ways. The first of those would not be very difficult to do, and would in fact be a good little project for anyone interested in getting their hands dirty with the MRtrix3 C++ code…


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Hi Rob
Sorry for the late reply. I have now picked up this issue again.
I found the following option under tcksift:
-out_selection path output a text file containing the binary selection of streamlines.
I think with this option the problem is solved.