The difference between @sabco’s usage and yours is the use of
-seeds <nonzero> -select 0 vs.
-select <nonzero>, and the consequences for what the command does as a result. This isn’t described in a manuscript, it’s just the MRtrix3
tckgen interface. In your usage (which is more common),
tckgen will continue seeding and propagating streamlines until it has written 100,000 streamlines to the output file. Each of those 100,000 streamlines satisfy all criteria imposed on reconstructed streamlines in order to be deemed “acceptable”.
In your method 1, 100,000 streamlines are generated, regardless of whether or not they intersect
tckedit will then select from those 100,000 streamlines only those that traverse
targetimage.nii.gz. Let’s say for the sake of the argument that about 1% of streamlines seeded in
filteredtracks.tck will contain about 1,000 streamlines.
In your method 2,
tckgen will continue until it has generated 100,000 streamlines that intersect
targetimage.nii.gz. If 1% of generated streamlines succeed in doing so, that means
tckgen will need to generate about 10,000,000 streamlines before it produces those 100,000 “acceptable” streamlines that satisfy the criterion of intersecting
targetimage.nii.gz. As a result,
output2.tck has about 100 times as many streamlines in it than does