The numerical differences between the two are likely principally stochastic, and if you were to run both experiments multiple times, the average number of streamlines between the two approaches would come out to about the same. This is specifically because you’re using “
-seeds 10000 -select 0”, which means that 10,000 streamline seeds are propagated from, regardless of how many are successful; under default
tckgen usage, where the number of output streamlines is fixed, the latter usage would always lead to an equal or lesser number of streamlines than the former.
The more esoteric answer is that in the former case, all three vertices of each half-voxel iFOD2 “step” are compared to any provided ROIs, whereas in the latter case, the streamlines data have already been “downsampled”, such that the vertices in the track file are half a voxel distance apart, prior to comparison to image
target_mask.mif. So there may be some rare instances where the latter usage would reject a streamline that would have been retained by the former usage, if it’s only one of those “in-between” vertices that resides within a voxel present in the mask.