Should I be specifying the step and angle to get better results?
You can certainly experiment with those: The default of 1/2 voxel step size and 45 degrees per step is fairly short compared to other data due to the smaller voxel size, using 1.25mm step size and 45 degrees per step would be closer to the “standard” “default”. But there really is no correct answer as to what these should be.
I am not sure if masks should be specified given this is a whole brain tractography approach.
For whole-brain tracking with ACT, assuming you don’t want to exclude any white matter, the best option is to not use any mask.
Also, on revision:
I was wondering about the accuracy of this particular approach, i.e. generating a complete whole brain connectome and then specifically selecting connections from the amygdala to all other nodes using
connectome2tck.
My suspicion is that the issue you describe is generic to streamlines tractography, and is not specific to the approach of generating whole-brain streamlines and subsequently selecting tracks. If you were to perform targeted tracking with both seed and target regions, this would simply be obscuring the large number of generated streamlines that connect only one of those two regions, which is precisely what you’re seeing in the whole-brain data.
Rob