Tckgen: Insights on -seed_image, -seed_grid_per_voxel, and -seed_cutoff Interaction in tckgen

1

Hello MRtrix Community,

I am currently utilizing tckgen and seeking clarifications regarding the seeding process, particularly with the -seed_image, -seed_grid_per_voxel, and -seed_cutoff options.

  1. When using -seed_image mask, I noticed that not all voxels in my mask are initiating fibers. Can you explain why this is the case? How does the -seed_cutoff parameter influence whether a voxel in the mask becomes a seed point for fiber tracking? Even if i lowered it, there were still no fibers from some parts of the mask.
  2. I’m also interested in understanding the use of -seed_grid_per_voxel in conjunction with the -seed_image option. How does -seed_grid_per_voxel function differently from -seed_image, and under what circumstances would one be preferred over the other?
  3. Regarding the -seed_cutoff option, how does it affect the seeding process in terms of fiber tracking initiation ?

Your insights into these parameters and how they interact in the tckgen command would be invaluable for my research.

Best regards and happy new year,
Nicolas