Hi there,
Firstly, thank you very much to the MRtrix creators and maintainers for a truly pleasant user experience and “well-oiled” tool.
tckgen has been working great for me and I generated some wonderful whole-brain tracks following the Beginner Tutorial.
Beginning to dabble in ROI-based analysis, I tried out the -seed_sphere option instead of -seed_image with the mask, and found a suitable midpoint and radius inside the neck as far in the inferior direction as there are tracks in my whole-brain tractogram. In other words, as far into the neck past the base of the brain as meaningful tracks are generated.
However, I wasn’t sure from the docs,
-seed_sphere spec (multiple uses permitted) spherical seed as four comma-separated values (XYZ position and radius)
what the units for x,y,z and radius are. However, after trying out generating tracks assuming
- voxels, then
- mm,
I’m fairly certain the sphere spec units are in mm? If so, should this be specified in the aforementioned docs?
Thank you. Best,
Tom