Cutoff value in tckgen

tractography

#1

Dear MRtrix community,

I have some doubts regarding the cutoff value for the function tckgen. In the documentation it is written that “set the FA or FOD amplitude cutoff for terminating tracks (default is 0.1)”.

  • If I use the CSD model with probabilistic or deterministic tracking, is the cutoff value always referred to the FOD amplitude threshold? And is it referred to the FA threshold only if I don’t use CSD?

  • Is the cutoff value used to terminate the tracking when the FOD amplitude is below the value? Or is it used to remove directions from the probability mass function for selecting the tracking direction (in the case of probabilistic tracking)?

Thank you in advance!

Best,
Giulia


#2

Yes, that’s correct - aside possibly from the FACT algorithm, where the cutoff presumably refers to the length of the vector (@rsmith will no doubt correct me if I’m wrong).

With deterministic tracking, it is used for termination. For probabilistic tracking, it serves both functions you suggest, but the latter is the more correct way of phrasing it: directions whose FOD amplitude is lower than the cutoff are not considered - they are effectively removed from the PDF being sampled. When no direction above the cutoff can be found within the allowed solid angle, then the streamline is terminated.

Cheers,
Donald.


Thresholding fixels using voxelwise threshold
#3

Thank you so much Donald for the fast reply!
Now it’s clear to me.

Best,
Giulia