I’m opening a new thread because I asked several different questions under one thread.
I am running deterministic tractography on FOD, using the FACT algorithm in tckgen. In many works (e.g., this one) I’ve seen that people use an absolute threshold on the peak FOD, which is defined as 3 “multiples of the amplitude of a spherical FOD obtained from an isotropic voxel of gray matter” .
I am not sure how to interpret this. I thought I should take the l=0 volume of the FOD file (as the amplitude of the 0th spherical harmonic), and average that across gray-matter voxels. Does this make sense to you?