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?

This happens to be one of the examples that @rsmith has been adding to the docs for mrcalc (still in development, this is a sneek preview):

Rescale the densities in a SH l=0 image:

$ mrcalc ODF_CSF.mif 4 pi -mult -sqrt -div ODF_CSF_scaled.mif

This applies the spherical harmonic basis scaling factor: 1.0/sqrt(4*pi), such that a single-tissue voxel containing the same intensities as the response function of that tissue should contain the value 1.0.