Hi everyone,
I’m having a little trouble understanding the exact meaning of the 20% default threshold used in the freeview -tv option and dmri_pathstats --pthr. I’ve seen multiple threads where Anastasia said that it is 20% of the maximum value in the probability distribution—which corresponds to the maximum number of sample paths intersecting a single voxel—but the default thresholds I’ve seen set by the -tv option are generally lower than that. For example, I have one subject in whom the right CST has a maximum value in its path.pd.nii.gz file of 300. I would expect based on what I’ve read in the mail archives that the threshold would be set at 60, but when I open the merged file with the -tv option the default threshold for the right CST is 35.
My current best guess is that the default threshold is set to produce a volume that has a probability sum equal to 20% of the sum of the pre-threshold volume. (That is, the sum of intensities of all voxels in the path.pd.nii.gz file should be 5 times the sum of the voxels above the default threshold.) Is that accurate?
Thanks for all you’ve done to develop this tool. It’s brilliant and I want to understand as much of it as I can.
-Dillan