Optimal QA Threshold Strategy for ADNI/PPMI Group Study (Auto vs Fixed?)

[Jaeyoung Kang]

Hi Frank,

I am processing a large group study (ADNI/PPMI data) using DSI Studio (command line via Docker). My current pipeline is:

1. Reconstruction: QSDR (Human Connectome Template)
2. Tracking: Whole-brain seeding, 1M seeds, threshold_index=qa.
3. Connectivity: Brainnetome atlas to generate connectivity matrices.

The Issue: I am currently leaving the threshold value unspecified (so it uses the Auto/Default threshold). However, when analyzing the resulting binary connectivity matrices, I am seeing cutoff regions / disconnected nodes (regions with 0 connections) in many subjects. Ideally, I want to minimize these false negatives for a valid network analysis.

My Questions:

1. Auto vs. Fixed: For a large heterogeneity dataset like ADNI/PPMI, is it safe to rely on the auto-threshold (Otsu-based)? Or is it standard practice to set a conservative fixed lower bound (e.g., fa_threshold=0.15 or 0.1) to ensure consistency across the group?
2. Individual Threshold: If "Auto" is inconsistent, is there a recommended way to determine the optimal "individual" threshold for each subject if I script it myself, or is a fixed group threshold preferred?

Thank you so much for your help!

Jae