Functional Connectivity and the CONN Toolbox | Alfonso Nieto-Castañón (Andy's BrainCast #007)

Dr. Alfonso Nieto-Castañón is the Director of the Computational Neuroscience Research Lab in Santiago de Compostela, Spain. He was previously a Research Affiliate at the McGovern Institute for Brain Research at MIT, where he developed the CONN toolbox, the most widely used functional connectivity analysis software package in the field. He has won several computing programming competitions, including the Microsoft and Chalearn data analysis competition and the Genentech data prediction competitions, along with being awarded Google's Kaggle Competition Grandmaster title. His research focuses on modeling and statistics, brain imaging methods, and machine learning, especially the understanding and characterization of human brain dynamics (https://en.wikipedia.org/wiki/Alfonso.... In this interview we discuss how he became interested in functional connectivity, his work on developing the CONN toolbox, and his views on the future of dynamic connectivity. Alfonso's Personal Website: https://web.alfnie.com/ The CONN Toolbox: https://web.conn-toolbox.org/ The CONN Workshop: https://web.conn-toolbox.org/workshops Ooi2025 Optimal Scan Time Calculator (Thomas Yeo's group): https://thomasyeolab.github.io/Optima... Table of Contents ============== 0:00 Introduction 1:54 Alfonso's Interest in Brain Research 7:58 Global Signal Regression vs. Anatomical Component Correction 22:49 The CONN Workshop 28:17 Current Recommendations for Preprocessing and Denoising 38:16 Analyzing High-Movement Populations 45:47 Thoughts on FIRMM and Data Scrubbing 52:01 Reliability and Scan Time 58:20 Dynamic Connectivity 1:09:36 Alfonso's Thoughts on Software Design and Its Influence on Science 1:12:24 Closing Remarks Interview recorded on November 24th, 2025.