MIND-Map; A Comprehensive Toolbox for Estimating Brain Dynamic States

Studying dynamic brain states has offered new insights into understanding functional connectivity. One of the promising approaches for estimating these brain states is the hidden semi-Markov model (HSMM). However, despite its potential, its adoption in the neuroscience community has been limited due to its complexity. We developed the Markov Inference Dynamic Mapping (MIND-Map) toolbox to overcome this limitation. This interactive user-friendly toolbox leverages HSMM to identify brain states, analyze their dynamics, and perform two-sample statistical comparisons of network dynamics. Furthermore, it introduces a new approach, not yet used in conjunction with these models, for determining the optimal number of states, addressing a key challenge in the field. We assessed the performance of the HSMM and our method for identifying the optimal number of states using two datasets, including a unique dataset explicitly developed for this purpose.