REST: A MATLAB-Based Toolkit for Resting-State fMRI Data Analysis

In the field of neuroimaging, resting-state functional magnetic resonance imaging (fMRI) is attracting growing research interest. However, specialized software for analyzing this type of data has been notably absent. To address this gap, we developed REST, a MATLAB-based toolkit that implements three primary analytical functions through optimized algorithms and custom scripts:

1. Functional Connectivity Analysis: This feature enables researchers to investigate functional relationships between different brain regions at the neural network level, revealing information transfer mechanisms within the nervous system. The implementation employs correlation analysis and seed-based approaches to compute connectivity matrices, with options for both voxel-wise and region-of-interest analyses using MATLAB's statistical toolbox.

2. Regional Homogeneity (ReHo) Analysis: This function helps researchers localize functional abnormalities in specific brain areas, thereby uncovering neural mechanisms underlying various disorders. The algorithm calculates Kendall's coefficient of concordance to measure synchronization of time series within clusters of adjacent voxels, implemented through sliding window techniques and neighborhood operations for robust local connectivity assessment.

3. Amplitude of Low-Frequency Fluctuations (ALFF) Analysis: This capability allows quantitative measurement of low-frequency signal amplitudes across different brain regions, revealing inter-regional differences and their relationships with disease pathogenesis. The computation involves Fast Fourier Transform (FFT) implementations to extract power spectra from preprocessed time series, with frequency band filtering (typically 0.01-0.08 Hz) and normalization procedures to ensure comparability across subjects.

Thus, the REST toolkit provides researchers with a powerful resource for investigating nervous system functionality and disease mechanisms. It facilitates deeper understanding of brain organization through standardized processing pipelines and offers valuable references for clinical research applications, all implemented within an extensible MATLAB framework that supports custom script integration and batch processing capabilities.