Design protocol data analysis methods form a well-known set of techniques used by design researchers to further understand the conceptual design process. Verbal protocols are a popular technique used to analyze design activities. However, verbal protocols are known to have some limitations. A recurring problem in design protocol analysis is to segment and code protocol data into logical and semantic units. This is usually a manual step and little work has been done on fully automated segmentation techniques. Physiological signals such as electroencephalograms (EEG) can provide assistance in solving this problem. Such problems are typical inverse problems that occur in the line of research. A thought process needs to be reconstructed from its output, an EEG signal. We propose an EEG-based method for design protocol coding and segmentation. We provide experimental validation of our methods and compare manual segmentation by domain experts to algorithmic segmentation using EEG. The best performing automated segmentation method (when manual segmentation is the baseline) is found to have an average deviation from manual segmentations of 2 s. Furthermore, EEG-based segmentation can identify cognitive structures that simple observation of design protocols cannot. EEG-based segmentation does not replace complex domain expert segmentation but rather complements it. Techniques such as verbal protocols are known to fail in some circumstances. EEG-based segmentation has the added feature that it is fully automated and can be readily integrated in engineering systems and subsystems. It is effectively a window into the mind.