TractEM: Fast Protocols for Whole Brain Deterministic Tractography-Based White Matter Atlas

Reproducible identification of white matter tracts across subjects is essential for the study of structural connectivity of the human brain. One of the key challenges is anatomical differences between subjects. Labeling white matter regions of interest presents many challenges due to the need to integrate both local and global information. Clearly communicating the human/manual processes to capture this information is cumbersome, and the state-of-the-art for white matter atlas is the population-averaged Johns Hopkins Eve atlas. A critical bottleneck with the Eve atlas framework is that manual labeling time is extensive and peripheral white matter regions are conservatively labeled. In this work, we developed and tested a protocol for a simpler and flexible approach based on modern tractography definitions. The TractEM protocols for whole brain tractography take less than 6 hours for one subject. We tested the protocols on 61 unique tracts for 20 subjects manually labeled at least twice per subject. We analyzed reproducibility of the fiber bundles using volumetric overlap metrics, Dice correlation coefficient, continuous Dice correlation coefficient; distance metric, root mean squared error; and probabilistic intraclass correlation (ICC). Raters with minimal neuroanatomical expertise attained good and high reproducibility for typical 3T research resolution and high-resolution Human Connectome Project datasets, respectively. While the existing tractography methods tend to cover larger tracts and target only a limited number of tracts, the TractEM manual labeling protocols allow for reconstruction of reproducible region-specific fiber bundles across the brain. The protocols and sample results have been made available in open source.