AFQ Browser A browser tool for tractometry data
Brain Connectivity Toolbox (BCT)
Circos Diagrams
dsi studio autotrack
How to Interpret dMRI metrics A really nice reference by DSI studio's Frank Yeh.
MRtrix3 Read-the-Docs Good documentation on fundamental concepts and on working with connectomes.
Daducci, A., Canales-Rodríguez, E. J., Descoteaux, M., Garyfallidis, E., Gur, Y., Lin, Y. C. et al. (2014). Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI. IEEE Trans Med Imaging, 33(2), 384-399.
Huber, E., Henriques, R. N., Owen, J. P., Rokem, A., & Yeatman, J. D. (2019). Applying microstructural models to understand the role of white matter in cognitive development. Dev Cogn Neurosci, 36, 100624.
Johansen-Berg, H., Behrens, T. E. J., Sillery, E. L., Ciccarelli, O., Thompson, A. J., Smith, S. M. et al. (2005). Functional-anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus. Cerebral Cortex, 15(1), 31-39.
Patterson, D. K., Van Petten, C., Beeson, P., Rapcsak, S. Z., & Plante, E. (2014). Bidirectional iterative parcellation of diffusion weighted imaging data: separating cortical regions connected by the arcuate fasciculus and extreme capsule. NeuroImage, 102 Pt 2, 704-716.
Radhakrishnan, H., Zhao, C., Sydnor, V. J., Baller, E. B., Cook, P. A., Fair, D. et al. (2023). Establishing the Validity of Compressed Sensing Diffusion Spectrum Imaging. bioRxiv, 2023.02.22.529546.
Scholz, J., Klein, M. C., Behrens, T. E. J., & Johansen-Berg, H. (2009). Training induces changes in white-matter architecture. Nature Neuroscience, 12(11), 1370-1371.
Song, S.-K., Yoshino, J., Le, T. Q., Lin, S.-J., Sun, S.-W., Cross, A. H. et al. (2005). Demyelination increases radial diffusivity in corpus callosum of mouse brain. NeuroImage, 26(1), 132-140.
Song, S.-K., Sun, S.-W., Ju, W.-K., Lin, S.-J., Cross, A. H., & Neufeld, A. H. (2003). Diffusion tensor imaging detects and differentiates axon and myelin degeneration in mouse optic nerve after retinal ischemia. NeuroImage, 20(3), 1714-1722.
Sporns, Olaf. (2016) Networks of the Brain. MIT Press.
Yeatman, J. D., Dougherty, R. F., Myall, N. J., Wandell, B. A., & Feldman, H. M. (2012). Tract profiles of white matter properties: automating fiber-tract quantification. PLoS One, 7(11), e49790.

dMRI from 10,000 Feet (~55-minutes)