AFQ Browser A browser tool for tractometry data
Brain Connectivity Toolbox (BCT) Olaf Sporn's Matlab toolbox for doing network analysis
Circos Diagrams Software for creating pretty circular charts sometimes used to illustrate connections
dMRI in 2023 (This is a PDF of the slides, including notes, that were used for this lesson presentation)
dsi studio autotrack A webpage and video explaining dsistudio autotrack, which is one of the reconstruction pipelines available in QSIrecon.
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.
Timeline of Tractography A 50 minute You Tube video by Dr Kurt Schilling on the history of tractography
dMRI scalars: My google spreadsheet of different scalars associated with different kinds of reconstruction
qsiprep reconstruction pipelines: My google spreadsheet of different reconstructions and their outputs and requirements
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.
Mori, Susumu and J-Donald Tournier Introduction to Diffusion Tensor Imaging 2014 This is an excellent book. Chapter 1 gave a pretty good introduction to dMRI acquisition.
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.
Tractography: a story of hope, dreams, excitement, broken dreams, delusions, renewed hope, renewed dreams, renewed excitement.,...? Thijs Dhollander, 2019 (22.5 minutes) An exceptionally friendly and exciting video presentation on tractography.
Timeline of Tractography Kurt Schilling ~40 minutes: YouTube lecture on the history of tractography
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 4 (10 pts): Modern dMRI