References

Avants, B. B., Epstein, C. L., Grossman, M., & Gee, J. C. (2008). Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain. Medical Image Analysis, 12(1), 26–41. https://doi.org/10.1016/j.media.2007.06.004

Daducci, A., Canales-Rodríguez, E. J., Zhang, H., Dyrby, T. B., Alexander, D. C., & Thiran, J.-P. (2015). Accelerated microstructure imaging via convex optimization (AMICO) from diffusion MRI data. NeuroImage, 105, 32–44. https://doi.org/10.1016/j.neuroimage.2014.10.026

Dhollander, T., Raffelt, D., & Connelly, A. (2016). Unsupervised 3-tissue response function estimation from single-shell or multi-shell diffusion MR data without a co-registered T1 image. ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 5.

Frazier, J. A., Chiu, S., Breeze, J. L., Makris, N., Lange, N., Kennedy, D. N., Herbert, M. R., Bent, E. K., Koneru, V. K., Dieterich, M. E., Hodge, S. M., Rauch, S. L., Grant, P. E., Cohen, B. M., Seidman, L. J., Caviness, V. S., & Biederman, J. (2005). Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder. American Journal of Psychiatry, 162(7), 1256–1265. https://doi.org/10.1176/appi.ajp.162.7.1256

Freedman, D., & Lane, D. (1983). A nonstochastic interpretation of reported significance levels. Journal of Business & Economic Statistics, 1(4), 292–298. https://doi.org/10.1080/07350015.1983.10509354

Garyfallidis, E., Brett, M., Correia, M. M., Williams, G. B., & Nimmo-Smith, I. (2012). QuickBundles, a method for tractography simplification. Frontiers in Neuroscience, 6, 175. https://doi.org/10.3389/fnins.2012.00175

Garyfallidis, E., Brett, M., Amirbekian, B., Rokem, A., van der Walt, S., Descoteaux, M., Nimmo-Smith, I., & DIPY Contributors. (2014). Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 8, 8. https://doi.org/10.3389/fninf.2014.00008

Hoopes, A., Mora, J. S., Dalca, A. V., Fischl, B., & Hoffmann, M. (2022). SynthStrip: Skull-stripping for any brain image. NeuroImage, 260, 119474. https://doi.org/10.1016/j.neuroimage.2022.119474

Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., & Smith, S. M. (2012). FSL. NeuroImage, 62(2), 782–790. https://doi.org/10.1016/j.neuroimage.2011.09.015

Jeurissen, B., Tournier, J.-D., Dhollander, T., Connelly, A., & Sijbers, J. (2014). Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage, 103, 411–426. https://doi.org/10.1016/j.neuroimage.2014.07.061

Kruper, J., Yeatman, J. D., Richie-Halford, A., Bloom, D., Grotheer, M., Caffarra, S., Kiar, G., Karipidis, I. I., Roy, E., Chandio, B. Q., Garyfallidis, E., & Rokem, A. (2021). Evaluating the reliability of human brain white matter tractometry. Aperture Neuro, 2021(1). https://doi.org/10.52294/e6198273-b8e3-4b63-babb-6e6b0da10669

Makris, N., Goldstein, J. M., Kennedy, D., Hodge, S. M., Caviness, V. S., Faraone, S. V., Tsuang, M. T., & Seidman, L. J. (2006). Decreased volume of left and total anterior insular lobule in schizophrenia. Schizophrenia Research, 83(2–3), 155–171. https://doi.org/10.1016/j.schres.2005.11.020

Murty, V. P., Shermohammed, M., Smith, D. V., Carter, R. M., Huettel, S. A., & Adcock, R. A. (2014). Resting state networks distinguish human ventral tegmental area from substantia nigra. NeuroImage, 100, 580–589. https://doi.org/10.1016/j.neuroimage.2014.06.047

Parker, C. S., Veale, T., Bocchetta, M., Slattery, C. F., Malone, I. B., Thomas, D. L., Schott, J. M., Cash, D. M., & Zhang, H. (2021). Not all voxels are created equal: Reducing estimation bias in regional NODDI metrics using tissue-weighted means. NeuroImage, 245, 118749. https://doi.org/10.1016/j.neuroimage.2021.118749

Pauli, W. M., Nili, A. N., & Tyszka, J. M. (2018). A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei. Scientific Data, 5, 180063. https://doi.org/10.1038/sdata.2018.63

Raffelt, D., Dhollander, T., Tournier, J.-D., Tabbara, R., Smith, R. E., Pierre, E., & Connelly, A. (2017). Bias field correction and intensity normalisation for quantitative analysis of apparent fibre density. Proceedings of the International Society for Magnetic Resonance in Medicine, 25, 3541.

Tournier, J.-D., Calamante, F., & Connelly, A. (2010). Improved probabilistic streamlines tractography by 2nd order integration over fibre orientation distributions. Proceedings of the International Society for Magnetic Resonance in Medicine, 18, 1670.

Tournier, J.-D., Smith, R., Raffelt, D., Tabbara, R., Dhollander, T., Pietsch, M., Christiaens, D., Jeurissen, B., Yeh, C.-H., & Connelly, A. (2019). MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 202, 116137. https://doi.org/10.1016/j.neuroimage.2019.116137

Trutti, A. C., Fontanesi, L., Mulder, M. J., Bazin, P.-L., Hommel, B., & Forstmann, B. U. (2021). A probabilistic atlas of the human ventral tegmental area (VTA) based on 7 Tesla MRI data. Brain Structure and Function, 226, 1155–1167. https://doi.org/10.1007/s00429-021-02231-w

Tziortzi, A. C., Haber, S. N., Searle, G. E., Tsoumpas, C., Long, C. J., Shotbolt, P., Douaud, G., Jbabdi, S., Behrens, T. E. J., Rabiner, E. A., Jenkinson, M., & Gunn, R. N. (2014). Connectivity-based functional analysis of dopamine release in the striatum using diffusion-weighted MRI and positron emission tomography. Cerebral Cortex, 24(5), 1165–1177. https://doi.org/10.1093/cercor/bhs397

Vu, A. T., Auerbach, E., Lenglet, C., Moeller, S., Sotiropoulos, S. N., Jbabdi, S., Andersson, J., Yacoub, E., & Ugurbil, K. (2015). High resolution whole brain diffusion imaging at 7T for the Human Connectome Project. NeuroImage, 122, 318–331. https://doi.org/10.1016/j.neuroimage.2015.08.004

Winkler, A. M., Ridgway, G. R., Webster, M. A., Smith, S. M., & Nichols, T. E. (2014). Permutation inference for the general linear model. NeuroImage, 92, 381–397. https://doi.org/10.1016/j.neuroimage.2014.01.060

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. https://doi.org/10.1371/journal.pone.0049790

Zhang, H., Schneider, T., Wheeler-Kingshott, C. A., & Alexander, D. C. (2012). NODDI: Practical in vivo neurite orientation dispersion and density imaging of the human brain. NeuroImage, 61(4), 1000–1016. https://doi.org/10.1016/j.neuroimage.2012.03.072