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Cieslak, M., Cook, P.A., He, X. et al. (2021) QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data. Nat Methods 18 (775–778) doi: https://doi.org/10.1038/s41592-021-01185-5

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Brett M, Leff AP, Rorden C, Ashburner J (2001) Spatial Normalization of Brain Images with Focal Lesions Using Cost Function Masking. NeuroImage 14(2) doi:10.006/nimg.2001.0845.

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[Huntenburg2014]

Huntenburg, J. M. (2014) Evaluating Nonlinear Coregistration of BOLD EPI and T1w Images. Berlin: Master Thesis, Freie Universität. PDF.

[Treiber2016]

Treiber, J. M. et al. (2016) Characterization and Correction of Geometric Distortions in 814 Diffusion Weighted Images, PLoS ONE 11(3): e0152472. doi:10.1371/journal.pone.0152472.

[Wang2017]

Wang S, et al. (2017) Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion MRI. Front. Neuroinform. 11:17.

[Jeurissen2014]

Jeurissen, B.; Tournier, J.-D.; Dhollander, T.; Connelly, A. & Sijbers, J. Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage, 2014, 103, 411-426

[Dhollander2016]

Dhollander, T. & Connelly, A. A novel iterative approach to reap the benefits of multi-tissue CSD from just single-shell (+b=0) diffusion MRI data. Proc Intl Soc Mag Reson Med, 2016, 3010

[Dhollander2019]

Dhollander, Thijs & Mito, Remika & Raffelt, David & Connelly, Alan. (2019). Improved white matter response function estimation for 3-tissue constrained spherical deconvolution.

[Smith2012]

Smith, R. E., Tournier, J. D., Calamante, F., & Connelly, A. (2012). Anatomically-constrained tractography: improved diffusion MRI streamlines tractography through effective use of anatomical information. Neuroimage, 62(3), 1924-1938.

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Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT2: Enabling dense quantitative assessment of brain white matter connectivity using streamlines tractography. NeuroImage, 2015, 119, 338-351

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F.-C. Yeh, T. D. Verstynen, Y. Wang, J. C. Fernández-Miranda, and W-Y. I. Tseng, Deterministic Diffusion Fiber Tracking Improved By Quantitative Anisotropy, PLoS ONE 8(11): e80713. doi:10.1371/journal.pone.0080713

[Yeh2019]

Yeh, F. C., Zaydan, I. M., Suski, V. R., Lacomis, D., Richardson, R. M., Maroon, J., & Barrios-Martinez, J. (2019). Differential tractography as a track-based biomarker for neuronal injury. NeuroImage, 576025.

[Yeh2020]

Yeh, F.-C. (2020). Shape analysis of the human association pathways. Neuroimage, 117329.

[Yeh2022]

Yeh, F.-C. (2022). Population-based tract-to-region connectome of the human brain and its hierarchical topology. Nat Comm (13), 4933.

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Schaefer, A., Kong, R., Gordon, E. M., Laumann, T. O., Zuo, X. N., Holmes, A. J., … & Yeo, B. T. (2017). Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI. Cerebral Cortex, 28(9), 3095-3114.

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Thomas Yeo, B. T., Krienen, F. M., Sepulcre, J., Sabuncu, M. R., Lashkari, D., Hollinshead, M., … & Fischl, B. (2011). The organization of the human cerebral cortex estimated by intrinsic functional connectivity. Journal of neurophysiology, 106(3), 1125-1165.

[Joliot2015]

Joliot M, Jobard G, Naveau M, Delcroix N, Petit L, Zago L, Crivello F, Mellet E, Mazoyer B, Tzourio-Mazoyer N (2015) AICHA: An atlas of intrinsic connectivity of homotopic areas. J Neurosci Methods 254:46-59.

[Fan2016]

Lingzhong Fan, Hai Li, Junjie Zhuo, Yu Zhang, Jiaojian Wang, Liangfu Chen, Zhengyi Yang, Congying Chu, # Sangma Xie, Angela R. Laird, Peter T. Fox, Simon B. Eickhoff, Chunshui Yu, and Tianzi Jiang, “The Human # Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture”, Cerebral Cortex, 2016

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Gordon, E. M., Laumann, T. O., Adeyemo, B., Huckins, J. F., Kelley, W. M., & Petersen, S. E. (2014). Generation and evaluation of a cortical area parcellation from resting-state correlations. Cerebral cortex, 26(1), 288-303.

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[Daducci2015]

Daducci, Alessandro, et al. “Accelerated microstructure imaging via convex optimization (AMICO) from diffusion MRI data.” NeuroImage 105 (2015): 32-44.

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Zhang, Hui, et al. “NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain.” Neuroimage 61.4 (2012): 1000-1016.

[Smith2020]

Smith, R.; Skoch, A.; Bajada, C.; Caspers, S.; Connelly, A. Hybrid Surface- Volume Segmentation for improved Anatomically-Constrained Tractography. In Proc OHBM 2020

[Irfanoglu]

Irfanoglu, M.O., et al. (2015) DR-BUDDI (Diffeomorphic Registration for Blip-Up blip-Down Diffusion Imaging) method for correcting echo planar imaging distortions.

Neuroimage 106:284-299

[Irfanoglu2017]

Irfanoglu, M.O., et al. TORTOISE v3: Improvements and new features of the NIH diffusion MRI processing pipeline.” Program and proceedings of the ISMRM 25th annual meeting and exhibition, Honolulu, HI, USA. 2017.