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  url       = {https://doi.org/10.1016/j.mri.2019.05.008},
  note      = {Artificial Intelligence in MRI}
}

@article{Smith2012,
  author    = {Robert E. Smith and Jacques-Donald Tournier and Fernando Calamante and Alan Connelly},
  title     = {{Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information}},
  journal   = {NeuroImage},
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  month     = {September},
  doi       = {10.1016/j.neuroimage.2012.06.005},
  url       = {https://doi.org/10.1016/j.neuroimage.2012.06.005}
}

@article{Soderman1995,
  author    = {Olle S\"{o}derman and Bengt J\"{o}onsson},
  title     = {{Restricted Diffusion in Cylindrical Geometry}},
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@article{Sotiropoulos2013,
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  title     = {{Advances in diffusion MRI acquisition and processing in the Human Connectome Project}},
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  year      = {2013},
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  url       = {https://doi.org/10.1016/j.neuroimage.2013.05.057},
  note      = {Mapping the Connectome},
}

@article{Stejskal1965,
  author    = {Edward O. Stejskal and John E. Tanner},
  title     = {{Spin Diffusion Measurements: Spin Echoes in the Presence of a Time-Dependent Field Gradient}},
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@article{StOnge2018,
  author    = {Etienne St-Onge and Alessandro Daducci and Gabriel Girard and Maxime Descoteaux},
  title     = {{Surface-enhanced tractography (SET)}},
  journal   = {NeuroImage},
  year      = {2018},
  volume    = {169},
  pages     = {524-539},
  doi       = {10.1016/j.neuroimage.2017.12.036},
  url       = {https://doi.org/10.1016/j.neuroimage.2017.12.036}
}

@article{StOnge2022,
  author    = {Etienne St-Onge and Eleftherios Garyfallidis and D. Louis Collins},
  title     = {{Fast Streamline Search: An Exact Technique for Diffusion MRI Tractography}},
  journal   = {Neuroinformatics},
  year      = {2022},
  volume    = {20},
  number    = {4},
  pages     = {1093--1104},
  doi       = {10.1007/s12021-022-09590-7},
  url       = {https://doi.org/10.1007/s12021-022-09590-7}
}

@article{Szczepankiewicz2019,
  author    = {Filip Szczepankiewicz and Scott Hoge and Carl-Fredrik Westin},
  title     = {{Linear, planar and spherical tensor-valued diffusion MRI data by free waveform encoding in healthy brain, water, oil and liquid crystals}},
  journal   = {Data in Brief},
  year      = {2019},
  volume    = {25},
  pages     = {104208},
  doi       = {10.1016/j.dib.2019.104208},
  url       = {https://doi.org/10.1016/j.dib.2019.104208}
}

@article{Tabesh2011,
  author    = {Ali Tabesh and Jens H. Jensen and Babak A. Ardekani and Joseph A. Helpern},
  title     = {{Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging}},
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  volume    = {65},
  number    = {3},
  pages     = {823-836},
  year      = {2011},
  doi       = {10.1002/mrm.22655},
  url       = {https://doi.org/10.1002/mrm.22655}
}

@article{Tariq2016,
  author    = {Maira Tariq and Torben Schneider and Daniel C. Alexander and Claudia A. Gandini Wheeler-Kingshott and Hui Zhang},
  journal   = {NeuroImage},
  title     = {{Bingham-Noddi: Mapping anisotropic orientation dispersion of neurites using diffusion MRI}},
  volume    = {133},
  year      = {2016},
  pages     = {207--223},
  doi       = {10.1016/j.neuroimage.2016.01.046},
  url       = {https://doi.org/10.1016/j.neuroimage.2016.01.046}
}

@article{Tax2015,
  author    = {Chantal M.W. Tax and Willem M. Otte and Max A. Viergever and Rick M. Dijkhuizen and Alexander Leemans},
  title     = {{REKINDLE: Robust extraction of kurtosis INDices with linear estimation}},
  journal   = {Magnetic Resonance in Medicine},
  volume    = {73},
  number    = {2},
  pages     = {794-808},
  year      = {2015},
  doi       = {10.1002/mrm.25165},
  url       = {https://doi.org/10.1002/mrm.25165}
}

@article{Tax2014,
  author    = {Chantal M.W. Tax and Ben Jeurissen and Sjoerd B. Vos and Max A. Viergever and Alexander Leemans},
  title     = {{Recursive calibration of the fiber response function for spherical deconvolution of diffusion MRI data}},
  journal   = {NeuroImage},
  volume    = {86},
  pages     = {67-80},
  year      = {2014},
  doi       = {10.1016/j.neuroimage.2013.07.067},
  url       = {https://doi.org/10.1016/j.neuroimage.2013.07.067}
}

@article{Tournier2019,
  author    = {Jacques-Donald Tournier and Robert Smith and David Raffelt and Rami Tabbara and Thijs Dhollander and Maximilian Pietsch and Daan Christiaens and Ben Jeurissen and Chun-Hung Yeh and Alan Connelly},
  title     = {{MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation}},
  journal   = {NeuroImage},
  volume    = {202},
  pages     = {116137},
  year      = {2019},
  month     = {November},
  doi       = {10.1016/j.neuroimage.2019.116137},
  url       = {https://doi.org/10.1016/j.neuroimage.2019.116137}
}

@article{Tournier2012,
  author    = {Jacques-Donald Tournier and Fernando Calamante and Alan Connelly},
  title     = {{MRtrix: Diffusion tractography in crossing fiber regions}},
  journal   = {International Journal of Imaging Systems and Technology},
  volume    = {22},
  number    = {1},
  pages     = {53-66},
  year      = {2012},
  doi       = {https://doi.org/10.1002/ima.22005},
  url       = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ima.22005}
}

@article{Tournier2007,
  author    = {Jacques-Donald Tournier and Fernando Calamante and Alan Connelly},
  title     = {{Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution}},
  journal   = {NeuroImage},
  volume    = {35},
  number    = {4},
  pages     = {1459-1472},
  year      = {2007},
  month     = {May},
  doi       = {10.1016/j.neuroimage.2007.02.016},
  url       = {https://doi.org/10.1016/j.neuroimage.2012.06.005}
}

@article{Tournier2004,
  author    = {Jacques-Donald Tournier and Fernando Calamante and David G. Gadian and Alan Connelly},
  title     = {{Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution}},
  journal   = {NeuroImage},
  volume    = {23},
  number    = {3},
  pages     = {1176-1185},
  year      = {2004},
  month     = {November},
  doi       = {10.1016/j.neuroimage.2004.07.037},
  url       = {https://doi.org/10.1016/j.neuroimage.2004.07.037}
}

@article{TristanVega2010,
  author    = {Antonio Trist\'{a}n-Vega and Carl-Fredrik Westin and Santiago Aja-Fern\'{a}ndez},
  title     = {{A new methodology for the estimation of fiber populations in the white matter of the brain with the Funk–Radon transform}},
  journal   = {NeuroImage},
  volume    = {49},
  number    = {2},
  pages     = {1301-1315},
  year      = {2010},
  doi       = {10.1016/j.neuroimage.2009.09.070},
  url       = {https://doi.org/10.1016/j.neuroimage.2009.09.070}
}

@article{TristanVega2009a,
  author    = {Antonio Trist\'{a}n-Vega and Carl-Fredrik Westin and Santiago Aja-Fern\'{a}ndez},
  title     = {{Estimation of fiber Orientation Probability Density Functions in High Angular Resolution Diffusion Imaging}},
  journal   = {NeuroImage},
  volume    = {47},
  number    = {2},
  pages     = {638-650},
  year      = {2009},
  month     = {August},
  doi       = {10.1016/j.neuroimage.2009.04.049},
  url       = {https://doi.org/10.1016/j.neuroimage.2009.04.049}
}

@article{Tuch2004,
  author    = {David S. Tuch},
  title     = {{Q-ball imaging}},
  journal   = {Magnetic Resonance in Medicine},
  volume    = {52},
  number    = {6},
  pages     = {1358-1372},
  year      = {2004},
  doi       = {10.1002/mrm.20279},
  url       = {https://doi.org/10.1002/mrm.20279}
}

@article{Veraart2016c,
  author    = {Jelle Veraart and Dmitry S. Novikov and Daan Christiaens and Benjamin Ades-aron and Jan Sijbers and Els Fieremans},
  title     = {{Denoising of diffusion MRI using random matrix theory}},
  journal   = {NeuroImage},
  volume    = {142},
  pages     = {394--406},
  year      = {2016},
  month     = {November},
  doi       = {10.1016/j.neuroimage.2016.08.016},
  url       = {https://doi.org/10.1016/j.neuroimage.2016.08.016}
}

@article{Veraart2016b,
  author    = {Jelle Veraart and Els Fieremans and Dmitry S. Novikov},
  title     = {{Diffusion MRI noise mapping using random matrix theory}},
  journal   = {Magnetic Resonance in Medicine},
  volume    = {76},
  number    = {5},
  pages     = {1582--1593},
  year      = {2016},
  month     = {November},
  doi       = {10.1002/mrm.26059},
  url       = {https://doi.org/10.1002/mrm.26059}
}

@article{Veraart2016a,
  author    = {Jelle Veraart and Els Fieremans and Ileana O. Jelescu and Florian Knoll and Dmitry S. Novikov},
  title     = {{Gibbs ringing in diffusion MRI}},
  journal   = {Magnetic Resonance in Medicine},
  volume    = {76},
  number    = {1},
  pages     = {301-314},
  year      = {2016},
  month     = {July},
  doi       = {10.1002/mrm.25866},
  url       = {https://doi.org/10.1002/mrm.25866}
}

@article{Veraart2013,
  author    = {Jelle Veraart and Jan Sijbers and Stefan Sunaert and Alexander Leemans and Ben Jeurissen},
  title     = {{Weighted linear least squares estimation of diffusion MRI parameters: Strengths, limitations, and pitfalls}},
  journal   = {NeuroImage},
  volume    = {81},
  pages     = {335-346},
  year      = {2013},
  doi       = {10.1016/j.neuroimage.2013.05.028},
  url       = {https://doi.org/10.1016/j.neuroimage.2013.05.028}
}

@article{Veraart2011,
  author    = {Jelle Veraart and Dirk H. J. Poot and Wim Van Hecke and Ines Blockx and Annemie Van der Linden and Marleen Verhoye and Jan Sijbers},
  title     = {{More accurate estimation of diffusion tensor parameters using diffusion kurtosis imaging}},
  journal   = {Magnetic Resonance in Medicine},
  volume    = {65},
  number    = {1},
  pages     = {138-145},
  year      = {2011},
  doi       = {10.1002/mrm.22603},
  url       = {https://doi.org/10.1002/mrm.22603},
}

@article{Vercauteren2009,
  author    = {Tom Vercauteren and Xavier Pennec and Aymeric Perchant and Nicholas Ayache},
  title     = {{Diffeomorphic demons: Efficient non-parametric image registration}},
  journal   = {NeuroImage},
  volume    = {45},
  number    = {1, Supplement 1},
  pages     = {S61-S72},
  year      = {2009},
  doi       = {10.1016/j.neuroimage.2008.10.040},
  url       = {https://doi.org/10.1016/j.neuroimage.2008.10.040},
  note      = {Mathematics in Brain Imaging}
}

@article{Wedeen2008,
  author    = {Van Jay Wedeen and Ruopeng P. Wang and Jeremy Dan Schmahmann and Thomas Benner and Wen Yih Isaac Tseng and Guangping Dai and Deepak N. Pandya and Patric Hagmann and Helen D'Arceuil and Alexander J. {de Crespigny}},
  title     = {{Diffusion spectrum magnetic resonance imaging (DSI) tractography of crossing fibers}},
  journal   = {NeuroImage},
  volume    = {41},
  number    = {4},
  pages     = {1267-1277},
  year      = {2008},
  doi       = {10.1016/j.neuroimage.2008.03.036},
  url       = {https://doi.org/10.1016/j.neuroimage.2008.03.036}
}

@article{Wedeen2005,
  author    = {Van Jay Wedeen and Patric Hagmann and Wen-Yih Tseng and Timothy G. Reese and Robert M. Weisskoff},
  title     = {{Mapping Complex Tissue Architecture with Diffusion Spectrum Magnetic Resonance Imaging}},
  journal   = {Magnetic Resonance in Medicine},
  volume    = {54},
  number    = {6},
  pages     = {1377-1386},
  year      = {2005},
  doi       = {10.1002/mrm.20642},
  url       = {https://doi.org/10.1002/mrm.20642}
}

@article{Westin2016,
  author    = {Carl-Fredrik Westin and Hans Knutsson and Ofer Pasternak and Filip Szczepankiewicz and Evren {\"O}zarslan and Danielle {van Westen} and Cecilia Mattisson and Mats Bogren and Lauren J. O'Donnell and Marek Kubicki and Daniel Topgaard and Markus Nilsson},
  title     = {{Q-space trajectory imaging for multidimensional diffusion MRI of the human brain}},
  journal   = {NeuroImage},
  volume    = {135},
  pages     = {345-362},
  year      = {2016},
  doi       = {10.1016/j.neuroimage.2016.02.039},
  url       = {https://doi.org/10.1016/j.neuroimage.2016.02.039}
}

@article{Wichmann2006,
  author    = {Brian A. Wichmann and Ian David Hill},
  title     = {{Generating good pseudo-random numbers}},
  journal   = {Computational Statistics \& Data Analysis},
  volume    = {51},
  number    = {3},
  pages     = {1614-1622},
  year      = {2006},
  doi       = {10.1016/j.csda.2006.05.019},
  url       = {https://doi.org/10.1016/j.csda.2006.05.019}
}

@article{Wu2008,
  author    = {Yu-Chien Wu and Aaron S. Field and Andrew L. Alexander},
  title     = {{Computation of Diffusion Function Measures in $q$-Space Using Magnetic Resonance Hybrid Diffusion Imaging}},
  journal   = {IEEE Transactions on Medical Imaging},
  year      = {2008},
  volume    = {27},
  number    = {6},
  pages     = {858-865},
  doi       = {10.1109/TMI.2008.922696}
}

@article{Wu2007,
  author    = {Yu-Chien Wu and Andrew L. Alexander},
  title     = {{Hybrid diffusion imaging}},
  journal   = {NeuroImage},
  volume    = {36},
  number    = {3},
  pages     = {617-629},
  year      = {2007},
  doi       = {10.1016/j.neuroimage.2007.02.050},
  url       = {https://doi.org/10.1016/j.neuroimage.2007.02.050}
}

@article{Yeatman2012,
  author    = {Jason D. Yeatman and Robert F. Dougherty and Nathaniel J. Myall and Brian A. Wandell and Heidi M. Feldman},
  title     = {{Tract Profiles of White Matter Properties: Automating Fiber-Tract Quantification}},
  journal   = {PLOS ONE},
  publisher = {Public Library of Science},
  volume    = {7},
  pages     = {1-15},
  number    = {11},
  year      = {2012},
  month     = {November},
  doi       = {10.1371/journal.pone.0049790},
  url       = {https://doi.org/10.1371/journal.pone.0049790}
}

@article{Yeh2019,
  author    = {Fang-Cheng Yeh and Islam M. Zaydan and Valerie R. Suski and David Lacomis and R. Mark Richardson and Joseph C. Maroon and Jessica Barrios-Martinez},
  title     = {{Differential tractography as a track-based biomarker for neuronal injury}},
  journal   = {NeuroImage},
  volume    = {202},
  pages     = {116131},
  year      = {2019},
  doi       = {10.1016/j.neuroimage.2019.116131},
  url       = {https://doi.org/10.1016/j.neuroimage.2019.116131}
}

@article{Yeh2018,
  author    = {Fang-Cheng Yeh and Sandip Panesar and David Fernandes and Antonio Meola and Masanori Yoshino and Juan C. Fernandez-Miranda and Jean M. Vettel and Timothy Verstynen},
  title     = {{Population-averaged atlas of the macroscale human structural connectome and its network topology}},
  journal   = {NeuroImage},
  volume    = {178},
  pages     = {57-68},
  year      = {2018},
  doi       = {10.1016/j.neuroimage.2018.05.027},
  url       = {https://doi.org/10.1016/j.neuroimage.2018.05.027}
}

@article{Yeh2010,
  author    = {Fang-Cheng Yeh and Van Jay Wedeen and Wen-Yih Isaac Tseng},
  title     = {{Generalized ${q}$-Sampling Imaging}},
  journal   = {IEEE Transactions on Medical Imaging},
  volume    = {29},
  number    = {9},
  pages     = {1626-1635},
  year      = {2010},
  doi       = {10.1109/TMI.2010.2045126},
  url       = {https://doi.org/10.1109/TMI.2010.2045126}
}

@article{Yendiki2014,
  author    = {Anastasia Yendiki and Kami Koldewyn and Sita Kakunoori and Nancy Kanwisher and Bruce Fischl},
  title     = {{Spurious group differences due to head motion in a diffusion MRI study}},
  journal   = {NeuroImage},
  volume    = {88},
  pages     = {79-90},
  year      = {2014},
  doi       = {10.1016/j.neuroimage.2013.11.027},
  url       = {https://doi.org/10.1016/j.neuroimage.2013.11.027}
}

@article{Zhang2001,
  author    = {Yongyue Zhang and Michael Brady and Stephen Smith},
  title     = {Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm},
  journal   = {IEEE Transactions on Medical Imaging},
  volume    = {20},
  number    = {1},
  pages     = {45-57},
  year      = {2001},
  doi       = {10.1109/42.906424}
}

@article{Zhang2012,
  author    = {Hui Zhang and Torben Schneider and Claudia A. Wheeler-Kingshott and Daniel C. Alexander},
  journal   = {NeuroImage},
  number    = {4},
  title     = {NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain},
  volume    = {61},
  pages     = {1000-1016},
  year      = {2012},
  doi       = {10.1016/j.neuroimage.2012.03.072},
  url       = {https://doi.org/10.1016/j.neuroimage.2012.03.072}
}

@article{Zou2005,
  author    = {Hui Zou and Trevor Hastie},
  title     = {{Regularization and Variable Selection Via the Elastic Net}},
  journal   = {Journal of the Royal Statistical Society Series B: Statistical Methodology},
  volume    = {67},
  number    = {2},
  pages     = {301-320},
  year      = {2005},
  month     = {March},
  doi       = {10.1111/j.1467-9868.2005.00503.x},
  url       = {https://doi.org/10.1111/j.1467-9868.2005.00503.x}
}

%% book
@book{Hastie2009,
  author    = {Trevor Hastie and Robert Tibshirani and Jerome Friedman},
  title     = {{The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition}},
  edition   = {2},
  publisher = {Springer},
  year      = {2009},
  pages     = {745},
  doi       = {https://doi.org/10.1007/978-0-387-84858-7},
}

%% incollection
@incollection{Topgaard2016,
  author    = {Daniel Topgaard},
  title     = {{NMR Methods for Studying Microscopic Diffusion Anisotropy}},
  booktitle = {Diffusion NMR of Confined Systems: Fluid Transport in Porous Solids and Heterogeneous Materials},
  publisher = {The Royal Society of Chemistry},
  year      = {2016},
  month     = {December},
  doi       = {10.1039/9781782623779-00226},
  url       = {https://doi.org/10.1039/9781782623779-00226},
  isbn      = {978-1-78262-190-4}
}

%% inproceedings
@inproceedings{Aganj2009,
  author    = {Iman Aganj and Christophe Lenglet and Guillermo Sapiro},
  title     = {{ODF reconstruction in q-ball imaging with solid angle consideration}},
  booktitle = {2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro},
  year      = {2009},
  volume    = {},
  number    = {},
  pages     = {1398-1401},
  doi       = {10.1109/ISBI.2009.5193327}
}

@inproceedings{ArceSantana2014,
  author    = {Edgar Arce-Santana and Daniel U. Campos-Delgado and Flavio Vigueras-G{\'o}mez and Isnardo Reducindo and Aldo R. Mej{\'i}a-Rodr{\'i}guez},
  title     = {{Non-rigid Multimodal Image Registration Based on the Expectation-Maximization Algorithm}},
  booktitle = {Image and Video Technology},
  editor    = {Reinhard Klette and Mariano Rivera and Shin'ichi Satoh},
  publisher = {Springer Berlin Heidelberg},
  address   = {Berlin, Heidelberg},
  pages     = {36--47},
  year      = {2014},
  isbn      = {978-3-642-53842-1}
}

@inproceedings{Bruhn2005,
  author    = {Andr\'{e}s Bruhn and Joachim Weickert},
  title     = {{Towards ultimate motion estimation: combining highest accuracy with real-time performance}},
  booktitle = {Tenth IEEE International Conference on Computer Vision (ICCV'05) Volume 1},
  volume    = {1},
  number    = {},
  pages     = {749-755},
  year      = {2005},
  doi       = {10.1109/ICCV.2005.240}
}

@inproceedings{Chandio2020b,
  author    = {Bramsh Qamar Chandio and Eleftherios Garyfallidis},
  title     = {{StND: Streamline-based Non-rigid partial-Deformation Tractography Registration}},
  booktitle = {Medical Imaging Meets NeurIPS Workshop},
  address   = {Online},
  year      = {2020},
  month     = {December}
}

@inproceedings{Cheng2011,
  author    = {Jian Cheng and Tianzi Jiang and Rachid Deriche},
  title     = {{Theoretical Analysis and Practical Insights on EAP Estimation via a Unified HARDI Framework}},
  booktitle = {MICCAI Workshop on Computational Diffusion MRI (CDMRI)},
  address   = {Toronto, Canada},
  year      = {2011},
  month     = {September}
}

@inproceedings{Correia2011a,
  author       = {Marta Morgado Correia and Guy B. Williams and Frank Yeh and Ian Nimmo-Smith and Eleftherios Garyfallidis},
  title        = {{Robustness of Diffusion Scalar Metrics When Estimated with Generalized Q-Sampling Imaging Acquisition Schemes}},
  booktitle    = {ISMRM 19th Annual Meeting \& Exhibition SMRT 20th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Montr\'{e}al, Canada},
  volume       = {},
  pages        = {},
  year         = {2011},
  month        = {May}
}

@inproceedings{DellAcqua2014,
  author       = {Flavio Dell'Acqua and Luis Lacerda and Marco Catani and Andrew Simmons},
  title        = {{Anisotropic Power Maps: A diffusion contrast to reveal low anisotropy tissues from HARDI data}},
  booktitle    = {Joint Annual Meeting ISMRM-ESMRMB 2014 SMRT 23rd Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Milan, Italy},
  volume       = {},
  pages        = {},
  year         = {2014}
}

@inproceedings{Descoteaux2008a,
  author    = {Maxime Descoteaux and Nicolas Wiest-Daessl\'{e} and Sylvain Prima and Christian Barillot and Rachid Deriche},
  title     = {{Impact of Rician adapted Non-Local Means filtering on HARDI}},
  booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
  editor    = {Dimitris Metaxas and Leon Axel and Gabor Fichtinger and G{\'a}bor Sz{\'e}kely},
  publisher = {Springer Berlin Heidelberg},
  address   = {Berlin, Heidelberg},
  volume    = {11},
  number    = {Pt 2},
  pages     = {122--130},
  year      = {2008},
  doi       = {10.1007/978-3-540-85990-1_15},
  isbn      = {978-3-540-85990-1}
}

@inproceedings{Fadnavis2024,
  author    = {Shreyas Fadnavis and Agniva Chowdhury and Joshua Batson and Petros Drineas and Eleftherios Garyfallidis},
  title     = {{Patch2Self2: Self-supervised Denoising on Coresets via Matrix Sketching}},
  booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  editor    = {},
  publisher = {},
  volume    = {},
  pages     = {27641--27651},
  year      = {2024},
  url       = {https://openaccess.thecvf.com/content/CVPR2024/papers/Fadnavis_Patch2Self2_Self-supervised_Denoising_on_Coresets_via_Matrix_Sketching_CVPR_2024_paper.pdf},
}

@inproceedings{Fadnavis2020,
  author    = {Shreyas Fadnavis and Joshua Batson and Eleftherios Garyfallidis},
  title     = {{Patch2Self: Denoising Diffusion MRI with Self-Supervised Learning}},
  booktitle = {Advances in Neural Information Processing Systems},
  editor    = {Hugo Larochelle and Marc'Aurelio Ranzato and Raia Hadsell and Maria-Florina Balcan and Hsuan-Tien Lin},
  publisher = {Curran Associates, Inc.},
  volume    = {33},
  pages     = {16293--16303},
  year      = {2020},
  url       = {https://proceedings.neurips.cc/paper_files/paper/2020/file/bc047286b224b7bfa73d4cb02de1238d-Paper.pdf},
}

@inproceedings{Fadnavis2019,
  author       = {Shreyas Fadnavis and Marco Reisert and Hamza Farooq and Maryam Afzali and Cheng Hu and Bago Amirbekian and Eleftherios Garyfallidis},
  title        = {{MicroLearn: Framework for machine learning, reconstruction, optimization and microstructure modeling}},
  booktitle    = {ISMRM 27th Annual Meeting \& Exhibition SMRT 28th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Montr\'{e}al, Canada},
  pages        = {},
  year         = {2019}
}

@inproceedings{Fick2016a,
  author    = {Rutger H. J. Fick and MArco Pizzolato and Demian Wassermann and Mauro Zucchelli and Gloria Menegaz and Rachid Deriche},
  title     = {{A sensitivity analysis of q-space indices with respect to changes in axonal diameter, dispersion and tissue composition}},
  booktitle = {IEEE 13th International Symposium on Biomedical Imaging (ISBI)},
  volume    = {},
  number    = {},
  pages     = {1241-1244},
  year      = {2016},
  month     = {April},
  doi       = {10.1109/ISBI.2016.7493491}
}

@inproceedings{Fick2015,
  author    = {Rutger Fick and Demian Wassermann and Marco Pizzolato and Rachid Deriche},
  title     = {{A Unifying Framework for Spatial and Temporal Diffusion in Diffusion MRI}},
  booktitle = {Information Processing in Medical Imaging},
  editor    = {Sebastien Ourselin and Daniel C. Alexander and Carl-Fredrik Westin and M. Jorge Cardoso},
  publisher = {Springer International Publishing},
  address   = {Cham},
  pages     = {167--178},
  year      = {2015},
  isbn      = {978-3-319-19992-4}
}

@inproceedings{Fieremans2012,
  author       = {Els Fieremans and Jens H. Jensen and Joseph A. Helpern and Sungheon Kim and Robert I. Grossman and Matilde Inglese and Dmitry S. Novikov},
  title        = {{Diffusion distinguishes between axonal loss and demyelination in brain white matter}},
  booktitle    = {ISMRM 20th Annual Meeting \& Exhibition SMRT 21st Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Melbourne, Australia},
  pages        = {},
  year         = {2012}
}

@inproceedings{Garyfallidis2019,
  author       = {Eleftherios Garyfallidis and Marc-Alexandre C\^{o}t\'{e} and Bramsh Qamar Chandio and Shreyas Fadnavis and Javier Guaje and Ranveer Aggarwal and Etienne St-Onge and Karandeep Singh Juneja and Serge Koudoro and David Reagan},
  title        = {{DIPY Horizon: fast, modular, unified and adaptive visualization}},
  booktitle    = {ISMRM 27th Annual Meeting \& Exhibition SMRT 28th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Montr\'{e}al, Canada},
  volume       = {},
  pages        = {},
  year         = {2019}
}

@inproceedings{Garyfallidis2016,
  author       = {Eleftherios Garyfallidis and Marc-Alexandre C\^{o}t\'{e} and Fran\c{c}ois Rheault and Maxime Descoteaux},
  title        = {{QuickBundlesX: Sequential clustering of millions of streamlines in multiple levels of detail at record execution time}},
  booktitle    = {ISMRM 24th Annual Meeting \& Exhibition SMRT 25th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Singapore},
  volume       = {},
  pages        = {},
  year         = {2016}
}

@inproceedings{Garyfallidis2014b,
  author       = {Eleftherios Garyfallidis and Demian Wassermann and Maxime Descoteaux},
  title        = {{Direct native-space fiber bundle alignment for group comparisons}},
  booktitle    = {Joint Annual Meeting ISMRM-ESMRMB 2014 SMRT 23rd Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Milan, Italy},
  pages        = {},
  year         = {2014},
  month        = {May}
}

@inproceedings{Garyfallidis2011,
  author       = {Eleftherios Garyfallidis and Matthew Brett and Bagrat Amirbekian and Chistopher Nguyen and Fang-Cheng Yeh and Emanuele Olivetti and Yaroslav Halchenko and Ian Nimmo-Smith},
  title        = {{Dipy - a novel software library for diffusion MR and tractography}},
  booktitle    = {17th annual meeting of the Organization for Human Brain Mapping},
  organization = {Organization for Human Brain Mapping (OHBM)},
  address      = {Quebec City, Canada},
  volume       = {},
  pages        = {},
  year         = {2011},
  month        = {June}
}

@inproceedings{Garyfallidis2010b,
  author       = {Eleftherios Garyfallidis and Matthew Brett and Ian Nimmo-Smith},
  title        = {{Fast Dimensionality Reduction for Brain Tractography Clustering}},
  booktitle    = {16th Annual Meeting of the Organization for Human Brain Mapping},
  organization = {Organization for Human Brain Mapping (OHBM)},
  address      = {Barcelona, Spain},
  volume       = {},
  pages        = {},
  year         = {2010},
  month        = {June}
}

@inproceedings{Garyfallidis2010a,
  author       = {Eleftherios Garyfallidis and Matthew Brett and Vassilis Tsiaras and George Vogiatzis and Ian Nimmo-Smith1},
  title        = {{Identification of corresponding tracks in diffusion MRI tractographies}},
  booktitle    = {Joint Annual Meeting ISMRM-ESMRMB 2010 SMRT 19th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Stockholm, Sweden},
  volume       = {},
  pages        = {},
  year         = {2010},
  month        = {May}
}

@inproceedings{Houde2015,
  author       = {Jean-Christophe Houde and Marc-Alexandre Ct-Harnois and Maxime Descoteaux},
  title        = {{How to Avoid Biased Streamlines-Based Metrics for Streamlines with Variable Step Sizes}},
  booktitle    = {ISMRM 23rd Annual Meeting \& Exhibition SMRT 24th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Toronto, Canada},
  volume       = {},
  pages        = {},
  year         = {2015}
}

@inproceedings{Lee2008,
  author    = {Agatha D. Lee and Natasha Lepore and Marina Barysheva and Yi-Yu Chou and Caroline Brun and Sarah K. Madsen and Katie L. McMahon and Greig I. {de Zubicaray} and Matthew Meredith and Margaret J. Wright and Arthur W. Toga and Paul M. Thompson},
  title     = {{Comparison of fractional and geodesic anisotropy in diffusion tensor images of 90 monozygotic and dizygotic twins}},
  booktitle = {2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro},
  volume    = {},
  pages     = {943-946},
  year      = {2008},
  month     = {May},
  doi       = {10.1109/ISBI.2008.4541153}
}

@inproceedings{Meesters2016b,
  author       = {Stephan Meesters and Gonzalo Sanguinetti and Eleftherios Garyfallidis and Jorg Portegies and Pauly Ossenblok and Remco Duits1},
  title        = {{Cleaning output of tractography via fiber to bundle coherence, a new open source implementation}},
  booktitle    = {The Organization for Human Brain Mapping Annual Meeting},
  organization = {Organization for Human Brain Mapping (OHBM)},
  address      = {Geneva, Switzerland},
  volume       = {},
  pages        = {},
  year         = {2016},
  month        = {June}
}

@inproceedings{Meesters2016a,
  author       = {Stephan Meesters and Gonzalo Sanguinetti and Eleftherios Garyfallidis and Jorg Portegies and Remco Duits1},
  title        = {{Fast implementations of contextual PDE's for HARDI data processing in DIPY}},
  booktitle    = {ISMRM 24th Annual Meeting \& Exhibition SMRT 25th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Singapore},
  volume       = {},
  pages        = {},
  year         = {2016},
  month        = {May}
}

@inproceedings{Nath2018
  author       = {Vishwesh Nath and Kurt G. Schilling and Prasanna Parvathaneni and Allison E. Hainline and Colin B. Hansen and Camilo Bermudez and Andrew J. Plassard and Justin A. Blaber and Vaibhav Janve and Yurui Gao and Iwona Stepniewska and Adam W. Anderson and Bennett A. Landman},
  title        = {{Deep Learning Captures More Accurate Diffusion Fiber Orientations Distributions than Constrained Spherical Deconvolution}},
  booktitle    = {Joint Annual Meeting ISMRM-ESMRMB 2018 SMRT 27th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Paris, France},
  pages        = {},
  year         = {2018}
}

@inproceedings{Niethammer2006,
  author    = {Marc Niethammer and Ra\'{u}l San Jos\'{e} Estepar and Sylvain Bouix and Martha Shenton and Carl-Fredrik Westin},
  title     = {{On Diffusion Tensor Estimation}},
  booktitle = {International Conference of the IEEE Engineering in Medicine and Biology Society},
  volume    = {},
  number    = {},
  pages     = {2622-2625},
  year      = {2006},
  doi       = {10.1109/IEMBS.2006.259826}
}

@inproceedings{Ozarslan2009,
  author       = {Evren {\"O}zarslan and Cheng Guan Koay and Timothy M. Shepherd and Stephen J. Blackband and Peter J. Basser},
  title        = {{Simple harmonic oscillator based reconstruction and estimation for three-dimensional q-space MRI}},
  booktitle    = {ISMRM 17th Scientific Meeting \& Exhibition SMRT 18th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Honolulu, HI, USA},
  volume       = {},
  pages        = {},
  year         = {2009}
}

@inproceedings{Ozarslan2008,
  author       = {Evren {\"O}zarslan and Cheng Guan Koay and Peter J. Basser},
  title        = {{Simple harmonic oscillator based reconstruction and estimation for one-dimensional q-space magnetic resonance (1D-SHORE)}},
  booktitle    = {ISMRM 16th Scientific Meeting \& Exhibition SMRT 17th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Toronto, Canada},
  volume       = {16},
  pages        = {35},
  year         = {2008}
}

@inproceedings{Portegies2015a,
  author    = {Jorg Portegies and Gonzalo Sanguinetti and Stephan Meesters and Remco Duits},
  title     = {{New Approximation of a Scale Space Kernel on SE(3) and Applications in Neuroimaging}},
  booktitle = {5th International Conference on Scale Space and Variational Methods in Computer Vision},
  editor    = {Jean-Fran{\c{c}}ois Aujol and Mila Nikolova and Nicolas Papadakis},
  publisher = {Springer International Publishing},
  address   = {Cham},
  pages     = {40--52},
  year      = {2015},
  isbn      = {978-3-319-18461-6}
}

@inproceedings{Rathi2011,
  author    = {Yogesh Rathi and Oleg Michailovich and Kawin Setsompop and Sylvain Bouix and Martha E. Shenton and Carl-Fredrik Westin},
  title     = {{Sparse Multi-Shell Diffusion Imaging}},
  booktitle = {Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2011},
  editor    = {Gabor Fichtinger and Anne Martel and Terry Peters},
  publisher = {Springer Berlin Heidelberg},
  address   = {Berlin, Heidelberg},
  pages     = {58--65},
  year      = {2011},
  isbn      = {978-3-642-23629-7}
}

@inproceedings{Rheault2015,
  author       = {Fran\c{c}ois Rheault and Jean-Christophe Houde and Maxime Descoteaux},
  title        = {{Real Time Interaction with Millions of Streamlines}},
  booktitle    = {ISMRM 23rd Annual Meeting \& Exhibition SMRT 24th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Toronto, Canada},
  volume       = {},
  pages        = {},
  year         = {2015}
}

@inproceedings{Rodrigues2010,
  author       = {Paulo Rodrigues and Remco Duits and Bart M. ter Haar Romeny and Anna Vilanova},
  title        = {{Accelerated Diffusion Operators for Enhancing DW-MRI}},
  booktitle    = {Eurographics Workshop on Visual Computing for Biology and Medicine},
  editor       = {Dirk Bartz and Charl Botha and Joachim Hornegger and Raghu Machiraju and Alexander Wiebel and Bernhard Preim},
  publisher    = {The Eurographics Association},
  year         = {2010},
  isbn         = {978-3-905674-28-6},
  doi          = {https://doi.org/10.2312/VCBM/VCBM10/049-056}
}

@inproceedings{Rokem2014,
  author       = {Ariel Rokem and Kimberly L. Chan and Jason D. Yeatman and Franco Pestilli and  Brian A. Wandel},
  title        = {{Evaluating the accuracy of diffusion models at multiple b-values with cross-validation}},
  booktitle    = {Joint Annual Meeting ISMRM-ESMRMB 2014 SMRT 23rd Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Milan, Italy},
  volume       = {},
  pages        = {},
  year         = {2014}
}

@inproceedings{TristanVega2009b,
  author       = {Antonio Trist{\'a}n-Vega and Santiago Aja-Fern{\'a}ndez and Carl-Fredrik Westin},
  title        = {{On the Blurring of the Funk-Radon Transform in Q-Ball Imaging}},
  booktitle    = {Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2009},
  editor       = {Guang-Zhong Yang and David Hawkes and Daniel Rueckert and Alison Noble and Chris Taylor},
  publisher    = {Springer Berlin Heidelberg},
  address      = {Berlin, Heidelberg},
  pages        = {415-422},
  year         = {2009},
  month        = {September},
  isbn         = {978-3-642-04271-3}
}

@inproceedings{RomeroBascones2022,
  author       = {David Romero-Bascones and Bramsh Qamar Chandio and Shreyas Fadnavis and Jong Sung Park and Serge Koudoro and Unai Ayala and Maitane Barrenechea and Eleftherios Garyfallidis},
  title        = {{BundleAtlasing: unbiased population-specific atlasing of bundles in streamline space}},
  booktitle    = {Joint Annual Meeting ISMRM-ESMRMB \& ISMRT 31st Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {London, UK},
  volume       = {},
  pages        = {},
  year         = {2022}
}

@inproceedings{Wanyan2017,
  author       = {Tingyi Wanyan and Eleftherios Garyfallidis},
  title        = {{Important new insights for the reduction of false positives in tractograms emerge from streamline-based registration and pruning}},
  booktitle    = {ISMRM 25th Annual Meeting \& Exhibition SMRT 26th Annual Meeting},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Honolulu, HI, USA},
  volume       = {},
  pages        = {},
  year         = {2017}
}

@inproceedings{Westin1997,
  author       = {Carl-Fredrik Westin and Sharon Peled and H\'{a}kon Gudbjartsson and Ron Kikinis and Ferenc Jolesz},
  title        = {{Geometrical diffusion measures for MRI from tensor basis analysis}},
  booktitle    = {5th Scientific Meeting and Exhibition},
  organization = {International Society for Magnetic Resonance in Medicine (ISMRM)},
  address      = {Vancouver, Canada},
  volume       = {},
  pages        = {},
  year         = {1997}
}

@inproceedings{Zucchelli2017,
  author    = {Mauro Zucchelli and Maxime Descoteaux and Gloria Menegaz},
  title     = {{A generalized SMT-based framework for Diffusion MRI microstructural model estimation}},
  booktitle = {Computational Diffusion MRI},
  editor    = {Enrico Kaden and Francesco Grussu and Lipeng Ning and Chantal M. W. Tax and Jelle Veraart},
  year      = {2018},
  publisher = {Springer International Publishing},
  address   = {Cham},
  pages     = {51--63}
}

%% mastersthesis
@mastersthesis{NetoHenriques2012,
  author    = {Rafael {Neto Henriques}},
  title     = {{Diffusion kurtosis imaging of the healthy human brain}},
  type      = {MSc thesis},
  school    = {Universidade de Lisboa},
  address   = {Lisboa, Portugal},
  year      = {2012},
  doi       = {},
  url       = {https://repositorio.ul.pt/bitstream/10451/8511/1/ulfc104137_tm_Rafael_Henriques.pdf}
}

%% misc
@misc{Chandio2023,
  author       = {Bramsh Qamar Chandio and Emanuele Olivetti and David Romero-Bascones and Jaroslaw Harezlak and Eleftherios Garyfallidis},
  title        = {{BundleWarp, streamline-based nonlinear registration of white matter tracts}},
  howpublished = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  year         = {2023},
  doi          = {https://doi.org/10.1101/2023.01.04.522802}
}

@misc{NetoHenriques2017,
  author       = {Rafael {Neto Henriques} and Ariel Rokem and Eleftherios Garyfallidis and Samuel St-Jean and Eric Thomas Peterson and Marta Morgado Correia},
  title        = {{[Re] Optimization of a free water elimination two-compartment model for diffusion tensor imaging}},
  howpublished = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  year         = {2017},
  doi          = {https://doi.org/10.1101/108795}
}

@misc{Valabregue2015,
  author       = {Romain Valabr\`{e}gue},
  title        = {{Diffusion MRI measured at multiple b-values}},
  howpublished = {University Libraries, eScience Institute Faculty Research},
  publisher    = {University of Washington},
  year         = {2015},
  doi          = {http://hdl.handle.net/1773/33311}
}

@misc{Wassermann2017,
  author       = {Demian Wassermann and Mathieu Santin and Anne-Charlotte Philippe and Rutger Fick and Rachid Deriche and Stephane Lehericy and Alexandra Petiet},
  title        = {{Test-Retest qt-dMRI datasets for Non-Parametric GraphNet-Regularized Representation of dMRI in Space and Time}},
  howpublished = {Zenodo},
  year         = {2017},
  month        = {September},
  doi          = {10.5281/zenodo.996889},
  url          = {https://zenodo.org/records/996889},
  note         = {Dataset}
}

%% phdthesis
@phdthesis{Amirbekian2016,
  author    = {Bagrat Amirbekian},
  title     = {{The Modeling of White Matter Architecture and Networks Using Diffusion MRI: Methods, Tools and Applications}},
  type      = {PhD thesis},
  school    = {University of California San Francisco},
  address   = {San Francisco, CA, USA},
  year      = {2016},
  doi       = {},
  url       = {}
}

@phdthesis{Cheng2012,
  author    = {Jian Cheng},
  title     = {{Estimation and Processing of Ensemble Average Propagator and Its Features in Diffusion MRI}},
  type      = {PhD thesis},
  school    = {Universit{\'e} Nice Sophia Antipolis},
  address   = {Valbonne, France},
  year      = {2012},
  doi       = {},
  url       = {}
}

@phdthesis{Descoteaux2008b,
  author    = {Maxime Descoteaux},
  title     = {{High Angular Resolution Diffusion MRI: from Local Estimation to Segmentation and Tractography}},
  type      = {PhD thesis},
  school    = {Universit{\'e} Nice Sophia Antipolis},
  address   = {Valbonne, France},
  year      = {2007},
  doi       = {},
  url       = {https://theses.hal.science/tel-00457458}
}

@phdthesis{Garyfallidis2012b,
  author    = {Eleftherios Garyfallidis},
  title     = {{Towards an accurate brain tractography}},
  type      = {PhD thesis},
  school    = {Cambridge University},
  address   = {Cambridge, United Kingdom},
  year      = {2012},
  doi       = {},
  url       = {}
}

@phdthesis{NetoHenriques2018,
  author    = {Rafael {Neto Henriques}},
  title     = {{Advanced Methods for Diffusion MRI Data Analysis and their Application to the Healthy Ageing Brain}},
  type      = {PhD thesis},
  school    = {Cambridge University},
  address   = {Cambridge, United Kingdom},
  year      = {2018},
  doi       = {10.17863/CAM.29356},
  url       = {https://doi.org/10.17863/CAM.29356}
}

@phdthesis{Tuch2002,
  author    = {David S. Tuch},
  title     = {{Diffusion MRI of Complex Tissue Structure}},
  type      = {PhD thesis},
  school    = {Massachusetts Institute of Technology},
  address   = {Cambridge, USA},
  year      = {2002},
  doi       = {},
  url       = {http://hdl.handle.net/1721.1/8348}
}
