# General bibliography

[ALS09]

Iman Aganj, Christophe Lenglet, and Guillermo Sapiro. ODF reconstruction in q-ball imaging with solid angle consideration. In 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, volume, 1398–1401. 2009. doi:10.1109/ISBI.2009.5193327.

[ALS+10]

Iman Aganj, Christophe Lenglet, Guillermo Sapiro, Essa Yacoub, Kamil Ugurbil, and Noam Harel. Reconstruction of the orientation distribution function in single- and multiple-shell q-ball imaging within constant solid angle. Magnetic Resonance in Medicine, 64(2):554–566, 2010. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.22365, doi:https://doi.org/10.1002/mrm.22365.

[AEA+17]

Lindsay M. Alexander, Jasmine Escalera, Lei Ai, Charissa Andreotti, Karina Febre, Alexander Mangone, Natan Vega-Potler, Nicolas Langer, Alexis Alexander, Meagan Kovacs, Shannon Litke, Bridget O'Hagan, Jennifer Andersen, Batya Bronstein, Anastasia Bui, Marijayne Bushey, Henry Butler, Victoria Castagna, Nicolas Camacho, Elisha Chan, Danielle Citera, Jon Clucas, Samantha Cohen, Sarah Dufek, Megan Eaves, Brian Fradera, Judith Gardner, Natalie Grant-Villegas, Gabriella Green, Camille Gregory, Emily Hart, Shana Harris, Megan Horton, Danielle Kahn, Katherine Kabotyanski, Bernard Karmel, Simon P. Kelly, Kayla Kleinman, Bonhwang Koo, Eliza Kramer, Elizabeth Lennon, Catherine Lord, Ginny Mantello, Amy Margolis, Kathleen R. Merikangas, Judith Milham, Giuseppe Minniti, Rebecca Neuhaus, Alexandra Levine, Yael Osman, Lucas C. Parra, Ken R. Pugh, Amy Racanello, Anita Restrepo, Tian Saltzman, Batya Septimus, Russell Tobe, Rachel Waltz, Anna Williams, Anna Yeo, Francisco X. Castellanos, Arno Klein, Tomas Paus, Bennett L. Leventhal, R. Cameron Craddock, Harold S. Koplewicz, and Michael P. Milham. An open resource for transdiagnostic research in pediatric mental health and learning disorders. Scientific Data, 4(1):170181, December 2017. URL: https://doi.org/10.1038/sdata.2017.181, doi:10.1038/sdata.2017.181.

[AHK+22]

Rita Alves, Rafael Neto Henriques, Leevi Kerkelä, Cristina Chavarrías, Sune N. Jespersen, and Noam Shemesh. Correlation Tensor MRI deciphers underlying kurtosis sources in stroke. NeuroImage, 247:118833, 2022. URL: https://doi.org/10.1016/j.neuroimage.2021.118833, doi:10.1016/j.neuroimage.2021.118833.

[Ami16]

Bagrat Amirbekian. The Modeling of White Matter Architecture and Networks Using Diffusion MRI: Methods, Tools and Applications. PhD thesis, University of California San Francisco, San Francisco, CA, USA, 2016. URL:, doi:.

[And05]

Adam W. Anderson. Measurement of fiber orientation distributions using high angular resolution diffusion imaging. Magnetic Resonance in Medicine, 54(5):1194–1206, 2005. URL: https://doi.org/10.1002/mrm.20667, doi:10.1002/mrm.20667.

[ASCDVGomez+14]

Edgar Arce-Santana, Daniel U. Campos-Delgado, Flavio Vigueras-Gómez, Isnardo Reducindo, and Aldo R. Mejía-Rodríguez. Non-rigid Multimodal Image Registration Based on the Expectation-Maximization Algorithm. In Reinhard Klette, Mariano Rivera, and Shin'ichi Satoh, editors, Image and Video Technology, 36–47. Berlin, Heidelberg, 2014. Springer Berlin Heidelberg.

[AFPA06]

Vincent Arsigny, Pierre Fillard, Xavier Pennec, and Nicholas Ayache. Log-Euclidean metrics for fast and simple calculus on diffusion tensors. Magnetic Resonance in Medicine, 56(2):411–421, 2006. URL: https://doi.org/10.1002/mrm.20965, doi:10.1002/mrm.20965.

[AFRB04]

Yaniv Assaf, Raisa Z. Freidlin, Gustavo K. Rohde, and Peter J. Basser. New modeling and experimental framework to characterize hindered and restricted water diffusion in brain white matter. Magnetic Resonance in Medicine, 52(5):965–978, 2004. URL: https://doi.org/10.1002/mrm.20274, doi:10.1002/mrm.20274.

[AEGG08]

Brian B. Avants, Charles L. Epstein, Murray Grossman, and James C. Gee. Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain. Medical Image Analysis, 12(1):26–41, 2008. Special Issue on The Third International Workshop on Biomedical Image Registration – WBIR 2006. URL: https://doi.org/10.1016/j.media.2007.06.004, doi:10.1016/j.media.2007.06.004.

[ATW+11]

Brian B. Avants, Nicholas J. Tustison, Jue Wu, Philip A. Cook, and James C. Gee. An Open Source Multivariate Framework for n-Tissue Segmentation with Evaluation on Public Data. Neuroinformatics, 9(4):381–400, 2011. URL: https://doi.org/10.1007/s12021-011-9109-y, doi:10.1007/s12021-011-9109-y.

[ATS09]

Brian B. Avants, Nick Tustison, and Gang Song. Advanced Normalization Tools: V1. 0. The Insight Journal, 2(365):1–35, July 2009.

[ASB+15]

Alexandru V. Avram, Joelle E Sarlls, Alan S Barnett, Evren Özarslan, Cibu Thomas, M. Okan Irfanoglu, Elizabeth Hutchinson, Carlo Pierpaoli, and Peter J. Basser. Clinical feasibility of using mean apparent propagator (MAP) MRI to characterize brain tissue microstructure. NeuroImage, 111:159–169, 2015. URL: https://doi.org/10.1016/j.neuroimage.2015.01.007, doi:10.1016/j.neuroimage.2015.01.007.

[AS47]

Dogu Baran Aydogan and Yonggang Shi. Ieee transactions on medical imaging. Parallel Transport Tractography, 2021(40):2, 635-647. doi:10.1109/TMI.2020.3034038.

[BMLeBihan94a]

Peter J. Basser, James Mattiello, and Denis Le Bihan. Estimation of the Effective Self-Diffusion Tensor from the NMR Spin Echo. Journal of Magnetic Resonance, Series B, 103(3):247–254, March 1994. URL: https://doi.org/10.1006/jmrb.1994.1037, doi:10.1006/jmrb.1994.1037.

[BMLeBihan94b]

Peter J. Basser, James Mattiello, and Denis Le Bihan. MR Diffusion Tensor Spectroscopy and Imaging. Biophysical Journal, 66(1):259–267, January 1994. doi:http://dx.doi.org/10.1016/S0006-3495(94)80775-1.

[BP96]

Peter J. Basser and Carlo Pierpaoli. Microstructural and Physiological Features of Tissues Elucidated by Quantitative-Diffusion-Tensor MRI. Journal of Magnetic Resonance, Series B, 111(3):209–219, 1996. URL: https://doi.org/10.1006/jmrb.1996.0086, doi:10.1006/jmrb.1996.0086.

[BMA+05]

Phillipp G. Batchelor, Maher Moakher, David Atkinson, Fernando Calamante, and Alan Connelly. A rigorous framework for diffusion tensor calculus. Magnetic Resonance in Medicine, 53(1):221–225, 2005. URL: https://doi.org/10.1002/mrm.20334, doi:10.1002/mrm.20334.

[BJBJ+07]

Timothy E. J. Behrens, Heidi Johansen-Berg, Saad Jbabdi, Matthew F.S. Rushworth, and Mark W. Woolrich. Probabilistic diffusion tractography with multiple fibre orientations: What can we gain? NeuroImage, 34(1):144–155, 2007. URL: https://doi.org/10.1016/j.neuroimage.2006.09.018, doi:10.1016/j.neuroimage.2006.09.018.

[BWMJ+03]

Timothy E. J. Behrens, Mark W. Woolrich, M. Mark Jenkinson, Heidi Johansen-Berg, Rita Gouveia Nunes, Stuart Clare, Paul M. Matthews, John Michael Brady, and Stephen M. Smith. Characterization and propagation of uncertainty in diffusion-weighted MR imaging. Magnetic Resonance in Medicine, 50(5):1077–1088, 2003. URL: https://doi.org/10.1002/mrm.10609, doi:10.1002/mrm.10609.

[BCM+08]

Jeffrey I. Berman, SungWon Chung, Pratik Mukherjee, Christopher P. Hess, Eric T. Han, and Roland G. Henry. Probabilistic streamline q-ball tractography using the residual bootstrap. NeuroImage, 39(1):215–222, 2008. URL: https://doi.org/10.1016/j.neuroimage.2007.08.021, doi:10.1016/j.neuroimage.2007.08.021.

[BA97]

David S. C. Biggs and Mark Andrews. Acceleration of iterative image restoration algorithms. Applied Optics, 36(8):1766–1775, March 1997. URL: https://doi.org/10.1364/AO.36.001766, doi:10.1364/AO.36.001766.

[BGP+23]

Benjamin Billot, Douglas N. Greve, Oula Puonti, Axel Thielscher, Koen Van Leemput, Bruce Fischl, Adrian V. Dalca, and Juan Eugenio Iglesias. SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining. Medical Image Analysis, 86:102789, 2023. URL: https://doi.org/10.1016/j.media.2023.102789, doi:10.1016/j.media.2023.102789.

[Bre65]

Jack E. Bresenham. Algorithm for computer control of a digital plotter. IBM Systems Journal, 4(1):25–30, 1965. doi:10.1147/sj.41.0025.

[BW05]

Andrés Bruhn and Joachim Weickert. Towards ultimate motion estimation: combining highest accuracy with real-time performance. In Tenth IEEE International Conference on Computer Vision (ICCV'05) Volume 1, volume 1, 749–755. 2005. doi:10.1109/ICCV.2005.240.

[CoteGBore+13]

Marc-Alexandre Côté, Gabriel Girard, Arnaud Boré, Eleftherios Garyfallidis, Jean-Christophe Houde, and Maxime Descoteaux. Tractometer: Towards validation of tractography pipelines. Medical Image Analysis, 17(7):844–857, October 2013. Special Issue on the 2012 Conference on Medical Image Computing and Computer Assisted Intervention. URL: 10.1016/j.media.2013.03.009, doi:https://doi.org/10.1016/j.media.2013.03.009.

[CRodriguezDS+15]

Erick J. Canales-Rodríguez, Alessandro Daducci, Stamatios N. Sotiropoulos, Emmanuel Caruyer, Santiago Aja-Fernández, Joaquim Radua, Jesús M. Yurramendi Mendizabal, Yasser Iturria-Medina, Lester Melie-García, Yasser Alemán-Gómez, Jean-Philippe Thiran, Salvador Sarró, Edith Pomarol-Clotet, and Raymond Salvador. Spherical Deconvolution of Multichannel Diffusion MRI Data with Non-Gaussian Noise Models and Spatial Regularization. PLOS ONE, 10(10):e0138910, 2015. URL: https://doi.org/10.1371/journal.pone.0138910, doi:10.1371/journal.pone.0138910.

[CRodriguezIMAlemanGomezMGarcia10]

Erick J. Canales-Rodríguez, Yasser Iturria-Medina, Yasser Alemán-Gómez, and Lester Melie-García. Deconvolution in diffusion spectrum imaging. NeuroImage, 50(1):136–149, 2010. URL: https://doi.org/10.1016/j.neuroimage.2009.11.066, doi:10.1016/j.neuroimage.2009.11.066.

[Car95]

Billie C. Carlson. Numerical computation of real or complex elliptic integrals. Numerical Algorithms, 10(1):13–26, 1995. URL: https://doi.org/10.1007/BF02198293, doi:10.1007/BF02198293.

[CLSD13]

Emmanuel Caruyer, Christophe Lenglet, Guillermo Sapiro, and Rachid Deriche. Design of multishell sampling schemes with uniform coverage in diffusion MRI. Magnetic Resonance in Medicine, 69(6):1534–1540, 2013. URL: https://doi.org/10.1002/mrm.24736, doi:10.1002/mrm.24736.

[CHM+10]

Samuel R. Chamberlain, Adam Hampshire, Lara A. Menzies, Eleftherios Garyfallidis, Jon E. Grant, Brian L. Odlaug, Kevin Craig, Naomi Fineberg, and Barbara J. Sahakian. Reduced Brain White Matter Integrity in Trichotillomania: A Diffusion Tensor Imaging Study. Archives of General Psychiatry, 67(9):965–971, September 2010. URL: https://doi.org/10.1001/archgenpsychiatry.2010.109, doi:10.1001/archgenpsychiatry.2010.109.

[Cha04]

Antonin Chambolle. An Algorithm for Total Variation Minimization and Applications. Journal of Mathematical Imaging and Vision, 20(1):89–97, 2004. URL: https://doi.org/10.1023/B:JMIV.0000011325.36760.1e, doi:10.1023/B:JMIV.0000011325.36760.1e.

[CG20]

Bramsh Qamar Chandio and Eleftherios Garyfallidis. StND: Streamline-based Non-rigid partial-Deformation Tractography Registration. In Medical Imaging Meets NeurIPS Workshop. Online, December 2020.

[CORB+23]

Bramsh Qamar Chandio, Emanuele Olivetti, David Romero-Bascones, Jaroslaw Harezlak, and Eleftherios Garyfallidis. BundleWarp, streamline-based nonlinear registration of white matter tracts. bioRxiv, 2023. doi:https://doi.org/10.1101/2023.01.04.522802.

[CRP+20]

Bramsh Qamar Chandio, Shannon Leigh Risacher, Franco Pestilli, Daniel Bullock, Fang-Cheng Yeh, Serge Koudoro, Ariel Rokem, Jaroslaw Harezlak, and Eleftherios Garyfallidis. Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. Scientific Reports, 10:17149, October 2020. URL: https://doi.org/10.1038/s41598-020-74054-4, doi:10.1038/s41598-020-74054-4.

[CVRN+24]

Bramsh Qamar Chandio, Julio E Villalon-Reina, Talia M Nir, Sophia I Thomopoulos, Yixue Feng, Sebastian Benavidez, Neda Jahanshad, Jaroslaw Harezlak, Eleftherios Garyfallidis, and Paul M Thompson. Bundle analytics based data harmonization for multi-site diffusion MRI tractometry. In 2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 1–7. IEEE, 2024. URL: https://doi.org/10.1109/EMBC53108.2024.10782419.

[CJP05]

Lin-Ching Chang, Derek K. Jones, and Carlo Pierpaoli. RESTORE: Robust estimation of tensors by outlier rejection. Magnetic Resonance in Medicine, 53(5):1088–1095, 2005. URL: https://doi.org/10.1002/mrm.20426, doi:10.1002/mrm.20426.

[CWP12]

Lin-Ching Chang, Lindsay Walker, and Carlo Pierpaoli. Informed RESTORE: A method for robust estimation of diffusion tensor from low redundancy datasets in the presence of physiological noise artifacts. Magnetic Resonance in Medicine, 68(5):1654–1663, 2012. URL: https://doi.org/10.1002/mrm.24173, doi:10.1002/mrm.24173.

[CNA+20]

Hu Cheng, Sharlene Newman, Maryam Afzali, Shreyas Fadnavis, and Eleftherios Garyfallidis. Segmentation of the brain using direction-averaged signal of DWI images. Magnetic Resonance Imaging, 69:1–7, June 2020. URL: https://doi.org/10.1016/j.mri.2020.02.010, doi:10.1016/j.mri.2020.02.010.

[CVBW+22]

Hu Cheng, Sophia Vinci-Booher, Jian Wang, Bradley Caron, Qiuting Wen, Sharlene Newman, and Franco Pestilli. Denoising diffusion weighted imaging data using convolutional neural networks. PLOS ONE, 17(9):1–24, September 2022. URL: https://doi.org/10.1371/journal.pone.0274396, doi:10.1371/journal.pone.0274396.

[Che12]

Jian Cheng. Estimation and Processing of Ensemble Average Propagator and Its Features in Diffusion MRI. PhD thesis, Université Nice Sophia Antipolis, Valbonne, France, 2012. URL:, doi:.

[CJD11]

Jian Cheng, Tianzi Jiang, and Rachid Deriche. Theoretical Analysis and Practical Insights on EAP Estimation via a Unified HARDI Framework. In MICCAI Workshop on Computational Diffusion MRI (CDMRI). Toronto, Canada, September 2011.

[CLH06]

SungWon Chung, Ying Lu, and Roland G. Henry. Comparison of bootstrap approaches for estimation of uncertainties of DTI parameters. NeuroImage, 33(2):531–541, 2006. URL: https://doi.org/10.1016/j.neuroimage.2006.07.001, doi:10.1016/j.neuroimage.2006.07.001.

[CADW11]

Julien Cohen-Adad, Maxime Descoteaux, and Lawrence L. Wald. Quality assessment of high angular resolution diffusion imaging data using bootstrap on Q-ball reconstruction. Journal of Magnetic Resonance Imaging, 33(5):1194–1208, 2011. URL: https://doi.org/10.1002/jmri.22535, doi:10.1002/jmri.22535.

[CVJ+15]

Quinten Collier, Jelle Veraart, Ben Jeurissen, Arno den Dekker, and Jan Sijbers. Iterative reweighted linear least squares for accurate, fast, and robust estimation of diffusion magnetic resonance parameters: IRLLS for Estimation of Diffusion MR Parameters. Magnetic Resonance in Medicine, 73(6):2174–2184, 2015. URL: https://doi.org/10.1002/mrm.25351, doi:10.1002/mrm.25351.

[CAM97]

Chris D. Constantinides, Ergin Atalar, and Elliot R. McVeigh. Signal-to-noise measurements in magnitude images from NMR phased arrays. Magnetic Resonance in Medicine, 38(5):852–857, 1997. URL: https://doi.org/10.1002/mrm.1910380524, doi:10.1002/mrm.1910380524.

[CSBA07]

Philip A. Cook, Mark Symms, Philip A. Boulby, and Daniel C. Alexander. Optimal acquisition orders of diffusion-weighted MRI measurements. Journal of Magnetic Resonance Imaging, 25(5):1051–1058, 2007. URL: https://doi.org/10.1002/jmri.20905, doi:10.1002/jmri.20905.

[CNW11]

Marta Morgado Correia, Virginia F. J. Newcombe, and Guy B. Williams. Contrast-to-noise ratios for indices of anisotropy obtained from diffusion MRI: A study with standard clinical b-values at 3T. NeuroImage, 57(3):1103–1115, August 2011. Special Issue: Educational Neuroscience. URL: https://doi.org/10.1016/j.neuroimage.2011.03.004, doi:10.1016/j.neuroimage.2011.03.004.

[CWY+11]

Marta Morgado Correia, Guy B. Williams, Frank Yeh, Ian Nimmo-Smith, and Eleftherios Garyfallidis. Robustness of Diffusion Scalar Metrics When Estimated with Generalized Q-Sampling Imaging Acquisition Schemes. In ISMRM 19th Annual Meeting & Exhibition SMRT 20th Annual Meeting, volume. Montréal, Canada, May 2011. International Society for Magnetic Resonance in Medicine (ISMRM).

[CoupeManjonRC12]

Pierrick Coupé, José V. Manjón, Montserrat Robles, and Louis D. Collins. Adaptive Multiresolution Non-Local Means Filter for 3D MR Image Denoising. IET Image Processing, 6(5):558–568, July 2012. URL: https://doi.org/10.1049/iet-ipr.2011.0161, doi:10.1049/iet-ipr.2011.0161.

[CoupeYP+08]

Pierrick Coupé, Pierre Yger, Sylvain Prima, Pierre Hellier, Charles Kervrann, and Christian Barillot. An Optimized Blockwise Nonlocal Means Denoising Filter for 3-D Magnetic Resonance Images. IEEE Transactions on Medical Imaging, 27(4):425–441, 2008. URL: https://doi.org/10.1109/TMI.2008.2008967, doi:10.1109/TMI.2007.906087.

[CAM+25]

Sam Coveney, Maryam Afzali, Lars Mueller, Irvin Teh, Arka Das, Erica Dall’Armellina, Filip Szczepankiewicz, Derek K. Jones, and Jurgen E. Schneider. Outlier detection in cardiac diffusion tensor imaging: Shot rejection or robust fitting? Medical Image Analysis, 101:103386, 2025. URL: https://doi.org/10.1016/j.media.2024.103386, doi:10.1016/j.media.2024.103386.

[CAM+26]

Sam Coveney, Maryam Afzali, Lars Mueller, Irvin Teh, Filip Szczepankiewicz, Derek K. Jones, and Jurgen E. Schneider. Robust constrained weighted least squares for in vivo human cardiac diffusion kurtosis imaging. Magnetic Resonance in Medicine, 95(1):220–233, 2026. URL: https://doi.org/10.1002/mrm.70037, doi:10.1002/mrm.70037.

[CW79]

Peter Craven and Grace Wahba. Smoothing Noisy Data with Spline Functions - Estimating the Correct Degree of Smoothing by the Method of Generalized Cross-Validation. Numerische Mathematik, 31(4):377–403, 1979. doi:.

[DellAcquaLCS14]

Flavio Dell'Acqua, Luis Lacerda, Marco Catani, and Andrew Simmons. Anisotropic Power Maps: A diffusion contrast to reveal low anisotropy tissues from HARDI data. In Joint Annual Meeting ISMRM-ESMRMB 2014 SMRT 23rd Annual Meeting, volume. Milan, Italy, 2014. International Society for Magnetic Resonance in Medicine (ISMRM).

[DellAcquaRS+07]

Flavio Dell'Acqua, Giovanna Rizzo, Paola Scifo, Rafael Alonso Clarke, Giuseppe Scotti, and Ferruccio Fazio. A Model-Based Deconvolution Approach to Solve Fiber Crossing in Diffusion-Weighted MR Imaging. IEEE Transactions on Biomedical Engineering, 54(3):462–472, 2007. doi:10.1109/TBME.2006.888830.

[Des07]

Maxime Descoteaux. High Angular Resolution Diffusion MRI: from Local Estimation to Segmentation and Tractography. PhD thesis, Université Nice Sophia Antipolis, Valbonne, France, 2007. URL: https://theses.hal.science/tel-00457458, doi:.

[DAFD07]

Maxime Descoteaux, Elaine Angelino, Shaun Fitzgibbons, and Rachid Deriche. Regularized, fast, and robust analytical Q-ball imaging. Magnetic Resonance in Medicine, 58(3):497–510, 2007. URL: https://doi.org/10.1002/mrm.21277, doi:10.1002/mrm.21277.

[DDKnoscheA09]

Maxime Descoteaux, Rachid Deriche, Thomas R. Knösche, and Alfred Anwander. Deterministic and Probabilistic Tractography Based on Complex Fibre Orientation Distributions. IEEE Transactions on Medical Imaging, 28(2):269–286, February 2009. URL: https://doi.org/10.1109/TMI.2008.2004424, doi:10.1109/TMI.2008.2004424.

[DDLeBihan+11]

Maxime Descoteaux, Rachid Deriche, Denis Le Bihan, Jean-François Mangin, and Cyril Poupon. Multiple q-shell diffusion propagator imaging. Medical Image Analysis, 15(4):603–621, 2011. Special section on IPMI 2009. URL: https://doi.org/10.1016/j.media.2010.07.001, doi:10.1016/j.media.2010.07.001.

[DWDaessleP+08]

Maxime Descoteaux, Nicolas Wiest-Daesslé, Sylvain Prima, Christian Barillot, and Rachid Deriche. Impact of Rician adapted Non-Local Means filtering on HARDI. In Dimitris Metaxas, Leon Axel, Gabor Fichtinger, and Gábor Székely, editors, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11, 122–130. Berlin, Heidelberg, 2008. Springer Berlin Heidelberg. doi:10.1007/978-3-540-85990-1_15.

[DE96]

Thomas J. DiCiccio and Bradley Efron. Bootstrap confidence intervals. Statistical Science, 11(3):189–228, 1996. URL: https://doi.org/10.1214/ss/1032280214, doi:10.1214/ss/1032280214.

[DF11]

Remco Duits and Erik Franken. Left-invariant diffusions on the space of positions and orientations and their application to crossing-preserving smoothing of hardi images. International Journal of Computer Vision, 92(3):231–264, 2011. URL: https://doi.org/10.1007/s11263-010-0332-z, doi:10.1007/s11263-010-0332-z.

[Efr79]

Bradley Efron. Bootstrap Methods: Another Look at the Jackknife. The Annals of Statistics, 7(1):1–26, 1979. URL: https://doi.org/10.1214/aos/1176344552, doi:10.1214/aos/1176344552.

[EK06]

Daniel B. Ennis and Gordon Kindlmann. Orthogonal tensor invariants and the analysis of diffusion tensor magnetic resonance images. Magnetic Resonance in Medicine, 55(1):136–146, 2006. URL: https://doi.org/10.1002/mrm.20741, doi:10.1002/mrm.20741.

[FBG20]

Shreyas Fadnavis, Joshua Batson, and Eleftherios Garyfallidis. Patch2Self: Denoising Diffusion MRI with Self-Supervised Learning. In Hugo Larochelle, Marc'Aurelio Ranzato, Raia Hadsell, Maria-Florina Balcan, and Hsuan-Tien Lin, editors, Advances in Neural Information Processing Systems, volume 33, 16293–16303. Curran Associates, Inc., 2020. URL: https://proceedings.neurips.cc/paper_files/paper/2020/file/bc047286b224b7bfa73d4cb02de1238d-Paper.pdf.

[FCB+24]

Shreyas Fadnavis, Agniva Chowdhury, Joshua Batson, Petros Drineas, and Eleftherios Garyfallidis. Patch2Self2: Self-supervised Denoising on Coresets via Matrix Sketching. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, volume, 27641–27651. 2024. URL: https://openaccess.thecvf.com/content/CVPR2024/papers/Fadnavis_Patch2Self2_Self-supervised_Denoising_on_Coresets_via_Matrix_Sketching_CVPR_2024_paper.pdf.

[FRF+19]

Shreyas Fadnavis, Marco Reisert, Hamza Farooq, Maryam Afzali, Cheng Hu, Bago Amirbekian, and Eleftherios Garyfallidis. MicroLearn: Framework for machine learning, reconstruction, optimization and microstructure modeling. In ISMRM 27th Annual Meeting & Exhibition SMRT 28th Annual Meeting. Montréal, Canada, 2019. International Society for Magnetic Resonance in Medicine (ISMRM).

[FXN+16]

Hamza Farooq, Junqian Xu, Jung Who Nam, Daniel F. Keefe, Essa Yacoub, Tryphon Georgiou, and Christophe Lenglet. Microstructure imaging of crossing (mix) white matter fibers from diffusion mri. Scientific Reports, 6(1):38927, December 2016. URL: https://doi.org/10.1038/srep38927, doi:10.1038/srep38927.

[FMOBrien+12]

Christian Federau, Philippe Maeder, Kieran O'Brien, Patrick Browaeys, Reto Meuli, and Patric Hagmann. Quantitative Measurement of Brain Perfusion with Intravoxel Incoherent Motion MR Imaging. Radiology, 265(3):874–881, 2012. URL: https://doi.org/10.1148/radiol.12120584, doi:10.1148/radiol.12120584.

[FWPD15]

Rutger Fick, Demian Wassermann, Marco Pizzolato, and Rachid Deriche. A Unifying Framework for Spatial and Temporal Diffusion in Diffusion MRI. In Sebastien Ourselin, Daniel C. Alexander, Carl-Fredrik Westin, and M. Jorge Cardoso, editors, Information Processing in Medical Imaging, 167–178. Cham, 2015. Springer International Publishing.

[FPS+18]

Rutger H. J. Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Rachid Deriche, and Demian Wassermann. Non-parametric graphnet-regularized representation of dMRI in space and time. Medical Image Analysis, 43:37–53, 2018. URL: https://doi.org/10.1016/j.media.2017.09.002, doi:10.1016/j.media.2017.09.002.

[FPW+16]

Rutger H. J. Fick, MArco Pizzolato, Demian Wassermann, Mauro Zucchelli, Gloria Menegaz, and Rachid Deriche. A sensitivity analysis of q-space indices with respect to changes in axonal diameter, dispersion and tissue composition. In IEEE 13th International Symposium on Biomedical Imaging (ISBI), volume, 1241–1244. April 2016. doi:10.1109/ISBI.2016.7493491.

[FWCD16]

Rutger H. J. Fick, Demian Wassermann, Emmanuel Caruyer, and Rachid Deriche. MAPL: Tissue microstructure estimation using Laplacian-regularized MAP-MRI and its application to HCP data. NeuroImage, 134:365–385, July 2016. URL: https://doi.org/10.1016/j.neuroimage.2016.03.046, doi:10.1016/j.neuroimage.2016.03.046.

[FBJ+13]

Els Fieremans, Andreana Benitez, Jens H. Jensen, Maria F. Falangola, Ali Tabesh, Rachael L. Deardorff, Maria Vittoria S. Spampinato, James S. Babb, Dmitry S. Novikov, Steven H. Ferris, and Joseph A. Helpern. Novel White Matter Tract Integrity Metrics Sensitive to Alzheimer Disease Progression. American Journal of Neuroradiology, 34(11):2105–2112, 2013. URL: https://www.ajnr.org/content/34/11/2105, doi:10.3174/ajnr.A3553.

[FJH11]

Els Fieremans, Jens H. Jensen, and Joseph A. Helpern. White matter characterization with diffusional kurtosis imaging. NeuroImage, 58(1):177–188, 2011. URL: https://doi.org/10.1016/j.neuroimage.2011.06.006, doi:10.1016/j.neuroimage.2011.06.006.

[FJH+12]

Els Fieremans, Jens H. Jensen, Joseph A. Helpern, Sungheon Kim, Robert I. Grossman, Matilde Inglese, and Dmitry S. Novikov. Diffusion distinguishes between axonal loss and demyelination in brain white matter. In ISMRM 20th Annual Meeting & Exhibition SMRT 21st Annual Meeting. Melbourne, Australia, 2012. International Society for Magnetic Resonance in Medicine (ISMRM).

[FEB+11]

Vladimir Fonov, Alan C. Evans, Kelly Botteron, C. Robert Almli, Robert C. McKinstry, and D. Louis Collins. Unbiased average age-appropriate atlases for pediatric studies. NeuroImage, 54(1):313–327, 2011. URL: https://doi.org/10.1016/j.neuroimage.2010.07.033, doi:10.1016/j.neuroimage.2010.07.033.

[FEM+09]

Vladimir S. Fonov, Alan C. Evans, Robert C. McKinstry, C. Robert Almli, and D. Louis Collins. Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. NeuroImage, 47:S102, 2009. Organization for Human Brain Mapping 2009 Annual Meeting. URL: https://doi.org/10.1016/S1053-8119(09)70884-5, doi:10.1016/S1053-8119(09)70884-5.

[Gar12]

Eleftherios Garyfallidis. Towards an accurate brain tractography. PhD thesis, Cambridge University, Cambridge, United Kingdom, 2012. URL:, doi:.

[GBA+11]

Eleftherios Garyfallidis, Matthew Brett, Bagrat Amirbekian, Chistopher Nguyen, Fang-Cheng Yeh, Emanuele Olivetti, Yaroslav Halchenko, and Ian Nimmo-Smith. Dipy - a novel software library for diffusion MR and tractography. In 17th annual meeting of the Organization for Human Brain Mapping, volume. Quebec City, Canada, June 2011. Organization for Human Brain Mapping (OHBM).

[GBA+14]

Eleftherios Garyfallidis, Matthew Brett, Bagrat Amirbekian, Ariel Rokem, Stefan Van Der Walt, Maxime Descoteaux, Ian Nimmo-Smith, and Dipy Contributors. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, February 2014. URL: https://doi.org/10.3389/fninf.2014.00008, doi:10.3389/fninf.2014.00008.

[GBC+12]

Eleftherios Garyfallidis, Matthew Brett, Marta M. Correia, Guy B. Williams, and Ian Nimmo-Smith. QuickBundles, a Method for Tractography Simplification. Frontiers in Neuroscience, 6():175, December 2012. URL: https://doi.org/10.3389/fnins.2012.00175, doi:10.3389/fnins.2012.00175.

[GBNS10]

Eleftherios Garyfallidis, Matthew Brett, and Ian Nimmo-Smith. Fast Dimensionality Reduction for Brain Tractography Clustering. In 16th Annual Meeting of the Organization for Human Brain Mapping, volume. Barcelona, Spain, June 2010. Organization for Human Brain Mapping (OHBM).

[GBT+10]

Eleftherios Garyfallidis, Matthew Brett, Vassilis Tsiaras, George Vogiatzis, and Ian Nimmo-Smith1. Identification of corresponding tracks in diffusion MRI tractographies. In Joint Annual Meeting ISMRM-ESMRMB 2010 SMRT 19th Annual Meeting, volume. Stockholm, Sweden, May 2010. International Society for Magnetic Resonance in Medicine (ISMRM).

[GCoteC+19]

Eleftherios Garyfallidis, Marc-Alexandre Côté, Bramsh Qamar Chandio, Shreyas Fadnavis, Javier Guaje, Ranveer Aggarwal, Etienne St-Onge, Karandeep Singh Juneja, Serge Koudoro, and David Reagan. DIPY Horizon: fast, modular, unified and adaptive visualization. In ISMRM 27th Annual Meeting & Exhibition SMRT 28th Annual Meeting, volume. Montréal, Canada, 2019. International Society for Magnetic Resonance in Medicine (ISMRM).

[GCoteRD16]

Eleftherios Garyfallidis, Marc-Alexandre Côté, François Rheault, and Maxime Descoteaux. QuickBundlesX: Sequential clustering of millions of streamlines in multiple levels of detail at record execution time. In ISMRM 24th Annual Meeting & Exhibition SMRT 25th Annual Meeting, volume. Singapore, 2016. International Society for Magnetic Resonance in Medicine (ISMRM).

[GCoteR+18]

Eleftherios Garyfallidis, Marc-Alexandre Côté, François Rheault, Jasmeen Sidhu, Janice Hau, Laurent Petit, David Fortin, Stephen Cunanne, and Maxime Descoteaux. Recognition of white matter bundles using local and global streamline-based registration and clustering. NeuroImage, 170:283–295, April 2018. Segmenting the Brain. URL: https://doi.org/10.1016/j.neuroimage.2017.07.015, doi:10.1016/j.neuroimage.2017.07.015.

[GKG+21]

Eleftherios Garyfallidis, Serge Koudoro, Javier Guaje, Marc-Alexandre Côté, Soham Biswas, David Reagan, Nasim Anousheh, Filipi Silva, Geoffrey Fox, and Fury Contributors. FURY: advanced scientific visualization. Journal of Open Source Software, 6(64):3384, 2021. URL: https://doi.org/10.21105/joss.03384, doi:10.21105/joss.03384.

[GOWD15]

Eleftherios Garyfallidis, Omar Ocegueda, Demian Wassermann, and Maxime Descoteaux. Robust and efficient linear registration of white-matter fascicles in the space of streamlines. NeuroImage, 117:124–140, August 2015. URL: https://doi.org/10.1016/j.neuroimage.2015.05.016, doi:10.1016/j.neuroimage.2015.05.016.

[GWD14]

Eleftherios Garyfallidis, Demian Wassermann, and Maxime Descoteaux. Direct native-space fiber bundle alignment for group comparisons. In Joint Annual Meeting ISMRM-ESMRMB 2014 SMRT 23rd Annual Meeting. Milan, Italy, May 2014. International Society for Magnetic Resonance in Medicine (ISMRM).

[GS78]

Walter Gautschi and Josef Slavik. On the computation of modified Bessel function ratios. Mathematics of Computation, 32(143):865–875, 1978. doi:10.1090/S0025-5718-1978-0470267-9.

[GWDD14]

Gabriel Girard, Kevin Whittingstall, Rachid Deriche, and Maxime Descoteaux. Towards quantitative connectivity analysis: reducing tractography biases. NeuroImage, 98:266–278, September 2014. URL: https://doi.org/10.1016/j.neuroimage.2014.04.074, doi:10.1016/j.neuroimage.2014.04.074.

[GHTJ15]

G. Russell Glenn, Joseph A. Helpern, Ali Tabesh, and Jens H. Jensen. Quantitative assessment of diffusional kurtosis anisotropy. NMR in Biomedicine, 28(4):448–459, 2015. URL: https://doi.org/10.1002/nbm.3271, doi:10.1002/nbm.3271.

[GAC+16]

Krzysztof J. Gorgolewski, Tibor Auer, Vince D. Calhoun, R. Cameron Craddock, Samir Das, Eugene P. Duff, Guillaume Flandin, Satrajit S. Ghosh, Tristan Glatard, Yaroslav O. Halchenko, Daniel A. Handwerker, Michael Hanke, David Keator, Xiangrui Li, Zachary Michael, Camille Maumet, B. Nolan Nichols, Thomas E. Nichols, John Pellman, Jean-Baptiste Poline, Ariel Rokem, Gunnar Schaefer, Vanessa Sochat, William Triplett, Jessica A. Turner, Gaël Varoquaux, and Russell A. Poldrack. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific Data, 3(1):160044, June 2016. URL: https://doi.org/10.1038/sdata.2016.44, doi:10.1038/sdata.2016.44.

[GCG18]

Clint Greene, Matt Cieslak, and Scott T. Grafton. Effect of different spatial normalization approaches on tractography and structural brain networks. Network Neuroscience, 2(3):362–380, September 2018. URL: https://doi.org/10.1162/netn\_a\_00035, doi:10.1162/netn_a_00035.

[GP95]

Hákon Gudbjartsson and Samuel Patz. The rician distribution of noisy mri data. Magnetic Resonance in Medicine, 34(6):910–914, 1995. URL: https://doi.org/10.1002/mrm.1910340618, doi:10.1002/mrm.1910340618.

[HJ16]

Brian Hansen and Sune Nørhøj Jespersen. Data for evaluation of fast kurtosis strategies, b-value optimization and exploration of diffusion MRI contrast. Scientific Data, 3(1):160072, August 2016. URL: https://doi.org/10.1038/sdata.2016.72, doi:10.1038/sdata.2016.72.

[HLSJ13]

Brian Hansen, Torben E. Lund, Ryan Sangill, and Sune Nørhøj Jespersen. Experimentally and computationally fast method for estimation of a mean kurtosis. Magnetic Resonance in Medicine, 69(6):1754–1760, 2013. URL: https://doi.org/10.1002/mrm.24743, doi:10.1002/mrm.24743.

[HSJ16]

Brian Hansen, Noam Shemesh, and Sune Nørhøj Jespersen. Fast imaging of mean, axial and radial diffusion kurtosis. NeuroImage, 142:381–393, November 2016. URL: https://doi.org/10.1016/j.neuroimage.2016.08.022, doi:10.1016/j.neuroimage.2016.08.022.

[HS96]

Ronald H. Hardin and Neil J. A. Sloane. Mclaren's improved snub cube and other new spherical designs in three dimensions. Discrete & Computational Geometry, 15(4):429–441, 1996. URL: https://doi.org/10.1007/BF02711518, doi:10.1007/BF02711518.

[HME+09]

Hamied A. Haroon, David M. Morris, Karl V. Embleton, Daniel C. Alexander, and Geoffrey J. M. Parker. Using the Model-Based Residual Bootstrap to Quantify Uncertainty in Fiber Orientations From $Q$-Ball Analysis. IEEE Transactions on Medical Imaging, 28(4):535–550, 2009. doi:10.1109/TMI.2008.2006528.

[HTF09]

Trevor Hastie, Robert Tibshirani, and Jerome Friedman. The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition. Springer, 2 edition, 2009. doi:https://doi.org/10.1007/978-0-387-84858-7.

[HBH+21]

Magnus Herberthson, Deneb Boito, Tom Dela Haije, Aasa Feragen, Carl-Fredrik Westin, and Evren Özarslan. Q-space trajectory imaging with positivity constraints (QTI+). NeuroImage, 238:118198, 2021. URL: https://doi.org/10.1016/j.neuroimage.2021.118198, doi:10.1016/j.neuroimage.2021.118198.

[HCWA13]

A. Pasha Hosseinbor, Moo K. Chung, Yu-Chien Wu, and Andrew L. Alexander. Bessel Fourier Orientation Reconstruction (BFOR): An analytical diffusion propagator reconstruction for hybrid diffusion imaging and computation of q-space indices. NeuroImage, 64:650–670, 2013. URL: https://doi.org/10.1016/j.neuroimage.2012.08.072, doi:10.1016/j.neuroimage.2012.08.072.

[HCHD15]

Jean-Christophe Houde, Marc-Alexandre Ct-Harnois, and Maxime Descoteaux. How to Avoid Biased Streamlines-Based Metrics for Streamlines with Variable Step Sizes. In ISMRM 23rd Annual Meeting & Exhibition SMRT 24th Annual Meeting, volume. Toronto, Canada, 2015. International Society for Magnetic Resonance in Medicine (ISMRM).

[HKKA14]

Andrew R. Hoy, Cheng Guan Koay, Steven R. Kecskemeti, and Andrew L. Alexander. Optimization of a free water elimination two-compartment model for diffusion tensor imaging. NeuroImage, 103:323–333, 2014. URL: 10.1016/j.neuroimage.2014.09.053, doi:https://doi.org/10.1016/j.neuroimage.2014.09.053.

[HCQW08]

Edward S. Hui, Matthew M. Cheung, Liqun Qi, and Ed X. Wu. Towards better MR characterization of neural tissues using directional diffusion kurtosis analysis. NeuroImage, 42(1):122–134, 2008. URL: https://doi.org/10.1016/j.neuroimage.2008.04.237, doi:10.1016/j.neuroimage.2008.04.237.

[JS01]

Mark Jenkinson and Stephen Smith. A global optimisation method for robust affine registration of brain images. Medical Image Analysis, 5(2):143–156, 2001. URL: https://doi.org/10.1016/S1361-8415(01)00036-6, doi:10.1016/S1361-8415(01)00036-6.

[JH10]

Jens H. Jensen and Joseph A. Helpern. MRI quantification of non-Gaussian water diffusion by kurtosis analysis. NMR in Biomedicine, 23(7):698–710, 2010. URL: https://doi.org/10.1002/nbm.1518, doi:10.1002/nbm.1518.

[JHR+05]

Jens H. Jensen, Joseph A. Helpern, Anita Ramani, Hanzhang Lu, and Kyle Kaczynski. Diffusional kurtosis imaging: The quantification of non-gaussian water diffusion by means of magnetic resonance imaging. Magnetic Resonance in Medicine, 53(6):1432–1440, 2005. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.20508, doi:https://doi.org/10.1002/mrm.20508.

[JLJ+11]

Ben Jeurissen, Alexander Leemans, Derek K. Jones, Jacques-Donald Tournier, and Jan Sijbers. Probabilistic fiber tracking using the residual bootstrap with constrained spherical deconvolution. Human Brain Mapping, 32(3):461–479, 2011. URL: https://doi.org/10.1002/hbm.21032, doi:10.1002/hbm.21032.

[JTD+14]

Ben Jeurissen, Jacques-Donald Tournier, Thijs Dhollander, Alan Connelly, and Jan Sijbers. Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage, 103:411–426, December 2014. URL: https://doi.org/10.1016/j.neuroimage.2014.07.061, doi:10.1016/j.neuroimage.2014.07.061.

[JHS99]

Derek K. Jones, Mark A. Horsfield, and Andrew Simmons. Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging. Magnetic Resonance in Medicine, 42(3):515–25, 1999. URL: http://www.ncbi.nlm.nih.gov/pubmed/10467296, doi:10.1002/(SICI)1522-2594(199909)42:3<515::AID-MRM14>3.0.CO;2-Q.

[JKnoscheT13]

Derek K. Jones, Thomas R. Knösche, and Robert Turner. White matter integrity, fiber count, and other fallacies: The do's and don'ts of diffusion MRI. NeuroImage, 73:239–254, 2013. URL: https://doi.org/10.1016/j.neuroimage.2012.06.081, doi:10.1016/j.neuroimage.2012.06.081.

[JMW+19]

Kesshi Jordan, Olivier Morin, Michael Wahl, Bagrat Amirbekian, Christopher Chapman, Julia Owen, Pratik Mukherjee, Steve Braunstein, and Roland Henry. An Open-Source Tool for Anisotropic Radiation Therapy Planning in Neuro-oncology Using DW-MRI Tractography. Frontiers in Oncology, 2019. URL: https://doi.org/10.3389/fonc.2019.00810, doi:10.3389/fonc.2019.00810.

[JAKH18]

Kesshi M. Jordan, Bagrat Amirbekian, Anisha Keshavan, and Roland G. Henry. Cluster Confidence Index: A Streamline-Wise Pathway Reproducibility Metric for Diffusion-Weighted MRI Tractography. Journal of Neuroimaging, 28(1):64–69, 2018. URL: https://doi.org/10.1111/jon.12467, doi:10.1111/jon.12467.

[JMPFS+15]

J. M. Jorg M. Portegies, Rutger H. J. Fick, Gonzalo Sanguinetti, Stephan P. L. Meesters, Gabriel Girard, and Remco Duits. Improving Fiber Alignment in HARDI by Combining Contextual PDE Flow with Constrained Spherical Deconvolution. PLOS ONE, 10(10):1–33, October 2015. URL: https://doi.org/10.1371/journal.pone.0138122, doi:10.1371/journal.pone.0138122.

[KKC+16]

Enrico Kaden, Nathaniel D. Kelm, Robert P. Carson, Mark D. Does, and Daniel C. Alexander. Multi-compartment microscopic diffusion imaging. NeuroImage, 139:346–359, October 2016. URL: https://doi.org/10.1016/j.neuroimage.2016.06.002, doi:10.1016/j.neuroimage.2016.06.002.

[KKA16]

Enrico Kaden, Frithjof Kruggel, and Daniel C. Alexander. Quantitative mapping of the per-axon diffusion coefficients in brain white matter. Magnetic Resonance in Medicine, 75(4):1752–1763, April 2016. URL: https://doi.org/10.1002/mrm.25734, doi:10.1002/mrm.25734.

[KYC+24]

Praitayini Kanakaraj, Tianyuan Yao, Leon Y. Cai, Ho Hin Lee, Nancy R. Newlin, Michael E. Kim, Chenyu Gao, Kimberly R. Pechman, Derek Archer, Timothy Hohman, Angela Jefferson, Lori L. Beason-Held, Susan M. Resnick, Eleftherios Garyfallidis, Adam Anderson, Kurt G. Schilling, Bennett A. Landman, Daniel Moyer, The Alzheimer's Disease Neuroimaging Initiative (ADNI), and The BIOCARD Study Team. DeepN4: Learning N4ITK Bias Field Correction for T1-weighted Images. Neuroinformatics, 22(2):193–205, April 2024. URL: https://doi.org/10.1007/s12021-024-09655-9, doi:10.1007/s12021-024-09655-9.

[KDKR16]

Elias Kellner, Bibek Dhital, Valerij G. Kiselev, and Marco Reisert. Gibbs-ringing artifact removal based on local subvoxel-shifts. Magnetic Resonance in Medicine, 76(5):1574–1581, 2016. URL: https://doi.org/10.1002/mrm.26054, doi:10.1002/mrm.26054.

[KBPS11]

Florian Knoll, Kristian Bredies, Thomas Pock, and Rudolf Stollberger. Second order total generalized variation (TGV) for MRI. Magnetic Resonance in Medicine, 65(2):480–491, 2011. URL: https://doi.org/10.1002/mrm.22595, doi:10.1002/mrm.22595.

[KB06]

Cheng Guan Koay and Peter J. Basser. Analytically exact correction scheme for signal extraction from noisy magnitude MR signals. Journal of Magnetic Resonance, 179(2):317–322, April 2006. URL: https://doi.org/10.1016/j.jmr.2006.01.016, doi:10.1016/j.jmr.2006.01.016.

[KCA+06]

Cheng Guan Koay, John D. Carew, Andrew L. Alexander, Peter J. Basser, and M. Elizabeth Meyerand. Investigation of anomalous estimates of tensor-derived quantities in diffusion tensor imaging. Magnetic Resonance in Medicine, 55(4):930–936, April 2006. URL: https://doi.org/10.1002/mrm.20832, doi:10.1002/mrm.20832.

[KCC+06]

Cheng Guan Koay, Lin-Ching Chang, John D. Carew, Carlo Pierpaoli, and Peter J. Basser. A unifying theoretical and algorithmic framework for least squares methods of estimation in diffusion tensor imaging. Journal of Magnetic Resonance, 182(1):115–125, September 2006. URL: https://doi.org/10.1016/j.jmr.2006.06.020, doi:10.1016/j.jmr.2006.06.020.

[KOzarslanB09]

Cheng Guan Koay, Evren Özarslan, and Peter J. Basser. A signal transformational framework for breaking the noise floor and its applications in MRI. Journal of Magnetic Resonance, 197(2):108–119, April 2009. URL: https://doi.org/10.1016/j.jmr.2008.11.015, doi:10.1016/j.jmr.2008.11.015.

[KOzarslanP09]

Cheng Guan Koay, Evren Özarslan, and Carlo Pierpaoli. Probabilistic Identification and Estimation of Noise (PIESNO): A self-consistent approach and its applications in MRI. Journal of Magnetic Resonance, 199(1):94–103, July 2009. URL: https://doi.org/10.1016/j.jmr.2009.03.005, doi:10.1016/j.jmr.2009.03.005.

[LLB+08]

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

[LKJones09]

Alexander Leemans and Derek K.Jones. The B-matrix must be rotated when correcting for subject motion in DTI data. Magnetic Resonance in Medicine, 61(6):1336–1349, 2009. URL: https://doi.org/10.1002/mrm.21890, doi:10.1002/mrm.21890.

[ManjonCoupeC+13]

José V. Manjón, Pierrick Coupé, Luis Concha, Antonio Buades, D. Louis Collins, and Montserrat Robles. Diffusion Weighted Image Denoising Using Overcomplete Local PCA. PLOS ONE, 8(9):e73021, 2013. URL: https://doi.org/10.1371/journal.pone.0073021, doi:10.1371/journal.pone.0073021.

[ManjonCoupeMartiBonmati+10]

José V. Manjón, Pierrick Coupé, Luis Martí-Bonmatí, D. Louis Collins, and Montserrat Robles. Adaptive non-local means denoising of MR images with spatially varying noise levels. Journal of Magnetic Resonance Imaging, 31(1):192–203, 2010. URL: https://doi.org/10.1002/jmri.22003, doi:10.1002/jmri.22003.

[MJL+11]

Kenneth Marek, Danna Jennings, Shirley Lasch, Andrew Siderowf, Caroline Tanner, Tanya Simuni, Chris Coffey, Karl Kieburtz, Emily Flagg, Sohini Chowdhury, Werner Poewe, Brit Mollenhauer, Paracelsus-Elena Klinik, Todd Sherer, Mark Frasier, Claire Meunier, Alice Rudolph, Cindy Casaceli, John Seibyl, Susan Mendick, Norbert Schuff, Ying Zhang, Arthur Toga, Karen Crawford, Alison Ansbach, Pasquale De Blasio, Michele Piovella, John Trojanowski, Les Shaw, Andrew Singleton, Keith Hawkins, Jamie Eberling, Deborah Brooks, David Russell, Laura Leary, Stewart Factor, Barbara Sommerfeld, Penelope Hogarth, Emily Pighetti, Karen Williams, David Standaert, Stephanie Guthrie, Robert Hauser, Holly Delgado, Joseph Jankovic, Christine Hunter, Matthew Stern, Baochan Tran, Jim Leverenz, Marne Baca, Sam Frank, Cathi-Ann Thomas, Irene Richard, Cheryl Deeley, Linda Rees, Fabienne Sprenger, Elisabeth Lang, Holly Shill, Sanja Obradov, Hubert Fernandez, Adrienna Winters, Daniela Berg, Katharina Gauss, Douglas Galasko, Deborah Fontaine, Zoltan Mari, Melissa Gerstenhaber, David Brooks, Sophie Malloy, Paolo Barone, Katia Longo, Tom Comery, Bernard Ravina, Igor Grachev, Kim Gallagher, Michelle Collins, Katherine L. Widnell, Suzanne Ostrowizki, Paulo Fontoura, Tony Ho, Johan Luthman, Marcel van der Brug, Alastair D. Reith, and Peggy Taylor. The Parkinson Progression Marker Initiative (PPMI). Progress in Neurobiology, 95(4):629–635, 2011. Biological Markers for Neurodegenerative Diseases. URL: https://doi.org/10.1016/j.pneurobio.2011.09.005, doi:10.1016/j.pneurobio.2011.09.005.

[MHV+03]

David Mattes, David R Haynor, Hubert Vesselle, Thomas K. Lewellen, and William Eubank. PET-CT image registration in the chest using free-form deformations. IEEE Transactions on Medical Imaging, 22(1):120–128, 2003. doi:10.1109/TMI.2003.809072.

[MSG+16a]

Stephan Meesters, Gonzalo Sanguinetti, Eleftherios Garyfallidis, Jorg Portegies, and Remco Duits1. Fast implementations of contextual PDE's for HARDI data processing in DIPY. In ISMRM 24th Annual Meeting & Exhibition SMRT 25th Annual Meeting, volume. Singapore, May 2016. International Society for Magnetic Resonance in Medicine (ISMRM).

[MSG+16b]

Stephan Meesters, Gonzalo Sanguinetti, Eleftherios Garyfallidis, Jorg Portegies, Pauly Ossenblok, and Remco Duits1. Cleaning output of tractography via fiber to bundle coherence, a new open source implementation. In The Organization for Human Brain Mapping Annual Meeting, volume. Geneva, Switzerland, June 2016. Organization for Human Brain Mapping (OHBM).

[MD13]

Sylvain L. Merlet and Rachid Deriche. Continuous diffusion signal, EAP and ODF estimation via Compressive Sensing in diffusion MRI. Medical Image Analysis, 17(5):556–572, July 2013. URL: https://doi.org/10.1016/j.media.2013.02.010, doi:10.1016/j.media.2013.02.010.

[MSdenDekker+23]

Jan Morez, Filip Szczepankiewicz, Arnold J. den Dekker, Floris Vanhevel, Jan Sijbers, and Ben Jeurissen. Optimal experimental design and estimation for q-space trajectory imaging. Human Brain Mapping, 44(4):1793–1809, 2023. URL: https://doi.org/10.1002/hbm.26175, doi:10.1002/hbm.26175.

[NSP+18]

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

[NSP+19]

Vishwesh Nath, Kurt G. Schilling, Prasanna Parvathaneni, Colin B. Hansen, Allison E. Hainline, Yuankai Huo, Justin A. Blaber, Ilwoo Lyu, Vaibhav Janve, Yurui Gao, Iwona Stepniewska, Adam W. Anderson, and Bennett A. Landman. Deep learning reveals untapped information for local white-matter fiber reconstruction in diffusion-weighted MRI. Magnetic Resonance Imaging, 62:220–227, 2019. URL: https://doi.org/10.1016/j.mri.2019.07.012, doi:10.1016/j.mri.2019.07.012.

[NEB+06]

Marc Niethammer, Raúl San José Estepar, Sylvain Bouix, Martha Shenton, and Carl-Fredrik Westin. On Diffusion Tensor Estimation. In International Conference of the IEEE Engineering in Medicine and Biology Society, volume, 2622–2625. 2006. doi:10.1109/IEMBS.2006.259826.

[NNetoHenriquesI+22]

Lisa Novello, Rafael Neto Henriques, Andrada Ianuş, Thorsten Feiweier, Noam Shemesh, and Jorge Jovicich. In vivo Correlation Tensor MRI reveals microscopic kurtosis in the human brain on a clinical 3T scanner. NeuroImage, 254:119137, 2022. URL: https://doi.org/10.1016/j.neuroimage.2022.119137, doi:10.1016/j.neuroimage.2022.119137.

[ODG+16]

Omar Ocegueda, Oscar Dalmau, Eleftherios Garyfallidis, Maxime Descoteaux, and Mariano Rivera. On the computation of integrals over fixed-size rectangles of arbitrary dimension. Pattern Recognition Letters, 79:68–72, 2016. URL: https://doi.org/10.1016/j.patrec.2016.05.008, doi:10.1016/j.patrec.2016.05.008.

[OAM19]

Daniel V. Olson, Volkan E. Arpinar, and L. Tugan Muftuler. Optimization of q-space sampling for mean apparent propagator MRI metrics using a genetic algorithm. NeuroImage, 199:237–244, 2019. URL: https://doi.org/10.1016/j.neuroimage.2019.05.078, doi:10.1016/j.neuroimage.2019.05.078.

[PP99]

Sinisa Pajevic and Carlo Pierpaoli. Color Schemes to Represent the Orientation of Anisotropic Tissues from Diffusion Tensor Data: Application to White Matter Fiber Tract Mapping in the Human Brain. Magnetic Resonance in Medicine, 42(3):526–540, 1999. URL: https://doi.org/10.1002/(SICI)1522-2594(199909)42:3<526::AID-MRM15>3.0.CO;2-J, doi:10.1002/(SICI)1522-2594(199909)42:3<526::AID-MRM15>3.0.CO;2-J.

[PMH+00]

Nikolaos G. Papadakis, Chris D. Murrills, Laurance D. Hall, Christopher L.-H. Huang, and T. Adrian Carpenter. Minimal gradient encoding for robust estimation of diffusion anisotropy. Magnetic Resonance Imaging, 18(6):671–679, 2000. URL: https://doi.org/10.1016/S0730-725X(00)00151-X, doi:10.1016/S0730-725X(00)00151-X.

[PFG24]

Jong Sung Park, Shreyas Fadnavis, and Eleftherios Garyfallidis. Multi-scale V-net architecture with deep feature CRF layers for brain extraction. Communications Medicine, 4(1):29, February 2024. URL: https://doi.org/10.1038/s43856-024-00452-8, doi:10.1038/s43856-024-00452-8.

[Par62]

Emanuel Parzen. On Estimation of a Probability Density Function and Mode. The Annals of Mathematical Statistics, 33(3):1065–1076, 1962. URL: https://doi.org/10.1214/aoms/1177704472, doi:10.1214/aoms/1177704472.

[PSG+09]

Ofer Pasternak, Nir Sochen, Yaniv Gur, Nathan Intrator, and Yaniv Assaf. Free water elimination and mapping from diffusion MRI. Magnetic Resonance in Medicine, 62(3):717–730, 2009. URL: 10.1002/mrm.22055, doi:https://doi.org/10.1002/mrm.22055.

[PAP+15]

Daniele Perrone, Jan Aelterman, Aleksandra Pižurica, Ben Jeurissen, Wilfried Philips, and Alexander Leemans. The effect of Gibbs ringing artifacts on measures derived from diffusion MRI. NeuroImage, 120:441–455, 2015. URL: https://doi.org/10.1016/j.neuroimage.2015.06.068, doi:10.1016/j.neuroimage.2015.06.068.

[PYR+14]

Franco Pestilli, Jason D. Yeatman, Ariel Rokem, Kendrick N. Kay, and Brian A. Wandell. Evaluation and statistical inference for human connectomes. Nature Methods, 11(10):1058–1063, 2014. URL: https://doi.org/10.1038/nmeth.3098, doi:10.1038/nmeth.3098.

[PSMD15]

Jorg Portegies, Gonzalo Sanguinetti, Stephan Meesters, and Remco Duits. New Approximation of a Scale Space Kernel on SE(3) and Applications in Neuroimaging. In Jean-François Aujol, Mila Nikolova, and Nicolas Papadakis, editors, 5th International Conference on Scale Space and Variational Methods in Computer Vision, 40–52. Cham, 2015. Springer International Publishing.

[PJHD15]

Caroline Presseau, Pierre-Marc Jodoin, Jean-Christophe Houde, and Maxime Descoteaux. A new compression format for fiber tracking datasets. NeuroImage, 109:73–83, 2015. URL: 10.1016/j.neuroimage.2014.12.058, doi:https://doi.org/10.1016/j.neuroimage.2014.12.058.

[RMS+11]

Yogesh Rathi, Oleg Michailovich, Kawin Setsompop, Sylvain Bouix, Martha E. Shenton, and Carl-Fredrik Westin. Sparse Multi-Shell Diffusion Imaging. In Gabor Fichtinger, Anne Martel, and Terry Peters, editors, Medical Image Computing and Computer-Assisted Intervention – MICCAI 2011, 58–65. Berlin, Heidelberg, 2011. Springer Berlin Heidelberg.

[RDB+16]

Emmanuelle Renauld, Maxime Descoteaux, Michaël Bernier, Eleftherios Garyfallidis, and Kevin Whittingstall. Semi-Automatic Segmentation of Optic Radiations and LGN, and Their Relationship to EEG Alpha Waves. PLOS ONE, 11(7):1–21, July 2016. URL: https://doi.org/10.1371/journal.pone.0156436, doi:10.1371/journal.pone.0156436.

[RHD15]

François Rheault, Jean-Christophe Houde, and Maxime Descoteaux. Real Time Interaction with Millions of Streamlines. In ISMRM 23rd Annual Meeting & Exhibition SMRT 24th Annual Meeting, volume. Toronto, Canada, 2015. International Society for Magnetic Resonance in Medicine (ISMRM).

[Ric72]

William Hadley Richardson. Bayesian-based iterative method of image restoration∗. Journal of the Optical Society of America, 62(1):55–59, January 1972. URL: https://doi.org/10.1364/JOSA.62.000055, doi:10.1364/JOSA.62.000055.

[RHCA+22]

Adam Richie-Halford, Matthew Cieslak, Lei Ai, Sendy Caffarra, Sydney Covitz, Alexandre R. Franco, Iliana I. Karipidis, John Kruper, Michael Milham, Bárbara Avelar-Pereira, Ethan Roy, Valerie J. Sydnor, Jason D. Yeatman, Nicholas J. Abbott, John A. E. Anderson, B. Gagana, MaryLena Bleile, Peter S. Bloomfield, Vince Bottom, Josiane Bourque, Rory Boyle, Julia K. Brynildsen, Navona Calarco, Jaime J. Castrellon, Natasha Chaku, Bosi Chen, Sidhant Chopra, Emily B. J. Coffey, Nigel Colenbier, Daniel J. Cox, James Elliott Crippen, Jacob J. Crouse, Szabolcs David, Benjamin De Leener, Gwyneth Delap, Zhi-De Deng, Jules Roger Dugre, Anders Eklund, Kirsten Ellis, Arielle Ered, Harry Farmer, Joshua Faskowitz, Jody E. Finch, Guillaume Flandin, Matthew W. Flounders, Leon Fonville, Summer B. Frandsen, Dea Garic, Patricia Garrido-Vásquez, Gabriel Gonzalez-Escamilla, Shannon E. Grogans, Mareike Grotheer, David C. Gruskin, Guido I. Guberman, Edda Briana Haggerty, Younghee Hahn, Elizabeth H. Hall, Jamie L. Hanson, Yann Harel, Bruno Hebling Vieira, Meike D. Hettwer, Harriet Hobday, Corey Horien, Fan Huang, Zeeshan M. Huque, Anthony R. James, Isabella Kahhale, Sarah L. H. Kamhout, Arielle S. Keller, Harmandeep Singh Khera, Gregory Kiar, Peter Alexander Kirk, Simon H. Kohl, Stephanie A. Korenic, Cole Korponay, Alyssa K. Kozlowski, Nevena Kraljevic, Alberto Lazari, Mackenzie J. Leavitt, Zhaolong Li, Giulia Liberati, Elizabeth S. Lorenc, Annabelle Julina Lossin, Leon D. Lotter, David M. Lydon-Staley, Christopher R. Madan, Neville Magielse, Hilary A. Marusak, Julien Mayor, Amanda L. McGowan, Kahini P. Mehta, Steven Lee Meisler, Cleanthis Michael, Mackenzie E. Mitchell, Simon Morand-Beaulieu, Benjamin T. Newman, Jared A. Nielsen, Shane M. O'Mara, Amar Ojha, Adam Omary, Evren Özarslan, Linden Parkes, Madeline Peterson, Adam Robert Pines, Claudia Pisanu, Ryan R. Rich, Matthew D. Sacchet, Ashish K. Sahoo, Amjad Samara, Farah Sayed, Jonathan Thore Schneider, Lindsay S. Shaffer, Ekaterina Shatalina, Sara A. Sims, Skyler Sinclair, Jae W. Song, Griffin Stockton Hogrogian, Christian K. Tamnes, Ursula A. Tooley, Vaibhav Tripathi, Hamid B. Turker, Sofie Louise Valk, Matthew B. Wall, Cheryl K. Walther, Yuchao Wang, Bertil Wegmann, Thomas Welton, Alex I. Wiesman, Andrew G. Wiesman, Mark Wiesman, Drew E. Winters, Ruiyi Yuan, Sadie J. Zacharek, Chris Zajner, Ilya Zakharov, Gianpaolo Zammarchi, Dale Zhou, Benjamin Zimmerman, Kurt Zoner, Theodore D. Satterthwaite, Ariel Rokem, and The Fibr Community Science Consortium. An analysis-ready and quality controlled resource for pediatric brain white-matter research. Scientific Data, 9(1):616, October 2022. URL: https://doi.org/10.1038/s41597-022-01695-7, doi:10.1038/s41597-022-01695-7.

[RSAK14]

Till W. Riffert, Jan Schreiber, Alfred Anwander, and Thomas R. Knösche. Beyond fractional anisotropy: Extraction of bundle-specific structural metrics from crossing fiber models. NeuroImage, 100:176–191, 2014. URL: https://www.sciencedirect.com/science/article/pii/S1053811914004923, doi:10.1016/j.neuroimage.2014.06.015.

[RDtHRV10]

Paulo Rodrigues, Remco Duits, Bart M. ter Haar Romeny, and Anna Vilanova. Accelerated Diffusion Operators for Enhancing DW-MRI. In Dirk Bartz, Charl Botha, Joachim Hornegger, Raghu Machiraju, Alexander Wiebel, and Bernhard Preim, editors, Eurographics Workshop on Visual Computing for Biology and Medicine. The Eurographics Association, 2010. doi:https://doi.org/10.2312/VCBM/VCBM10/049-056.

[RCY+14]

Ariel Rokem, Kimberly L. Chan, Jason D. Yeatman, Franco Pestilli, and Brian A. Wandel. Evaluating the accuracy of diffusion models at multiple b-values with cross-validation. In Joint Annual Meeting ISMRM-ESMRMB 2014 SMRT 23rd Annual Meeting, volume. Milan, Italy, 2014. International Society for Magnetic Resonance in Medicine (ISMRM).

[RYP+15]

Ariel Rokem, Jason D. Yeatman, Franco Pestilli, Kendrick N. Kay, Aviv Mezer, Stefan van der Walt, and Brian A. Wandell. Evaluating the Accuracy of Diffusion MRI Models in White Matter. PLOS ONE, 10(4):1–26, April 2015. URL: https://doi.org/10.1371/journal.pone.0123272, doi:10.1371/journal.pone.0123272.

[RBCF+22]

David Romero-Bascones, Bramsh Qamar Chandio, Shreyas Fadnavis, Jong Sung Park, Serge Koudoro, Unai Ayala, Maitane Barrenechea, and Eleftherios Garyfallidis. BundleAtlasing: unbiased population-specific atlasing of bundles in streamline space. In Joint Annual Meeting ISMRM-ESMRMB & ISMRT 31st Annual Meeting, volume. London, UK, 2022. International Society for Magnetic Resonance in Medicine (ISMRM).

[ROF92]

Leonid I. Rudin, Stanley Osher, and Emad Fatemi. Nonlinear total variation based noise removal algorithms. Physica D: Nonlinear Phenomena, 60(1):259–268, 1992. URL: https://doi.org/10.1016/0167-2789(92)90242-F, doi:10.1016/0167-2789(92)90242-F.

[SodermanJoonsson95]

Olle Söderman and Bengt Jöonsson. Restricted Diffusion in Cylindrical Geometry. Journal of Magnetic Resonance, Series A, 117(1):94–97, 1995. URL: https://doi.org/10.1006/jmra.1995.0014, doi:10.1006/jmra.1995.0014.

[SBH+20]

Kurt G. Schilling, Justin Blaber, Colin Hansen, Leon Cai, Baxter Rogers, Adam W. Anderson, Seth Smith, Praitayini Kanakaraj, Tonia Rex, Susan M. Resnick, Andrea T. Shafer, Laurie E. Cutting, Neil Woodward, David Zald, and Bennett A. Landman. Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps. PLOS ONE, 15(7):1–15, July 2020. URL: https://doi.org/10.1371/journal.pone.0236418, doi:10.1371/journal.pone.0236418.

[SBH+19]

Kurt G. Schilling, Justin Blaber, Yuankai Huo, Allen Newton, Colin Hansen, Vishwesh Nath, Andrea T. Shafer, Owen Williams, Susan M. Resnick, Baxter Rogers, Adam W. Anderson, and Bennett A. Landman. Synthesized b0 for diffusion distortion correction (Synb0-DisCo). Magnetic Resonance Imaging, 64:62–70, 2019. Artificial Intelligence in MRI. URL: https://doi.org/10.1016/j.mri.2019.05.008, doi:10.1016/j.mri.2019.05.008.

[SHRM+25]

Atharva Jaydeep Shah, Rafael Neto Henriques, Alonso Ramirez-Manzanares, Patryk Filipiak, Steven Baete, Kaustav Deka, Maharshi Gor, Serge Koudoro, and Eleftherios Garyfallidis. FORCE: FORward modeling for Complex microstructure Estimation. Research Square (Preprint), 2025. Under review at Nature Portfolio. URL: https://www.researchsquare.com/article/rs-8151109/v1, doi:10.21203/rs.3.rs-8151109/v1.

[STCC12]

Robert E. Smith, Jacques-Donald Tournier, Fernando Calamante, and Alan Connelly. Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. NeuroImage, 62(3):1924–1938, September 2012. URL: https://doi.org/10.1016/j.neuroimage.2012.06.005, doi:10.1016/j.neuroimage.2012.06.005.

[SJX+13]

Stamatios N. Sotiropoulos, Saad Jbabdi, Junqian Xu, Jesper L. Andersson, Steen Moeller, Edward J. Auerbach, Matthew F. Glasser, Moises Hernandez, Guillermo Sapiro, Mark Jenkinson, David A. Feinberg, Essa Yacoub, Christophe Lenglet, David C. Van Essen, Kamil Ugurbil, and Timothy E.J. Behrens. Advances in diffusion MRI acquisition and processing in the Human Connectome Project. NeuroImage, 80:125–143, 2013. Mapping the Connectome. URL: https://doi.org/10.1016/j.neuroimage.2013.05.057, doi:10.1016/j.neuroimage.2013.05.057.

[SODGD18]

Etienne St-Onge, Alessandro Daducci, Gabriel Girard, and Maxime Descoteaux. Surface-enhanced tractography (SET). NeuroImage, 169:524–539, 2018. URL: https://doi.org/10.1016/j.neuroimage.2017.12.036, doi:10.1016/j.neuroimage.2017.12.036.

[SOGC22]

Etienne St-Onge, Eleftherios Garyfallidis, and D. Louis Collins. Fast Streamline Search: An Exact Technique for Diffusion MRI Tractography. Neuroinformatics, 20(4):1093–1104, 2022. URL: https://doi.org/10.1007/s12021-022-09590-7, doi:10.1007/s12021-022-09590-7.

[ST65]

Edward O. Stejskal and John E. Tanner. Spin Diffusion Measurements: Spin Echoes in the Presence of a Time-Dependent Field Gradient. The Journal of Chemical Physics, 42(1):288–292, January 1965. doi:http://dx.doi.org/10.1063/1.1695690.

[SHW19]

Filip Szczepankiewicz, Scott Hoge, and Carl-Fredrik Westin. Linear, planar and spherical tensor-valued diffusion MRI data by free waveform encoding in healthy brain, water, oil and liquid crystals. Data in Brief, 25:104208, 2019. URL: https://doi.org/10.1016/j.dib.2019.104208, doi:10.1016/j.dib.2019.104208.

[TJAH11]

Ali Tabesh, Jens H. Jensen, Babak A. Ardekani, and Joseph A. Helpern. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Magnetic Resonance in Medicine, 65(3):823–836, 2011. URL: https://doi.org/10.1002/mrm.22655, doi:10.1002/mrm.22655.

[TSA+16]

Maira Tariq, Torben Schneider, Daniel C. Alexander, Claudia A. Gandini Wheeler-Kingshott, and Hui Zhang. Bingham-Noddi: Mapping anisotropic orientation dispersion of neurites using diffusion MRI. NeuroImage, 133:207–223, 2016. URL: https://doi.org/10.1016/j.neuroimage.2016.01.046, doi:10.1016/j.neuroimage.2016.01.046.

[TJV+14]

Chantal M.W. Tax, Ben Jeurissen, Sjoerd B. Vos, Max A. Viergever, and Alexander Leemans. Recursive calibration of the fiber response function for spherical deconvolution of diffusion MRI data. NeuroImage, 86:67–80, 2014. URL: https://doi.org/10.1016/j.neuroimage.2013.07.067, doi:10.1016/j.neuroimage.2013.07.067.

[TOV+15]

Chantal M.W. Tax, Willem M. Otte, Max A. Viergever, Rick M. Dijkhuizen, and Alexander Leemans. REKINDLE: Robust extraction of kurtosis INDices with linear estimation. Magnetic Resonance in Medicine, 73(2):794–808, 2015. URL: https://doi.org/10.1002/mrm.25165, doi:10.1002/mrm.25165.

[Top16]

Daniel Topgaard. NMR Methods for Studying Microscopic Diffusion Anisotropy. In Diffusion NMR of Confined Systems: Fluid Transport in Porous Solids and Heterogeneous Materials. The Royal Society of Chemistry, December 2016. URL: https://doi.org/10.1039/9781782623779-00226, doi:10.1039/9781782623779-00226.

[TCC07]

Jacques-Donald Tournier, Fernando Calamante, and Alan Connelly. Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution. NeuroImage, 35(4):1459–1472, May 2007. URL: https://doi.org/10.1016/j.neuroimage.2012.06.005, doi:10.1016/j.neuroimage.2007.02.016.

[TCC12]

Jacques-Donald Tournier, Fernando Calamante, and Alan Connelly. MRtrix: Diffusion tractography in crossing fiber regions. International Journal of Imaging Systems and Technology, 22(1):53–66, 2012. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/ima.22005, doi:https://doi.org/10.1002/ima.22005.

[TCGC04]

Jacques-Donald Tournier, Fernando Calamante, David G. Gadian, and Alan Connelly. Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution. NeuroImage, 23(3):1176–1185, November 2004. URL: https://doi.org/10.1016/j.neuroimage.2004.07.037, doi:10.1016/j.neuroimage.2004.07.037.

[TSR+19]

Jacques-Donald Tournier, Robert Smith, David Raffelt, Rami Tabbara, Thijs Dhollander, Maximilian Pietsch, Daan Christiaens, Ben Jeurissen, Chun-Hung Yeh, and Alan Connelly. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 202:116137, November 2019. URL: https://doi.org/10.1016/j.neuroimage.2019.116137, doi:10.1016/j.neuroimage.2019.116137.

[TristanVWAFernandez09]

Antonio Tristán-Vega, Carl-Fredrik Westin, and Santiago Aja-Fernández. Estimation of fiber Orientation Probability Density Functions in High Angular Resolution Diffusion Imaging. NeuroImage, 47(2):638–650, August 2009. URL: https://doi.org/10.1016/j.neuroimage.2009.04.049, doi:10.1016/j.neuroimage.2009.04.049.

[TristanVWAFernandez10]

Antonio Tristán-Vega, Carl-Fredrik Westin, and Santiago Aja-Fernández. A new methodology for the estimation of fiber populations in the white matter of the brain with the Funk–Radon transform. NeuroImage, 49(2):1301–1315, 2010. URL: https://doi.org/10.1016/j.neuroimage.2009.09.070, doi:10.1016/j.neuroimage.2009.09.070.

[TristanVAFernandezW09]

Antonio Tristán-Vega, Santiago Aja-Fernández, and Carl-Fredrik Westin. On the Blurring of the Funk-Radon Transform in Q-Ball Imaging. In Guang-Zhong Yang, David Hawkes, Daniel Rueckert, Alison Noble, and Chris Taylor, editors, Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009, 415–422. Berlin, Heidelberg, September 2009. Springer Berlin Heidelberg.

[Tuc02]

David S. Tuch. Diffusion MRI of Complex Tissue Structure. PhD thesis, Massachusetts Institute of Technology, Cambridge, USA, 2002. URL: http://hdl.handle.net/1721.1/8348, doi:.

[Tuc04]

David S. Tuch. Q-ball imaging. Magnetic Resonance in Medicine, 52(6):1358–1372, 2004. URL: https://doi.org/10.1002/mrm.20279, doi:10.1002/mrm.20279.

[Valabregue15]

Romain Valabrègue. Diffusion MRI measured at multiple b-values. University Libraries, eScience Institute Faculty Research, 2015. doi:http://hdl.handle.net/1773/33311.

[VFJ+16]

Jelle Veraart, Els Fieremans, Ileana O. Jelescu, Florian Knoll, and Dmitry S. Novikov. Gibbs ringing in diffusion MRI. Magnetic Resonance in Medicine, 76(1):301–314, July 2016. URL: https://doi.org/10.1002/mrm.25866, doi:10.1002/mrm.25866.

[VFN16]

Jelle Veraart, Els Fieremans, and Dmitry S. Novikov. Diffusion MRI noise mapping using random matrix theory. Magnetic Resonance in Medicine, 76(5):1582–1593, November 2016. URL: https://doi.org/10.1002/mrm.26059, doi:10.1002/mrm.26059.

[VNC+16]

Jelle Veraart, Dmitry S. Novikov, Daan Christiaens, Benjamin Ades-aron, Jan Sijbers, and Els Fieremans. Denoising of diffusion MRI using random matrix theory. NeuroImage, 142:394–406, November 2016. URL: https://doi.org/10.1016/j.neuroimage.2016.08.016, doi:10.1016/j.neuroimage.2016.08.016.

[VPH+11]

Jelle Veraart, Dirk H. J. Poot, Wim Van Hecke, Ines Blockx, Annemie Van der Linden, Marleen Verhoye, and Jan Sijbers. More accurate estimation of diffusion tensor parameters using diffusion kurtosis imaging. Magnetic Resonance in Medicine, 65(1):138–145, 2011. URL: https://doi.org/10.1002/mrm.22603, doi:10.1002/mrm.22603.

[VSS+13]

Jelle Veraart, Jan Sijbers, Stefan Sunaert, Alexander Leemans, and Ben Jeurissen. Weighted linear least squares estimation of diffusion MRI parameters: Strengths, limitations, and pitfalls. NeuroImage, 81:335–346, 2013. URL: https://doi.org/10.1016/j.neuroimage.2013.05.028, doi:10.1016/j.neuroimage.2013.05.028.

[VPPA09]

Tom Vercauteren, Xavier Pennec, Aymeric Perchant, and Nicholas Ayache. Diffeomorphic demons: Efficient non-parametric image registration. NeuroImage, 45(1, Supplement 1):S61–S72, 2009. Mathematics in Brain Imaging. URL: https://doi.org/10.1016/j.neuroimage.2008.10.040, doi:10.1016/j.neuroimage.2008.10.040.

[WG17]

Tingyi Wanyan and Eleftherios Garyfallidis. Important new insights for the reduction of false positives in tractograms emerge from streamline-based registration and pruning. In ISMRM 25th Annual Meeting & Exhibition SMRT 26th Annual Meeting, volume. Honolulu, HI, USA, 2017. International Society for Magnetic Resonance in Medicine (ISMRM).

[WSP+17]

Demian Wassermann, Mathieu Santin, Anne-Charlotte Philippe, Rutger Fick, Rachid Deriche, Stephane Lehericy, and Alexandra Petiet. Test-Retest qt-dMRI datasets for Non-Parametric GraphNet-Regularized Representation of dMRI in Space and Time. Zenodo, September 2017. Dataset. URL: https://zenodo.org/records/996889, doi:10.5281/zenodo.996889.

[WHT+05]

Van Jay Wedeen, Patric Hagmann, Wen-Yih Tseng, Timothy G. Reese, and Robert M. Weisskoff. Mapping Complex Tissue Architecture with Diffusion Spectrum Magnetic Resonance Imaging. Magnetic Resonance in Medicine, 54(6):1377–1386, 2005. URL: https://doi.org/10.1002/mrm.20642, doi:10.1002/mrm.20642.

[WWS+08]

Van Jay Wedeen, Ruopeng P. Wang, Jeremy Dan Schmahmann, Thomas Benner, Wen Yih Isaac Tseng, Guangping Dai, Deepak N. Pandya, Patric Hagmann, Helen D'Arceuil, and Alexander J. de Crespigny. Diffusion spectrum magnetic resonance imaging (DSI) tractography of crossing fibers. NeuroImage, 41(4):1267–1277, 2008. URL: https://doi.org/10.1016/j.neuroimage.2008.03.036, doi:10.1016/j.neuroimage.2008.03.036.

[WKP+16]

Carl-Fredrik Westin, Hans Knutsson, Ofer Pasternak, Filip Szczepankiewicz, Evren Özarslan, Danielle van Westen, Cecilia Mattisson, Mats Bogren, Lauren J. O'Donnell, Marek Kubicki, Daniel Topgaard, and Markus Nilsson. Q-space trajectory imaging for multidimensional diffusion MRI of the human brain. NeuroImage, 135:345–362, 2016. URL: https://doi.org/10.1016/j.neuroimage.2016.02.039, doi:10.1016/j.neuroimage.2016.02.039.

[WPG+97]

Carl-Fredrik Westin, Sharon Peled, Hákon Gudbjartsson, Ron Kikinis, and Ferenc Jolesz. Geometrical diffusion measures for MRI from tensor basis analysis. In 5th Scientific Meeting and Exhibition, volume. Vancouver, Canada, 1997. International Society for Magnetic Resonance in Medicine (ISMRM).

[WH06]

Brian A. Wichmann and Ian David Hill. Generating good pseudo-random numbers. Computational Statistics & Data Analysis, 51(3):1614–1622, 2006. URL: https://doi.org/10.1016/j.csda.2006.05.019, doi:10.1016/j.csda.2006.05.019.

[WA07]

Yu-Chien Wu and Andrew L. Alexander. Hybrid diffusion imaging. NeuroImage, 36(3):617–629, 2007. URL: https://doi.org/10.1016/j.neuroimage.2007.02.050, doi:10.1016/j.neuroimage.2007.02.050.

[WFA08]

Yu-Chien Wu, Aaron S. Field, and Andrew L. Alexander. Computation of Diffusion Function Measures in $q$-Space Using Magnetic Resonance Hybrid Diffusion Imaging. IEEE Transactions on Medical Imaging, 27(6):858–865, 2008. doi:10.1109/TMI.2008.922696.

[YDM+12]

Jason D. Yeatman, Robert F. Dougherty, Nathaniel J. Myall, Brian A. Wandell, and Heidi M. Feldman. Tract Profiles of White Matter Properties: Automating Fiber-Tract Quantification. PLOS ONE, 7(11):1–15, November 2012. URL: https://doi.org/10.1371/journal.pone.0049790, doi:10.1371/journal.pone.0049790.

[YPF+18]

Fang-Cheng Yeh, Sandip Panesar, David Fernandes, Antonio Meola, Masanori Yoshino, Juan C. Fernandez-Miranda, Jean M. Vettel, and Timothy Verstynen. Population-averaged atlas of the macroscale human structural connectome and its network topology. NeuroImage, 178:57–68, 2018. URL: https://doi.org/10.1016/j.neuroimage.2018.05.027, doi:10.1016/j.neuroimage.2018.05.027.

[YWT10]

Fang-Cheng Yeh, Van Jay Wedeen, and Wen-Yih Isaac Tseng. Generalized $q$-Sampling Imaging. IEEE Transactions on Medical Imaging, 29(9):1626–1635, 2010. URL: https://doi.org/10.1109/TMI.2010.2045126, doi:10.1109/TMI.2010.2045126.

[YZS+19]

Fang-Cheng Yeh, Islam M. Zaydan, Valerie R. Suski, David Lacomis, R. Mark Richardson, Joseph C. Maroon, and Jessica Barrios-Martinez. Differential tractography as a track-based biomarker for neuronal injury. NeuroImage, 202:116131, 2019. URL: https://doi.org/10.1016/j.neuroimage.2019.116131, doi:10.1016/j.neuroimage.2019.116131.

[YKK+14]

Anastasia Yendiki, Kami Koldewyn, Sita Kakunoori, Nancy Kanwisher, and Bruce Fischl. Spurious group differences due to head motion in a diffusion MRI study. NeuroImage, 88:79–90, 2014. URL: https://doi.org/10.1016/j.neuroimage.2013.11.027, doi:10.1016/j.neuroimage.2013.11.027.

[ZSWKA12]

Hui Zhang, Torben Schneider, Claudia A. Wheeler-Kingshott, and Daniel C. Alexander. Noddi: practical in vivo neurite orientation dispersion and density imaging of the human brain. NeuroImage, 61(4):1000–1016, 2012. URL: https://doi.org/10.1016/j.neuroimage.2012.03.072, doi:10.1016/j.neuroimage.2012.03.072.

[ZBS01]

Yongyue Zhang, Michael Brady, and Stephen Smith. Segmentation of brain mr images through a hidden markov random field model and the expectation-maximization algorithm. IEEE Transactions on Medical Imaging, 20(1):45–57, 2001. doi:10.1109/42.906424.

[ZH05]

Hui Zou and Trevor Hastie. Regularization and Variable Selection Via the Elastic Net. Journal of the Royal Statistical Society Series B: Statistical Methodology, 67(2):301–320, March 2005. URL: https://doi.org/10.1111/j.1467-9868.2005.00503.x, doi:10.1111/j.1467-9868.2005.00503.x.

[ZDM18]

Mauro Zucchelli, Maxime Descoteaux, and Gloria Menegaz. A generalized SMT-based framework for Diffusion MRI microstructural model estimation. In Enrico Kaden, Francesco Grussu, Lipeng Ning, Chantal M. W. Tax, and Jelle Veraart, editors, Computational Diffusion MRI, 51–63. Cham, 2018. Springer International Publishing.

[OzarslanKB08]

Evren Özarslan, Cheng Guan Koay, and Peter J. Basser. Simple harmonic oscillator based reconstruction and estimation for one-dimensional q-space magnetic resonance (1D-SHORE). In ISMRM 16th Scientific Meeting & Exhibition SMRT 17th Annual Meeting, volume 16, 35. Toronto, Canada, 2008. International Society for Magnetic Resonance in Medicine (ISMRM).

[OzarslanKS+09]

Evren Özarslan, Cheng Guan Koay, Timothy M. Shepherd, Stephen J. Blackband, and Peter J. Basser. Simple harmonic oscillator based reconstruction and estimation for three-dimensional q-space MRI. In ISMRM 17th Scientific Meeting & Exhibition SMRT 18th Annual Meeting, volume. Honolulu, HI, USA, 2009. International Society for Magnetic Resonance in Medicine (ISMRM).

[OzarslanKS+13]

Evren Özarslan, Cheng Guan Koay, Timothy M. Shepherd, Michal E. Komlosh, M. Okan İrfanoǧlu, Carlo Pierpaoli, and Peter J. Basser. Mean apparent propagator (MAP) MRI: A novel diffusion imaging method for mapping tissue microstructure. NeuroImage, 78:16–32, 2013. URL: https://doi.org/10.1016/j.neuroimage.2013.04.016, doi:10.1016/j.neuroimage.2013.04.016.

[DelaHaijeOzarslanF20]

Tom Dela Haije, Evren Özarslan, and Aasa Feragen. Enforcing necessary non-negativity constraints for common diffusion MRI models using sum of squares programming. NeuroImage, 209:116405, 2020. URL: https://doi.org/10.1016/j.neuroimage.2019.116405, doi:10.1016/j.neuroimage.2019.116405.

[LeBihanBL+88]

Denis Le Bihan, Eric Breton, Denis Lallemand, M. L. Aubin, Jacqueline Vignaud, and Maurice Laval-Jeantet. Separation of diffusion and perfusion in intravoxel incoherent motion MR imaging. Radiology, 168(2):497–505, 1988. URL: https://doi.org/10.1148/radiology.168.2.3393671, doi:10.1148/radiology.168.2.3393671.

[NetoHenriques12]

Rafael Neto Henriques. Diffusion kurtosis imaging of the healthy human brain. Master's thesis, Universidade de Lisboa, Lisboa, Portugal, 2012. URL: https://repositorio.ul.pt/bitstream/10451/8511/1/ulfc104137_tm_Rafael_Henriques.pdf, doi:.

[NetoHenriques18]

Rafael Neto Henriques. Advanced Methods for Diffusion MRI Data Analysis and their Application to the Healthy Ageing Brain. PhD thesis, Cambridge University, Cambridge, United Kingdom, 2018. URL: https://doi.org/10.17863/CAM.29356, doi:10.17863/CAM.29356.

[NetoHenriquesCM+21]

Rafael Neto Henriques, Marta M. Correia, Maurizio Marrale, Elizabeth Huber, John Kruper, Serge Koudoro, Jason D. Yeatman, Eleftherios Garyfallidis, and Ariel Rokem. Diffusional Kurtosis Imaging in the Diffusion Imaging in Python Project. Frontiers in Human Neuroscience, July 2021. Sec. Brain Imaging and Stimulation. Advanced Diffusion MRI for Brain Microstructure: Methodology, Consistency, and Application. URL: https://doi.org/10.3389/fnhum.2021.675433, doi:10.3389/fnhum.2021.675433.

[NetoHenriquesCNF15]

Rafael Neto Henriques, Marta Morgado Correia, Rita Gouveia Nunes, and Hugo Alexandre Ferreira. Exploring the 3D geometry of the diffusion kurtosis tensor—Impact on the development of robust tractography procedures and novel biomarkers. NeuroImage, 111:85–99, 2015. URL: https://doi.org/10.1016/j.neuroimage.2015.02.004, doi:10.1016/j.neuroimage.2015.02.004.

[NetoHenriquesJS19]

Rafael Neto Henriques, Sune N. Jespersen, and Noam Shemesh. Microscopic anisotropy misestimation in spherical-mean single diffusion encoding MRI. Magnetic Resonance in Medicine, 81(5):3245–3261, 2019. URL: https://doi.org/10.1002/mrm.27606, doi:10.1002/mrm.27606.

[NetoHenriquesJS20]

Rafael Neto Henriques, Sune N. Jespersen, and Noam Shemesh. Correlation tensor magnetic resonance imaging. NeuroImage, 211:116605, 2020. URL: https://doi.org/10.1016/j.neuroimage.2020.116605, doi:10.1016/j.neuroimage.2020.116605.

[NetoHenriquesJS21]

Rafael Neto Henriques, Sune N. Jespersen, and Noam Shemesh. Evidence for microscopic kurtosis in neural tissue revealed by correlation tensor MRI. Magnetic Resonance in Medicine, 86(6):3111–3130, December 2021. URL: https://doi.org/10.1002/mrm.28938, doi:10.1002/mrm.28938.

[NetoHenriquesRG+17]

Rafael Neto Henriques, Ariel Rokem, Eleftherios Garyfallidis, Samuel St-Jean, Eric Thomas Peterson, and Marta Morgado Correia. [Re] Optimization of a free water elimination two-compartment model for diffusion tensor imaging. bioRxiv, 2017. doi:https://doi.org/10.1101/108795.