Dipy, a library for the analysis of diffusion MRI data

Aganj, 2010, Reconstruction of the orientation distribution function in single- and multiple-shell q-ball imaging within constant solid angle, Magn. Reson. Med, 64, 554, 10.1002/mrm.22365

Alexander, 2002, Detection and modeling of non-gaussian apparent diffusion coefficient profiles in human brain data, Magn. Reson. Med, 48, 331, 10.1002/mrm.10209

Anderson, 2005, Measurements of fiber orientation distributions using high angular resolution diffusion imaging, Magnet. Reson. Med, 54, 1194, 10.1002/mrm.20667

Arsigny, 2006, Log-euclidean metrics for fast and simple calculus on diffusion tensors, Magn. Reson. Med, 56, 411, 10.1002/mrm.20965

Assaf, 2008, Axcaliber: a method for measuring axon diameter distribution from diffusion mri, Magn. Reson. Med, 59, 1347, 10.1002/mrm.21577

Basser, 1994, MR diffusion tensor spectroscopy and imaging, Biophys. J, 66, 259, 10.1016/S0006-3495(94)80775-1

Basser, 2000, In vivo fiber tractography using DT-MRI data, Magn. Reson. Med, 44, 625, 10.1002/1522-2594(200010)44:4625::AID-MRM173.0.CO;2-O

Basser, 1996, Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI, J. Magn. Reson, 213, 560, 10.1016/j.jmr.2011.09.022

Beaulieu, 2002, The basis of anisotropic water diffusion in the nervous system - a technical review, NMR Biomed, 15, 435, 10.1002/nbm.782

Beaulieu, 1996, Changes in water diffusion due to Wallerian degeneration in peripheral nerve, Magn. Reson. Med, 36, 627, 10.1002/mrm.1910360419

2009, Diffusion MRI

Ben-Shachar, 2007, White matter pathways in reading, Curr. Opin. Neurobiol, 17, 258, 10.1016/j.conb.2007.03.006

Berman, 2008, Probabilistic streamline q-ball tractography using the residual bootstrap, Neuroimage, 39, 215, 10.1016/j.neuroimage.2007.08.021

Bilgic, 2012, Accelerated diffusion spectrum imaging with compressed sensing using adaptive dictionaries, Magn. Reson. Med, 68, 1747, 10.1002/mrm.24505

Callaghan, 1988, Rapid communication: NMR microscopy of dynamic displacements: k-space and q-space imaging, J. Phys. E Sci. Instrum, 21, 820, 10.1088/0022-3735/21/8/017

Callaghan, 1991, Principles of Nuclear Magnetic Resonance Microscopy, 10.1093/oso/9780198539445.001.0001

Canales-Rodréiguez, 2010, Deconvolution in diffusion spectrum imaging, Neuroimage, 50, 136, 10.1016/j.neuroimage.2009.11.066

Caruyer, 2013, Design of multishell sampling schemes with uniform coverage in diffusion MRI, Magn. Reson. Med, 69, 1534, 10.1002/mrm.24736

Chamberland, 2013, Explore the brain white matter networks in real-time: multi-sticks fiber tracking, The International Society for Magnetic Resonance in Medicine

Chang, 2005, RESTORE: robust estimation of tensors by outlier rejection, Magn. Reson. Med, 53, 1088, 10.1002/mrm.20426

Chang, 2012, Informed RESTORE: a method for robust estimation of diffusion tensor from low redundancy datasets in the presence of physiological noise artifacts, Magn. Reson. Med, 68, 1654, 10.1002/mrm.24173

Chung, 2006, Comparison of bootstrap approaches for estimation of uncertainties of DTI parameters, Neuroimage, 33, 531, 10.1016/j.neuroimage.2006.07.001

Clayden, 2011, TractoR: magnetic resonance imaging and tractography with R, J. Stat. Softw, 44, 1, 10.18637/jss.v044.i08

Conturo, 1999, Tracking neuronal fiber pathways in the living human brain, Proc. Natl. Acad. Sci. U.S.A, 96, 10422, 10.1073/pnas.96.18.10422

Cook, 2006, Camino: open-source diffusion-MRI reconstruction and processing, Int. Soc. Magn. Reson. Med, 14, 2759

Côté, 2013, Tractometer: towards validation of tractography pipelines, Med. Image Anal, 17, 844, 10.1016/j.media.2013.03.009

Cox, 2012, AFNI: what a long strange trip it's been, Neuroimage, 62, 743, 10.1016/j.neuroimage.2011.08.056

Daducci, 2012, The connectome mapper: an open-source processing pipeline to map connectomes with MRI, PLoS ONE, 7, e48121, 10.1371/journal.pone.0048121

Descoteaux, 2008, “High Angular Resolution Diffusion MRI: From Local Estimation to Segmentation and Tractography.”

Descoteaux, 2006, Apparent diffusion coefficients from high angular resolution diffusion imaging: estimation and applications, Magn. Reson. Med, 56, 395, 10.1002/mrm.20948

Descoteaux, 2007, Regularized, fast, and robust analytical q-ball imaging, Magn. Reson. Med, 58, 497, 10.1002/mrm.21277

Descoteaux, 2011, Multiple q-shell diffusion propagator imaging, Med. Image Anal, 15, 603, 10.1016/j.media.2010.07.001

Descoteaux, 2009, Deterministic and probabilistic tractography based on complex fibre orientation distributions, IEEE Trans. Med. Imaging, 28, 269, 10.1109/TMI.2008.2004424

Donoho, 2010, An invitation to reproducible computational research, Biostatistics, 11, 385, 10.1093/biostatistics/kxq028

Ennis, 2006, Orthogonal tensor invariants and the analysis of diffusion tensor magnetic resonance images, Magn. Reson. Med, 55, 136, 10.1002/mrm.20741

Fischl, 2012, Freesurfer, Neuroimage, 62, 774, 10.1016/j.neuroimage.2012.01.021

Fortin, 2012, Tractography in the study of the human brain: a neurosurgical perspective, Can. J. Neurol. Sci, 39, 747, 10.1017/S0317167100015560

Frank, 2001, Anisotropy in high angular resolution diffusion-weighted MRI, Magn. Reson. Med, 45, 935, 10.1002/mrm.1125

Frank, 2002, Characterization of anisotropy in high angular resolution diffusion-weighted MRI, Magn. Reson. Med, 47, 1083, 10.1002/mrm.10156

Fritzsche, 2012, MITK diffusion imaging, Methods Inform. Med, 51, 441, 10.3414/ME11-02-0031

Garyfallidis, 2012, Towards an Accurate Brain Tractography

Garyfallidis, 2011, Dipy - a novel software library for diffusion MR and tractography, 17th Annual Meeting of the Organization for Human Brain Mapping

Garyfallidis, 2012, QuickBundles, a method for tractography simplification, Front. Neurosci, 6, 10.3389/fnins.2012.00175

Garyfallidis, 2013, Constrained spherical deconvolution on signal and ODF values, ISBI HARDI reconstruction challenge 2013

Goebel, 2012, Brainvoyager past, present, future, Neuroimage, 62, 748, 10.1016/j.neuroimage.2012.01.083

Gorgolewski, 2011, Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python, Front. Neuroinform, 5, 10.3389/fninf.2011.00013

Gramfort, 2013, Denoising and fast diffusion imaging with physically constrained sparse dictionary learning, Med. Image Anal, 18, 36-49, 10.1016/j.media.2013.08.006

Halchenko, 2012, Open is not enough. letÅ s take the next step: an integrated, community-driven computing platform for neuroscience, Front. Neuroinform, 6, 10.3389/fninf.2012.00022

Hess, 2006, Q-ball reconstruction of multimodal fiber orientations using the spherical harmonic basis, Magn. Reson. Med, 56, 104, 10.1002/mrm.20931

Jeurissen, 2011, Probabilistic fiber tracking using the residual bootstrap with constrained spherical deconvolution, Hum. Brain Mapp, 32, 461, 10.1002/hbm.21032

2010, Diffusion MRI: Theory, Methods And Applications

Jones, 1999, Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging, Magn. Reson. Med, 42, 515, 10.1002/(SICI)1522-2594(199909)42:3515::AID-MRM143.3.CO;2-H

Jones, 2013, White matter integrity, fiber count, and other fallacies: the do's and don'ts of diffusion MRI, Neuroimage, 73, 239, 10.1016/j.neuroimage.2012.06.081

Koay, 2006, A unifying theoretical and algorithmic framework for least squares methods of estimation in diffusion tensor imaging, J. Magn. Reson, 182, 115, 10.1016/j.jmr.2006.06.020

LeBihan, 1985, Imagerie de diffusion in vivo par résonance magnétique nucléaire, C. R. Acad. Sci. Paris, 301, 1109

Leemans, 2009, ExploreDTI: a graphical toolbox for processing, analyzing, and visualizing diffusion MR data, Proc. Int. Soc. Magn. Reson. Med, 17, 3537

Lenglet, 2006, Statistics on the manifold of multivariate normal distributions: theory and application to diffusion tensor mri processing, J. Math. Imaging Vis, 25, 423, 10.1007/s10851-006-6897-z

Maas, 2005, Diffusion MRI: overview and clinical applications in neuroradiology, Appl. Radiol, 34, 44, 10.37549/AR1383

Maximilien, 2013, Assessing test-driven development at IBM, Proceedings of the 25th International Conference on Software Engineering, 2003

McKinney, 2012, Python for Data Analysis

Menzel, 2011, Accelerated diffusion spectrum imaging in the human brain using compressed sensing, Magn. Reson. Med, 66, 1226, 10.1002/mrm.23064

Merboldt, 1985, Self-diffusion NMR imaging using stimulated echoes, J. Magn. Reson, 64, 479

Mori, 1999, Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging, Annal. Neurol, 45, 265, 10.1002/1531-8249(199902)45:2265::AID-ANA213.0.CO;2-3

Mori, 2005, MRI Atlas of Human White Matter

Morris, 2008, Probabilistic fibre tracking: differentiation of connections from chance events, Neuroimage, 42, 1329, 10.1016/j.neuroimage.2008.06.012

Numano, 2006, In vivo isotropic 3d diffusion tensor mapping of the rat brain using diffusion-weighted 3d mp-rage MRI, Magn. Reson. Imaging, 24, 287, 10.1016/j.mri.2005.12.011

Otsu, 1979, Threshold selection method from gray-level histograms, IEEE Trans. Syst. Man Cybern, 62, 10.1109/TSMC.1979.4310076

Özarslan, 2013, Mean apparent propagator (map) mri: a novel diffusion imaging method for mapping tissue microstructure, Neuroimage, 78, 16, 10.1016/j.neuroimage.2013.04.016

Pajevic, 1999, Color schemes to represent the orientation of anisotropic tissues from diffusion tensor data: application to white matter fiber tract mapping in the human brain, Magn. Reson. Med, 42, 526, 10.1002/(SICI)1522-2594(199909)42:3526::AID-MRM153.3.CO;2-A

Pérez, 2007, Ipython: a system for interactive scientific computing, Comput. Sci. Eng, 9, 21, 10.1109/MCSE.2007.53

Pérez, 2011, Python: an ecosystem for scientific computing, Comput. Sci. Eng, 13, 13, 10.1109/MCSE.2010.119

Pieper, 2006, The NA-MIC Kit: ITK, VTK, pipelines, grids and 3D slicer as an open platform for the medical image computing community, 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro, 2006, 698, 10.1109/ISBI.2006.1625012

Pierpaoli, 1996, Diffusion Tensor MR imaging of human brain, Radiology, 201, 637, 10.1148/radiology.201.3.8939209

Schroeder, 2001, The Visualization Toolkit-User's Guide

Setsompop, 2012, Improving diffusion mri using simultaneous multi-slice echo planar imaging, Neuroimage, 63, 569, 10.1016/j.neuroimage.2012.06.033

Sherbondy, 2005, Exploring connectivity of the brain's white matter with dynamic queries, IEEE Trans. Vis. Comput. Graph, 11, 419, 10.1109/TVCG.2005.59

Smith, 2004, Advances in functional and structural MR image analysis and implementation as FSL, Neuroimage, 23, S208, 10.1016/j.neuroimage.2004.07.051

Song, 2002, Dysmyelination revealed through MRI as increased radial (but unchanged axial) diffusion of water, Neuroimage, 17, 1429, 10.1006/nimg.2002.1267

Sporns, 2005, The human connectome: a structural description of the human brain, PLoS Comput. Biol, 1, e42, 10.1371/journal.pcbi.0010042

Taylor, 1985, The spatial mapping of translational diffusion coefficients by the nmr imaging technique, Phys. Med. Biol, 30, 345, 10.1088/0031-9155/30/4/009

Thomason, 2011, Diffusion imaging, white matter, and psychopathology, Annu. Rev. Clin. Psychol, 7, 63, 10.1146/annurev-clinpsy-032210-104507

Tournier, 2007, Robust determination of the fibre orientation distribution in diffusion mri: non-negativity constrained super-resolved spherical deconvolution, Neuroimage, 35, 1459, 10.1016/j.neuroimage.2007.02.016

Tournier, 2012, MRtrix: diffusion tractography in crossing fiber regions, Int. J. Imaging Syst. Technol, 22, 53, 10.1002/ima.22005

Tournier, 2004, Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution, Neuroimage, 23, 1176, 10.1016/j.neuroimage.2004.07.037

Toussaint, 2007, MedINRIA: medical image navigation and research tool by INRIA, MICCAI'07 Workshop on Interaction in medical image analysis and visualization

Tristan-Vega, 2009, Estimation of fiber orientation probability density functions in high angular resolution diffusion imaging, Neuroimage, 47, 638, 10.1016/j.neuroimage.2009.04.049

Tuch, 2004, Q-ball imaging, Magn. Reson. Med, 52, 1358, 10.1002/mrm.20279

Tuch, 2002, High angular resolution diffusion imaging reveals intravoxel white matter fiber heterogeneity, Magn. Reson. Med, 48, 577, 10.1002/mrm.10268

Tuch, 2002, Diffusion MRI of Complex Tissue Structure

Vaillancourt, 2011, A fiber navigator for neurosurgical planning, Organization for Human Brain Mapping

van der Walt, 2011, The NumPy array: a structure for efficient numerical computation, Comput. Sci. Eng, 13, 22, 10.1109/MCSE.2011.37

Van Essen, 2013, The WU-Minn human connectome project: an overview, Neuroimage, 80, 62, 10.1016/j.neuroimage.2013.05.041

Wandell, 2013, Biological development of reading circuits, Curr. Opin. Neurobiol, 23, 261, 10.1016/j.conb.2012.12.005

Wang, 2007, Diffusion toolkit: a software package for diffusion imaging data processing and tractography, Proc. Int. Soc. Magn. Reson. Med, 15, 3720

Wedeen, 2005, Mapping complex tissue architecture with diffusion spectrum magnetic resonance imaging, Magn. Reson. Med, 54, 1377, 10.1002/mrm.20642

Westin, 1997, Geometrical diffusion measures for MRI from tensor basis analysis, Proc. ISMRM, 97, 1742

Yeatman, 2012, Tract profiles of white matter properties: automating fiber-tract quantification, PLoS ONE, 7, e49790, 10.1371/journal.pone.0049790

Yeh, 2010, Generalized Q-sampling imaging, IEEE Trans. Med. Imaging, 29, 1626, 10.1109/TMI.2010.2045126