Publications - Peter Basser Lab | NICHD - Eunice Kennedy Shriver National Institute of Child Health and Human Development

2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 | 1990

Abstracts

Patents

2024

Kristofor E. Pas, Kadharbatcha S. Saleem, Peter J. Basser, Alexandru V. Avram. Direct segmentation of cortical cytoarchitectonic domains using ultra-high-resolution whole-brain diffusion MRI. bioRxiv 2024.10.14.618245; doi: https://doi.org/10.1101/2024.10.14.618245
B. J. Roth and P. J. Basser, "Correction to "a model of the stimulation of a nerve fiber by electromagnetic induction"," in IEEE Transactions on Biomedical Engineering, vol. 39, no. 11, pp. 1121-1121, Nov. 1992, doi: 10.1109/TBME.1992.10659064 .
Horkay F, Basser PJ, Geissler E. Cartilage extracellular matrix polymers: hierarchical structure, osmotic properties, and function. Soft Matter. 2024 Jul 31;20(30):6033-6043. doi: 10.1039/d4sm00617h. PMID: 39028032.
Teddy X. Cai, Nathan H. Williamson, Rea Ravin, Peter J. Basser. The Diffusion Exchange Ratio (DEXR): A minimal sampling of diffusion exchange spectroscopy to probe exchange, restriction, and time-dependence. Journal of Magnetic Resonance, 2024, 107745, ISSN 1090-7807, https://doi.org/10.1016/j.jmr.2024.107745 .
F Abate, A Adu-Amankwah, KA Ae-Ngibise, FA Agbokey, VA Agyemang, CT Agyemang, C Akgun, J Ametepe, T Arichi, KP Asante, S Balaji, L Baljer, PJ Basser, J Beauchemin, C Bennallick, Y Berhane, Y Boateng-Mensah, NJ Bourke, L Bradford, MMK Bruchhage, R Cano Lorente, P Cawley, M Cercignani, V D Sa, A de Canha, N de Navarro, DC Dean, J Delarosa, KA Donald, A Dvorak, AD Edwards, D Field, H Frail, B Freeman, T George, J Gholam, J Guerrero-Gonzalez, JV Hajnal, R Haque, W Hollander, Z Hoodbhoy, M Huentelman, SK Jafri, DK Jones, F Joubert, T. Karaulanov, MP Kasaro, S Knackstedt, S Kolind, B Koshy, R Kravitz, S Lecurieux Lafayette, AC Lee, B Lena, N Lepore, M Linguraru, E Ljungberg, Z Lockart, E Loth, P Mannam, KM Masemola, R Moran, D Murphy, FL Nakwa, V Nankabirwa, CA Nelson, K North, S Nyame, R O Halloran, J O'Muircheartaigh, BF Oakley, H Odendaal, CM Ongeti, D Onyango, SA Oppong, F Padormo, D Parvez, T Paus, MS Pepper, KS Phiri, M Poorman, JE Ringshaw, J Rogers, M Rutherford, H Sabir, L Sacolick, M Seal, ML Sekoli, T Shama, K Siddiqui, N Sindano, MB Spelke, PE Springer, FE Suleman, PC Sundgren, R Teixeira, W Terekegn, M Traughber, MG Tuuli, J van Rensburg, F Váša, S Velaphi, P Velasco, IM Viljoen, M Vokhiwa, A Webb, C Weiant, N Wiley, P Wintermark, K Yibetal, SCL Deoni, SCR Williams. UNITY: A Low-Field Magnetic Resonance Neuroimaging Initiative to Characterize Neurodevelopment in Low and Middle-Income Settings. Developmental Cognitive Neuroscience, 2024, https://doi.org/10.1016/j.dcn.2024.101397 .
Horkay, F., Basser, P.J. Organization of hyaluronic acid molecules in solutions. MRS Advances (2024). https://doi.org/10.1557/s43580-024-00875-4
Kadharbatcha S Saleem, Alexandru V Avram, Daniel Glen, Vincent Schram, Peter J Basser, The Subcortical Atlas of the Marmoset (“SAM”) monkey based on high-resolution MRI and histology, Cerebral Cortex, Volume 34, Issue 4, April 2024, bhae120, https://doi.org/10.1093/cercor/bhae120
Magdoom KN, Avram AV, Witzel TE, Huang SY, Basser PJ. Water Diffusion in the Live Human Brain is Gaussian at the Mesoscale. bioRxiv [Preprint]. 2024 Apr 14:2024.04.10.588939. doi: 10.1101/2024.04.10.588939. PMID: 38645264; PMCID: PMC11030434.
Ravin R, Cai TX, Li A, Briceno N, Pursley RH, Garmendia-Cedillos M, Pohida T, Wang H, Zhuang Z, Cui J, Morgan NY, Williamson NH, Gilbert MR, Basser PJ. "Tumor Treating Fields" delivered via electromagnetic induction have varied effects across glioma cell lines and electric field amplitudes. Am J Cancer Res. 2024 Feb 15;14(2):562-584. PMID: 38455403.
Erin Santos, William C. Huffman, R. Douglas Fields. Recovery of Node of Ranvier Structure in Optic Nerve under Visual Deprivation. Neuroscience Research, 2024, ISSN 0168-0102. https://doi.org/10.1016/j.neures.2024.03.005.
Witherspoon VJ, Komlosh ME, Benjamini D, Özarslan E, Lavrik N, Basser PJ. Novel pore size-controlled, susceptibility matched, 3D-printed MRI phantoms. Magn Reson Med. 2024; 1-12. http://doi.org/10.1002/mrm.30029

2023

Julian A. Rey, Uzair M. Farid, Christopher M. Najjoum, Alec Brown, Kulam Najmudeen Magdoom, Thomas H. Mareci, and Malisa Sarntinoranont. Perivascular network segmentations derived from high-field MRI and their implications for perivascular and parenchymal mass transport in the rat brain. Sci Rep 13, 9205 (2023). https://doi.org/10.1038/s41598-023-34850-0
Chremos A, Mussel M, Douglas JF, Horkay F. Ion Partition in Polyelectrolyte Gels and Nanogels. Gels. 2023; 9(11):881. https://doi.org/10.3390/gels9110881
Ravin, R., Cai, T. X., Li, A., Briceno, N., Pursley, R. H., Garmendia-Cedillos, M., Pohida, T., Wang, H., Zhuang, Z., Cui, J., Morgan, N. Y., Williamson, N. H., Gilbert, M. R., & Basser, P. J. (2023). "Tumor Treating Fields" delivered via electromagnetic induction have varied effects across glioma cell lines and electric field amplitudes. Preprint. bioRxiv. 2023;2023.01.18.524504. Published 2023 Jan 20. https://pmc.ncbi.nlm.nih.gov/articles/PMC10915321/
Bouhrara, M., Avram, A. V., Kiely, M., Trivedi, A., & Benjamini, D. (2023). Adult lifespan maturation and degeneration patterns in gray and white matter: A mean apparent propagator (MAP) MRI study. Neurobiology of aging, 124, 104–116. https://doi.org/10.1016/j.neurobiolaging.2022.12.016
Edlow BL, Gilmore N, Tromly SL, Deary KB, McKinney IR, Hu CG, Kelemen JN, Maffei C, Tseng CJ, Llorden GR, Healy BC, Masood M, Cali RJ, Baxter T, Yao EF, Belanger HG, Benjamini D, Basser PJ, Priemer DS, Kimberly WT, Polimeni JR, Rosen BR, Fischl B, Zurcher NR, Greve DN, Hooker JM, Huang SY, Caruso A, Smith GA, Szymanski TG, Perl DP, Dams-O'Connor K, Mac Donald CL, Bodien YG. (2023). Optimizing Brain Health of United States Special Operations Forces. Journal of special operations medicine : a peer reviewed journal for SOF medical professionals, 23(4), 47–56. https://doi.org/10.55460/99QW-K0HG
Ferenc Horkay, Peter J. Basser, Erik Geissler. Ion-induced changes in DNA gels. Soft Matter, 2023. https://doi.org/10.1039/D3SM00666B
Mihika Gangolli, Sinisa Pajevic, Joong Hee Kim, Elizabeth B Hutchinson, Dan Benjamini, Peter J Basser. Correspondence of mean apparent propagator MRI metrics with phosphorylated tau and astrogliosis in chronic traumatic encephalopathy. Brain Communications, 2023;. fcad253. https://doi.org/10.1093/braincomms/fcad253
Horkay F, Douglas JF. Evidence of Many-Body Interactions in the Virial Coefficients of Polyelectrolyte Gels. Gels. 2022; 8(2):96. https://doi.org/10.3390/gels8020096
Ferenc Horkay and J. F. Douglas. Influence of solvent quality on the swelling and deswelling and the shear modulus of semi-dilute solution cross-linked poly(vinyl acetate) gels. The Journal of Chemical Physics 158(24). June 2023. https://doi.org/10.1063/5.0156604
Shinjini Kundu, Stephanie Barsoum, Jeanelle Ariza, Amber L Nolan, Caitlin S Latimer, C Dirk Keene, Peter J Basser, Dan Benjamini. Mapping the individual human cortex using multidimensional MRI and unsupervised learning. Brain Communications, 2023;. fcad258, https://doi.org/10.1093/braincomms/fcad258
Alexandros Chremos and Ferenc Horkay. Coexistence of Crumpling and Flat Sheet Conformations in Two-Dimensional Polymer Networks: An Understanding of Aggrecan Self-Assembly. Phys. Rev. Lett. 131, 138101. (September 28 2023). https://doi.org/10.1103/PhysRevLett.131.138101
Kadharbatcha S Saleem, Alexandru V Avram, Cecil Chern-Chyi Yen, Kulam Najmudeen Magdoom, Vincent Schram, Peter J Basser. Multimodal anatomical mapping of subcortical regions in Marmoset monkeys using high-resolution MRI and matched histology with multiple stains. bioRxiv 2023.03.30.534950; doi: https://doi.org/10.1101/2023.03.30.534950
Nathan H. Williamson, Velencia J. Witherspoon, Teddy X. Cai, Rea Ravin, Ferenc Horkay, Peter J. Basser. Low-field, high-gradient NMR shows diffusion contrast consistent with localization or motional averaging of water near surfaces. Magnetic Resonance Letters, 2023. ISSN 2772-5162. https://doi.org/10.1016/j.mrl.2023.03.009
Sinisa Pajevic, Dietmar Plenz, Peter J Basser, R. Douglas Fields. Oligodendrocyte-mediated myelin plasticity and its role in neural synchronization.eLife 12:e81982. https://doi.org/10.7554/eLife.81982
Kulam Najmudeen Magdoom, Alexandru V. Avram, Joelle E. Sarlls, Gasbarra Dario, Peter J. Basser. A Novel Framework for In-vivo Diffusion Tensor Distribution MRI of the Human Brain. NeuroImage, 2023. 120003. https://doi.org/10.1016/j.neuroimage.2023.120003
Nathan H Williamson, Rea Ravin, Teddy X Cai, Melanie Falgairolle, Michael J O’Donovan, Peter J Basser, Water exchange rates measure active transport and homeostasis in neural tissue, PNAS Nexus, 2023;, pgad056, https://doi.org/10.1093/pnasnexus/pgad056

2022

Chremos A, Douglas JF, Basser PJ, Horkay F. Prestressed Composite Polymer Gels as a Model of the Extracellular-Matrix of Cartilage. Gels. 2022; 8(11):707. https://doi.org/10.3390/gels8110707
Alexandru V. Avram, Kadharbatcha S. Saleem, Peter J. Basser. COnstrained Reference frame diffusion TEnsor Correlation Spectroscopic (CORTECS) MRI: A practical framework for high-resolution diffusion tensor distribution imaging. Frontiers. 2022.10.20.512879; https://www.frontiersin.org/articles/10.3389/fnins.2022.1054509/full
Alexandru V. Avram, Kadharbatcha S. Saleem, Michal E. Komlosh, Cecil C. Yen, Frank Q. Ye, Peter J. Basser. High-resolution cortical MAP-MRI reveals areal borders and laminar substructures observed with histological staining. NeuroImage. 2022. https://doi.org/10.1016/j.neuroimage.2022.119653.
Velencia Witherspoon, Michal E Komlosh, Dan Benjamini, Evren Özarslan, Nickolay Lavrik, Peter Basser. Novel Pore Size-Controlled, Susceptibility Matched, 3D-Printed MRI Phantoms. bioRxiv 2022.10.10.511634; doi: https://doi.org/10.1101/2022.10.10.511634
Nathan H Williamson, Rea Ravin, Teddy Cai, Melanie Falgairolle, Michael O'Donovan, Peter Basser. Water exchange rates measure active transport and homeostasis in neural tissue. bioRxiv 2022.09.23.483116; doi: https://doi.org/10.1101/2022.09.23.483116
Dan Benjamini, David S Priemer, Daniel P Perl, David L Brody, Peter J Basser, Mapping astrogliosis in the individual human brain using multidimensional MRI, Brain, 2022. https://doi.org/10.1093/brain/awac298
Chremos A, Douglas JF, Basser PJ, Horkay F. Molecular dynamics study of the swelling and osmotic properties of compact nanogel particles. Soft Matter. 2022 Aug 24;18(33):6278-6290. doi: 10.1039/d2sm00681b. PMID: 35968626.
Kulam Najmudeen Magdoom, Alexandru V. Avram, Joelle E Sarlls, Dario E Gasbarra, Peter J Basser. A Novel Framework for In-vivo Diffusion Tensor Distribution MRI of the Human Brain. bioRxiv 2022.08.15.503969. https://doi.org/10.1101/2022.08.15.503969
Ryan C. Nieuwendaal, Jeffrey D. Wilbur, Dean Welsh, Velencia Witherspoon, Christopher M. Stafford. A method to quantify composition, purity, and cross-link density of the active polyamide layer in reverse osmosis composite membranes using 13C cross polarization magic angle spinning nuclear magnetic resonance spectroscopy. Journal of Membrane Science, Volume 648, 2022, 120346, ISSN 0376-7388, https://doi.org/10.1016/j.memsci.2022.120346 .
Horkay, F and Basser, PJ. Hydrogel composite mimics biological tissues. Soft Matter 18 (23) , pp.4414-4426. https://doi.org/10.1039/D2SM00505K
Zhen Ni, Sinisa Pajevic, Li Chen, Giorgio Leodori, Felipe Vial, Alexandru V. Avram, Yong Zhang, Patrick McGurrin, Leonardo G. Cohen, Peter J. Basser, Mark Hallett. Identifying magnetic stimulation induced electroencephalographic signatures of different neuronal elements in primary motor cortex. Clinical Neurophysiology, 2022.
Magdoom Kulam Najmudeen, Komlosh Michal E., Saleem Kadharbatcha, Gasbarra Dario, Basser Peter J. High Resolution Ex Vivo Diffusion Tensor Distribution MRI of Neural Tissue. Frontiers in Physics 10 2022. https://doi.org/10.3389/fphy.2022.807000
A Chremos, F Horkay, JF Douglas. Influence of network defects on the conformational structure of nanogel particles: From “closed compact” to “open fractal” nanogel particles. The Journal of Chemical Physics 156 (9), 094903. https://doi.org/10.1063/5.0072274
Basser, P. Detection of stroke by portable, low-field MRI: A milestone in medical imaging. Science Advances, Vol 8, Issue 16. (April 20, 2022). https://doi.org/10.1126/sciadv.abp9307
Cai Teddy X., Williamson Nathan H., Ravin Rea, Basser Peter J. Disentangling the Effects of Restriction and Exchange With Diffusion Exchange Spectroscopy. Frontiers in Physics. (March 23, 2022). https://www.frontiersin.org/articles/10.3389/fphy.2022.805793/full
M Mussel, O Lewis, PJ. Basser, F Horkay. Dynamic model of monovalent-divalent cation exchange in polyelectrolyte gels. Physical Review Materials, Vol. 6, Issue 3. (March 2022). https://link.aps.org/doi/10.1103/PhysRevMaterials.6.035602
Dan Benjamini, David S Priemer, Daniel P Perl, David L Brody, Peter J Basser. Astrogliosis mapping in individual brains using multidimensional MRI. bioRxiv 2022.01.10.475717. https://doi.org/10.1101/2022.01.10.475717

2021

Mussel M, Basser PJ, Horkay F. Ion-Induced Volume Transition in Gels and Its Role in Biology. Gels. 2021; 7(1):20. https://doi.org/10.3390/gels7010020
Matan Mussel, Marshall Slemrod. Conservation laws in biology: Two new applications. Quarterly of Applied Mathematics 79 (2021), 479-492. https://doi.org/10.1090/qam/1590
Matan Mussel, Matthias F Schneider. Sound pulses in lipid membranes and their potential function in biology. Progress in Biophysics and Molecular Biology Volume 162, July 2021, Pages 101-110. https://doi.org/10.1016/j.pbiomolbio.2020.08.001
Ferenc Horkay, Jack F. Douglas, and Srinivasa R. Raghavan. Rheological Properties of Cartilage Glycosaminoglycans and Proteoglycans. Macromolecules 2021, 54, 5, 2316–2324. https://doi.org/10.1021/acs.macromol.0c02709
Magdoom, K.N., Pajevic, S., Dario, G. Basser, P. A new framework for MR diffusion tensor distribution. Sci Rep 11, 2766 (2021). https://doi.org/10.1038/s41598-021-81264-x
Zhao, H., Cheng, J., Liu, T., Jiang, J., Koch, F., Sachdev, P. S., Basser, P. J., Wen, W. Orientational changes of white matter fibers in Alzheimer's disease and amnestic mild cognitive impairment. Human brain mapping, 42(16), 5397–5408. https://doi.org/10.1002/hbm.25628
Kadharbatcha S. Saleem, Alexandru V. Avram, Daniel Glen, Cecil Chern-Chyi Yen, Frank Q. Ye, Michal Komlosh, Peter J. Basser. High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology. NeuroImage. 118759. (2021)
Faisal KS, Clulow AJ, Krasowska M, Gillam T, Miklavcic SJ, Williamson NH, Blencowe A. Interrogating the relationship between the microstructure of amphiphilic poly(ethylene glycol-b-caprolactone) copolymers and their colloidal assemblies using non-interfering techniques. J Colloid Interface Sci. Aug 17;606(Pt 2):1140-1152. (2021)
Slator PJ, Palombo M, Miller KL, Westin CF, Laun F, Kim D, Haldar JP, Benjamini D, Lemberskiy G, de Almeida Martins JP, Hutter J. Combined diffusion-relaxometry microstructure imaging: Current status and future prospects. Magn Reson Med. Aug 19. (2021)
F Horkay, A Chremos, JF Douglas, R Jones, J Lou, Y Xia. Comparative experimental and computational study of synthetic and natural bottlebrush polyelectrolyte solutions. The Journal of Chemical Physics 155 (7), 074901. (2021)
Zhao H, Cheng J, Liu T, Jiang J, Koch F, Sachdev PS, Basser PJ, Wen W; Alzheimer's Disease Neuroimaging Initiative. Orientational changes of white matter fibers in Alzheimer's disease and amnestic mild cognitive impairment. Hum Brain Mapp. 2021 Nov;42(16):5397-5408. doi: 10.1002/hbm.25628. Epub 2021 Aug 19. PMID: 34412149.
Alexandros Chremos, Ferenc Horkay, Jack F. Douglas. Structure and conformational properties of ideal nanogel particles in athermal solutions. J. Chem. Phys. 155, 134905 (2021).
Benjamini Dan, Bouhrara Mustapha, Komlosh Michal E., Iacono Diego, Perl Daniel P., Brody David L., Basser Peter J. Multidimensional MRI for Characterization of Subtle Axonal Injury Accelerated Using an Adaptive Nonlocal Multispectral Filter. Frontiers in Physics, Volume 9. (2021)
Susie Y. Huang, Thomas Witzel, Boris Keil, Alina Scholz, Mathias Davids, Peter Dietz, Elmar Rummert, Rebecca Ramb, John E. Kirsch, Anastasia Yendiki, Qiuyun Fan, Qiyuan Tian, Gabriel Ramos-Llordén, Hong-Hsi Lee, Aapo Nummenmaa, Berkin Bilgic, Kawin Setsompop, Fuyixue Wang, Alexandru V. Avram, Michal Komlosh, Dan Benjamini, Kulam Najmudeen Magdoom, Sudhir Pathak, Walter Schneider, Dmitry S. Novikov, Els Fieremans, Slimane Tounekti, Choukri Mekkaoui, Jean Augustinack, Daniel Berger, Alexander Shapson-Coe, Jeff Lichtman, Peter J. Basser, Lawrence L. Wald, Bruce R. Rosen. Connectome 2.0: Developing the next-generation ultra-high gradient strength human MRI scanner for bridging studies of the micro-, meso- and macro-connectome. NeuroImage, Volume 243. (2021)
W Zhang, JF Douglas, A Chremos, FW Starr. (2021). Structure and Dynamics of Star Polymer Films from Coarse-Grained Molecular Simulations. Macromolecules, 54 (12), 5344-5353. https://doi.org/10.1021/acs.macromol.1c00504
Miller, S. R., Yu, S., Pajevic, S., & Plenz, D. Long-term stability of avalanche scaling and integrative network organization in prefrontal and premotor cortex. Network Neuroscience, 5(2), 505–526. (2021). https://doi.org/10.1162/netn_a_00188
Alexandru V. Avram, Joelle E. Sarlls, Peter J. Basser. Whole-Brain Imaging of Subvoxel T1-Diffusion Correlation Spectra in Human Subjects. Frontiers in Neuroscience. (2021). https://doi.org/10.3389/fnins.2021.671465
Dan Benjamini, Diego Iacono, Michal E Komlosh, Daniel P Perl, David L Brody, Peter J Basser. Diffuse axonal injury has a characteristic multidimensional MRI signature in the human brain. Brain. (2021). https://doi.org/10.1093/brain/awaa447
Teddy X. Cai, Nathan H. Williamson, Velencia J. Witherspoon, Rea Ravin, and Peter J. Basser. A single-shot measurement of time-dependent diffusion over sub-millisecond timescales using static field gradient NMR. J. Chem. Phys. (2021). https://doi.org/10.1063/5.0041354
Mussel, M.; Basser, P.J.; Horkay, F. Ion-Induced Volume Transition in Gels and Its Role in Biology. Gels. (2021). https://doi.org/10.3390/gels7010020
Kulam Najmudeen Magdoom, Sinisa Pajevic, Gasbarra Dario, Peter J. Basser. A new framework for MR diffusion tensor distribution. Scientific Reports. (2021). https://doi.org/10.1038/s41598-021-81264-x

2020

JM Sarapas, TB Martin, A Chremos, D Jack F., B Kathryn L. Bottlebrush polymers in the melt and polyelectrolytes in solution share common structural features. Proceedings of National Academy of Science 117(10) 5168-5175. https://www.pnas.org/content/pnas/117/10/5168.full.pdf (PDF 1.2 MB)
A Giuntoli, A Chremos, JF Douglas. Influence of polymer topology on crystallization in thin films. The Journal of Chemical Physics 152 (4), 044501. https://doi.org/10.1063/1.5134983
Lopez, C. G., Horkay, F., Mussel, M., Jones, R. L., & Richtering, W. (2020). Screening lengths and osmotic compressibility of flexible polyelectrolytes in excess salt solutions. Soft Matter, 16(31), 7289-7298. https://doi.org/10.1039/D0SM00464B
Kulam Najmudeen Magdoom, Sinisa Pajevic, Gasbarra Dario, Peter J. Basser. A New Framework for MR Diffusion Tensor Distribution. bioRxiv. (2020). https://doi.org/10.1101/2020.05.01.071118
Dan Benjamini, Elizabeth B. Hutchinson, Michal E. Komlosh, Courtney J. Comrie, Susan C. Schwerin, Guofeng Zhang, Carlo Pierpaoli, Peter J. Basser. Direct and specific assessment of axonal injury and spinal cord microenvironments using diffusion correlation imaging. NeuroImage (2020). http://dx.doi.org/10.1016/j.neuroimage.2020.117195
A Aldroubi, P Basser, N Vieira . Optimal sampling for the determination of calcium metabolism. Kinetic Models of Trace Element 2020.
Horkay Ferenc; Basser, Peter J . Composite Hydrogel Model of Cartilage Predicts Its Load-Bearing Ability. Scientific Reports (Nature Publisher Group) Vol. 10, Iss. 1, (2020). DOI:10.1038/s41598-020-64917-1.
Nathan H. Williamson, Michal E. Komlosh, Dan Benjamini, Peter J. Basser. Limits to flow detection in phase contrast MRI. Journal of Magnetic Resonance Open: 2–3 (2020). https://doi.org/10.1016/j.jmro.2020.100004
Dan Benjamini, Peter J. Basser. Multidimensional correlation MRI. NMR in Biomedicine, (2020). https://doi.org/10.1002/nbm.4226
Zhen Ni, Giorgio Leodori, Felipe Viala, Yong Zhang, Alexandru V. Avram, Sinisa Pajevic, Peter J. Basser, Mark Hallett. Measuring latency distribution of transcallosal fibers using transcranial magnetic stimulation. Brain Stimulation 13:5 (2020). https://doi.org/10.1016/j.brs.2020.08.004
R Ravin, TX Cai, RH Pursley, T Pohida, RZ Freidlin, H Wang, Z Zhuang, AJ Giles, NH Williamson, MR Gilbert, PJ Basser. A Novel In Vitro Device to Deliver Induced Electromagnetic Fields to Cell and Tissue Cultures. Biophysical Journal 13 (2020). https://doi.org/10.1016/j.bpj.2020.11.002
Pas, K., Komlosh, M.E., Perl, D.P. et al. Retaining information from multidimensional correlation MRI using a spectral regions of interest generator. Sci Rep 10, 3246 (2020). https://doi.org/10.1038/s41598-020-60092-5
Horkay, F., Basser, P.J., Geissler, E. Static and dynamic behavior of aggrecan solutions. MRS Advances, (2020). https://www.cambridge.org/core/journals/mrs-advances/article/static-and-dynamic-behavior-of-aggrecan-solutions/B4FE235CE74E4AA9F4D0D888CE5D11E5
Ruiliang Bai, Zhaoqing Li, Chaoliang Sun, Yi-Cheng Hsu, Hui Liang, Peter Basser. Feasibility of filter-exchange imaging (FEXI) in measuring different exchange processes in human brain. NeuroImage 219, 2020. https://doi.org/10.1016/j.neuroimage.2020.117039
A Chremos, F Horkay. (PDF 1.3 MB) Comparison of neutral and charged polyelectrolyte bottlebrush polymers in dilute salt-free conditions. 2020. MRS Advances.
F Horkay, A Chremos, JF Douglas, R L. Jones, J Lou, Y Xia. (PDF 7.7 MB) 2020. Systematic investigation of synthetic polyelectrolyte bottlebrush solutions by neutron and dynamic light scattering, osmometry, and molecular dynamics simulation. The Journal of Chemical Physics 152, 194904.
A Chremos, F Horkay. (PDF 1.2 MB) Disappearance of the polyelectrolyte peak in salt-free solutions. 2020. Physical Review E 102, 012611.
A Chremos. (PDF 3.4 MB) Design of nearly perfect hyperuniform polymeric materials. 2020. Journal of Chemical Physics 153, 054902.
Benjamini D. Nonparametric inversion of relaxation and diffusion correlation data. Advanced Diffusion Encoding Methods in MRI, Ed Topgaard D. Royal Society of Chemistry, London, UK, 2020. DOI: 10.1039/9781788019910-00278
Williamson N, Ravin R, Cai T, Benjamini D, Falgairolle M, O’Donovan M, Basser P. 2020. Real-time measurement of diffusion exchange rate in biological tissue. Journal of Magnetic Resonance 317:106782. DOI: 10.1016/j.jmr.2020.106782
Ni Z, Vial F, Avram A, Leodori G, Pajevic S, Basser P, Hallett M. 2020. Measuring conduction velocity distributions in peripheral nerves using neurophysiological techniques. Clinical Neurophysiology 131:1581-1588. DOI: 10.1016/j.clinph.2020.04.008

2019

Mussel, M., Schneider, M.F. Similarities between action potentials and acoustic pulses in a van der Waals fluid. Sci Rep 9, 2467 (2019). https://doi.org/10.1038/s41598-019-38826-x
Pajevic, S. 2019. “Exploring the Dynamics of Brain Extracellular Space”, Biophysical Journal, 117, 1781–1782.
Mussel M, Horkay F. 2019. Experimental Evidence for Universal Behavior of Ion-Induced Volume Phase Transition in Sodium Polyacrylate Gels. The Journal of Physical Chemistry Letters 10, 7831-7835.
Williamson NH, Ravin R, Benjamini D, Merkle H, Falgairolle M, O’Donovan MJ, Blivis D, Ide D, Cai TX, Ghorashi NS, Bai R, and Basser PJ. 2019. Magnetic resonance measurements of cellular and sub-cellular membrane structures in live and fixed neural tissue. eLife 8:e51101.
Avram A, Bernstein A, Irfanoglu M, Weinkauf C, Cota M, Gai N, Simmons A, Moses A, Turtzo L, Jikaria N et al. 2019. A framework for spatial normalization and voxelwise analysis of diffusion propagators in multiple MAP-MRI data sets. bioRxiv doi: 10.1101/697284
Bernstein AS, Chen NK, Trouard TP. 2019. Bootstrap analysis of diffusion tensor and mean apparent propagator parameters derived from multiband diffusion MRI. Magn Reson Med 82(5):1796-1803.
Ferenc Horkay, Miroslava Dušková-Smrcková (Eds.) Polymer Networks: Structure, Properties and Function. Macromol. Symp, 385, Wiley-VCH. 2019
Horkay F. 2019. Effect of the Ionic Environment on the Supramolecular Structure and Thermodynamics of DNA Gels. Macromol Symp 385:1800199 (1-5).
Mussel M, Basser PJ, Horkay F. 2019. Effects of mono- and divalent cations on the structure and thermodynamic properties of polyelectrolyte gels. Soft Matter 22:4153-4161.
Kaur S, Law C, Williamson N, Kempson I, Popat A, Kumeria T, Santos A. 2019. Environmental Copper Sensor Based on Polyethylenimine-Functionalized Nanoporous Anodic Alumina Interferometers. Analytical Chemistry 91:5011-5020.
Turnbull T, Douglass M, Williamson N, Howard D, Bhardwaj R, Lawrence M, Paterson D, Bezak E, Thierry B, Kempson I. 2019. Cross-Correlative Single-Cell Analysis Reveals Biological Mechanisms of Nanoparticle Radiosensitization. ACS Nano 13:5077-5090.
Williamson N, Dower A, Codd S, Broadbent A, Gross D, Seymour J. 2019. Glass Dynamics and Domain Size in a Solvent-Polymer Weak Gel Measured by Multidimensional Magnetic Resonance Relaxometry and Diffusometry. Phys Rev Lett. 122(6):068001.
Benjamini D, Basser P. 2019. Water mobility spectral imaging of the spinal cord: Parametrization of model-free Laplace MRI. Magnetic Resonance Imaging 56:187-193.
Komlosh M, Benjamini D, Williamson N, Horkay F, Hutchinson E, Basser P. 2019. A novel MRI phantom to study interstitial fluid transport in the glymphatic system. Magnetic Resonance Imaging 56:181-186.
Benjamini D, Komlosh M, Williamson N, Basser P. 2019. Generalized mean apparent propagator (GMAP) MRI to measure and image advective and dispersive flows in medicine and biology. IEEE Transactions on Medical Imaging 38:11-20.
Bai R, Springer C, Plenz D, Basser P. 2019. Brain active transmembrane water cycling measured by MR is associated with neuronal activity. Magn Reson Med 81(2):1280-1295.

2018

Hutchinson EB, Schwerin SC, Radomski KL, Sadeghi N, Komlosh ME, Irfanoglu MO, Juliano SL, and Pierpaoli C. Detection and Distinction of Mild Brain Injury Effects in a Ferret Model Using Diffusion Tensor MRI (DTI) and DTI-Driven Tensor-Based Morphometry (D-TBM).Front Neurosci 12: 573.
Cheng J, Liu T, Shi F, Bai R, Zhang J, Zhu H, Tao D, Basser P. 2018. On Quantifying Local Geometric Structures of Fiber Tracts. Medical Image Computing and Computer Assisted Intervention – MICCAI 2018:392-400.
Hutchinson EB, Schwerin SC, Radomski KL, Sadeghi N, Komlosh ME, Irfanoglu MO, Juliano SL, and Pierpaoli C. (2018) Detection and Distinction of Mild Brain Injury Effects in a Ferret Model Using Diffusion Tensor MRI (DTI) and DTI-Driven Tensor-Based Morphometry (D-TBM). Front Neurosci 12: 573.
Chandran P, Dimitriadis E, Mertz E, Horkay F. 2018. Microscale mapping of extracellular matrix elasticity of mouse joint cartilage: an approach to extracting bulk elasticity of soft matter with surface roughness. Soft Matter 14:2879-2892.
Horkay F, Basser P, Hecht AM, Geissler E. 2018. Microstructure and Dynamic Properties of Aggrecan Assemblies. MRS Advances 3:1589-1595.
Horkay F, Basser P, Hecht AM, Geissler E. 2018. Ionic effects in semi-dilute biopolymer solutions: A small angle scattering study. The Journal of Chemical Physics 149:163312.
Chandran P, Dimitriadis EK, Basser PJ, and Horkay F. 2018. A Nanoindentation Approach To Assess the Mechanical Properties of Heterogeneous Biological Tissues with Poorly Defined Surface Characteristics. In: Horkay F, Douglas JF, Del Gado E, ed. by. ACS Symposium Series Volume 1296: Gels and Other Soft Amorphous Solids. Washington, DC: American Chemical Society. p. 265-290.
Horkay F, Douglas JF. 2018. Polymer Gels: Basics, Challenges, and Perspectives. In: Horkay F, Douglas JF, Del Gado E, ed. by. ACS Symposium Series Volume 1296: Gels and Other Soft Amorphous Solids. Washington, DC: American Chemical Society. p. 1-13.
Horkay F, Douglas JF, Del Gado E. 2018. Preface. In: Horkay F, Douglas JF, Del Gado E, ed. by. ACS Symposium Series Volume 1296: Gels and Other Soft Amorphous Solids. Washington, DC: American Chemical Society. p. ix-x.
Dutta D, Woo D, Lee P, Pajevic S, Bukalo O, Huffman W, Wake H, Basser P, SheikhBahaei S, Lazarevic V et al. (PDF 1.5 MB) 2018. Regulation of myelin structure and conduction velocity by perinodal astrocytes. Proceedings of the National Academy of Sciences:201811013.
Komlosh M, Benjamini D, Hutchinson E, King S, Haber M, Avram A, Holtzclaw L, Desai A, Pierpaoli C, Basser P. (PDF 1.2 MB) 2018. Using double pulsed-field gradient MRI to study tissue microstructure in traumatic brain injury (TBI). Microporous and Mesoporous Materials 269:156-159.
Benjamini D, Basser P. 2018. Towards clinically feasible relaxation-diffusion correlation MRI using MADCO. Microporous and Mesoporous Materials 269:93-96.
Avram A, Sarlls J, Basser P. 2018. Measuring non-parametric distributions of intravoxel mean diffusivities using a clinical MRI scanner. NeuroImage 185:255-262.
Cai T, Benjamini D, Komlosh M, Basser P, Williamson N. 2018. Rapid detection of the presence of diffusion exchange. Journal of Magnetic Resonance 297:17-22.
Yongqin Zhang, Feng Shi, Jian Cheng, Li Wang, Pew-Thian Yap, Dinggang Shen , "Longitudinally Guided Super-Resolution of Neonatal Brain Magnetic Resonance Images", IEEE Transactions on Cybernetics, 2018.
Cheng J and Basser PJ. 2018. Director Field Analysis (DFA): Exploring Local White Matter Geometric Structure in Diffusion MRI. Medical Image Analysis 43:112-128.
Thomas C, Sadeghi N, Nayak A, Trefler A, Sarlls J, Baker CI, Pierpaoli C. 2018. Impact of time-of-day on diffusivity measures of brain tissue derived from diffusion tensor imaging. NeuroImage 173:25-34.
Avram AV, Sarlls JE, Hutchinson E, and Basser PJ. 2018. Efficient experimental designs for isotropic generalized diffusion tensor MRI (IGDTI). Magn Reson Med 79:180–194.
Cheng J, Shen D, Yap PT, and Basser PJ. 2018. Single- and Multiple-Shell Uniform Sampling Schemes for Diffusion MRI Using Spherical Codes. IEEE Trans Med Imaging 37(1):185–199.
Bai R, Springer CS, Plenz D, and Basser PJ. 2018. Fast, Na+/K+ pump driven, steady-state transcytolemmal water exchange in neuronal tissue: A study of rat brain cortical cultures. Magn Reson Med 79:3207–3217. doi:10.1002/mrm.26980.
Hutchinson EB, Schwerin SC, Avram AV, Juliano SL, Pierpaoli C. 2018. Diffusion MRI and the detection of alterations following traumatic brain injury. J Neurosci Res 96(4):612-625.

2017

Guan H, Liu T, Jiang J, Tao D, Zhang J, Niu H, Zhu W, Wang Y, Cheng J, Kochan N et al. 2017. Classifying MCI Subtypes in Community-Dwelling Elderly Using Cross-Sectional and Longitudinal MRI-Based Biomarkers. Frontiers in Aging Neuroscience 9:309.
Horkay F, Nishi K, and Shibayama M. 2017. Decisive test of the ideal behavior of tetra-PEG gels. J Chem Phys 146:164905.
Hutchinson E, Avram A, Irfanoglu M, Koay C, Barnett A, Komlosh M, Özarslan E, Schwerin S, Juliano S, Pierpaoli C. 2017. Analysis of the effects of noise, DWI sampling, and value of assumed parameters in diffusion MRI models. Magnetic Resonance in Medicine 78:1767-1780.
Schwerin S, Hutchinson E, Radomski K, Ngalula K, Pierpaoli C, Juliano S. 2017. Establishing the ferret as a gyrencephalic animal model of traumatic brain injury: Optimization of controlled cortical impact procedures. Journal of Neuroscience Methods 285:82-96.
Haber M, Hutchinson E, Sadeghi N, Cheng W, Namjoshi D, Cripton P, Irfanoglu M, Wellington C, Diaz-Arrastia R, Pierpaoli C. 2017. Defining an Analytic Framework to Evaluate Quantitative MRI Markers of Traumatic Axonal Injury: Preliminary Results in a Mouse Closed Head Injury Model. eNeuro 4:ENEURO.0164-17.2017.
Benjamini D and Basser PJ. 2017. Magnetic resonance microdynamic imaging reveals distinct tissue microenvironments. NeuroImage 163:183-196.
Gasbarra D, Pajevic S, and Basser PJ. 2017. Eigenvalues of Random Matrices with Isotropic Gaussian Noise and the Design of Diffusion Tensor Imaging Experiments. SIAM J Imaging Sci 10(3):1511-1548.
Hutchinson EB, Schwerin SC, Radomski KL, Sadeghi N, Jenkins J, Komlosh ME, Irfanoglu MO, Juliano SL, Pierpaoli C. 2017. Population based MRI and DTI templates of the adult ferret brain and tools for voxelwise analysis. NeuroImage 152:575-589.
Horkay F, Jonsson E. 2017. Polymer Gels: Synthesis, Characterization and Applications. 1st ed. Weinheim, Germany: Wiley-VCH.
Horkay F, Basser P, Hecht A, Geissler E. 2017. Structure and Properties of Cartilage Proteoglycans. Macromolecular Symposia 372:43-50.
Cheng J, Basser PJ. 2017. Director Field Analysis to Explore Local White Matter Geometric Structure in Diffusion MRI. In: Niethammer M. et al. (eds) Information Processing in Medical Imaging. IPMI 2017. Lecture Notes in Computer Science, vol 10265. Springer, Cham.
Komlosh ME, Benjamini D, Barnett AS, Schram V, Horkay F, Avram AV, and Basser PJ. 2017. Anisotropic phantom to calibrate high-q diffusion MRI methods. Journal of Magnetic Resonance 275:19–28.
Benjamini D, Komlosh ME, and Basser PJ. 2017. Imaging Local Diffusive Dynamics Using Diffusion Exchange Spectroscopy MRI. Phys. Rev. Lett. 118:158003.
Puwal S, Roth BJ, and Basser PJ. 2017. Heterogeneous anisotropic magnetic susceptibility of the myelin-water layers causes local magnetic field perturbations in axons. NMR in Biomedicine 30(4):e3628.

2016

Arrigoni F, Peruzzo D, Gagliardi C, Maghini C, Colombo P, Iammarrone F, Pierpaoli C, Triulzi F, Turconi A. 2016. Whole-Brain DTI Assessment of White Matter Damage in Children with Bilateral Cerebral Palsy: Evidence of Involvement beyond the Primary Target of the Anoxic Insult. American Journal of Neuroradiology 37(7):1347-53.
Jenkins J, Chang L, Hutchinson E, Irfanoglu M, Pierpaoli C. 2016. Harmonization of methods to facilitate reproducibility in medical data processing: Applications to diffusion tensor magnetic resonance imaging. 2016 IEEE International Conference on Big Data (Big Data):3992-3994.
Rao S, Ibrahim JG, Cheng J, Yap P-T, and Zhu H. 2016. SR-HARDI: Spatially Regularizing High Angular Resolution Diffusion Imaging. J Comput Graph Stat. 25(4):1195–1211.
Cheng J, Zhu H. 2016. Diffusion Magnetic Resonance Imaging (dMRI). In: Ombao H, Lindquist M, Thompson W, Aston J, ed. by. Handbook of Neuroimaging Data Analysis. Boca Raton, Florida: CRC Press. p. 65-107.
Curtis KA, Miller D, Millard P, Basu S, Horkay F, Chandran PL. 2016. Unusual Salt and pH Induced Changes in Polyethylenimine Solutions. PLoS One 11(9):e0158147.
Gao Y, Nieuwendaal R, Dimitriadis E, Hammouda B, Douglas J, Xu B, Horkay F. 2016. Supramolecular Self-Assembly of a Model Hydrogelator: Characterization of Fiber Formation and Morphology. Gels 2(4). pii: 27.
Horkay F, Basser PJ, Hecht A-M, and Geissler E. 2016. Cartilage: Multiscale Structure and Biomechanical Properties. MRS Advances 1(8):509–519.
Bai R, Benjamini D, Cheng J, and Basser PJ. 2016. Fast, accurate 2D-MR relaxation exchange spectroscopy (REXSY): Beyond compressed sensing. J. Chem. Phys. 145:154202.
Hutchinson EB, Schwerin SC, Radomski KL, Irfanoglu MO, Juliano SL, Pierpaoli CM. 2016. Quantitative MRI and DTI Abnormalities During the Acute Period Following CCI in the Ferret. Shock 46(3 Suppl 1):167-76.
Walker L, Chang LC, Nayak A, Irfanoglu MO, Botteron KN, McCracken J, McKinstry RC, Rivkin MJ, Wang DJ, Rumsey J, Pierpaoli C, Brain Development Cooperative Group. 2016. The diffusion tensor imaging (DTI) component of the NIH MRI study of normal brain development (PedsDTI). Neuroimage 124(Pt B):1125-30.
Avram AV, Sarlls JE, Barnett AS, Özarslan E, Thomas C, Irfanoglu MO, Hutchinson E, Pierpaoli C, Basser PJ. 2016. Clinical feasibility of using mean apparent propagator (MAP) MRI to characterize brain tissue microstructure. Neuroimage 127:422-34.
Horkay F and Basser PJ. 2016. Osmotic Properties of Cartilage. In: Xia Y, Momot K, editors. Biophysics and Biochemistry of Cartilage by NMR and MRI. Cambridge: Royal Soc Of Chemistry.
Wenger C, Salvador R, Basser P, Miranda P. 2016. Improving TTFields treatment efficacy in patients with glioblastoma using personalized array layouts. International Journal of Radiation Oncology • Biology • Physics 94(5):1137-1143.
Benjamini D and Basser PJ. 2016. Use of marginal distributions constrained optimization (MADCO) for accelerated 2D MRI relaxometry and diffusometry. Journal of Magnetic Resonance 271:40-5.
Benjamini D, Komlosh ME, Holtzclaw LA, Nevo U, Basser PJ. 2016. White matter microstructure from nonparametric axon diameter distribution mapping. NeuroImage 135:333-44.
Irfanoglu MO, Nayak A, Jenkins J, Hutchinson EB, Sadeghi N, Thomas CP, and Pierpaoli C. 2016. DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures. Neuroimage 132:439–454.
Bai R, Stewart CV, Plenz D, and Basser PJ. 2016. Assessing the sensitivity of diffusion MRI to detect neuronal activity directly. Proc Natl Acad Sci USA 113(12):E1728-37.
Trefler A, Sadeghi N, Thomas AG, Pierpaoli C, Baker CI, and Thomas, C. 2016. Impact of time-of-day on brain morphometric measures derived from T1-weighted magnetic resonance imaging. NeuroImage 133:41–52.
Koay CG, Yeh P-H, Ollinger JM, Irfanoglu MO, Pierpaoli C, Basser PJ, Oakes TR, Riedy G. 2016. Tract Orientation and Angular Dispersion Deviation Indicator (TOADDI): A framework for single-subject analysis in diffusion tensor imaging. NeuroImage 126:151–63.
Wu Y, Liang J, Horkay F, and Libera M. 2016. Antimicrobial Loading into and Release from Poly(ethylene glycol)/Poly(acrylic acid) Semi-interpenetrating Hydrogels. Inc. J. Polym. Sci. Part B: Polym. Phys. 54:64–72.

2015

Bai R. 2015. Quantitative Study of Water Dynamics in Biomimetic Models and Living Tissue by NMR and MRI: Perspective on Direct Detection Neuronal Activity [thesis]. College Park: University of Maryland, College Park.
Berl MM, Walker L, Modi P, Irfanoglu MO, Sarlls JE, Nayak A, and Pierpaoli C. 2015. Investigation of vibration-induced artifact in clinical diffusion-weighted imaging of pediatric subjects. Hum Brain Mapp 36(12):4745-57.
Polonara G, Mascioli G, Foschi N, Salvolini U, Pierpaoli C, Manzoni T, Fabri M, Barbaresi P. 2015. Further Evidence for the Topography and Connectivity of the Corpus Callosum: An fMRI Study of Patients with Partial Callosal Resection. Journal of Neuroimaging 25(3):465–73.
Reveley C, Seth AK, Pierpaoli C, Silva AC, Yu D, Saunders RC, Leopold DA, Ye FQ. 2015. Superficial white matter fiber systems impede detection of long-range cortical connections in diffusion MR tractography. Proc Natl Acad Sci USA 112(21):E2820-8.
Mascioli G, Berlucchi G, Pierpaoli C, Salvolini U, Barbaresi P, Fabri M, Polonara G. 2015. Functional MRI cortical activations from unilateral tactile-taste stimulations of the tongue. Physiol Behav 151:221-9.
Pujol S, Wells W, Pierpaoli C, Brun C, Gee J, Cheng G, Vemuri B, Commowick O, Prima S, Stamm A, Goubran M, Khan A, Peters T, Neher P, Maier-Hein KH, Shi Y, Tristan-Vega A, Veni G, Whitaker R, Styner M, Westin CF, Gouttard S, Norton I, Chauvin L, Mamata H, Gerig G, Nabavi A, Golby A, Kikinis R. 2015. The DTI Challenge: Toward Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery. J Neuroimaging 25(6):875-82.
Horkay F. 2015. Interaction of Cartilage Biopolymers. Macromol. Symp. 358:78–84.
Horkay F and Shibayama M. 2015. Preface. Macromol. Symp. 358:9.
Paulsen JL, Özarslan E, Komlosh ME, Basser PJ, and Song Y-Q. 2015. Detecting compartmental non-Gaussian diffusion with symmetrized double-PFG MRI. NMR Biomed. 28(11):1550-6.
Huang P, Gao Y, Lin J, Hu H, Liao HS, Yan X, Tang Y, Jin A, Song J, Niu G, Zhang G, Horkay F, Chen X. 2015. Tumor-Specific Formation of Enzyme-Instructed Supramolecular Self-Assemblies as Cancer Theranostics. ACS Nano 9(10):9517-27.
Horkay F, Basser PJ, Hecht AM, Geissler E. 2015. Effect of calcium/sodium ion exchange on the osmotic properties and structure of polyelectrolyte gels. Proc Inst Mech Eng H. 229(12):895-904.
Horkay F. (PDF 383 KB) 2015. Tissue science and stem cell research [editorial]. Stem Cell Fundamentals and Practice 1:9.
Roth BJ, Puwal S, and Basser PJ. 2015. Local magnetic field perturbations caused by magnetic susceptibility heterogeneity in myelin-water layers within an axon. J. Coupled Syst. Multiscale Dyn. 3(3):228–232.
Bai R, Klaus A, Bellay T, Stewart C, Pajevic S, Nevo U, Merkle H, Plenz D, and Basser PJ. 2015. Simultaneous calcium fluorescence imaging and MR of ex vivo organotypic cortical cultures: a new test bed for functional MRI. NMR Biomed 28(12):1726-38.
Ozarslan E, Memic M, Avram AV, Afzali M, Basser PJ, Westin C-F. 2015. Rotating field gradient (RFG) MR offers improved orientational sensitivity. In Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, New York, NY. 16-19 April 2015. p 955-958.
Moakher M and Basser PJ. 2015. Fiber Orientation Distribution Functions and Orientation Tensors for Different Material Symmetries. In: Hotz I, Schultz T, editors. Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Switzerland: Springer International Publishing. p 37-71.
Wenger C, Salvador R, Basser PJ, and Miranda PC. 2015. The electric field distribution in the brain during TTFields therapy and its dependence on tissue dielectric properties and anatomy: a computational study. Physics in Medicine and Biology 60(18):7339-57.
Shi F, Cheng J, Wang L, Yap P-T, Shen D. 2015. LRTV: MR image super-resolution with low-rank and total variation regularizations. IEEE transactions on Medical Imaging 34(12):2459–66.
Cheng J, Shen D, Basser PJ, Yap P-T. 2015. Joint 6D k-q Space Compressed Sensing for Accelerated High Angular Resolution Diffusion MRI. In: Ourselin S, Alexander DC, Westin C-F, Cardoso MJ, editors. Information Processing in Medical Imaging. 24th International Conference, IPMI; 2015 June 28 – July 3; Sabhal Mor Ostaig, Isle of Skye, UK. Switzerland: Springer International Publishing. doi: 10.1007/978-3-319-19992-4_62
Bai R, Cloninger A, Czaja W, Basser PJ. 2015. Efficient 2D MRI relaxometry using compressed sensing. J Magn Reson. 255:88-99.
Fields RD, Woo DH, and Basser PJ. 2015. Glial regulation of the neuronal connectome through local and long-distant communication. Neuron 86(2):374-86.
Irfanoglu MO, Modi P, Nayak A, Hutchinson EB, Sarlls J, and Pierpaoli C. 2015. DR-BUDDI (Diffeomorphic Registration for Blip-Up blip-Down Diffusion Imaging) method for correcting echo planar imaging distortions. NeuroImage 106:284–299.
Thomas C, Avram A, Pierpaoli C, and Baker C. 2015. Diffusion MRI properties of the human uncinate fasciculus correlate with the ability to learn visual associations. Cortex 72:65–78.
Sadeghi N, Nayak A, Walker L, Irfanoglu MO, Albert P, Pierpaoli C, and Brain Development Cooperative Group. 2015. Analysis of the contribution of experimental bias, experimental noise, and inter-subject biological variability on the assessment of developmental trajectories in diffusion MRI studies of the brain. NeuroImage 109:480-92.

2014

Eliav U, Komlosh ME, Basser PJ, and Navon G. 2014. Collagen composition and content-dependent contrast in porcine annulus fibrosus achieved by using double quantum and magnetization transfer filtered UTE MRI. Magn Reson Med 71(1):388-93.
Pierpaoli C, Ferrante L, Manzoni T, Fabri M. 2014. Anatomical or mirror mode imitation? A behavioral approach. Arch Ital Biol 152(1):20-31.
Toke ER, Lorincz O, Csiszovszki Z, Somogyi E, Felföldi G, Molnár L, Szipocs R, Kolonics A, Malissen B, Lori F, Trocio J, Bakare N, Horkay F, Romani N, Tripp CH, Stoitzner P, Lisziewicz J. 2014. Exploitation of Langerhans cells for in vivo DNA vaccine delivery into the lymph nodes. Gene Ther 21(6):566-74.
Ducharme S, Albaugh MD, Hudziak JJ, Botteron KN, Nguyen TV, Truong C, Evans AC, Karama S, Brain Development Cooperative Group. 2014. Anxious/depressed symptoms are linked to right ventromedial prefrontal cortical thickness maturation in healthy children and young adults. Cereb Cortex 24(11):2941-50.
Gao Y, Nieuwendaal R, Hammouda B, Berciu C, Nicastro D, Douglas J, Xu B, and Horkay F. 2014. Supramolecular Self-Assembly Inside Living Mammalian Cells. MRS Proceedings 1622:85-93.
Horkay, Ferenc, Noshir A. Langrana, Mitsuhiro Shibayama, and Sandip Basu. (PDF 114 KB) "Preface." Preface. Fundamentals of Gels and Self-assembled Polymer Systems: Symposium Held December 1-6, 2013, Boston, Massachusetts, U.S.A. Warrendale, PA: Materials Research Society, 2014.
Chandran PL, Dimitriadis EK, Lisziewicz J, Speransky V, and Horkay F. 2014. DNA Nanoparticles with Core–shell Morphology. Soft Matter 10(38):7653-60.
Benjamini D and Basser PJ. 2014. Joint radius-length distribution as a measure of anisotropic pore eccentricity: An experimental and analytical framework. J Chem Phys 141(21):214202.
Thomas C, Ye FQ, Irfanoglu MO, Modi P, Kadharbatcha SS, Leopold DA, and Pierpaoli C. 2014. Anatomical accuracy of brain connections derived from diffusion MRI tractography is inherently limited. Proc Natl Acad Sci USA 111(46):16574–9.
Irfanoglu MO, Modi P, Nayak A, Knutsen A, Sarlls J, Pierpaoli C. 2014. DR-BUDDI: diffeomorphic registration for blip up-down diffusion imaging. Med Image Comput Comput Assist Interv 17(Pt 1):218-26.
Steffen-Smith E, Sarlls J, Pierpaoli C, Shih J, Bent R, Walker L, Warren K. 2014. Diffusion Tensor Histogram Analysis of Pediatric Diffuse Intrinsic Pontine Glioma. BioMed Research International 2014:1-9.
Cloninger A, Czaja W, Bai R, and Basser PJ. 2014. Solving 2D Fredholm Integral from Incomplete Measurements Using Compressive Sensing. SIAM J. Imaging Sci. 7(3):1775–1798.
Pajevic S, Basser PJ, and Fields RD. 2014. Role of myelin plasticity in oscillations and synchrony of neuronal activity. Neuroscience 276:135–147.
Benjamini D, Komlosh ME, Basser PJ, Nevo U. 2014. Nonparametric pore size distribution using d-PFG: Comparison to s-PFG and migration to MRI. J Magn Reson 246:36-45.
Bai R, Koay CG, Hutchinson E, and Basser PJ. 2014. A framework for accurate determination of the T2 distribution from multiple echo magnitude MRI images. J Magn Reson 244:53-63.
Basser PJ, Pajevic S, Pierpaoli C, Duda J, and Aldroubi A. 2000. In Vivo Fiber Tractography Using DT-MRI Data. Magn Reson Med 44:625–632. Rpt. in "Magnetic Resonance in Medicine at 30: 30 Magnetic Resonance in Medicine Papers That Helped Shape Our Field." Ed. Matt A. Bernstein. Magn Reson Med (2014): n. pag. Wiley Online Library. Web.
- * Reproduced for a special Magnetic Resonance in Medicine honorary issue
Miranda PC, Mekonnen A, Salvador R, and Basser PJ. 2014. Predicting the electric field distribution in the brain for the treatment of glioblastoma. Phys. Med. Biol. 59(15):4137-47.
Avram AV, Guidon A, Truong T, Liu C, and Song AW. 2014. Dynamic and Inherent B0 Correction for DTI Using Stimulated Echo Spiral Imaging. Magnetic Resonance in Medicine 71(3):1044-53.
Boukari H, Silva C, Nossal R, Horkay F. 2014. Nanoprobe Diffusion in Poly(Vinyl-alcohol) Gels and Solutions: Effects of pH and Dehydration. MRS Proceedings 1622:135-145.
Anyaeji C, Basser P, Horkay F. 2014. Cartilage: Biomimetic Study of the Extracellular Matrix. MRS Proceedings 1622:61-68.
Benjamini D, Eliav U, Nevo U, Basser P, Horkay F. 2014. Assessment of Functional Properties of Cartilage using Double Quantum Filtered MRI. MRS Proceedings 1622:41-48.
Bai R, Basser PJ, Briber RM, and Horkay F. (PDF 396 KB) 2014. NMR water self-diffusion and relaxation studies on sodium polyacrylate solutions and gels in physiologic ionic solutions. J Appl Polym Sci 131(6).
Basser PJ and Özarslan E. 2014. Introduction to Diffusion MR. In: H. Johansen-Berg and T. Behrens, editors. Diffusion MRI: From Quantitative Measurement to In-vivo Neuroanatomy. 2nd edition. Waltham, MA: Academic Press. p. 3-9.

2013

Gao Y, Kuang Y, Du X, Zhou J, Chandran P, Horkay F, and Xu B. 2013. Imaging self-assembly dependent spatial distribution of small molecules in a cellular environment. Langmuir 29(49):15191-200.
Horkay F. 2013. Ion Polymer Interactions in DNA Solutions and Gels. Macromol. Symp. 329:19–26.
Horkay F, Basser PJ, Hecht A-M and Geissler E. (PDF 668 KB) 2013. Structure and Interactions in Hyaluronic Acid Solutions. Polymeric Materials: Science & Engineering 108:111-112.
Bowman CN, and Ferenc Horkay. 2013. Preface. Macromolecular Symposia 329:1.
Horkay F. 2013. Large-Scale Structural Characterization of Biopolymer Systems by Small-Angle Neutron Scattering. In: Thomas S, Durand D, Chassenieux C, and Jyotishkumar P, editors. Handbook of Biopolymer-Based Materials: From Blends and Composites to Gels and Complex Networks. 1st edition. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA. p. 583-610.
Walker L, Curry M, Nayak A, Lange N, Pierpaoli C, and the Brain Development Cooperative Group. 2013. A Framework for the Analysis of Phantom Data in Multicenter Diffusion Tensor Imaging Studies. Human Brain Mapping 34:2439–2454.
Kateb B, Yamamoto V, Basser P, Roy M, Levy L, Tajbakhsh J, Steinberg G, Rosen A, Black KL, Teo C, Sidhu K, Berger M, and Grundfest W. 2013. Nanoneuroscience and Nanoneurosurgery: A Key Component of President Obama's Brain Mapping Initiative. In Kateb B, Heiss JD, editors. The Textbook of Nanoneuroscience and Nanoneurosurgery. Boca Raton, Florida: CRC Press. p. 547-556.
Özarslan E, Koay CG, Shepherd TM, Komlosh ME, Irfanoglu MO, Pierpaoli C, and Basser PJ. 2013. Mean Apparent Propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure. Neuroimage 78:16-32.
Komlosh ME, Özarslan E, Lizak MJ, Horkayne-Szakaly I, Freidlin RZ, Horkay F, and Basser PJ. (PDF 1.5 MB) 2013. Mapping average axon diameters in porcine spinal cord white matter and rat corpus callosum using d-PFG MRI. Neuroimage 78:210–216.
Albaugh MD, Ducharme S, Collins DL, Botteron KN, Althoff RR, Evans AC, Karama S, Hudziak JJ. 2013. Evidence for a cerebral cortical thickness network anti-correlated with amygdalar volume in healthy youths: Implications for the neural substrates of emotion regulation. NeuroImage 71:42-9.
Pajevic, S and Basser, PJ. 2013. An optimum principle predicts the distribution of axon diameters in normal white matter. PLoS ONE 8(1): e54095.
Özarslan E, Koay CG, Basser PJ. 2013. Simple harmonic oscillator based reconstruction and estimation for one-dimensional q-space magnetic resonance (1D-SHORE). In: Andrews TD, Balan R, Benedetto JJ, Czaja W, and Okoudjou KA, editors. Excursions in Harmonic Analysis: The February Fourier Talks at the Norbert Wiener Center. New York: Springer Science + Business Media. p. 373–400.
Avram AV, Özarslan E, Sarlls JE, Basser PJ. 2013. In vivo detection of microscopic anisotropy using quadruple pulsed-field gradient (qPFG) diffusion MRI on a clinical scanner. Neuroimage 64:229–39.

2012

Walker L, Gozzi M, Lenroot R, Thurm A, Behseta B, Swedo S, Pierpaoli C. 2012. Diffusion tensor imaging in young children with autism: biological effects and potential confounds. Biol Psychiatry 72(12):1043–51.
Ducharme S, Hudziak JJ, Botteron KN, Albaugh MD, Nguyen TV, Karama S, Evans AC. 2013. Decreased regional cortical thickness and thinning rate are associated with inattention symptoms in healthy children. J Am Acad Child Adolesc Psychiatry 51(1):18–27.e2.
Waber DP, Forbes PW, Almli CR, Blood EA. 2012. Four-year longitudinal performance of a population-based sample of healthy children on a neuropsychological battery: the NIH MRI study of normal brain development. J Int Neuropsychol Soc 18(2):179–90.
Nguyen TV, McCracken J, Ducharme S, Botteron KN, Mahabir M, Johnson W, Israel M, Evans AC, Karama S. 2012. Testosterone-Related Cortical Maturation Across Childhood and Adolescence. Cereb Cortex 23(6):1424–32.
Khundrakpam BS, Reid A, Brauer J, Carbonell F, Lewis J, Ameis S, Karama S, Lee J, Chen Z, Das S, Evans AC; Brain Development Cooperative Group. 2012. Developmental Changes in Organization of Structural Brain Networks. Cereb Cortex 23(9):2072–85.
Pasternak O, Sochen N, and Basser PJ. Metric Selection and Diffusion Tensor Swelling. In: Laidlaw DH, Vilanova A, editors. New Developments in the Visualization and Processing of Tensor Fields. Berlin: Springer Berlin Heidelberg; 2012. p. 323–336.
Chandran PL, Horkay F. 2012. Aggrecan, an Unusual Polyelectrolyte: Review of Solution Behavior and Physiological Implications. Acta Biomaterialia 8(1):3–12.
Lorincz O, Toke ER, Somogyi E, Horkay F, Chandran PJ, Douglas JF, Szebeni J, Lisziewicz J. 2012. Structure and Biological Activity of Pathogen-like Synthetic Nanomedicines. Nanomedicine 8(4):497-506.
Chandran PL, Dimitriadis EK, Horkay F. 2012. Probing DNA assembly into nanoparticles with short DNA. MRS Proceedings 1418:mrsf11–1418-ll02–09.
Silva C, Horkayne-Szakaly I, Chandran P, Dimitriadis EK, Lin D, Papanicolas C, Basser PJ, Horkay F. 2012. Depth dependent osmotic and swelling properties of cartilage. MRS Proceedings 1418:mrsf11–1418-ll03–08.
Horkay F. 2012. Interactions of Cartilage Extracellular Matrix Macromolecules. J Polym Sci B Polym Phys 50(24):1699-1705.
Horkay F, Narayan R, Langrana N, Weiss R. et al. (eds) Gels and Biomedical Materials, Materials Research Society, Volume 1418, 1-253, Cambridge University Press, 2012.
Freidlin RZ, Kakareka JW, Pohida TJ, Komlosh ME, Basser PJ. 2012. A spin echo sequence with a single-sided bipolar diffusion gradient pulse to obtain snapshot diffusion weighted images in moving media. J Mag Res. 221:24–31.
Horkay F, Basser PJ, Hecht AM, Geissler E. 2012. Chondroitin Sulfate in Solution: Effects of Mono- and Divalent Salts. Macromolecules 45(6):2882-2890.
Brain Development Cooperative Group. 2012. Total and Regional Brain Volumes in a Population-Based Normative Sample from 4 to 18 Years: The NIH MRI Study of Normal Brain Development. Cerebral Cortex 22(1):1-12.
Eliav U, Komlosh M, Basser PJ, and Navon G. 2012. Characterization and mapping of dipolar interactions within macromolecules in tissues using a combination of DQF, MT and UTE MRI. NMR Biomed 25(10):1152-9.
Chang L-C, Walker L, and Pierpaoli C. 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(5):1654-63.
Irfanoglu MO, Walker L, Sarlls J, Marenco S, Pierpaoli C. 2012. Effects of image distortions originating from susceptibility variations and concomitant fields on diffusion MRI tractography results. Neuroimage 61(1):275-88.
Koay CG, Özarslan E, Johnson KM, and Meyerand ME. 2012. Sparse and optimal acquisition design for diffusion MRI and beyond. Med Phys 39(5):2499-511.
Özarslan E, Shepherd TM, Koay CG, Blackband SJ, and Basser PJ. 2012. Temporal scaling characteristics of diffusion as a new MRI contrast: Findings in rat hippocampus. NeuroImage 60(2):1380-93.
Shemesh N, Özarslan E, Basser PJ, and Cohen Y. 2012. Accurate noninvasive measurement of cell size and compartment shape anisotropy in yeast cells using double-pulsed field gradient MR. NMR Biomed 25(2):236-46.

2011

Irfanoglu MO, Walker L, Sammet S, Pierpaoli C, Machiraju R. 2011. Susceptibility distortion correction for echo planar images with non-uniform B-spline grid sampling: a diffusion tensor image study. Med Image Comput Comput Assist Interv. 14(Pt 2):174-81.
Ducharme S, Hudziak JJ, Botteron KN, Ganjavi H, Lepage C, Collins DL, Albaugh MD, Evans AC, Karama S; Brain Development Cooperative Group. 2011. Right anterior cingulate cortical thickness and bilateral striatal volume correlate with child behavior checklist aggressive behavior scores in healthy children. Biological Psychiatry 70(3):283-90.
Ganjavi H, Lewis J D, Bellec P, MacDonald P A, Waber D P, Evans A C, Karama S. 2011. Negative associations between corpus callosum midsagittal area and IQ in a representative sample of healthy children and adolescents. PloS One 6(5):e19698.
Karama S, Colom R, Johnson W, Deary IJ, Haier R, Waber DP, Lepage C, Ganjavi H, Jung R, Evans AC. 2011. Cortical thickness correlates of specific cognitive performance accounted for by the general factor of intelligence in healthy children aged 6 to 18. NeuroImage 55(4):1443-53.
Basser PJ and Pierpaoli C. 2011. Recollections about our 1996 JMR paper on diffusion anisotropy. J Magn Reson 213(2):571-2.
Sarlls JE, Pierpaoli C, Talagala SL, and Luh W-M. 2011. Robust Fat Suppression at 3T in High-Resolution Diffusion-Weighted Single-Shot Echo-Planar Imaging of Human Brain. Magnetic Resonance in Medicine 66(6):1658-65.
Özarslan E, Komlosh ME, Lizak MJ, Horkay F, and Basser PJ. 2011. Double pulsed field gradient (double-PFG) MR imaging (MRI) as a means to measure the size of plant cells. Magn Reson Chem 49 Suppl 1:S79-84.
Horkay F, Cho SH, Tathireddy P, Rieth L, Solzbacker F, and Magda J. 2011. Thermodynamic analysis of the selectivity enhancement obtained by using smart hydrogels that are zwitterionic when detecting glucose with boronic acid moieties. Sens Actuators B Chem 160(1):1363-71.
Jiang FX, Lin DC, Horkay F, and Langrana NA. 2011. Probing Mechanical Adaptation of Neurite Outgrowth on a Hydrogel Material Using Atomic Force Microscopy. Annals of Biomedical Engineering 39(2):706–13.
Horkay F, Basser PJ, Hecht A-M, and Geissler E. 2011. Hierarchical Organization of Cartilage Proteoglycans. Macromol. Symp. 306-307(1):11–17.
Salvador R, Silva S, Basser PJ, and Miranda PC. 2011. Determining which mechanisms lead to activation in the motor cortex: A modeling study of transcranial magnetic stimulation using realistic stimulus waveforms and sulcal geometry. Clinical Neurophysiology 122(4):748–58.
Komlosh ME, Özarslan E, Lizak MJ, Horkay F, Schram V, Shemesh N, Cohen Y, and Basser PJ. 2011. Pore diameter mapping using double pulsed-field gradient MRI and its validation using a novel glass capillary array phantom. J Magn Reson 208(1):128-35.
Özarslan E, Shemesh N, Koay CG, Cohen Y, and Basser PJ. 2011. NMR characterization of general compartment size distributions. New J Phys 13:15010.
Fonov V, Evans AC, Botteron K, Almli CR, McKinstry RC, Collins DL, and the Brain Development Cooperative Group. 2011. Unbiased average age-appropriate atlases for pediatric studies. NeuroImage 54(1):313-27.
Walker L, Chang L-C, Koay CG, Sharma N, Cohen L, Verma R, and Pierpaoli C. 2011. Effects of physiological noise in population analysis of diffusion tensor MRI data. NeuroImage 54(2):1168-77.

2010

Lange N, Froimowitz MP, Bigler ED, Lainhart JE, Brain Development Cooperative Group. 2010. Associations between IQ, total and regional brain volumes, and demography in a large normative sample of healthy children and adolescents. Dev Neuropsychol 35(3):296-317.
Chandran P, Dimitriadis E, Basser P, Horkay F. 2010. Probing interactions between aggrecan and mica surface by the atomic force microscopy. J Polym Sci B Polym Phys 48:2575-81.
Basser PJ and Özarslan E. 2010. Anisotropic Diffusion: From the Apparent Diffusion Coefficient to the Apparent Diffusion Tensor. In: Jones DK, editor. Diffusion MRI: Theory, Methods, and Applications. New York, NY: Oxford University Press. p. 79-91.
Koay CG. 2010. Least Squares Approaches to Diffusion Tensor Estimation. In: Jones DK, editor. Diffusion MRI: Theory, Methods, and Applications. New York, NY: Oxford University Press. p. 272-284.
Pierpaoli C. 2010. Artifacts in Diffusion MRI. In: Jones DK, editor. Diffusion MRI: Theory, Methods, and Applications. New York, NY: Oxford University Press. p. 303-318.
Basser PJ. 2010. Invention and Development of Diffusion Tensor MRI (DT-MRI or DTI) at the NIH. In: Jones DK, editor. Diffusion MRI: Theory, Methods, and Applications. New York, NY: Oxford University Press. p. 730-734.
Basser PJ, Özarslan E. 2010. Characterizing Compartment Distributions from Diffusion Weighted Magnetic Resonance (MR) Data. OTT Reference No: E-273-2010/0
Horkay F, Falus P, Hecht A-M, and Geissler E. 2010. Length Scale Dependence of the Dynamic Properties of Hyaluronic Acid Solutions in the Presence of Salt. J. Phys. Chem. B 114(47):15445-50.
Nevo U, Özarslan E, Komlosh ME, Koay CG, Sarlls JE, and Basser, PJ. 2010. A system and mathematical framework to model shear flow effects in biomedical DW-imaging and spectroscopy. NMR in Biomedicine 23(7):734–44.
Author's Comments
Intravoxel Coherent Motion (IVCM)

Colleagues David Taylor and Mary Clare Bushell, prophetically wrote in 1984, “Thus this additional parameter [i.e., the apparent diffusion coefficient,] could be of use in aiding contrast between tissues, in looking at cell size through restricted diffusion and perhaps most importantly in monitoring blood perfusion through tissues. Perfusion rates are only an order of magnitude greater than the diffusion rates and well within the range of the measurement technique. However, the technique must be used with care on living subjects as the sequence is sensitive to all types of movement”. There’s a lot to unpack in this quote. When we measure the apparent diffusion coefficients (ADCs) in MRI we use MRI sequences that are, as they wrote, sensitive to all types of water motion. For example, in living tissue where there is water diffusing in extracellular spaces and water flowing in blood vessels, one observes not only the diffusion of water in the tissue compartment but also the pseudo-diffusion of water flowing in roughly randomly oriented capillaries within the tissue. This is what Taylor and Bushell were referring to, which was later called “Intravoxel Incoherent Motion” or IVIM by Denis Le Bihan and his colleagues.

Characterizing pseudo-diffusion in tissues has been a challenging from the beginnings of preclinical and clinical diffusion MRI. We know that in different domains or pools, water is moving as a result of different biophysical and physiological processes. There can be convection, advection (e.g. arising from laminar, turbulent or shear flow), dispersion, cardiac pulsation, exchange between compartments, … to name a few. All of these, as Taylor and Bushell prophetically wrote, could affect the ADC.

One reason we undertook this study of measuring pseudo-diffusion in a well characterized shear flow was to create a quantitative model system in which we could measure the effects of one form of enhance mixing on the ADC and try to present a theory that explains these findings. We repurposed an NMR compatible Couette flow viscometer for this study. It is well known that within the concentric rings of a Couette cell, there is a linear velocity distribution established between the stationary cylinder and the rotating one, as a function of distance from a wall. Another way of saying this is that there is a constant velocity gradient or shear rate. While the Couette cell cylinder is rotating, water molecules diffusing within it may stay on the same streamline or may jump to one moving faster or slower than the one they were on. This impressed velocity distribution causes additional mixing and thus additional dephasing of the water spins as compared to the case where the Rheometer is not spinning. In other word, when the Rheometer is spinning, there is a greater spread of net displacements these molecules exhibit.

Here, this NMR diffusion shear flow experiment was combined with a novel MRI acquisition and analysis pipeline in that we chose voxels shaped like sectors of the Couette cell itself so that water was flowing perpendicular to two ends of the voxel and parallel to the four sides of the voxel.

While intravoxel incoherent motion (IVIM) is supposed to describe the random motion of water molecules in capillaries, this experiment effectively exhibits intravoxel coherent motion (IVCM) in which a well-defined velocity distribution is impressed upon the diffusing spins leads to enhanced mixing or higher apparent diffusion. In fact, the diffusivity of water hasn’t increased in this experiment but it appears to because of the enhanced mixing caused by an impressed shear flow.

T his seemingly simple experiment gives us a glimpse of the complexity of different types of motion that exist in biological tissue. It reminds us that we should examine all of the different types of water motion or transport in a voxel when interpreting diffusion weighted imaging data in vivo.
Shemesh N, Özarslan E, Komlosh ME, Basser PJ, and Cohen Y. 2010. From single-pulsed field gradient to double-pulsed field gradient MR: gleaning new microstructural information and developing new forms of contrast in MRI. NMR in Biomedicine 23(7):757–80.
Horkay F, Magda J, Alcoutlabi M, Atzet S, and Zarembinski T. 2010. Structural, mechanical and osmotic properties of injectable hyaluronan-based composite hydrogels. Polymer (Guildf) 51(19):4424-4430.
Horkay F, Basser PJ, Hecht A-M, and Geissler E. 2010. Counterion and pH-Mediated Structural Changes in Charged Biopolymer Gels. Macromol Symp 291-292(1):354-361.
Lin DC, Douglas JF, and Horkay F. 2010. Development of minimal models of the elastic properties of flexible and stiff polymer networks with permanent and thermoreversible cross-links. Soft Matter 6:3548–3561.
Geissler E, Hecht A-M, and Horkay F. 2010. Scaling Behavior of Hyaluronic Acid in Solution with Mono- and Divalent Ions. Macromol. Symp. 291-292(1):362-370.
Shemesh N, Özarslan E, Adiri T, Basser PJ, Cohen Y. 2010. Noninvasive bipolar double-pulsed-field-gradient NMR reveals signatures for pore size and shape in polydisperse, randomly oriented, inhomogeneous porous media. J Chem Phys 133(4):044705.
Pasternak O, Sochen N, and Basser PJ. 2010. The effect of metric selection on the analysis of diffusion tensor MRI data. Neuroimage 49(3):2190-204.
Shemesh N, Özarslan E, Basser PJ, and Cohen Y. 2010. Detecting diffusion-diffraction patterns in size distribution phantoms using double-pulsed field gradient NMR: Theory and experiments. J Chem Phys 132(3):034703.

2009

Horkay F, Langrana N, Richtering W, editors. 2009. Responsive Gels and Biopolymer Assemblies, MRS Symposium Series, Volume 1234. Warrendale (PA): Cambridge University Press.
Leppert IR, Almli CR, McKinstry RC, Mulkern RV, Pierpaoli C, Rivkin MJ, Pike GB, Brain Development Cooperative Group. 2009. T(2) relaxometry of normal pediatric brain development. J Magn Reson Imaging 29(2):258-67.
Karama S, Ad-Dab'bagh Y, Haier RJ, Deary IJ, Lyttelton OC, Lepage C, Evans AC, and the Brain Development Cooperative Group. 2009. Erratum to "Positive association between cognitive ability and cortical thickness in a representative US sample of healthy 6 to 18 year-olds." Intelligence 37(4):432–442.
Sarlls JE and Pierpaoli C. 2009. In vivo diffusion tensor imaging of the human optic chiasm at sub-millimeter resolution. NeuroImage 47:1244–1251.
Basser PJ. 2009. Method And System For Measuring The Diffusion Tensor And For Diffusion Tensor Imaging. OTT Reference No: E-203-1993/0.
Horkay F, Basser PJ, Pierpaoli C. 2009. A Novel Diffusion MRI Phantom, and a Method for Enhancing MR Image Quality. OTT Reference No: E-249-2008/0.
Basser PJ. 2009. Non-Invasive In Vivo MRI Method to Image Salient Features of Axons and Nerves. OTT Reference No: E-079-2003/1.
Basser PJ, Özarslan E. 2009. Magnetic Resonance Specimen Evaluation Using Multiple Pulse Field Gradient Sequences. OTT Reference No: E-276-2008/0.
Basser PJ. 2009. Diffusion Tensor and q-Space MRI Specimen Characterization. OTT Reference No: E-079-2003/0.
Yoon U, Fonov VS, Perusse D, Evans AC, Brain Development Cooperative Group. (2009) The effect of template choice on morphometric analysis of pediatric brain data. Neuroimage 45:769–777.
Jian B, Vemuri BC, Özarslan E. A Mixture of Wisharts (MOW) Model for Multifiber Reconstruction. In: Laidlaw D, Weickert J, editors. Visualization and Processing of Tensor Fields. Berlin: Springer Berlin Heidelberg; 2009. p. 39–56.
Horkay F, Basser PJ, Londono DJ, Hecht AM, Geissler E. 2009. Ions in hyaluronic acid solutions. J Chem Phys 131(18):184902.
Bencherif SA, Siegwart DJ, Srinivasan A, Horkay F, Hollinger JO, Washburn NR, and Matyjaszewski K. 2009. Nanostructured hybrid hydrogels prepared by a combination of atom transfer radical polymerization and free radical polymerization. Biomaterials 30(29):5270-8.
Lin DC, Shreiber DI, Dimitriadis EK, and Horkay F. 2009. Spherical indentation of soft matter beyond the Hertzian regime: numerical and experimental validation of hyperelastic models. Biomech Model Mechanobiol 8(5):345-58.
Horkay F, Lin DC. 2009. Mapping the Local Osmotic Modulus of Polymer Gels. Langmuir 25(15):8735–41.
Irfanoglu MO, Koay CG, Pajevic S, Machiraju R, and Basser PJ. 2009. Diffusion Tensor Field Registration in the Presence of Uncertainty. MICCAI 12(Pt 1):181-9.
McGraw T, Vemuri BC, Özarslan E, Chen Y, and Mareci TH. 2009. Variational denoising of diffusion weighted MRI. Inverse Probl Imag 3:625-648.
Leppert IR, Almli CR, McKinstry RC, Mulkern RV, Pierpaoli C, Rivkin MJ, Pike GB, and The Brain Development Cooperative Group. 2009. Response to "T2 relaxometry of maturing brains." Journal of Magnetic Resonance Imaging 30:912.
Shemesh N, Özarslan E, Bar-Shir A, Basser PJ, and Cohen Y. 2009. Observation of restricted diffusion in the presence of a free diffusion compartment: Single- and double-PFG experiments. J Magn Reson 200(2):214-25.
Freidlin RZ, Özarslan E, Assaf Y, Komlosh ME, and Basser PJ. 2009. A multivariate hypothesis testing framework for tissue clustering and classification of DTI data. NMR Biomed 22(7):716-29.
Koay CG. 2009. On the six-dimensional orthogonal tensor representation of the rotation in three dimensions: A simplified approach. Mech Mater 41(8):951-953.
Koay CG, Özarslan E and Pierpaoli C. 2009. Probabilistic Identification and Estimation of Noise (PIESNO): A self-consistent approach and its applications in MRI. J Magn Reson 199(1):94-103. (Software URL:http://sites.google.com/site/hispeedpackets/ )
Koay CG, Özarslan E and Basser PJ. 2009. A signal transformational framework for breaking the noise floor and its applications in MRI. J Magn Reson 197(2):108-19. (Software URL:http://sites.google.com/site/hispeedpackets/ )
Özarslan E. 2009. Compartment shape anisotropy (CSA) revealed by double pulsed field gradient MR. J Magn Reson 199:56-67.
Basser PJ and Özarslan E. Introduction to Diffusion MR. In: Johansen-Berg H, Behrens TEJ, editors. Diffusion MRI: From Quantitative Measurement to In vivo Neuroanatomy. Amsterdam (Netherlands): Elsevier Academic Press; 2009. p. 1-9.
Leppert IR, Almli CR, McKinstry RC, Mulkern RV, Pierpaoli C, Rivkin MJ, Pike GB; Brain Development Cooperative Group. 2009. T-2 Relaxometry of Normal Pediatric Brain Development. J Magn Reson Imaging 29(2):258-67.
Karama S, Ad-Dab'bagh Y, Haier RJ, Deary IJ, Lyttelton OC, Lepage C, Evans AC, and the Brain Development Cooperative Group. 2009. Positive association between cognitive ability and cortical thickness in a representative US sample of healthy 6 to 18 year-olds. Intelligence 37(2):145-155.
Shemesh N, Ozarslan E, Basser PJ, and Cohen Y. 2009. Measuring small compartmental dimensions with low-q angular double-PGSE NMR: The effect of experimental parameters on signal decay. J Magn Reson 198(1):15-23.
Özarslan E, Shemesh N, and Basser PJ. 2009. A general framework to quantify the effect of restricted diffusion on the NMR signal with applications to double pulsed field gradient NMR experiments. J Chem Phys 130(10):104702 (1-9). Erratum
Özarslan E, Koay CG, and Basser PJ. 2009. Remarks on q-space MR propagator in partially restricted, axially-symmetric, and isotropic environments. Magn Reson Imaging 27(6):834-44.
Barazany D, Basser PJ, and Assaf Y. 2009. In vivo measurement of axon diameter distribution in the corpus callosum of rat brain. Brain 132(Pt 5):1210-20.
Roth BJ, and Basser PJ. 2009. Mechanical Model of Neural Tissue Displacement During Lorentz Effect Imaging. Magn Reson Med 61(1):59-64.

2008

Basser PJ, Pajevic S. 2008. Quantitative Assessment Of Changes In Tissue Status In Disease, Development, Aging, Or Degeneration Using Diffusion Tensor Magnetic Resonance Imaging. OTT Reference No: E-192-1999/0.
Horkay F and Basser PJ. 2008. Ionic and pH Effects on the Osmotic Properties and Structure of Polyelectrolyte Gels. J Polym Sci B Polym Phys 46(24):2803-2810.
Yin DW, Horkay F, Douglas JF, and de Pablo JJ. 2008. Molecular simulation of the swelling of polyelectrolyte gels by monovalent and divalent counterions. J Chem Phys 129(15):154902.
Tasaki I. 2008. On the Reversible Abrupt Structural Changes in Nerve Fibers Underlying Their Excitation and Conduction Processes. In: Pollack GH, Chin WC, editors. Phase Transitions in Cell Biology. Dordrecht, Netherlands: Springer Netherlands. p.1-21.
Lin DC, Dimitriadis EK, and Horkay F. 2008. Elasticity models for the spherical indentation of gels and soft biological tissues. In Bioinspired Polymer Gels and Networks. F. Horkay, A. Ryan, N. Langrana, and D. Londono, editors. MRS Symposium Series, Warrendale, PA. 1-6.
Horkay F. 2008. Biopolymer Gels: Nanostructure and Macroscopic Properties. Progr Colloid Polym Sci 135:10–15.
Basser PJ. 2008. Diffusion and Diffusion Tensor MR Imaging: Fundamentals. In Magnetic Resonance Imaging of the Brain and Spine. S. W. Atlas, editor. Lippincott Williams and Wilkins, Philadelphia.
Bar-Shir A, Avram L, Özarslan E, Basser PJ, and Cohen Y. 2008. The effect of the diffusion time and pulse gradient duration ratio on the diffraction pattern and the structural information estimated from q-space diffusion MR: Experiments and simulations. J Magn Reson 194(2):230-6.
Horkay F, Basser PJ, Hecht AM, and Geissler E. 2008. Insensitivity to Salt of Assembly of a Rigid Biopolymer Aggrecan. Phys Rev Lett 101(6):068301.
Pasternak O, Verma R, Sochen N, and Basser PJ. 2008. On What Manifold Do Diffusion Tensors Live? IJ - 2008 MICCAI Workshop - Manifolds in Medical Imaging: Metrics, Learning and Beyond.
Silva S, Basser PJ, and Miranda PC. 2008. Elucidating the mechanisms and loci of neuronal excitation by transcranial magnetic stimulation using a finite element model of a cortical sulcus. Clin Neurophysiol 119(10): 2405–13.
Wu M, Chang LC, Walker L, Lemaitre H, Barnett AS, Marenco S, and Pierpaoli C. 2008. Comparison of EPI Distortion Correction Methods in Diffusion Tensor MRI Using a Novel Framework. Med Image Comput Comput Assist Interv 11(Pt 2):321-9.
Irfanoglu MO, Machiraju R, Sammet S, Pierpaoli C, and Knopp MV. 2008. Automatic Deformable Diffusion Tensor Registration for Fiber Population Analysis. Med Image Comput Comput Assist Interv 11(Pt 2):1014-22.
Chang LC, Koay CG, Basser PJ, and Pierpaoli C. 2008. Linear Least-Squares Method for Unbiased Estimation of T1 From SPGR Signals. Magn Reson Med 60(2):496-501.
Sarlls JE and Pierpaoli C. 2008. Diffusion-Weighted Radial Fast Spin-Echo for High-Resolution Diffusion Tensor Imaging at 3T. Magn Reson Med 60(2):270-6.
Bencherif SA, Srinivasan A, Horkay F, Hollinger JO, Matyjaszewski K, and Washburn NR. 2008. Influence of the degree of methacrylation on hyaluronic acid hydrogels properties. Biomaterials 29(12):1739-49.
Horkay F and Hammouda B. 2008. Small-angle neutron scattering from typical synthetic and biopolymer solutions. Colloid Polym Sci 286:611–620.
Avram L, Ozarslan E, Assaf Y, Bar-Shir A, Cohen Y, and Basser PJ. 2008. Three-dimensional water diffusion in impermeable cylindrical tubes: theory versus experiments. NMR Biomed 21(8):888-98.
Author's Comments
This paper, while not widely cited, provides a critical framework for using NMR and MRI methods to assess porous media microstructure non invasively. It also provides the basis for our later CHARMED and AxCaliber NMR and MRI methods that have had broad applications in neuroscience and even neuroradiology.
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This paper presents a mathematical model that describes complex diffusion NMR and MRI signal attenuation data obtained in a pack of impermeable tubes. When one looks at water diffusion in these tubes in an arbitrary frame of reference, i.e., not aligned with the tubes’ axis, the diffusive motion appears complicated. However, if you rotate the frame of reference so that one axis is aligned with the tubes’ axis, the diffusion process becomes simple and tractable to describe mathematically. Then, we show that the diffusion MR signal is explained by the product of two functions, one describing the diffusion attenuation parallel to the tube axis, and the second one describing the diffusion attenuation perpendicular to it. Water diffusion along the tube axis is considered “free” and is described by a Gaussian or normal net displacement distribution whereas diffusion perpendicular to the tube axis is called “restricted” and is described by well-known restricted diffusion models previously derived by Callaghan, Neumann, van Gelderen, inter alia. To be able to model restricted diffusion using a general gradient waveform, Evren Ozarslan implemented and improved upon Callaghan’s ‘operator method’, which more accurately models the relationship between the NMR signal, the tube inner diameter, and the diffusivity of the liquid in the tube. The agreement with data obtained by Liat Avram from Yoram Cohen’s lab and the model is excellent for the extreme cases with water diffusing parallel and perpendicular to the tube axis, and for all other orientations, as well. This parallel/perpendicular decomposition extends the notion we previously used when introducing diffusion tensor NMR and MRI, i.e., in the principal frame of reference, i.e., the one aligned with the principal axes of diffusion, the joint 3D net displacement distribution can be written simply as the product of the three marginal net displacement distributions along the three principal directions. Here, this concept is extended so that it can be used to obtain analytical expressions that describe diffusion in more complex objects, like within impermeable cylindrical pores with impermeable endcaps, between parallel plates and within pores that are 3D rectangular prisms, all having arbitrary orientations. This information is useful to describe and infer microstructural features of some porous media, but also can be useful in constructing NMR or MRI phantoms where the “ground truth” is known.

An issue which has only recently gained the attention of the larger diffusion MRI community is the effect of orientational dispersion or tube “splay” on the MR signal. Evren, I believe, was the first one to model the effect of tubes having a distribution of orientations on the overall diffusion weighted MR signal, and showed its blurring effect on diffraction peaks this produces. Evren also modeled the effect of there being a distribution of tube diameters rather than the tubes all having the same diameter, and similarly showed the smoothing of the diffusion attenuation profile. These two features have come to the forefront in attempts to explain the geometry and morphology of packs of axons in white matter pathways in the brain, particularly in tractography applications.

The restricted diffusion model presented here became the basis of our description of water diffusion in a uniform pack of axons in the CHARMED MRI model, which we later extended to estimate the axon diameter distribution (ADD) in our subsequent AxCaliber MRI model, in which we used the signal attenuation profile to infer or estimate the diameter distribution of a pack of axons that are assumed to be impermeable.
Kim S, Barnett AS, Pierpaoli C, and Chi-Fishman G. 2008. Three-dimensional mapping of lingual myoarchitecture by diffusion tensor MRI. NMR Biomed 21(5):479-88.
Assaf Y, Blumenfeld-Katzir T, Yovel Y, and Basser PJ. 2008. AxCaliber: A Method for Measuring Axon Diameter Distribution from Diffusion MRI. Magnetic Resonance in Medicine 59(6):1347-54.
Koay CG, Nevo U, Chang LC, Pierpaoli C, and Basser PJ. 2008. The elliptical cone of uncertainty and its normalized measures in diffusion tensor imaging. IEEE Trans Med Imag 27(6):834-46.
Lin DC and Horkay F. 2008. Nanomechanics of polymer gels and biological tissues: A critical review of analytical approaches in the Hertzian regime and beyond. Soft Matter 4:669-682.
Horkay F, Basser PJ, Hecht AM, and Geissler E. 2008. Gel-like behavior in aggrecan assemblies. J Chem Phys 128(13):135103.
Özarslan E and Basser PJ. 2008. Microscopic anisotropy revealed by NMR double pulsed field gradient experiments with arbitrary timing parameters. J Chem Phys 128(15):154511.
Komlosh ME, Lizak MJ, Horkay F, Freidlin RZ, and Basser PJ. 2008. Observation of Microscopic Diffusion Anisotropy in the Spinal Cord Using Double-Pulsed Gradient Spin Echo MRI. Magn Reson Med 59(4):803-9.
Özarslan E, Nevo U and Basser PJ. 2008. Anisotropy induced by macroscopic boundaries: Surface normal mapping using diffusion-weighted imaging. Biophys J 94(7):2809-18.

2007

Horkay F, Langrana NA, Ryan AJ, and Londono JD, editors. 2007. Bioinspired Polymer Gels and Networks, MRS Symposium Series, Volume 1060. Warrendale (PA): Cambridge University Press.
Freidlin RZ, Komlosh ME, Loew MH, and Basser PJ. 2007. Parsimonious model selection for tissue classification: A DTI study of zebrafish. Medical Imaging 2007: Image Processing. Edited by Pluim, Josien P. W.; Reinhardt, Joseph M. Proceedings of the SPIE, Volume 6512, pp. 65122T, Mar 2007.
McMillan KM, Rogers BP, Koay CG, Laird AR, Price RR, and Meyerand ME. 2007. An objective method for combining multi-parametric MRI datasets to characterize malignant tumors. Med Phys 34(3):1053-61.
Horkay F and McKenna GB. 2007. Polymer Networks and Gels. In Physical Properties of Polymers Handbook. James E. Mark, editor. Springer, New York.
Horkay F, Basser PJ, Hecht A-M, and Geissler E. 2007. Comparative study of scattering and osmotic properties of synthetic and biopolymer gels. Macromol. Symp. 256:80-87.
Geissler E, Hecht A-M, and Horkay F. 2007. Scaling Equations for a Biopolymer in Salt Solution. Phys Rev Lett 99(26):267801.
Silva CC, Lin DC, Horkayne-Szakaly I, Basser PJ, and Horkay F. 2007. Novel Applications of the QCM Technique in Biomaterials Science. Bioinspired Polymer Gels and Networks, edited by F. Horkay, N.A. Langrana, A.J. Ryan, and J.D. Londono (Mater. Res. Soc. Symp. Proc. Volume 1060E, Warrendale, PA, 2007), 1060-LL03-06.
Boukari H, Silva C, Nossal R, and Horkay F. 2007. Monitoring nanoprobe diffusion in osmotically-stressed hydrogels. Bioinspired Polymer Gels and Networks, edited by F. Horkay, N.A. Langrana, A.J. Ryan, and J.D. Londono (Mater. Res. Soc. Symp. Proc. Volume 1060E, Warrendale, PA, 2007), 1060-LL07-03.
Lin DC, Dimitriadis EK, and Horkay F. 2007. Robust strategies for automated AFM force curve analysis - I. Non-adhesive indentation of soft, inhomogeneous materials. J Biomech Eng 129(3):430-40.
Lin DC, Dimitriadis EK, and Horkay F. 2007. Robust strategies for automated AFM force curve analysis - II. Adhesion-influenced indentation of soft, elastic materials. J Biomech Eng 129(6):904-12.
Lin DC, Dimitriadis EK, and Horkay F. 2007. Elasticity of rubber-like materials measured by AFM nanoindentation. eXPRESS Polymer Letters 1:576-584.
Hauben E, Roncarolo MG, Draghici E, and Nevo U. 2007. The role of tissue adaptation and graft size in immune tolerance. Transpl Immunol 18(2):122-5.
Nevo U and Hauben E. 2007. Ecoimmunity: immune tolerance by symmetric co-evolution. Evol Dev 9(6):632-42.
Van Thienen TG, Horkay F, Braeckmans K, Stubbe BG, Demeester J, and De Smedt SC. 2007. Influence of free chains on the swelling pressure of PEG-HEMA and dex-HEMA hydrogels. Int J Pharm 337(1-2):31-9.
Michelman-Ribeiro A, Horkay F, Nossal R, and Boukari H. 2007. Probe diffusion in aqueous poly(vinyl alcohol) solutions studied by fluorescence correlation spectroscopy. Biomacromolecules 8(5):1595-600.
Basser PJ and Pajevic S. 2007. Spectral decomposition of a 4th-order covariance tensor: Applications to diffusion tensor MRI. Signal Processing 87:220-236.
Chang LC, Koay CG, Pierpaoli C, and Basser PJ. 2007. Variance of estimated DTI-derived parameters via first-order perturbation methods. Magn Reson Med 57(1):141-9.
Koay CG, Chang LC, Pierpaoli C, and Basser PJ. 2007. Error Propagation Framework for Diffusion Tensor Imaging via Diffusion Tensor Representations. IEEE Trans Med Imaging 26(8):1017-34.
Koay CG, Sarlls JE, and Ozarslan E. 2007. Three-dimensional analytical magnetic resonance imaging phantom in the Fourier domain. Magn Reson Med. 58(2):430-436.
Jian B, Vemuri BC, Ozarslan E, Carney PR, and Mareci TH. 2007. A novel tensor distribution model for diffusion weighted MR signal. NeuroImage 37(1):164-176. Erratum.
Shepherd TM, Ozarslan E, Yachnis AT, King MA, and Blackband SJ. 2007. Diffusion tensor microscopy indicates the cytoarchitectural basis for diffusion anisotropy in the human hippocampus. Am J Neuroradiol 28(5):958-64.
Miranda PC, Correia L, Salvador R, and Basser PJ. 2007. Tissue heterogeneity as a mechanism for localized neural stimulation by applied electric fields. Phys Med Biol 52(18):5603-17.
Özarslan E, and Basser PJ. 2007. MR diffusion-"diffraction" phenomenon in multi-pulse-field-gradient experiments. J Magn Reson 188(2):285-94.
Waber DP, De Moor C, Forbes PW, Almli CR, Botteron KN, Leonard G, Milovan D, Paus T, Rumsey J and Brain Development Cooperative Group. 2007. The NIH MRI study of normal brain development: Performance of a population based sample of healthy children aged 6 to 18 years on a neuropsychological battery. J Int Neuropsychol Soc 13(5):729-46.
Almli CR, Rivkin MJ, McKinstry RC and Brain Development Cooperative Group. 2007. The NIH MRI study of normal brain development (Objective-2): Newborns, infants, toddlers, and preschoolers. NeuroImage 35(1):308-25.
Marenco S, Siuta MA, Kippenhan JS, Grodofsky S, Chang WL, Kohn P, Mervis CB, Morris CA, Weinberger DR, Meyer-Lindenberg A, Pierpaoli C, and Berman KF. 2007. Genetic contributions to white matter architecture revealed by diffusion tensor imaging in Williams syndrome. Proc Natl Acad Sci USA 104(38):15117-22.
Komlosh ME, Horkay F, Freidlin RZ, Nevo U, Assaf Y, and Basser PJ. 2007. Detection of microscopic anisotropy in gray matter and in a novel tissue phantom using double Pulsed Gradient Spin Echo MR. J Magn Reson 189(1):38-45.
Freidlin RZ, Ozarslan E, Komlosh ME, Chang LC, Koay CG, Jones DK, and Basser PJ. 2007. Parsimonious model selection for tissue segmentation and classification applications: A study using simulated and experimental DTI data. IEEE Trans Med Imaging 26(11):1576-84.

2006

Basser PJ, Pickalov V. 2006. In vivo Assessment of Tissue Microstructure and Microdynamics: Estimation of the Average Propagator from Magnetic Resonance Data. OTT Reference No: E-164-2006/0.
Marenco, S., R. Rawlings, G.K. Rohde, A.S. Barnett, R.A. Honea, C. Pierpaoli, and D.R. Weinberger. (PDF 447 KB) 2006. Regional distribution of measurement error in diffusion tensor imaging. Psychiatry Research 147:69-78.
Basser PJ. 2006. Diffusion Tensor MR Imaging Fundamentals. In: Edelman RR, Hesselink J, Zlatkin M, and Crues VC III, editors. Clinical Magnetic Resonance Imaging. Philadelphia (PA): Saunders Elsevier. p. 320-332.
Horkay F, Hecht AM, Geissler E. 2006. Similarities between polyelectrolyte gels and biopolymer solutions. Journal of Polymer Science Part B: Polymer Physics 44:3679-3686.
Horkay F, Han MH, Han IS, Bang IS, and Magda JJ. 2006. Separation of the effects of pH and polymer concentration on the swelling pressure and elastic modulus of a pH-responsive hydrogel. Polymer (Guildf) 47(21):7335-7338.
Assaf Y, Ben-Sira L, Constantini S, Chang LC, and Beni-Adani L. 2006. Diffusion tensor imaging in hydrocephalus: Initial Experience. AJNR Am J Neuroradiol 27(8):1717-24.
Carew JD, Koay CG, Wahba G, Alexander AL, Meyerand ME, and Basser PJ. 2006. The asymptotic behavior of the nonlinear estimators of the diffusion tensor and tensor-derived quantities with implications for group analysis. University of Wisconsin Department of Statistics, Technical Report No. 1132.
Horkay F, Hecht AM, Rochas C, Basser PJ, and Geissler E. 2006. Anomalous small angle x-ray scattering determination of ion distribution around a polyelectrolyte biopolymer in salt solution. J Chem Phys 125(23):234904.
Jones DK, Catani M, Pierpaoli C, Reeves SJ, Shergill SS, O'Sullivan M, Golesworthy P, McGuire P, Horsfield MA, Simmons A, Williams SC, Howard RJ. 2006. Age Effects on Diffusion Tensor Magnetic Resonance Imaging Tractography Measures of Frontal Cortex Connections in Schizophrenia. Hum Brain Mapp 27(3):230-8.
Koay CG and Basser PJ. 2006. Analytically exact correction scheme for signal extraction from noisy magnitude MR signals. J Magn Reson 179(2):317-22.
Koay CG, Carew JD, Alexander AL, Basser PJ, and Meyerand ME. 2006. Investigation of anomalous estimates of tensor-derived quantities in diffusion tensor imaging. Magn Reson Med 55(4):930-6.
Koay CG, Chang LC, Carew JD, Pierpaoli C, and Basser PJ. 2006. A unifying theoretical and algorithmic framework for least squares methods of estimation in diffusion tensor imaging. J Magn Reson 182(1):115-25. [For software request, please write to the corresponding author at guankoac@mail.nih.gov]
Lin DC, Dimitriadis EK, and Horkay F. 2006. Advances in the mechanical characterization of soft materials by nanoindentation. In Recent Research Developments in Biophysics (Ed: Pandalai, S.G.), Vol. 5 Part II, pp. 333-370, Transworld Research Network, Kerala, India, 2006.
Özarslan E, Basser PJ, Shepherd TM, Thelwall PE, Vemuri BC, and Blackband SJ. 2006. Observation of anomalous diffusion in excised tissue by characterizing the diffusion-time dependence of the MR signal. J Magn Reson 183(2):315-23.
Özarslan E, Shepherd TM, Vemuri BC, Blackband SJ, and Mareci TH. 2006. Resolution of complex tissue microarchitecture using the diffusion orientation transform (DOT). NeuroImage 31(3):1086-103.
Pajevic S, Aldroubi A, and Basser PJ. 2006. Continuous Tensor Field Approximation of Diffusion Tensor MRI data. In: Weickert J, Hagen H, editors. Visualization and Processing of Tensor Fields. Berlin Germany: Springer. p. 299-314.
Shepherd TM, Ozarslan E, King MA, Mareci TH, and Blackband SJ. 2006. Structural insights from high-resolution diffusion tensor imaging and tractography of the isolated rat hippocampus. NeuroImage 32(4):1499-509.
Tasaki I. 2006. A note on the local current associated with the rising phase of a propagating impulse in nonmyelinated nerve fibers. Bull Math Biol 68(2):483-90.
Evans AC and the Brain Development Cooperative Group. 2006. The NIH MRI study of normal brain development. NeuroImage 30(1):184-202.

2005

Michelman-Ribeiro A, Horkay F, Nossal R, Boukari H. 2005. Fluorescence Correlation Spectroscopy Study of TAMRA Diffusion in Poly(vinyl-alcohol) and Ficoll70 Solutions. MRS Proceedings 897.
Horkay F, Basser PJ, Hecht AM, and Geissler E. 2005. Effect of calcium ions on the structure of synthetic and biopolymer gels. Polymeric Materials: Scientific Engineering 93:105–106.
Horkay F and Amis EJ, editors. 2005. Biological and Synthetic Polymer Networks and Gels. Wiley VCH, Weinheim.
Michelman-Ribeiro A, Boukari H, Nossal R, and Horkay F. 2005. Fluorescence Correlation Spectroscopy Study of Probe Diffusion in Poly(vinyl alcohol) Solutions and Gels. Macromol Symp 227:221-230.
Jones DK, Catani M, Pierpaoli C, Reeves SJ, Shergill SS, O'Sullivan M, Maguire P, Horsfield MA, Simmons A, Williams SC, and Howard RJ. 2005. A diffusion tensor magnetic resonance imaging study of frontal cortex connections in very-late-onset schizophrenia-like psychosis. Am J Geriatr Psychiatry 13(12):1092-9.
Geissler E, Hecht AM, and Horkay F. 2005. Nanoscale inhomogeneities and thermodynamics of unfulfilled polymer gels. Journal of Macromolecular Science, Part B: Physics 44:873-880.
Lin-Gibson S, Bencherif S, Antonucci JM, Jones RL, and Horkay F. 2005. Synthesis and characterization of poly(ethylene glycol) dimethacrylate hydrogels. Macromol Symp 227:243-254.
Hammouda B, Horkay F, and Becker ML. 2005. Clustering and Solvation in Poly(acrylic acid) Polyelectrolyte Solutions. Macromolecules 38:2019-2021.
Assaf Y and Basser PJ. 2005. Composite hindered and restricted model of diffusion (CHARMED) MR imaging of the human brain. NeuroImage 27:48-58.
Basser PJ and Horkay F. 2005. Toward a constitutive law of cartilage: A polymer physics perspective. Macromol Symp 227:53-64.
Boguñá M, Pajevic S, Basser PJ, and Weiss GH. 2005. A model for noise effects on fibre tract trajectories in diffusion tensor imaging: theory and simulations. New Journal of Physics 7:1-7.
Chang LC, Jones DK, and Pierpaoli C. 2005. RESTORE: Robust estimation of tensors by outlier rejection. Magn Reson Med 53(5):1088-95.
Geissler E, Hecht AM, Rochas C, Horkay F, and Basser PJ. 2005. Light, small angle neutron and X-Ray scattering from gels. Macromol Symp 227:27-38.
Hauben E, Roncarolo MG, Nevo U, and Schwartz M. 2005. Beneficial autoimmunity in Type 1 diabetes mellitus. Trends Immunol 26(5):248-53.
Horkay F, Basser PJ, Hecht AM, and Geissler E. 2005. Structural investigations of a neutralized polyelectrolyte gel and an associating neutral hydrogel. Polymer 46:4242-47.
Horkay F, Horkayne-Szakaly I, and Basser PJ. 2005. Measurement of the osmotic properties of thin polymer films and biological tissue samples. Biomacromolecules 6(2):988-93.
Jones DK and Pierpaoli C. 2005. Confidence mapping in diffusion tensor magnetic resonance iImaging tractography using a bootstrap approach. Magn Reson Med 53(5):1143-9.
Jones DK, Travis AR, Eden G, Pierpaoli C, and Basser PJ. 2005. PASTA: pointwise assessment of streamline tractography attributes. Magn Reson Med 53(6):1462-7.
Kim S, Chi-Fishman G, Barnett AS, and Pierpaoli C. 2005. Dependence on diffusion time of apparent diffusion tensor of ex vivo calf tongue and heart. Magn Reson Med 54(6):1387-96.
Lin-Gibson S, Jones RL, Washburn NR, and Horkay F. 2005. Structure-property relationships of photopolymerizable poly(ethylene glycol) dimethacrylate hydrogels. Macromolecules 38:2897-2902.
Rohde GK, Barnett AS, Basser PJ, and Pierpaoli C. 2005. Estimating intensity variance due to noise in registered images: Applications to diffusion tensor MRI. NeuroImage 26(3):673-84.
Sen PN and Basser PJ. 2005. A model for diffusion in white matter in the brain. Biophys J 89(5):2927-38.
Sen PN and Basser PJ. 2005. Modeling diffusion in white matter in the brain: A composite porous medium. Magn Reson Imaging 23(2):215-20.
Tasaki I. 2005. Repetitive abrupt structural changes in polyanionic gels: a comparison with analogous processes in nerve fibers. J Theor Biol 236(1):2-11.

2004

Rohde GK, Pajevic S, and Pierpaoli C. Multi-channel registration of diffusion-tensor images using directional information. 2004 2nd IEEE International Symposium on Biomedical Imaging: Nano to Macro (IEEE Cat No. 04EX821), Arlington, VA, USA, 2004, pp. 712-715 Vol. 1.
Lange N, Jones DK, and Pierpaoli C. A closed-form method for improving inter-subject coherence in diffusion tensor magnetic resonance imaging. 2004 2nd IEEE International Symposium on Biomedical Imaging: Nano to Macro (IEEE Cat No. 04EX821), Arlington, VA, USA, 2004, pp. 1506-1509 Vol. 2.
Michelman-Ribeiro A, Boukari H, Nossal R, and Horkay F. 2004. Structural Changes in Polymer Gels Probed by Fluorescence Correlation Spectroscopy. Macromolecules 37:10212-10214.
Amsden BG, Stubbe BG, Horkay F, De Smedt SC, and Demeester J. 2004. Modeling the swelling pressure of degrading hydroxyethylmethacrylate-grafted dextran hydrogels. J Polym Sci Part B: Polym Phys 42(18):3397-3404.
Assaf Y, Freidlin RZ, Rohde GK, and Basser PJ. 2004. New modeling and experimental framework to characterize hindered and restricted water diffusion in brain white matter. Magn Reson Med 52(5):965-78.
Basser PJ. 2004. Scaling laws for myelinated axons derived from an electrotonic core-conductor model. J Integr Neurosci 3(2):227-44.
Horkay F and Basser PJ. 2004. Osmotic observations on chemically cross-linked DNA gels in physiological salt solutions. Biomacromolecules 5(1):232-7.
Jones DK. 2004. The effect of gradient sampling schemes on measures derived from diffusion tensor MRI: a Monte Carlo study. Magn Reson Med 51(4):807-15.
Jones DK and Basser PJ. 2004. Squashing Peanuts and Smashing Pumpkins: How Noise Distorts Diffusion-Weighted MR Data. Magn Reson Med 52(5):979-93.
Lin-Gibson S, Bencherif S, Cooper JA, Wetzel SJ, Antonucci JM, Vogel BM, Horkay F, and Washburn NR. 2004. Synthesis and characterization of PEG dimethacrylates and their hydrogels. Biomacromolecules 5(4):1280-7.
Morfin I, Horkay F, Basser PJ, Bley F, Hecht AM, Rochas C, and Geissler E. 2004. Adsorption of Divalent Cations on DNA. Biophys J 87(4):2897-904.
Rohde GK, Barnett AS, Basser PJ, Marenco S, and Pierpaoli C. 2004. Comprehensive approach for correction of motion and distortion in diffusion-weighted MRI. Magn Reson Med 51(1):103-14.
Tasaki I. 2004. On the conduction velocity of nonmyelinated nerve fibers. J Integr Neurosci 3(2):115-24.
Washburn NR, Weir M, Anderson P, and Potter K. 2004. Bone formation in polymeric scaffolds evaluated by proton magnetic resonance microscopy and x-ray microtomography. J Biomed Mater Res A 69(4):738-47.

2003

Jones DK. 2003. Determining and visualizing uncertainty in estimates of fiber orientation from diffusion tensor MRI. Magn Reson Med 49(1):7-12.
Basser PJ and Pajevic S. 2003. A normal distribution for tensor-valued random variables: applications to diffusion tensor MRI. IEEE Trans Med Imaging 22(7):785-94.
Basser PJ and Pajevic S. 2003. Dealing with uncertainty in diffusion tensor MR data. Israel Journal of Chemistry 43:129-144.
Horkay F and Basser PJ. 2003. Osmotic properties of polyelectrolyte hydrogels in physiological salt solutions. Recent Res. Devel. Macromol. 7:293-313.
Horkay F, Basser PJ, Hecht AM, and Geissler E. 2003. Calcium induced volume transition in polyelectrolyte gels. Macromol Symp. 200:21-30.
Miranda PC, Hallett M, and Basser PJ. 2003. The electric field induced in the brain by magnetic stimulation: a 3-D finite element analysis of the effect of tissue heterogeneity and anisotropy. IEEE Trans Biomed Eng 50(9):1074-85.
Morfin I, Horkay F, Basser PJ, Bley F, Ehrburger-Dolle F, Hecht A, and Geissler E. 2003. Ion condensation in a polyelectrolyte gel. Macromol Symp 200:227-234.
Pajevic S and Basser PJ. 2003. Parametric and non-parametric statistical analysis of DT-MRI data. J Magn Reson 161(1):1-14.
Rohde GK, Aldroubi A, and Dawant BM. 2003. The adaptive bases algorithm for intensity-based nonrigid image registration. IEEE Trans Med Imaging 22(11):1470-9.
Stubbe BG, Horkay F, Amsden B, Hennink WE, De Smedt SC, and Demeester J. 2003. Tailoring the swelling pressure of degrading dextran hydroxyethyl methacrylate hydrogels. Biomacromolecules 4(3):691-5.

2002

Basser PJ. 2002. Relationships between diffusion tensor and q-space MRI. Magn Reson Med 47(2):392-7.
Basser PJ and Jones DK. 2002. Diffusion-tensor MRI: theory, experimental design and data analysis — a technical review. NMR Biomed 15(7-8):456-67.
Basser PJ, Pajevic S, Pierpaoli C, and Aldroubi A. 2002. Fiber tract following in the human brain using DT-MRI data. IEICE Trans. Inf. & Syst. E85-D(1):15-21.
Dimitriadis EK, Horkay F, Maresca J, Kachar B, and Chadwick RS. 2002. Determination of elastic moduli of thin layers of soft material using the atomic force microscope. Biophys J 82(5):2798-810.
Han IS, Han MH, Kim J, Lew S, Lee YJ, Horkay F, and Magda JJ. 2002. Constant-volume hydrogel osmometer: a new device concept for miniature biosensors. Biomacromolecules 3(6):1271-5.
Hecht A, Horkay F, Schleger P, and Geissler E. 2002. Thermal fluctuations in polymer gels investigated by neutron spin echo and dynamic light scattering. Macromolecules 35:8552-5.
Horkay F, Basser PJ, Hecht A, and Geissler E. 2002. Calcium-induced volume transition in polyacrylate hydrogels swollen in physiological salt solutions. Macromol Biosci 2:207-13.
Horkay F, Hecht A, Grillo I, Basser PJ, and Geissler E. 2002. Experimental evidence for two thermodynamic length scales in neutralized polyacrylate gels. J Chem Phys 117(20):9103-9106.
Pajevic S, Aldroubi A, and Basser PJ. 2002. A continuous tensor field approximation of discrete DT-MRI data for extracting microstructural and architectural features of tissue. J of Magn Reson 154(1):85-100.
Pierpaoli C. 2002. Inferring structural and architectural features of brain tissue from DT-MRI measurements. CNS Spectrums 7:510-5.
Potter K, Leapman RD, Basser PJ, and Landis WJ. (PDF 1.5 MB) 2002. Cartilage calcification studied by proton nuclear magnetic resonance microscopy. J Bone Miner Res 17(4):652-60.
Stubbe BG, Braeckmans K, Horkay F, Hennink WE, De Smedt SC, and Demeester J. (PDF 104 KB) 2002. Swelling pressure observations on degrading Dex-HEMA hydrogels. Macromolecules 35(7):2501-5.
Tasaki I. (PDF 283 KB) 2002. Spread of discrete structural changes in synthetic polyanionic gel: a model of propagation of a nerve impulse. J Theor Biol 218(4):497-505.
Tasaki I and Matsumoto G. (PDF 137 KB) 2002. On the cable theory of nerve conduction. Bulletin of Mathematical Biology 64:1069-1082.

2001

Hasan KM, Basser PJ, Parker DL, and Alexander AL. 2001. Analytical Computation of the Eigenvalues and Eigenvectors in DT-MRI. Journal of Magnetic Resonance 152(1):41-47.
Alexander DC, Pierpaoli C, Basser PJ, and Gee JC. 2001. Spatial transformations of diffusion tensor magnetic resonance images. IEEE Trans Med Imaging 20(11):1131-9.
Hecht A, Horkay F, and Geissler E. 2001. Neutron scattering investigations on a bimodal polymer gel. J Phys Chem 105(24):5637-42.
Hecht A, Horkay F, and Geissler E. 2001. Structure of polymer solutions containing fumed silica. Phys Rev E Stat Nonlin Soft Matter Phys 64(4 Pt 1):041402.
Horkay F, Hecht AM, Basser PJ, and Geissler E. 2001. Comparison between neutral gels and neutralized polyelectrolyte gels in the presence of divalent cations. Macromolecules 34(12):4285-7.
Horkay F, Tasaki I, and Basser PJ. 2001. Effect of monovalent-divalent cation exchange on the swelling of polyacrylate hydrogels in physiological salt solutions. Biomacromolecules 2(1):195-9.
Pierpaoli C, Barnett A, Pajevic S, Chen R, Penix LR, Virta A, and Basser PJ. 2001. Water diffusion changes in Wallerian degeneration and their dependence on white matter architecture. NeuroImage 13(6 Pt 1):1174-85.

2000

Basser PJ, Pajevic S. 2000. Statistical artifacts in diffusion tensor MRI (DT-MRI) caused by background noise. Magn Reson Med 44(1):41-50.
Basser PJ, Pajevic S, Pierpaoli C, Duda J, and Aldroubi A. 2000. In vivo fiber tractography using DT-MRI data. Magn Reson Med 44(4):625-32.
Basser PJ, Roth BJ. 2000. New currents in electrical stimulation of excitable tissues. Annu Rev Biomed Eng. 2:377-97.
Horkay F, Basser P, Hecht A, and Geissler E. 2000. Osmotic and SANS Observations on Sodium Polyacrylate Hydrogels in Physiological Salt Solutions. Macromolecules 33(22):8329-33.
Horkay F, McKenna GB, Deschamps P, and Geissler E. 2000. Neutron scattering properties of randomly cross-linked polyisoprene gels. Macromolecules 33(14):5215-20.
Horkay F, Tasaki I, Basser PJ. 2000. Osmotic swelling of polyacrylate hydrogels in physiological salt solutions. Biomacromolecules 1(1):84-90. PMID: 11709847, DOI: 10.1021/bm9905031

1999

Pierpaoli C, Basser PJ. 1999. Method to Reduce the Bias in the Mean and Variance of Indices of Water Diffusion Anisotropy as Measured by Diffusion Tensor MRI. OTT Reference No: E-157-1996/0.
Aldroubi A and Basser PJ. 1999. Reconstruction of vector and tensor fields from sampled discrete data. Contemporary Mathematics 247:1-15.
Barratti C, Barnett AS, Pierpaoli C. 1999. Comparative MR imaging study of brain maturation in kittens with T1, T2, and the trace of the diffusion tensor. Radiology 210(1):133-42.
Pajevic S, Pierpaoli C. 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(3):526-40.
Tasaki I. 1999. Evidence for phase transition in nerve fibers, cells and synapses. Ferroelectrics 220:305-16.DOI: 10.1080/00150199908216221
Tasaki I. 1999. Rapid structural changes in nerve fibers and cells associated with their excitation processes. Jpn J Physiol 49(2):125-38. DOI: 10.2170/jjphysiol.49.125
Virta A, Barnett A, Pierpaoli C. 1999. Visualizing and characterizing white matter fiber structure and architecture in the human pyramidal tract using diffusion tensor MRI. Magn Reson Imaging 17(8):1121-33.

1998

Basser PJ, Pierpaoli C. 1998. A simplified method to measure the diffusion tensor from seven MR images. Magn Reson Med 39(6):928-34.
Basser PJ, Schneiderman R, Bank RA, Wachtel E, Maroudas A. 1998. Mechanical properties of the collagen network in human articular cartilage as measured by osmotic stress technique. Arch Biochem Biophys 351(2):207-19.
Shrager RI, Basser PJ. 1998. Anisotropically weighted MRI. Magn Reson Med 40(1):160-5.
Tasaki I. 1998. Repetitive mechanical responses of the amphibian skin to adrenergic stimulation. Jpn J Physiol 48(4):297-300. DOI: 10.2170/jjphysiol.48.297

1997

Basser PJ. 1997. New histological and physiological stains derived from diffusion-tensor MR images. Ann N Y Acad Sci 820:123-38.
Mattiello J, Basser PJ, Le Bihan D. 1997. The b matrix in diffusion tensor echo-planar imaging. Magn Reson Med 37(2):292-300.
Tasaki I. 1997. Rapid volume expansion in the torpedo electric organ associated with its postsynaptic potential. Biochem Biophys Res Commun. 233(2):305-8. PDF version (PDF 366 KB) PMID: 9144529, DOI: 10.1006/bbrc.1997.6451

1996

Basser PJ, Pierpaoli C. 1996. Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B 111(3):209-19.
George MS, Wassermann EM, Williams WA, Steppel J, Pascual-Leone A, Basser PJ, Hallett M, Post RM. 1996. Changes in mood and hormone levels after rapid-rate transcranial magnetic stimulation (rTMS) of the prefrontal cortex. J Neuropsychiatry Clin Neurosci 8(2):172-80.
Pierpaoli C, Jezzard P, Basser PJ, Barnett A, Chiro G. 1996. Diffusion tensor MR imaging of the human brain. Radiology 201(3):637-48.
Pierpaoli C, Basser PJ. 1996. Toward a quantitative assessment of diffusion anisotropy [published erratum appears in Magn Reson Med 37(6):972]. Magn Reson Med 36(6):893-906.

1995

Basser PJ. (1995) Inferring microstructural features and the physiological state of tissue from diffusion weighted images. NMR Biomed. 8(7-8):333-44. PMID: 8739270
George MS, Wassermann EM, Williams WA, Callahan A, Ketter TA, Basser PJ, Hallett M, Post RM. (1995) Daily repetitive transcranial magnetic stimulation (rTMS) improves mood in depression. Neuroreport. 6(14):1853-6. PMID: 8547583
Author's Comments
This paper is important because it is the first publication to propose and demonstrate the use of transcranial magnetic stimulation (TMS) to alter mood, and specifically to treat depression. This work had a surprising origin, which isn’t widely known. Two years before this paper was published, in April, 1993, I had a chance meeting with the lead author, Mark George, in a cloakroom in the Ritz Carlton Hotel in Fairfax County, Virginia, where we were both attending a workshop on diffusion MRI sponsored by the ISMRM. For several years, a long time our mutual friend and colleague, Susan Weiss, Ph.D., who at that time was a post-doctoral fellow in NIMH studying “kindling” in rodent epilepsy models, had been telling each of us that we should meet since we had many interests in common. Mark was a psychiatry fellow in NIMH interested in anger and other primitive emotions, the function of the amygdala, PET scanning, and electroconvulsive therapy (ECT); I was a Staff Fellow in the Biomedical Engineering Program at NIH, having recently written a group of papers with my colleagues, Brad Roth and Mark Hallett, inter alia, explaining the physical underpinnings of “magnetic stimulation” of nerves in the peripheral nervous system (PNS) and “transcranial magnetic stimulation” or TMS of neural tissue in the central nervous system (CNS).

I recall that Mark George started telling me about his interests and eventually moved to the subject of treating clinical depression using ECT. He then briefly described the details of that therapy. It seemed like a crude treatment methodology; I immediately suggested to him that perhaps he should consider using “transcranial magnetic stimulation” or TMS as an alternative to ECT. I recall he had never heard of it. I then explained to him that TMS was a new neurological technique that I had been researching with Dr. Hallett and others. I outlined some of its potential benefits over ECT … that TMS would be non-contacting, painless, could be done without anesthesia on an out-patient basis, and wouldn’t have the stigma or risks associated with ECT, which required eliciting convulsions in the patient to work. My only reservations/questions were whether TMS could elicit a sufficient stimulus to improve mood and whether this could be done without the patient convulsing. Mark was excited about this idea and this prospect, and the following day he and I began exchanging emails about collaborating on developing this idea and moving it forward. After some time elapsed, I remember introducing Mark to my collaborator in NINDS, Mark Hallett, a noted neurologist. I organized a meeting with Mark Hallett, Brad Roth, Mark George, and myself in Mark Hallett’s office where we began discussing how this technology could possibly be tested on human subjects to assess its efficacy in changing mood. Not being a clinician, this “translational” part of the project was out of my “wheelhouse”, so I began to provide technical support for this project going forward. For instance, I remember Mark George called me to determine what electromagnetic “dose” of TMS he should use to see if a response in mood could expected to be elicited. I suggested that he use at least the minimum dose of TMS to elicit a motor response in the motor cortex as a baseline level of stimulation for which he might expect to see a biological effect in other parts of the brain, such as the left frontal cortex, where ECT electrodes are generally placed. Other questions related to how one can perform a “sham” TMS experiment. The list goes on.

Since then, TMS has become an important FDA-approved method for treating intractable clinical depression. Even after almost thirty years, however, I don’t believe there is a deep mechanistic understanding how induced electric fields affect mood.
Basser, P.J., Mattiello, J., and Le Bihan, D. (1995) Anisotropic diffusion: MR diffusion tensor imaging. In D. Le Bihan (Ed.), Diffusion and Perfusion Magnetic Resonance Imaging. (pp. 140-149). New York: Raven Press, Ltd.
Mattiello J, Basser PJ, Le Bihan D. (1995) Analytical calculation of the b matrix in diffusion imaging. In D. Le Bihan (Ed.), Diffusion and Perfusion Magnetic Resonance Imaging. (pp. 77-99). New York: Raven Press, Ltd.
Le Bihan, D. and Basser, P.J. (1995) Molecular diffusion and nuclear magnetic resonance. In D. Le Bihan (Ed.) ,Diffusion and Perfusion Magnetic Resonance Imaging (pp. 5-17). New York: Raven Press, Ltd.

1994

Basser PJ. (1994) Focal magnetic stimulation of an axon. IEEE Trans Biomed Eng. 41(6):601-6. PMID: 7927380, DOI: 10.1109/10.293248
Author's Comments
Once my colleague, Brad Roth and I had established the basic physical underpinnings of electromagnetic stimulation (a.k.a. magnetic stimulation) of a nerve fiber or axon in our 1990 papers, several questions naturally arose. How localized is the stimulation? Can magnetic stimulation be focused or made focal? What physical parameters determine how concentrated or focal such excitation can be, such as the depth of the nerve from the coil, the diameter of the coil, the current flowing in the coil, the location of the nerve with respect to the coil center, etc.? Even though at the time I was experimenting with inductive coils wound around tapered iron cores as a possible means to focus the magnetic field, and thus the induced electric field gradients, I knew that magnetic fields don’t “like” to be concentrated and tend to spread out left to their own devices. One wouldn’t expect to be able to direct concentrated magnetic fields using this approach as you could light using lenses. In this light, a good case to consider is electromagnetic stimulation of a nerve placed in a water bath with a circular coil placed above and parallel to the water’s free surface. In this case, analytical expressions can be derived to predict the induced electric field and field gradient caused by the current flowing in the coil, which forces current to flow across the nerve membrane to depolarize it. The expression for the induced electric field and electric field gradient from a circular coil involves elliptic integrals and a number of independent experimental parameters. While these formulae cannot be written as simple closed form expressions, they can be evaluated numerically and spatial distributions of the “activating function”, the quantity that drives magnetic stimulation, can be calculated throughout the medium to determine how concentrated the site of stimulation is, i.e., where the stimulus is above threshold. This paper shows the results of these calculations and explores the behavior when we systematically vary key independent experimental parameters to assess the prospects of focal delivery of magnetic stimulation, primarily in the peripheral nervous system (PNS). I believe this was the first paper addressing focality of magnetic stimulation. This issue has significant consequences for the use of magnetic stimulation in vivo, both in the PNS and the CNS, and has been addressed subsequently by many others.
Basser PJ, Mattiello J, Le Bihan D. (1994) Estimation of the effective self-diffusion tensor from the NMR spin echo. J Magn Reson B. 103(3):247-54. PMID: 8019776, DOI: 10.1006/jmrb.1994.1037 PDF File (518 KB)
Author's Comments
This paper presents the theory and a novel experimental design to measure a translation diffusion tensor via NMR of a spin labeled medium, like water, in an excited volume, which had never been done previously. This work is the basis of what is now called diffusion tensor MRI or DTI, in which the measurement described in this paper is performed in each voxel within an imaging volume. The precursor to DTI, which was called diffusion imaging or diffusion MRI, used a model and MR pulse sequences originally proposed by Stejskal and Tanner to measure a scalar diffusion coefficient in an excited volume. The idea of diffusion imaging (dMRI) performed on a voxel by voxel basis within an imaging volume was conceived of and clearly articulated by Paul Lauterbur in has classic ’73 paper introducing “Zeugmatography” or MRI. Wesby et al. later demonstrated or reduced Lauterbur’s idea to practice in 1984, showing that they could measure and map apparent diffusion coefficients (ADCs) of different liquids within different test tubes within an imaging volume, and my colleague, Denis Lebihan, and contemporaries Merbolt et al., and Taylor and Bushell all developed clinically viable diffusion MRI sequences based upon Wesby et al’s earlier work. However, Moseley, Doran, and others soon discovered that in some biological tissues, like brain, Stejskal and Tanner’s diffusion model used in diffusion MR imaging wasn’t adequate. Brain tissue was “anisotropic”, which meant that when you measured the scalar diffusivity in one direction using diffusion imaging you obtain a different value of the diffusivity than if you measured it in another direction. Therefore, diffusivity was not an intrinsic quantity or property of the tissue but depended on the orientation in which you measured it. This created a radiological confound that made it confusing to interpret the varying contrasts obtained in diffusion images of patients (and research subjects), particularly in conditions like stroke, making it challenging to identify the ischemic areas of the brain with certainty. The problem with diffusion imaging was, as Moseley pointed out, that the model of the diffusion process was not complex enough to describe this anisotropic diffusion process. A diffusion tensor was needed.
Without having had the benefit of having read these earlier works, I independently proposed a theoretical and experimental pipeline for anisotropic diffusion MR measurements to my colleagues, Denis LeBihan, Robert Turner, and Brad Roth to overcome the deficiencies of diffusion MRI or diffusion imaging to describing anisotropic water diffusion in biological tissue like brain, skeletal muscle, cardiac muscle, etc. This required extending the theory of Stejskal and Tanner to be able to a) relate the NMR diffusion weighted signal to the apparent or effective diffusion tensor, to b) formulate and implement an expanded experimental design and new pulse sequences to measure the diffusion tensor using this relation, which entailed applying for the first time gradients in a multiplicity of directions, not just along x, y or z, to c) develop of means to estimate each element of the effective or apparent diffusion tensor from these measurements, and to d) propose new and useful intrinsic tensor-derived quantities to measure and map features of the diffusion process in anisotropic media. This particular paper addresses points a, b and c, above, concentrating on the theory and experimental design undergirding diffusion tensor NMR and MRI, whereas the issues discussed in d above and applications of diffusion tensor MRI or DTI were presented in “MR diffusion tensor spectroscopy and imaging.” It is notable that this journal article reports the first measurements (to my knowledge) of a translational diffusion tensor obtained in any medium. Here I used water and skeletal muscle as examples of isotropic and anisotropic diffusion, respectively.
Basser PJ, Mattiello J, Le Bihan D. (1994) MR diffusion tensor spectroscopy and imaging. Biophys J. 66(1):259-67. PMID: 8130344, PMCID: PMC1275686, DOI: 10.1016/S0006-3495(94)80775-1
Author's Comments
Having already presented the theory and method for estimating a diffusion tensor of water (or other spin labeled species) in an excited volume, this paper presented the theory behind the measurement of diffusion tensors in each voxel of an imaging volume and proposed the new and useful information contained in the diffusion tensor, and that can be derived from it, which has become the basis of what is now called “diffusion tensor MRI” or DTI. The precursor to DTI, which was called diffusion imaging or diffusion MRI, incorporated a model and MR pulse sequences originally proposed by Stejskal and Tanner into an imaging sequence to measure and map a scalar diffusion coefficient. The idea of diffusion imaging (dMRI) performed on a voxel by voxel basis within an imaging volume was actually conceived of and clearly articulated by Paul Lauterbur in has classic ’73 paper introducing “Zeugmatography” or MRI. Wesby et al. demonstrated or reduced Lauterbur’s idea to practice in 1984, showing that they could measure and map apparent diffusion coefficients of different liquids within different test tubes, and my colleague, Denis Lebihan, and contemporaries Merbolt et al., and Taylor and Bushell all developed clinically viable diffusion MRI sequences based upon Wesby, et al’s work. However, Moseley, Doran, and others soon discovered that in some biological tissues, like brain, Stejskal and Tanner’s diffusion model used in diffusion imaging wasn’t adequate. Brain tissue was “anisotropic”, which meant that when you measured the scalar diffusivity in one direction using diffusion imaging, you obtained a different value than if you measured it in another direction. Therefore, diffusivity was not an intrinsic quantity or property of the tissue but depended on the orientation along which it was measured. In fact, this created a radiological confound that made it confusing to interpret the varying contrasts of diffusion images in patients, particularly in conditions like stroke, making it challenging to identify the ischemic areas of the brain with certainty. The problem with diffusion imaging was, as Moseley pointed out, that the model of the diffusion process was not complex enough to describe this anisotropic diffusion process. A diffusion tensor was needed.

Without the benefit of having read Moseley’s and other previous works, however, I independently proposed a theoretical and experimental pipeline for anisotropic diffusion MR measurements to my colleagues, Denis LeBihan, Robert Turner, and Brad Roth to overcome the deficiencies of diffusion MRI or diffusion imaging for describing anisotropic water diffusion in biological tissues like brain, skeletal muscle, cardiac muscle, etc. This required extending the theory of Stejskal and Tanner to be able to a) relate the NMR diffusion weighted signal to an apparent or effective diffusion tensor, to b) formulate and implement an expanded experimental design and new MR pulse sequences to measure the diffusion tensor using this relation, which entailed applying gradients simultaneously in a multiplicity of directions, not just along x, y or z, and to c) propose new and useful intrinsic tensor-derived quantities to measure and map features of the diffusion process in anisotropic media. This particular paper addresses only points c above, whereas points a and b were considered at length in our paper on “Estimation of the effective self-diffusion tensor from the NMR spin echo”.

Once we showed how to estimate a diffusion tensor in an excited volume (in diffusion tensor NMR) or within a voxel (in diffusion tensor MRI), there are many new and important parameters and descriptors that I proposed as potential quantitative MR imaging biomarkers and features to measure and map. The first of these is the Trace of the diffusion tensor, or one-third of this quantity, which has come to become known as the mean apparent diffusion coefficient or mADC. The mADC is the simplest DTI-derived quantity but probably the most widely used and important in radiology and other disciplines of any DTI parameter. The mADC represents an orientationally averaged bulk diffusivity that removes the effects of diffusion anisotropy. Because of its beautiful mathematical properties, i.e., it is “rotationally invariant”-- it provides a stain or image contrast that is the same -- independent of the experimental design (i.e., the size of the diffusion gradients and their directions) and the position of the subject in the scanner. It has proven to be a very robust and useful imaging biomarker, particularly in evaluating patients suffering from stroke, or for assessing the severity or recovery from brain and other cancers. Other scalar invariants proposed in this work can help characterize features of diffusion anisotropy. I also suggested the use of a new glyph in this paper -- the diffusion ellipsoid. It elegantly depicts the “fiber frame of reference” or the frame in which anisotropic diffusion process appears simplest. The diffusion ellipsoid shows both the principal axes or eigenvector frame and the corresponding principal diffusivities along those fiber axes. The size, shape and orientation of the diffusion ellipsoid help characterize anisotropic diffusion in a voxel. These are determined by eigenvectors and eigenvalues of the diffusion tensor, which we can also be estimated from the diffusion tensor itself.

Another important point made in this work was that because of the similarity of the equations describing different transport processes, i.e., mass, charge, heat, momentum, …) I suggested that the diffusion tensor can be used to predict the form other tensors, like the electrical, thermal, and hydraulic conductivity tensors, elasticity tensors and other parameters that could find wide use in materials sciences, engineering and physics applications by availing oneself of the so-called “cross-property” relationships. This allows DTI data to be repurposed in many new application areas using the diffusion tensor field as a scaffolding to build models of transport of other physical and chemical quantities.
Mattiello J, Basser PJ, Le Bihan D. (1994) Analytical expressions for the b matrix in NMR diffusion imaging and spectroscopy. J Magn Reson A 108:131-141. DOI: 10.1006/jmra.1994.1103
Roth BJ, Basser PJ, and Wikswo JP. (1994) A theoretical model for magneto-acoustic imaging of bioelectric currents. IEEE Trans Biomed Eng. 41(8):723-8. PMID: 7927394, DOI: 10.1109/10.310087

1993

Basser PJ. (1993) Cable equation for a myelinated axon derived from its microstructure. Med Biol Eng Comput. 31 Suppl:S87-92. PMID: 8231331
Basser PJ, Grodzinsky AJ. (1993) The Donnan model derived from microstructure. Biophys Chem. 46(1):57-68. PMID: 8443336
Author's Comments
It is fascinating that many complex materials, including tissues, require study at many length and time scales to understand the basis of their functional properties. Such is the case with cartilage and other soft extracellular matrix (ECM) tissues, which are hierarchically organized over length scales ranging from nanometers to centimeters. One issue of great importance in tissue sciences is understanding the basis of cartilage’s remarkable load bearing ability and its loss in disease and trauma. In particular, how can this tissue, which is made up of a soft and squishy collagen network and gooey proteoglycan gel aggregates, form a stiff, tough material that can bear enormous static and dynamic loads? That question is more directly addressed by another paper of ours, which we wrote in 1998 with colleagues at the Technion, but a prerequisite to addressing that question is understanding the origin and action of the various intermolecular forces between and among various biomacromolecular components of cartilage that underlie its macroscopic behavior. One remarkable feature of the proteoglycan, Aggrecan, a key constituent of cartilage, is the enormous electrostatic repulsive forces that it generates between the tines of its “bottlebrushes”; its biopolymeric bristles are composed of negatively charged long-chain molecules, mostly chondroitin sulfate and keratin sulfate. These intermolecular repulsive electrostatic interactions are challenging to model at the molecular length scale, but at the macroscopic tissue length scale, many have used the Donnan model to relate the charge density of these proteoglycans to the swelling or osmotic pressure these molecules exert, which tends to “inflate” the tissue. The goal of this paper was to understand whether this macroscopic Donnan model could be reconciled or explained by a more fundamental intermolecular model that describes the electrostatic repulsive forces between and among charged proteoglycan molecular assemblies that are bathed in a physiological salt solution. Primarily, these molecular-scale electrostatic interactions are described by the Poisson-Boltzmann (PB) equation. To address this question, I considered a composite model of the Aggrecan bottlebrush molecule consisting of a stack of charged plates having a given fixed charge density, separated by thin salt water layers. To analyze this composite medium, I used a mathematical method originally developed by Burridge and Keller to “homogenize” or smooth over the microcontinuum PB equations describing the electrostatic repulsion between these microscopic charged plates. To make a long story short, I was able to derive the macroscopic Donnan model as a first-order perturbation approximation to the microcontinuum PB equations. This derivation also addressed and resolved an important conundrum in the biomechanics community about the physical origin of the osmotic swelling pressure of cartilage and its relationship to the electrostatic repulsion among its molecular constituents.

1992

Chiarelli P, Basser PJ, Derossi D, and Goldstein S. (1992) The dynamics of a hydrogel strip. Biorheology 29(4):383-98. PMID: 1306365
Nilsson J, Panizza M, Roth BJ, Basser PJ, Cohen LG, Caruso G, Hallett M. Determining the site of stimulation during magnetic stimulation of a peripheral nerve. Electroencephalogr Clin Neurophysiol. 85(4):253-64. PMID: 1380913
Basser PJ, Wijesinghe RS, and Roth BJ. (1992) The activating function for magnetic stimulation derived from a three-dimensional volume conductor model. IEEE Trans Biomed Eng. 39(11):1207-10. PMID: 1487283, DOI: 10.1109/10.168686
Basser PJ. (1992) Interstitial pressure, volume, and flow during infusion into brain tissue. Microvascular Research 44(2):143-65. PMID: 1474925
Author's Comments
To my knowledge, this is the first paper describing a method to infuse drugs directly into brain tissue or brain “parenchyma”—now known as “Convection Enhanced Delivery,” or CED. CED is now an FDA-approved semi-invasive neurosurgical technique for regional delivery of chemotherapeutic agents, oncolytic viruses, etc. e.g., to treat brain tumors and other conditions without causing systemic toxicity. NIH colleagues Bob Dedrick and Paul Morrison suggested this clever approach because many drugs, particularly ones intended to treat brain tumors, could not cross the blood-brain-barrier when delivered via the vasculature. CED circumvented the blood-brain-barrier altogether, allowing the drug to be delivered locally, where it was needed, without causing systemic toxicity.

This paper describes a model of how a solute (or drug) is distributed within brain tissue when infused through a cannula under pressure. A unique feature of this model is that it takes into account the spongy porous-elastic properties of live brain tissue and its hydraulic properties that resist the flow of the infusate. The pressure and velocity distributions of the solute or drug are predicted as well as the deformation of the surrounding tissue. Interestingly, the injected fluid drags the tissue away from the end of the cannula. Some key ideas raised in this paper were that a) it would be possible to incorporate the anisotropy of the hydraulic conductivity of white matter into the model to predict pressure and drug distribution along white matter pathways, and b) that one could consider infusing not just drugs but “proteins, nucleic acids, viruses, and cells” into the brain parenchyma. Overall, CED is now a widely used minimally invasive neurosurgical technique for delivering a wide spectrum of agents into the brain. Many ideas in this paper have subsequently been incorporated into commercial medical devices to help plan and guide these CED therapeutic procedures in patients by being able to predict the transport of the infusate throughout the brain.

1991

Basser PJ, Roth BJ. (1991) Stimulation of a myelinated nerve axon by electromagnetic induction. Med Biol Eng Comput. 29(3):261-268. PMID: 1943258
Author's Comments
This paper extends our 1990 “A model of the stimulation of a nerve fiber by electromagnetic induction” to consider stimulation of myelinated nerves in the PNS or myelinated axons in the CNS by electromagnetic induction. Our previous model of stimulation of uniform nerve fibers had to be adapted and extended to consider these composite electrically insulated myelinated nerves and axons. Notable in this paper was the introduction and use of non-dimensional parameters appearing in the governing equations to help us rescale and simplify the underlying differential equations describing the excitation process and provide simple threshold criteria to predict whether, where and when a nerve would fire. Another innovation was the use of a “space curve” to describe the path of nerves or axons which may have sinuous trajectories. I later used this idea when proposing a new “tractography” algorithm that used diffusion tensor MRI (DTI) data to follow nerve, axon or other fiber pathways or trajectories.

1990

Roth B, Basser P. (1990) A model of the stimulation of a nerve fiber by electromagnetic induction. IEEE Trans. Bio. Med. Eng. 37:588-597. PMID: 2354840, DOI: 10.1109/10.55662
Author's Comments
Although time-varying magnetic fields have been used to stimulate living tissue since d'Arsonval first reported this observation in 1896, it had since been a mystery what the underlying mechanism of action was causing this remarkable phenomenon to occur. This paper provided the first comprehensive physics-based model of nerve stimulation by electromagnetic induction, which later became known as “magnetic stimulation”, “peripheral magnetic stimulation” (PMS) or “transcutaneous magnetic stimulation”. When used in the brain, it became known as “transcranial magnetic stimulation” (TMS). The basic idea was that if there were an electric field gradient induced along the direction of a nerve fiber, current would be injected or withdrawn across the nerve membrane, causing the transmembrane potential to change. We first proposed a “subthreshold” model that showed quantitatively how discharging a capacitor through a nearby circular inductive coil, predicting the change in transmembrane potential distribution along a nerve. We then considered the same type of excitation, this time of an active Hodgkin-Huxley nerve model. Once we clarified how the nerve fibers fired, we established the conditions whether, where, and when they would fire. More than 30 years later, FDA-approved medical devices that electromagnetically stimulate nerves in the PNS and axons in the CNS are “workhorses” in neurology both diagnostically and therapeutically.