| Peer Reviewed Articles (Alphabetically ordered, updates October 2012) |
1. Alexander, D. C. & Dyrby, T. B. Diffusion imaging with stimulated echoes: signal models, and experiment design. Submitted |
2. Alexander, D. C. et al. Orientationally invariant indices of axon diameter and density from diffusion MRI. Neuroimage 52, 1374–89 (2010). |
3. Azadbakht, H. et al. Validation of high resolution tractography against in vivo tracing in the macaque visual cortex. in preparation |
4. Barazany, D., Jones, D. K. & Assaf, Y. AxCaliber 3D. in preparation |
5. Behrens, T. E. J. & Sporns, O. Human connectomics. Curr Opin Neurobiol 22, 144–53 (2012). |
6. Ben-Amitay, S., Jones, D. K. & Assaf, Y. Motion correction and registration of high b-value diffusion weighted images. Magn Reson Med 67, 1694–702 (2012). |
7. Bizzi, A. et al. Aphasia induced by gliomas growing in the ventrolateral frontal region: assessment with diffusion MR tractography, functional MR imaging and neuropsychology. Cortex 48, 255–72 (2012). |
8. Blumenfeld-Katzir, T., Pasternak, O., Dagan, M. & Assaf, Y. Diffusion MRI of structural brain plasticity induced by a learning and memory task. PLoS One 6, e20678 (2011). |
9. Broser, P., Vargha-Khadem, F. & Clark, C. A. Robust subdivision of the thalamus in children based on probability distribution functions calculated from probabilistic tractography. Neuroimage 57, 403–15 (2011). |
10. Ciaraffa, F., Castelli, G., Parati, E. A., Bartolomeo, P. & Bizzi, A. Visual neglect as a disconnection syndrome? A confirmatory case report. Neurocase (2012).doi:10.1080/13554794.2012.667130 |
11. Clayden, J. D. et al. Normative development of white matter tracts: similarities and differences in relation to age, gender, and intelligence. Cereb Cortex 22, 1738–47 (2012). |
12. Clayden, J. D., King, M. D. & Clark, C. A. Shape modelling for tract selection. Med Image Comput Comput Assist Interv 12, 150–7 (2009). |
13. Clayden, J. D. et al. TractoR: Magnetic resonance imaging and tractography with R. Journal of Statistical Software 44, 1–18 (2011). |
14. Clayden, J. D., Nagy, Z., Hall, M. G., Clark, C. A. & Alexander, D. C. Active imaging with dual spin-echo diffusion MRI. Inf Process Med Imaging 21, 264–75 (2009). |
15. De Santis, S., Assaf, Y., Evans, C. J. & Jones, D. K. Improved precision in CHARMED assess- ment of white matter through sampling scheme optimisation and model parsimony testing. Submitted |
16. De Santis, S., Assaf, Y. & Jones, D. K. Using the biophysical CHARMED model to elucidate the underpinnings of contrast in diffusional kurtosis analysis of diffusion-weighted MRI. MAGMA 25, 267–76 (2012). |
17. De Santis, S., Assaf, Y. & Jones, D. K. Characterizing variation in white matter microstructure: an atlas-based approach. in preparation |
18. Douaud, G. et al. In vivo evidence for the selective subcortical degeneration in Huntington's disease. Neuroimage 46, 958–66 (2009). |
19. Douaud, G. et al. DTI measures in crossing-fibre areas: increased diffusion anisotropy reveals early white matter alteration in MCI and mild Alzheimer's disease. Neuroimage 55, 880–90 (2011). |
20. Drobnjak, I. & Alexander, D. C. Optimising time-varying gradient orientation for microstructure sensitivity in diffusion-weighted MR. J Magn Reson 212, 344–54 (2011). |
21. Drobnjak, I., Siow, B. & Alexander, D. C. Optimizing gradient waveforms for microstructure sensitivity in diffusion-weighted MR. J Magn Reson 206, 41–51 (2010). |
22. Dubois, J. et al. Brain development of infant and MRI by diffusion tensor imaging. Neurophysiol Clin 42, 1–9 |
23. Dyrby, T. B., Sřgaard, L. V., Hall, M. G., Ptito, M. & Alexander, D. C. Contrast and stability of the axon diameter index from microstructure imaging with diffusion MRI. Magn Reson Med (2012).doi:10.1002/mrm.24501 |
24. Eickhoff, S. B. et al. Anatomical and functional connectivity of cytoarchitectonic areas within the human parietal operculum. J Neurosci 30, 6409–21 (2010). |
25. Fischi-Gomez, E. et al. Effects of prematurity on brain Connectivity at age 6 years: a full Connectom analysis. in preparation |
26. Gallichan, D. et al. Addressing a systematic vibration artifact in diffusion-weighted MRI. Hum Brain Mapp 31, 193–202 (2010). |
27. Guevara, P. et al. Automatic fiber bundle segmentation in massive tractography datasets using a multi-subject bundle atlas. Neuroimage 61, 1083–99 (2012). |
28. Heidemann, R. M., Anwander, A., Feiweier, T., Knösche, T. R. & Turner, R. k-space and q-space: combining ultra-high spatial and angular resolution in diffusion imaging using ZOOPPA at 7 T. Neuroimage 60, 967–78 (2012). |
29. Heidemann, R. M. et al. Diffusion imaging in humans at 7T using readout-segmented EPI and GRAPPA. Magn Reson Med 64, 9–14 (2010). |
30. Hofstetter, S., Tavor, I., Tzur-Moryosef, S. & Assaf, Y. Short term learning induced white matter plasticity in the fornix. Submitted |
31. Hubbard, P. L., Zhou, F.-L., Eichhorn, S. J. & Parker, G. J. M. A bulk biomimetic phantom for the validation of diffusion MRI – sensitivity to microstructure. in preparation |
32. Hunt, L. T. et al. Mechanisms underlying cortical activity during value-guided choice. Nat Neurosci 15, 470–6, S1–3 (2012). |
33. Iima, M. et al. Reduced-distortion diffusion MRI of the craniovertebral junction. AJNR Am J Neuroradiol 33, 1321–5 (2012). |
34. Jbabdi, S. & Behrens, T. E. J. Specialization: the connections have it. Nat Neurosci 15, 171–2 (2012). |
35. Jbabdi, S., Behrens, T. E. J. & Smith, S. M. Crossing fibres in tract-based spatial statistics. Neuroimage 49, 249–56 (2010). |
36. Jbabdi, S., Sotiropoulos, S. N., Savio, A. M., Grańa, M. & Behrens, T. E. J. Model-based analysis of multishell diffusion MR data for tractography: How to get over fitting problems. Magn Reson Med (2012) |
37. Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W. & Smith, S. M. Fsl. Neuroimage 62, 782–90 (2012). |
38. Jocham, G., Hunt, L. T., Near, J. & Behrens, T. E. J. A mechanism for value-guided choice based on the excitation-inhibition balance in prefrontal cortex. Nat Neurosci 15, 960–1 (2012). |
39. Jones, D. K., Knösche, T. R. & Turner, R. White matter integrity, fiber count, and other fallacies: The do's and don'ts of diffusion MRI. Neuroimage (2012). |
40. King, A. V. et al. Microstructure of a three-way anatomical network predicts individual differences in response inhibition: a tractography study. Neuroimage 59, 1949–59 (2012). |
41. King, M. D., Calamante, F., Clark, C. A. & Gadian, D. G. Markov Chain Monte Carlo Random Effects Modeling in Magnetic Resonance Image Processing Using the BRugs Interface to WinBUGS. Journal of Statistical Software 44, (2011). |
42. Klein-Flügge, M. C., Hunt, L. T., Bach, D. R., Dolan, R. J. & Behrens, T. E. J. Dissociable reward and timing signals in human midbrain and ventral striatum. Neuron 72, 654–64 (2011). |
43. Knösche, T. R. & Tittgemeyer, M. The role of long-range connectivity for the characterization of the functional-anatomical organization of the cortex. Front Syst Neurosci 5, 58 (2011). |
44. Kunz, N. et al. Probing micro-structural information using the CHARMED model in the non-myelinated human newborn brain at 3T. in preparation |
45. Kunz, N. et al. brain development using the NODDI model in the non-myelinated human newborn brain at 3T. in preparation |
46. Le Bihan, D. et al. Brain tissue water comes in two pools: evidence from diffusion and R2' measurements with USPIOs in non human primates. Neuroimage 62, 9–16 (2012). |
47. Le Bihan, D. Diffusion, confusion and functional MRI. Neuroimage 62, 1131–6 (2012). |
48. Lundell, H. et al. Fast diffusion tensor imaging and tractography of the whole cervical spinal cord using point spread function corrected echo planar imaging. Magn Reson Med (2012).doi:10.1002/mrm.24235 |
49. Lundell, H., Nielsen, J. B., Ptito, M. & Dyrby, T. B. Distribution of collateral fibers in the monkey cervical spinal cord detected with diffusion-weighted magnetic resonance imaging. Neuroimage 56, 923–9 (2011). |
50. Mars, R. B. et al. Diffusion-weighted imaging tractography-based parcellation of the human parietal cortex and comparison with human and macaque resting-state functional connectivity. J Neurosci 31, 4087–100 (2011). |
51. McNab, J. A. et al. High resolution diffusion-weighted imaging in fixed human brain using diffusion-weighted steady state free precession. Neuroimage 46, 775–85 (2009). |
52. Miller, K. L. et al. Diffusion imaging of whole, post-mortem human brains on a clinical MRI scanner. Neuroimage 57, 167–81 (2011). |
53. Panagiotaki, E. et al. Compartment models of the diffusion MR signal in brain white matter: a taxonomy and comparison. Neuroimage 59, 2241–54 (2012). |
54. Richardson, S., Siow, B., Batchelor, A. M., Lythgoe, M. F. & Alexander, D. C. A viable isolated tissue system: A tool for detailed MR measurements and controlled perturbation in physiologically stable tissue. Magn Reson Med (2012). |
55. Richardson, S., Siow, B., Batchelor, A. M., Lythgoe, M. F. & Alexander, D. C. A viable isolated tissue system: A tool for detailed MR measurements and controlled perturbation in physiologically stable tissue. Magn Reson Med (2012). |
56. Rilling, J. K., Glasser, M. F., Jbabdi, S., Andersson, J. & Preuss, T. M. Continuity, divergence, and the evolution of brain language pathways. Front Evol Neurosci 3, 11 (2011). |
57. Rilling, J. K. et al. Differences between chimpanzees and bonobos in neural systems supporting social cognition. Soc Cogn Affect Neurosci 7, 369–79 (2012). |
58. Sagi, Y. et al. Learning in the fast lane: new insights into neuroplasticity. Neuron 73, 1195–203 (2012). |
59. Sasson, E., Doniger, G. M., Pasternak, O., Tarrasch, R. & Assaf, Y. Structural correlates of cognitive domains in normal aging with diffusion tensor imaging. Brain Struct Funct 217, 503–15 (2012). |
60. Schneider, T., Wheeler-Kingshott, C. A. M. & Alexander, D. C. In-vivo estimates of axonal characteristics using optimized diffusion MRI protocols for single fibre orientation. Med Image Comput Comput Assist Interv 13, 623–30 (2010). |
61. Schubotz, R. I., Anwander, A., Knösche, T. R., von Cramon, D. Y. & Tittgemeyer, M. Anatomical and functional parcellation of the human lateral premotor cortex. Neuroimage 50, 396–408 (2010). |
62. Shemesh, N., Adiri, T. & Cohen, Y. Probing microscopic architecture of opaque heterogeneous systems using double-pulsed-field-gradient NMR. J Am Chem Soc 133, 6028–35 (2011). |
63. Shemesh, N. et al. Mapping apparent eccentricity and residual ensemble anisotropy in the gray matter using angular double-pulsed-field-gradient MRI. Magn Reson Med 68, 794–806 (2012). |
64. Shemesh, N. & Cohen, Y. Overcoming apparent susceptibility-induced anisotropy (aSIA) by bipolar double-pulsed-field-gradient NMR. J Magn Reson 212, 362–9 (2011). |
65. Shemesh, N. & Cohen, Y. Microscopic and compartment shape anisotropies in gray and white matter revealed by angular bipolar double-PFG MR. Magn Reson Med 65, 1216–27 (2011). |
66. Shemesh, N., Ozarslan, E., Adiri, T., Basser, P. J. & Cohen, Y. 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, 044705 (2010). |
67. Shemesh, N., Özarslan, E., Basser, P. J. & Cohen, Y. Accurate noninvasive measurement of cell size and compartment shape anisotropy in yeast cells using double-pulsed field gradient MR. NMR Biomed 25, 236–46 (2012). |
68. Sherbondy, A. J., Rowe, M. C. & Alexander, D. C. MicroTrack: an algorithm for concurrent projectome and microstructure estimation. Med Image Comput Comput Assist Interv 13, 183–90 (2010). |
69. Siow, B., Drobnjak, I., Chatterjee, A., Lythgoe, M. F. & Alexander, D. C. Estimation of pore size in a microstructure phantom using the optimised gradient waveform diffusion weighted NMR sequence. J Magn Reson 214, 51–60 (2012). |
70. Sotiropoulos, S. N., Behrens, T. E. J. & Jbabdi, S. Ball and rackets: Inferring fiber fanning from diffusion-weighted MRI. Neuroimage 60, 1412–25 (2012). |
71. Tariq, M. et al. Scan-rescan reproducibility of neurite microstructure estimates using NODDI. edical Image Understanding and Analysis 255 – 261 (2012). |
72. Tavor, I., Hofstetter, S. & Assaf, Y. Micro-structural assessment of short term plasticity. in preparation |
73. Valette, J. et al. A new sequence for single-shot diffusion-weighted NMR spectroscopy by the trace of the diffusion tensor. Magn Reson Med (2012). |
74. Van de Looij, Y., Kunz, N., Hüppi, P., Gruetter, R. & Sizonenko, S. Diffusion tensor echo planar imaging using surface coil transceiver with a semiadiabatic RF pulse sequence at 14.1T. Magn Reson Med 65, 732–7 (2011). |
75. Woolrich, M., Hunt, L., Groves, A. & Barnes, G. MEG beamforming using Bayesian PCA for adaptive data covariance matrix regularization. Neuroimage 57, 1466–79 (2011). |
76. Yendiki, A. et al. Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy. Front Neuroinformatics 5, 23 (2011). |
77. Zhang, H., Dyrby, T. B. & Alexander, D. C. Axon diameter mapping in crossing fibers with diffusion MRI. Med Image Comput Comput Assist Interv 14, 82–9 (2011). |
78. Zhang, H., Hubbard, P. L., Parker, G. J. M. & Alexander, D. C. Axon diameter mapping in the presence of orientation dispersion with diffusion MRI. Neuroimage 56, 1301–15 (2011). |
79. Zhou, F.-L., Hubbard, P. L., Eichhorn, S. J. & Parker, G. J. M. Jet deposition in near-field electrospinning of patterned polycaprolactone and sugar-polycaprolactone core–shell fibres. Polymer (Guildf) 52, 3603–3610 (2011). |
80. Zhou, F.-L., Hubbard, P. L., Eichhorn, S. J. & Parker, G. J. M. Coaxially Electrospun Axon-Mimicking Fibers for Diffusion Magnetic Resonance Imaging. Submitted |
