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