Evaluation and statistical inference for human connectomes

Nature Methods

Volumn 11, Issue 10, 2014, Pages 1058-1063

  Pestilli, Franco ^a   Yeatman, Jason D ^a   Rokem, Ariel ^a   Kay, Kendrick N ^a,b   Wandell, Brian A ^a  

^a STANFORD UNIVERSITY   (United States)

^b WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; BOOTSTRAPPING; BRAIN MAPPING; BRAIN REGION; BRAIN SIZE; CONNECTOME; CORPUS CALLOSUM; DIFFUSION WEIGHTED IMAGING; EFFECT SIZE; HUMAN; INFORMATION PROCESSING; NERVE FIBER; NEUROMODULATION; PREDICTION; PRIORITY JOURNAL; SIGNAL NOISE RATIO; TEST RETEST RELIABILITY; TRACTOGRAPHY; WHITE MATTER; ALGORITHM; BIOLOGY; BRAIN; COGNITION; COMPUTER PROGRAM; MYELINATED NERVE; NUCLEAR MAGNETIC RESONANCE IMAGING; PATHOLOGY; PHYSIOLOGY; PROBABILITY; PROCEDURES; REPRODUCIBILITY; STATISTICAL ANALYSIS; STATISTICS;

ALGORITHMS; BRAIN; BRAIN MAPPING; COGNITION; COMPUTATIONAL BIOLOGY; CONNECTOME; DATA INTERPRETATION, STATISTICAL; HUMANS; MAGNETIC RESONANCE IMAGING; NERVE FIBERS, MYELINATED; PROBABILITY; REPRODUCIBILITY OF RESULTS; SOFTWARE; STATISTICS AS TOPIC;

EID: 84921822613     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3098     Document Type: Article

References (61)

1. Zhang, Y. et al. Atlas-guided tract reconstruction for automated and comprehensive examination of the white matter anatomy. Neuroimage 52, 1289-1301 (2010).
2. Yendiki, A. et al. Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy. Front. Neuroinform. 5, 23 (2011).
3. Yeatman, J.D., Dougherty, R.F., Myall, N.J., Wandell, B.A. & Feldman, H.M. Tract profiles of white matter properties: Automating fiber-tract quantification. PLoS ONE 7, e49790 (2012).
4. Yeatman, J.D., Dougherty, R.F., Ben-Shachar, M. & Wandell, B.A. Development of white matter and reading skills. Proc. Natl. Acad. Sci. USA 109, E3045-E3053 (2012).
5. Samanez-Larkin, G.R., Levens, S.M., Perry, L.M., Dougherty, R.F. & Knutson, B. Frontostriatal white matter integrity mediates adult age differences in probabilistic reward learning. J. Neurosci. 32, 5333-5337 (2012).
6. Thomason, M.E. & Thompson, P.M. Diffusion imaging, white matter, and psychopathology. Annu. Rev. Clin. Psychol. 7, 63-85 (2011).
7. Lebel, C., Walker, L., Leemans, A., Phillips, L. & Beaulieu, C. Microstructural maturation of the human brain from childhood to adulthood. Neuroimage 40, 1044-1055 (2008).
8. Scholz, J., Klein, M.C., Behrens, T.E.J. & Johansen-Berg, H. Training induces changes in white-matter architecture. Nat. Neurosci. 12, 1370-1371 (2009).
9. Hoeft, F. et al. Neural systems predicting long-term outcome in dyslexia. Proc. Natl. Acad. Sci. USA 108, 361-366 (2011).
10. Sporns, O., Tononi, G. & Kötter, R. The human connectome: A structural description of the human brain. PLoS Comput. Biol. 1, e42 (2005).
11. Hagmann, P. et al. MR connectomics: principles and challenges. J. Neurosci. Methods 194, 34-45 (2010).
12. Craddock, R.C. et al. Imaging human connectomes at the macroscale. Nat. Methods 10, 524-539 (2013).
13. Wedeen, V.J. et al. The geometric structure of the brain fiber pathways. Science 335, 1628-1634 (2012).
14. Catani, M., Bodi, I. & Dell'Acqua, F. Comment on "The geometric structure of the brain fiber pathways". Science 337, 1605 (2012).
15. Kim, D., Sra, S. & Dhillon, S.I. A non-monotonic method for large-scale nonnegative least squares. Optim. Methods Softw. 28, 1012-1039 (2013).
16. Tournier, J.-D., Calamante, F. & Connelly, A. MRtrix: diffusion tractography in crossing fiber regions. Int. J. Imaging Syst. Technol. 22, 53-66 (2012).
17. Markov, N.T. et al. Cortical high-density counterstream architectures. Science 342, 1238406 (2013).
18. Braitenberg, V. & Schuz, A. Cortex: Statistics and Geometry of Neuronal Connectivity (Springer, 1998).
19. Aboitiz, F., Scheibel, A.B., Fisher, R.S. & Zaidel, E. Fiber composition of the human corpus callosum. Brain Res. 598, 143-153 (1992).
20. 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, 183-190 (2010).
21. Smith, R.E., Tournier, J.-D., Calamante, F. & Connelly, A. SIFT: spherical-deconvolution informed filtering of tractograms. Neuroimage 67, 298-312 (2013).
22. Bastiani, M., Shah, N.J., Goebel, R. & Roebroeck, A. Human cortical connectome reconstruction from diffusion weighted MRI: the effect of tractography algorithm. Neuroimage 62, 1732-1749 (2012).
23. Basser, P.J., Pajevic, S., Pierpaoli, C., Duda, J. & Aldroubi, A. In vivo fiber tractography using DT-MRI data. Magn. Reson. Med. 44, 625-632 (2000).
24. Lazar, M. et al. White matter tractography using diffusion tensor deflection. Hum. Brain Mapp. 18, 306-321 (2003).
25. Behrens, T.E.J. et al. Non-invasive mapping of connections between human thalamus and cortex using diffusion imaging. Nat. Neurosci. 6, 750-757 (2003).
26. Parker, G.J.M., Haroon, H.A. & Wheeler-Kingshott, C.A.M. A framework for a streamline-based probabilistic index of connectivity (PICo) using a structural interpretation of MRI diffusion measurements. J. Magn. Reson. Imaging 18, 242-254 (2003).
27. Efron, B. & Tibshirani, R.J. An Introduction to the Bootstrap (Chapman & Hall, 1993).
28. Green, D.M. & Swets, J.A. Signal Detection Theory and Psychophysics (Wiley, 1966).
29. Rubner, Y., Tomasi, C. & Guibas, L.J. The Earth Mover's Distance as a metric for image retrieval. Int. J. Comput. Vis. 40, 99-121 (2000).
30. Maunsell, J.H. & van Essen, D.C. The connections of the middle temporal visual area (MT) and their relationship to a cortical hierarchy in the macaque monkey. J. Neurosci. 3, 2563-2586 (1983).
31. Boussaoud, D., Ungerleider, L.G. & Desimone, R. Pathways for motion analysis: cortical connections of the medial superior temporal and fundus of the superior temporal visual areas in the macaque. J. Comp. Neurol. 296, 462-495 (1990).
32. Greenblatt, S.H. Alexia without agraphia or hemianopsia. Anatomical analysis of an autopsied case. Brain 96, 307-316 (1973).
33. Yeatman, J.D., Rauschecker, A.M. & Wandell, B.A. Brain & Language. Brain Lang. 125, 146-155 (2013).
34. Kriegeskorte, N. et al. Human cortical object recognition from a visual motion flowfield. J. Neurosci. 23, 1451-1463 (2003).
35. Orban, G.A. A motion area in human visual cortex. Proc. Natl. Acad. Sci. USA 92, 993-997 (1995).
36. Braddick, O.J., O'Brien, J.M., Wattam-Bell, J., Atkinson, J. & Turner, R. Form and motion coherence activate independent, but not dorsal/ventral segregated, networks in the human brain. Curr. Biol. 10, 731-734 (2000).
37. Colby, C.L., Duhamel, J.R. & Goldberg, M.E. Ventral intraparietal area of the macaque: Anatomic location and visual response properties. J. Neurophysiol. 69, 902-914 (1993).
38. Conturo, T.E. et al. Tracking neuronal fiber pathways in the living human brain. Proc. Natl. Acad. Sci. USA 96, 10422-10427 (1999).
39. Mangin, J.F. et al. Toward global tractography. Neuroimage 80, 290-296 (2013).
40. Aganj, I. et al. Medical image analysis. Med. Image Anal. 15, 414-425 (2011).
41. Neher, P.F. et al. MITK global tractography. in Proc. SPIE, Vol. 8314 (eds. Haynor, D.R. & Ourselin, S.) (SPIE, 2012).
42. Jbabdi, S., Woolrich, M.W., Andersson, J.L.R. & Behrens, T.E.J. A Bayesian framework for global tractography. Neuroimage 37, 116-129 (2007).
43. Sherbondy, A.J., Dougherty, R.F., Ananthanarayanan, R., Modha, D.S. & Wandell, B.A. Think global, act local; projectome estimation with BlueMatter. Med. Image Comput. Comput. Assist. Interv. 12, 861-868 (2009).
44. Sherbondy, A.J., Dougherty, R.F., Ben-Shachar, M., Napel, S. & Wandell, B.A. ConTrack: finding the most likely pathways between brain regions using diffusion tractography. J. Vis. 8, 15 (2008).
45. Schreiber, J., Riffert, T., Anwander, A. & Knösche, T.R. Plausibility tracking: A method to evaluate anatomical connectivity and microstructural properties along fiber pathways. Neuroimage 90, 163-178 (2014).
46. Parker, G.J.M. et al. Initial demonstration of in vivo tracing of axonal projections in the macaque brain and comparison with the human brain using diffusion tensor imaging and fast marching tractography. Neuroimage 15, 797-809 (2002).
47. Seehaus, A.K. et al. Histological validation of DW-MRI tractography in human postmortem tissue. Cereb. Cortex 23, 442-450 (2013).
48. Jones, D.K., Knosche, T.R. & Turner, R. White matter integrity, fiber count, and other fallacies: the do's and don'ts of diffusion MRI. Neuroimage 73, 239-254 (2013).
49. Fillard, P. et al. NeuroImage quantitative evaluation of 10 tractography algorithms on a realistic diffusion MR phantom. Neuroimage 56, 220-234 (2011).
50. Assaf, Y. et al. The CONNECT project: combining macro-and micro-structure. Neuroimage 80, 273-282 (2013).
51. Close, T.G. et al. A software tool to generate simulated white matter structures for the assessment of fibre-tracking algorithms. Neuroimage 47, 1288-1300 (2009).
52. Mezer, A. et al. Quantifying the local tissue volume and composition in individual brains with magnetic resonance imaging. Nat. Med. 19, 1667-1672 (2013).
53. Jones, D.K., Horsfield, M.A. & Simmons, A. Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging. Magn. Reson. Med. 42, 515-525 (1999).
54. Friston, K.J. et al. Spatial registration and normalization of images. Hum. Brain Mapp. 3, 165-189 (1995).
55. Van Essen, D.C. et al. The Human Connectome Project: A data acquisition perspective. Neuroimage 62, 2222-2231 (2012).
56. Van Essen, D.C. et al. The WU-Minn Human Connectome Project: An overview. Neuroimage 80, 62-79 (2013).
57. Fischl, B. FreeSurfer. Neuroimage 62, 774-781 (2012).
58. Destrieux, C., Fischl, B., Dale, A. & Halgren, E. Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. Neuroimage 53, 1-15 (2010).
59. Fischl, B. et al. Cortical folding patterns and predicting cytoarchitecture. Cereb. Cortex 18, 1973-1980 (2008).
60. Stejskal, E.O. & Tanner, J.E. Spin diffusion measurements: spin echoes in the presence of a time-dependent field gradient. J. Chem. Phys. 42, 288 (1965).
61. Basser, P.J. & Pierpaoli, C. Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J. Magn. Reson. B. 111, 209-219 (1996).