Plausibility Tracking: A method to evaluate anatomical connectivity and microstructural properties along fiber pathways

NeuroImage

Volumn 90, Issue , 2014, Pages 163-178

  Schreiber, Jan ^a   Riffert, Till ^a   Anwander, Alfred ^a   Knösche, Thomas R ^a  

^a MAX PLANCK INSTITUTE FOR HUMAN COGNITIVE AND BRAIN SCIENCES   (Germany)

Author keywords

Diffusion MRI; Fiber density; Global tractography; Microstructural metrics; Spherical deconvolution; Tract based analysis; Tractography

Indexed keywords

DIFFUSION MRI; FIBER DENSITY; GLOBAL TRACTOGRAPHY; MICROSTRUCTURAL METRICS; SPHERICAL DECONVOLUTION; TRACT-BASED ANALYSIS; TRACTOGRAPHY;

ADULT; BRAIN; BRAIN MAPPING; CHILD; DIFFUSION TENSOR IMAGING; FEMALE; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MALE; NERVE FIBERS; NEURAL PATHWAYS;

EID: 84893546588     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2014.01.002     Document Type: Article

References (95)

1. Aboitiz F., Scheibel A.B., Fisher R.S., Zaidel E. Fiber composition of the human corpus callosum. Brain Res. 1992, 598:143-153.
2. Aganj I., Lenglet C., Sapiro G., Yacoub E., Ugurbil K., Harel N. Reconstruction of the orientation distribution function in single- and multiple-shell q-ball imaging within constant solid angle. Magn. Reson. Med. 2010, 64:554-566.
3. Aganj I., Lenglet C., Jahanshad N., Yacoub E., Harel N., Thompson P.M., Sapiro G. A Hough transform global probabilistic approach to multiple-subject diffusion MRI tractography. Med. Image Anal. 2011, 15:414-425.
4. Alexander D.C. Multiple-fiber reconstruction algorithms for diffusion MRI. Ann. N. Y. Acad. Sci. 2005, 1064:113-133.
5. Alexander A.L., Hasan K.M., Lazar M., Tsuruda J.S., Parker D.L. Analysis of partial volume effects in diffusion-tensor MRI. Magn. Reson. Med. 2001, 45:770-780.
6. Alexander D.C., Barker G.J., Arridge S.R. Detection and modeling of non-Gaussian apparent diffusion coefficient profiles in human brain data. Magn. Reson. Med. 2002, 48:331-340.
7. Alexander D.C., Hubbard P.L., Hall M.G., Moore E.A., Ptito M., Parker G.J.M., Dyrby T.B. Orientationally invariant indices of axon diameter and density from diffusion MRI. NeuroImage 2010, 52:1374-1389.
8. Anwander A., Tittgemeyer M., von Cramon D.Y., Friederici A.D., Knösche T.R. Connectivity-based parcellation of broca's area. Cereb. Cortex 2007, 17:816-825.
9. Ashburner J., Friston K.J. Voxel-based morphometry - the methods. NeuroImage 2000, 11:805-821.
10. Ashburner J., Friston K.J. Unified segmentation. NeuroImage 2005, 26:839-851.
11. Assaf Y., Freidlin R.Z., Rohde G.K., Basser P.J. New modeling and experimental framework to characterize hindered and restricted water diffusion in brain white matter. Magn. Reson. Med. 2004, 52:965-978.
12. Assaf Y., Blumenfeld-Katzir T., Yovel Y., Basser P.J. AxCaliber: a method for measuring axon diameter distribution from diffusion MRI. Magn. Reson. Med. 2008, 59:1347-1354.
13. Avants B., Epstein C., Grossman M., Gee J. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med. Image Anal. 2008, 12:26-41.
14. Basser P.J. Inferring microstructural features and the physiological state of tissues from diffusion-weighted images. NMR Biomed. 1995, 8:333-344.
15. Basser P.J., Pierpaoli C. Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J. Magn. Reson. B 1996, 111:209-219.
16. Basser P.J., Mattiello J., LeBihan D. Estimation of the effective self-diffusion tensor from the NMR spin echo. J. Magn. Reson. B 1994, 103:247-254.
17. Bastiani M., Shah N.J., Goebel R., Roebroeck A. Human cortical connectome reconstruction from diffusion weighted MRI: the effect of tractography algorithm. NeuroImage 2012, 62:1732-1749.
18. Beaulieu C. The basis of anisotropic water diffusion in the nervous system-a technical review. NMR Biomed. 2002, 15(7-8):435-455.
19. Behrens T.E.J., Woolrich M.W., Jenkinson M., Johansen-Berg H., Nunes R.G., Clare S., Matthews P.M., Brady J.M., Smith S.M. Characterization and propagation of uncertainty in diffusion-weighted MR imaging. Magn. Reson. Med. 2003, 50:1077-1088.
20. Behrens T.E.J., Berg H.J., Jbabdi S., Rushworth M.F.S., Woolrich M.W. Probabilistic diffusion tractography with multiple fibre orientations: what can we gain?. NeuroImage 2007, 34:144-155.
21. Brauer J., Anwander A., Friederici A.D. Neuroanatomical prerequisites for language functions in the maturing brain. Cereb. Cortex 2011, 21:459-466.
22. Brauer J., Anwander A., Perani D., Friederici A.D. Dorsal andventral pathways in language development. Brain Lang 2013, 127(2):289-295.
23. Brodmann K. Vergleichende Lokalisationslehre der Großhirnrinde 1909, Barth, Leipzig.
24. Catmull E., Rom R. A Class of Local Interpolating Splines. Computer Aided Geometric Design 1974, 317-326. Academic Press.
25. Colby J.B., Soderberg L., Lebel C., Dinov I.D., Thompson P.M., Sowell E.R. Along-tract statistics allow for enhanced tractography analysis. NeuroImage 2012, 59:3227-3242.
26. Collins D.L., Zijdenbos A.P., Kollokian V., Sled J.G., Kabani N.J., Holmes C.J., Evans A.C. Design and construction of a realistic digital brain phantom. IEEE Trans. Med. Imaging 1998, 17:463-468.
27. Corouge I., Fletcher P.T., Joshi S., Gouttard S., Gerig G. Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis. Med. Image Anal. 2006, 10:786-798.
28. Dell'Acqua F., Rizzo G., Scifo P., Clarke R.A., Scotti G., Fazio F. A model-based deconvolution approach to solve fiber crossing in diffusion-weighted MR imaging. IEEE Trans. Biomed. Eng. 2007, 54:462-472.
29. Dell'Acqua F., Simmons A., Williams S.C., Catani M. Can sphericaldeconvolution provide more information than fiber orientations? Hindrancemodulated orientational anisotropy, a true-tract specific index tocharacterize white matter diffusion. Hum. Brain Mapp 2013, 34(10):2464-2483.
30. Descoteaux M., Deriche R., Knösche T.R., Anwander A. Deterministic and probabilistic tractography based on complex fibre orientation distributions. IEEE Trans. Med. Imaging 2009, 28:269-286.
31. Douaud G., Jbabdi S., Behrens T.E.J., Menke R.A., Gass A., Monsch A.U., Rao A., Whitcher B., Kindlmann G., Matthews P.M., Smith S. DTI measures in crossing-fibre areas: increased diffusion anisotropy reveals early white matter alteration in MCI and mild Alzheimer's disease. NeuroImage 2011, 55:880-890.
32. Faria A.V., Zhang J., Oishi K., Li X., Jiang H., Akhter K., Hermoye L., Lee S.-K., Hoon A., Stashinko E., Miller M.I., van Zijl P.C.M., Mori S. Atlas-based analysis of neurodevelopment from infancy to adulthood using diffusion tensor imaging and applications for automated abnormality detection. NeuroImage 2010, 52:415-428.
33. Fillard P., Poupon C., Mangin J.-F. A novel global tractography algorithm based on an adaptive spin glass model. Proc Med Image Comput Comput Assist Interv 2009, vol. 1:927-934. MICCAI, London, UK.
34. Fillard P., Descoteaux M., Goh A., Gouttard S., Jeurissen B., Malcolm J., Ramirez-Manzanares A., Reisert M., Sakaie K., Tensaouti F., et al. Quantitative evaluation of 10 tractography algorithms on a realistic diffusion mr phantom. NeuroImage 2011, 56:220-234.
35. Frank L.R. Characterization of anisotropy in high angular resolution diffusion-weighted MRI. Magn. Reson. Med. 2002, 47:1083-1099.
36. Gong G., Jiang T., Zhu C., Zang Y., Wang F., Xie S., Xiao J., Guo X. Asymmetry analysis of cingulum based on scale-invariant parameterization by diffusion tensor imaging. Hum. Brain Mapp. 2005, 24:92-98.
37. Heidemann R.M., Porter D.A., Anwander A., Feiweier T., Heberlein K., Knösche T.R., Turner R. Diffusion imaging in humans at 7T using readout-segmented EPI and GRAPPA. Magn. Reson. Med. 2010, 64:9-14.
38. 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 7T. NeuroImage 2012, 60:967-978.
39. Jbabdi S., Woolrich M.W., Andersson J.L.R., Behrens T.E.J. A Bayesian framework for global tractography. NeuroImage 2007, 37:116-129.
40. Jbabdi S., Behrens T.E.J., Smith S.M. Crossing fibres in tract-based spatial statistics. NeuroImage 2010, 49:249-256.
41. Jeurissen B., Leemans A., Tournier J.D., Sijbers J. Fiber tracking on the 'fiber cup phantom' using constrained spherical deconvolution. MICCAI Workshop on Diffusion Modelling and the Fiber Cup (DMFC'09), London, United Kingdom 2009.
42. Jeurissen B., Leemans A., Jones D.K., Tournier J.-D., Sijbers J. Probabilistic fiber tracking using the residual bootstrap with constrained spherical deconvolution. Hum. Brain Mapp. 2011, 32:461-479.
43. Joachims T. Making large-scale SVM learning practical. Advances in Kernel Methods - Support Vector Learning 1999, 169-184. MIT Press, Cambridge, USA. B. Schölkopf, C. Burges, A. Smola (Eds.).
44. Jones D.K. Studying connections in the living human brain with diffusion MRI. Cortex 2008, 44:936-952.
45. Jones D.K. Challenges and limitations of quantifying brain connectivity in vivo with diffusion MRI. Imaging 2010, 2(3):341-355.
46. Jones D.K., Symms M.R., Cercignani M., Howard R.J. The effect of filter size on VBM analyses of DT-MRI data. NeuroImage 2005, 26:546-554.
47. 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 2013, 73:239-254.
48. Kaden E., Knösche T.R., Anwander A. Parametric spherical deconvolution: Inferring anatomical connectivity using diffusion MR imaging. NeuroImage 2007, 37:474-488.
49. Kaden E., Anwander A., Knösche T.R. Variational inference of the fiber orientation density using diffusion MR imaging. NeuroImage 2008, 42:1366-1380.
50. Klein A., Andersson J., Ardekani B.A., Ashburner J., Avants B., Chiang M.C., Christensen G.E., Collins D.L., Gee J., Hellier P., Song J.H., Jenkinson M., Lepage C., Rueckert D., Thompson P., Vercauteren T., Woods R.P., Mann J.J., Parsey R.V. Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. NeuroImage 2009, 46:786-802.
51. Koch M.A., Norris D.G., Hund-Georgiadis M. An investigation of functional and anatomical connectivity using magnetic resonance imaging. NeuroImage 2002, 16:241-250.
52. Kreher B.W., Mader I., Kiselev V.G. Gibbs tracking: a novel approach for the reconstruction of neuronal pathways. Magn. Reson. Med. 2008, 60:953-963.
53. Lazar M., Weinstein D.M., Tsuruda J.S., Hasan K.M., Arfanakis K., Meyerand M.E., Badie B., Rowley H.A., Haughton V., Field A., Alexander A.L. White matter tractography using diffusion tensor deflection. Hum. Brain Mapp. 2003, 18:306-321.
54. Lebel C., Walker L., Leemans A., Phillips L., Beaulieu C. Microstructural maturation of the human brain from childhood to adulthood. NeuroImage 2008, 40:1044-1055.
55. Leergaard T.B., White N.S., de Crespigny A., Bolstad I., D'Arceuil H., Bjaalie J.G., Dale A.M. Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain. PLoS One 2010, 5:e8595.
56. Lenglet C., Campbell J.S.W., Descoteaux M., Haro G., Savadjiev P., Wassermann D., Anwander A., Deriche R., Pike G.B., Sapiro G., Siddiqi K., Thompson P.M. Mathematical methods for diffusion MRI processing. NeuroImage 2009, 45:S111-S122.
57. Leuze C.W.U., Anwander A., Bazin P.-L., Dhital B., Stüber C., Reimann K., Geyer S., Turner R. Layer-specific intracortical connectivityrevealed with diffusion. MRI. Cereb. Cortex 2014, 24(2):328-339.
58. Malcolm J.G., Kubicki M., Shenton M.E., Rathi Y. The effect of local fiber model on population studies. In Diffusion Modeling and Fiber Cup 2009, 33-40. MICCAI, London, UK.
59. Melonakos J., Mohan V., Niethammer M., Smith K., Kubicki M., Tannenbaum A. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. Medical Image Computing and Computer-Assisted Intervention-MICCAI 2007 2007, 36-43. Springer, Berlin Heidelberg.
60. Mori S., van Zijl P.C.M. Fiber tracking: principles and strategies - a technical review. NMR Biomed. 2002, 15:468-480.
61. Mori S., Oishi K., Jiang H., Jiang L., Li X., Akhter K., Hua K., Faria A.V., Mahmood A., Woods R., Toga A.W., Pike G.B., Neto P.R., Evans A., Zhang J., Huang H., Miller M.I., van Zijl P., Mazziotta J. Stereotaxic white matter atlas based on diffusion tensor imaging in an ICBM template. NeuroImage 2008, 40:570-582.
62. Nelder J.A., Mead R. A simplex method for function minimization. Comput. J. 1965, 7:308-313.
63. Nichols T.E., Holmes A.P. Nonparametric permutation tests for functional neuroimaging: a primer with examples. Hum. Brain Mapp. 2002, 15:1-25.
64. O'Donnell L.J., Westin C.-F., Golby A.J. Tract-based morphometry for white matter group analysis. NeuroImage 2009, 45:832-844.
65. Pichon E., Westin C.-F., Tannenbaum A.R. A Hamilton-Jacobi-Bellman Approach to High Angular Resolution Diffusion Tractography. Medical Image Computing and Computer-Assisted Intervention-MICCAI 2005 2005, 180-187. Springer, Berlin Heidelberg.
66. Poupon C., Rieul B., Kezele I., Perrin M., Poupon F., Mangin J.F. New diffusion phantoms dedicated to the study and validation of high-angular-resolution diffusion imaging (HARDI) models. Magn. Reson. Med. 2008, 60:1276-1283.
67. Raffelt D., Tournier J.D., Rose S., Ridgway G.R., Henderson R., Crozier S., Salvado O., Connelly A. Apparent fibre density: a novel measure for the analysis of diffusion-weighted magnetic resonance images. NeuroImage 2012, 59:3976-3994.
68. Reisert M., Mader I., Kiselev V. Tracking a physical phantom by global fibre reconstruction. MICCAI Workshop on Diffusion Modelling and the Fiber Cup, London, United Kingdom 2009, MICCAI, Springer.
69. Reisert M., Mader I., Anastasopoulos C., Weigel M., Schnell S., Kiselev V. Global fiber reconstruction becomes practical. NeuroImage 2011, 54:955-962.
70. Riffert T., Knösche T.R., Anwander A. Quantification of fiber bundle properties using a decomposition of the fiber orientation distribution function. Proc. Int. Soc. Magn. Reson. Med. 2012, 20:3592. (Melbourne, Australia).
71. Riffert T., Schreiber J., Anwander A., Knösche T.R. Beyond Fractional Anisotropy: Extraction of Bundle-Specific Structural Metrics from Crossing-Fiber Models 2014, (under review).
72. Ros C., Güllmar D., Stenze M., Mentzel H.J., Reichenbach J.R. Quantitative fiber bundle-based analysis of diffusion-weighted MRI data. Biomed. Tech. (Berl.) 2012, 57:530-533.
73. Savadjiev P., Rathi Y., Bouix S., Smith A.R., Schultz R.T., Verma R., Westin C.F. Combining surface and fiber geometry: an integrated approach to brain morphology. MICCAI 2013 2013, 50-57. Springer, Berlin Heidelberg.
74. Schultz T., Seidel H.P. Estimating crossing fibers: a tensor decomposition approach. IEEE Trans. Vis. Comput. Graph. 2008, 14:1635-1642.
75. Smith S.M., Nichols T.E. Threshold-free cluster enhancement: addressing problems of smoothing, threshold dependence and localisation in cluster inference. NeuroImage 2009, 44:83-98.
76. Smith S.M., Jenkinson M., Woolrich M.W., Beckmann C.F., Behrens T.E.J., Johansen-Berg H., Bannister P.R., Luca M.D., Drobnjak I., Flitney D.E., Niazy R.K., Saunders J., Vickers J., Zhang Y., Stefano N.D., Brady J.M., Matthews P.M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage 2004, 23(Suppl. 1):S208-S219.
77. Smith S.M., Jenkinson M., Johansen-Berg H., Rueckert D., Nichols T.E., Mackay C.E., Watkins K.E., Ciccarelli O., Cader M.Z., Matthews P.M., Behrens T.E.J. Tract-based spatial statistics: voxelwise analysis of multi-subject diffusion data. NeuroImage 2006, 31:1487-1505.
78. Smith R.E., Tournier J.-D., Calamante F., Connelly A. SIFT: spherical-deconvolution informed filtering of tractograms. NeuroImage 2013, 67:298-312.
79. Snook L., Plewes C., Beaulieu C. Voxel based versus region of interest analysis in diffusion tensor imaging of neurodevelopment. NeuroImage 2007, 34:243-252.
80. Song S.-K., Sun S.-W., Ramsbottom M.J., Chang C., Russell J., Cross A.H. Dysmyelination revealed through MRI as increased radial (but unchanged axial) diffusion of water. NeuroImage 2002, 17:1429-1436.
81. Sotiropoulos S.N., Behrens T.E., Jbabdi S. Ball and rackets: inferring fiber fanning from diffusion-weighted MRI. NeuroImage 2012, 60(2):1412-1425.
82. Tournier J.D., Calamante F., Gadian D.G., Connelly A. Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution. NeuroImage 2004, 23:1176-1185.
83. Tournier J.D., Calamante F., Connelly A. Robust determination of the fibre orientation distribution in diffusion MRI: non-negativity constrained super-resolved spherical deconvolution. NeuroImage 2007, 35:1459-1472.
84. Tournier J.D., Calamante F., Connelly A. MRtrix: diffusion tractography in crossing fiber regions. Int. J. Imaging Syst. Technol. 2012, 22:53-66.
85. Tuch D. Diffusion MRI of Complex Tissue Structure 2002, (PhD Thesis), Harvard University and Massachusetts Institute of Technology, Boston, USA.
86. Tuch D.S. Q-ball imaging. Magn. Reson. Med. 2004, 52:1358-1372.
87. Tuch D.S., Reese T.G., Wiegell M.R., Makris N., Belliveau J.W., Wedeen V.J. High angular resolution diffusion imaging reveals intravoxel white matter fiber heterogeneity. Magn. Reson. Med. 2002, 48:577-582.
88. Turken A.U., Dronkers N.F. The neural architecture of the language comprehension network: converging evidence from lesion and connectivity analyses. Front. Syst. Neurosci. 2011, 5.
89. Wedeen V.J., Reese T.G., Tuch D.S., Dou J.G., Weiskoff R.M., Chessler D. Mapping fiber orientation spectra in cerebral white matter with Fourier-transform diffusion MRI. Proc. Int. Soc. Magn. Reson. Med. 2000, 321. (Denver, USA).
90. Woolrich M.W., Jbabdi S., Patenaude B., Chappell M., Makni S., Behrens T., Beckmann C., Jenkinson M., Smith S.M. Bayesian analysis of neuroimaging data in FSL. NeuroImage 2009, 45:S173-S186.
91. Yo T.-S., Anwander A., Descoteaux M., Fillard P., Poupon C., Knösche T. Quantifying brain connectivity: a comparative tractography study. Proc Med Image Comput Comput Assist Interv 2009, vol. 1:886-893. MICCAI, London, UK.
92. Yushkevich P.A., Zhang H., Simon T.J., Gee J.C. Structure-specific statistical mapping of white matter tracts. NeuroImage 2008, 41:448-461.
93. 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 2011, 56:1301-1315.
94. Zhang H., Dyrby T.B., Alexander D.C. Axon diameter mapping in crossing fibers with diffusion MRI. Proc Med Image Comput Comput Assist Interv 2011, vol. 2:82-89. MICCAI, Toronto, Canada.
95. Zhang H., Schneider T., Wheeler-Kingshott C.A., Alexander D.C. NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain. NeuroImage 2012, 61(4):1000-1016.