A

List of abbreviations

The following table describes the significance of various abbreviations and acronyms used
throughout the thesis. The page on which each one is defined or first used is also given.
Nonstandard acronyms that are used in some places to abbreviate the names of certain white
matter structures are not in this list.

Abbreviation Meaning Page

 anisotropic volume fraction 51
 Bayesian Estimation of Diffusion Parameters Obtained using 51
Sampling Techniques
c.d.f. cumulative density function 11
 cerebrospinal fluid 4
 coefficient of variation 71
d diffusion magnetic resonance imaging 3
 diffusion spectrum imaging 56
 diffusion tensor imaging 40
 Expectation–Maximisation 16
 echo planar imaging 34
 fractional anisotropy 41
 Fibre Assignment by Continuous Tracking 47
 ’s Linear Image Registration Tool 69
f functional magnetic resonance imaging 45
 Centre for Functional Magnetic Resonance Imaging of the 53
Brain (Oxford, )
 fast marching tractography 53
  software library 53
 free induction decay 31
 full width at half maximum 62
 high angular resolution diffusion imaging 54
i.i.d. independent and identically distributed 14
 maximum a posteriori 16
 Monte Carlo 19
 Markov chain Monte Carlo 22
 mean diffusivity 41
 maximum likelihood 14
 Montréal Neurological Institute 69
 magnetic resonance imaging 3
 nuclear magnetic resonance 4
continued on next page
116 Appendix A. List of abbreviations

Abbreviation Meaning Page

 neighbourhood tractography 64
 orientation distribution function 56
 persistent angular structure 56
p.d.f. probability density function 11
p.m.f. probability mass function 10
 radiofrequency 29
 region of interest 63
 tract-based spatial statistics 62
 echo time 32
 inversion time 32
 repetition time 32
 voxel-based morphometry 61
 vascular cognitive impairment 103
 B
Summary of publications

The following is a list of works published by the author during the course of the doctorate.
Many of these works are cited in the text and therefore also appear in the full bibliography
which follows.

Journal papers
• M.E. Bastin, J.D. Clayden, A. Pattie, I.F. Gerrish, J.M. Wardlaw & I.J. Deary (in press).
Diffusion tensor and magnetization transfer MRI measurements of periventricular white
matter hyperintensities in old age. To appear in Neurobiology of Aging.

• J.D. Clayden, A.J. Storkey & M.E. Bastin (2007). A probabilistic model-based approach
to consistent white matter tract segmentation. IEEE Transactions on Medical Imaging
26(11):1555–1561.

• J.D. Clayden, M.E. Bastin & A.J. Storkey (2006). Improved segmentation reproducibil-
ity in group tractography using a quantitative tract similarity measure. NeuroImage
33(2):482–492.

• I.J. Deary, M.E. Bastin, A. Pattie, J.D. Clayden, L.J. Whalley, J.M. Starr & J.M. Ward-
law (2006). White matter integrity and cognition in childhood and old age. Neurology
66(4):505–512.

Peer-reviewed conference abstracts

• J.D. Clayden, A.J. Storkey & M.E. Bastin (2007). A probabilistic model-based approach to
consistent white matter tract segmentation. In Proceedings of the ISMRM-ESMRMB Joint
Annual Meeting, p. 78.

• J.D. Clayden, S. Zhang, S. Correia & D.H. Laidlaw (2007). Fine-grained comparison
of anisotropy differences between groups of white matter tracts. In Proceedings of the
ISMRM-ESMRMB Joint Annual Meeting, p. 82.

• M.E. Bastin, J.D. Clayden, A. Pattie, I.F. Gerrish, J.M. Wardlaw & I.J. Deary (2007). DTI
and MTI parameters correlate in periventricular white matter hyperintensities in old age.
In Proceedings of the ISMRM-ESMRMB Joint Annual Meeting, p. 2160.

• J.D. Clayden, M.E. Bastin & A.J. Storkey (2006). Neighbourhood tractography: a new
approach to seed point placement for group fibre tracking. In Proceedings of the British
Chapter of the ISMRM, p. P34.

• J.D. Clayden, M.E. Bastin & A.J. Storkey (2006). Automated assessment of tract similarity
in group diffusion MRI data. In Proceedings of the ISMRM 14th Scientific Meeting &
Exhibition, p. 2742.
118 Appendix B. Summary of publications

• J.D. Clayden, D.K.S. Marjoram, M.E. Bastin, E.C. Johnstone & S.M. Lawrie (2005). To-
wards an automated method for white matter integrity comparison between populations.
In Proceedings of the ESMRMB 22nd Annual Meeting, p. 508.
• I.J. Deary, M.E. Bastin, A. Pattie, J.D. Clayden & J.M. Wardlaw (2005). Cognitive ageing
and white matter integrity: a diffusion tensor and magnetisation transfer MRI study. In
Proceedings of the ISMRM 13th Scientific Meeting & Exhibition.
• I.J. Deary, M.E. Bastin, A. Pattie, J.D. Clayden, J.M. Starr & J.M. Wardlaw (2005). White
matter integrity and cognition in childhood and old age: a diffusion tensor MRI study.
Methods for Quantitative MRI of Human Brain. ISMRM Workshop, Lake Louise, Canada.
 Bibliography

Abe O., Aoki S., Hayashi N., Yamada H., Kunimatsu A., Mori H., Yoshikawa T., Okubo T. &
Ohtomo K. (2002). Normal aging in the central nervous system: quantitative MR diffusion-
tensor analysis. Neurobiology of Aging 23:433–441.

Abe O., Yamada H., Masutani Y., Aoki S., Kunimatsu A., Yamasue H., Fukuda R., Kasai
K., Hayashi N., Masumoto T., Mori H., Soma T. & Ohtomo K. (2004). Amyotrophic lat-
eral sclerosis: diffusion tensor tractography and voxel-based analysis. NMR in Biomedicine
17(6):411–416.

Alexander A., Hasan K., Lazar M., Tsuruda J. & Parker D. (2001). Analysis of partial volume
effects in diffusion-tensor MRI. Magnetic Resonance in Medicine 45(5):770–780.

Alexander D. (2005). Maximum entropy spherical deconvolution for diffusion MRI. In Infor-
mation Processing in Medical Imaging, vol. 3565 of Lecture Notes in Computer Science, pp. 76–87.
Springer-Verlag.

Alexander D., Barker G. & Arridge S. (2002). Detection and modeling of non-Gaussian apparent
diffusion coefficient profiles in human brain data. Magnetic Resonance in Medicine 48(2):331–
340.

Andrieu C., Freitas N., Doucet A. & Jordan M. (2003). An introduction to MCMC for machine
learning. Machine Learning 50:5–43.

Anjari M., Srinivasan L., Allsop J., Hajnal J., Rutherford M., Edwards A. & Counsell S. (2007).
Diffusion tensor imaging with tract-based spatial statistics reveals local white matter abnor-
malities in preterm infants. NeuroImage 35:1021–1027.

Ardekani B., Nierenberg J., Hoptman M., Javitt D. & Lim K. (2003). MRI study of white matter
diffusion anisotropy in schizophrenia. Neuroreport 14:2025–2029.

Ashburner J. & Friston K. (2000). Voxel-based morphometry–the methods. NeuroImage

11(6):805–821.

Ashburner J. & Friston K. (2001). Why voxel-based morphometry should be used. NeuroImage
14:1238–1243.

Assaf Y., Ben-Bashat D., Chapman J., Peled S., Biton I., Kafri M., Segev Y., Hendler T., Korczyn
A., Graif M. & Cohen Y. (2002). High b-value q-space analyzed diffusion-weighted MRI:
application to multiple sclerosis. Magnetic Resonance in Medicine 47(1):115–126.

Assaf Y., Chapman J., Ben-Bashat D., Hendler T., Segev Y., Korczyn A., Graif M. & Cohen Y.
(2005). White matter changes in multiple sclerosis: correlation of q-space diffusion MRI and
1H MRS. Magnetic Resonance Imaging 23(6):703–710.

119
120 Bibliography

Baird A. & Warach S. (1998). Magnetic resonance imaging of acute stroke. Journal of Cerebral
Blood Flow & Metabolism 18(6):583–609.

Basser P., Mattiello J. & Le Bihan D. (1994a). Estimation of the effective self-diffusion tensor
from the NMR spin echo. Journal of Magnetic Resonance, Series B 103(3):247–254.

Basser P., Mattiello J. & Le Bihan D. (1994b). MR diffusion tensor spectroscopy and imaging.
Biophysical Journal 66(1):259–267.

Basser P., Pajevic S., Pierpaoli C., Duda J. & Aldroubi A. (2000). In vivo fiber tractography
using DT-MRI data. Magnetic Resonance in Medicine 44(4):625–632.

Basser P. & Pierpaoli C. (1996). Microstructural and physiological features of tissues elucidated
by quantitative-diffusion-tensor MRI. Journal of Magnetic Resonance, Series B 111(3):209–219.

Bastin M., Clayden J., Pattie A., Gerrish I., Wardlaw J. & Deary I. (2007). Diffusion tensor and
magnetization transfer MRI measurements of periventricular white matter hyperintensities
in old age. Neurobiology of Aging in press.

Batchelor P., Atkinson D., Hill D., Calamante F. & Connelly A. (2003). Anisotropic noise
propagation in diffusion tensor MRI sampling schemes. Magnetic Resonance in Medicine
49(6):1143–1151.

Batchelor P., Calamante F., Tournier J.D., Atkinson D., Hill D. & Connelly A. (2006). Quantifi-
cation of the shape of fiber tracts. Magnetic Resonance in Medicine 55:894–903.

Behrens T., Johansen-Berg H., Jbabdi S., Rushworth M. & Woolrich M. (2007). Probabilistic
diffusion tractography with multiple fibre orientations: What can we gain? NeuroImage
34(1):144–155.

Behrens T., Johansen-Berg H., Woolrich M., Smith S., Wheeler-Kingshott C., Boulby P., Barker
G., Sillery E., Sheehan K., Ciccarelli O., Thompson A., Brady J. & Matthews P. (2003a).
Non-invasive mapping of connections between human thalamus and cortex using diffusion
imaging. Nature Neuroscience 6(7):750–757.

Behrens T., Woolrich M., Jenkinson M., Johansen-Berg H., Nunes R., Clare S., Matthews P.,
Brady J. & Smith S. (2003b). Characterization and propagation of uncertainty in diffusion-
weighted MR imaging. Magnetic Resonance in Medicine 50(5):1077–1088.

Bishop C. (2006). Pattern recognition and machine learning. Springer, New York.

Biton I., Duncan I. & Cohen Y. (2006). High b-value q-space diffusion MRI in myelin-deficient
rat spinal cords. Magnetic Resonance Imaging 24:161–166.

Bloch F. (1946). Nuclear induction. Physics Review 70(7-8):460–474.

Böhm W., Farin G. & Kahmann J. (1984). A survey of curve and surface methods in CAGD.
Computer Aided Geometric Design 1(1):1–60.

Bransden B. & Joachain C. (1989). Introduction to quantum mechanics. Longman.

Brun A., Knutsson H., Park H.J., Shenton M. & Westin C.F. (2004). Clustering fiber traces using
normalized cuts. In Medical Image Computing and Computer-Assisted Intervention, vol. 3216 of
Lecture Notes in Computer Science, pp. 368–375. Springer-Verlag.

Bürgel U., Amunts K., Hoemke L., Mohlberg H., Gilsbach J. & Zilles K. (2006). White matter
fiber tracts of the human brain: Three-dimensional mapping at microscopic resolution,
topography and intersubject variability. NeuroImage 29(4):1092–1105.

Burns J., Job D., Bastin M., Whalley H., Macgillivray T., Johnstone E. & Lawrie S. (2003).
Structural disconnectivity in schizophrenia: a diffusion tensor magnetic resonance imaging
study. British Journal of Psychiatry 182:439–443.
Bibliography 121

Callaghan P. (1991). Principles of nuclear magnetic resonance microscopy. Oxford University Press,
UK.

Callaghan P., Eccles C. & Xia Y. (1988). NMR microscopy of dynamic displacements: k-space
and q-space imaging. Journal of Physics E: Scientific Instruments 21(8):820–822.

Campbell J., Siddiqi K., Rymar V., Sadikot A. & Pike G. (2005). Flow-based fiber tracking with
diffusion tensor and q-ball data: validation and comparison to principal diffusion direction
techniques. NeuroImage 27(4):725–736.

Catani M. & ffytche D. (2005). The rises and falls of disconnection syndromes. Brain
128(10):2224–2239.

Cherubini A., Luccichenti G., Péran P., Hagberg G., Barba C., Formisano R. & Sabatini U. (2007).
Multimodal fMRI tractography in normal subjects and in clinically recovered traumatic brain
injury patients. NeuroImage 34(4):1331–1341.

Chung S., Lu Y. & Henry R. (2006). Comparison of bootstrap approaches for estimation of
uncertainties of DTI parameters. NeuroImage 33(2):531–541.

Ciccarelli O., Parker G., Toosy A., Wheeler-Kingshott C., Barker G., Boulby P., Miller D.
& Thompson A. (2003a). From diffusion tractography to quantitative white matter tract
measures: a reproducibility study. NeuroImage 18(2):348–359.

Ciccarelli O., Werring D., Barker G., Griffin C., Wheeler-Kingshott C., Miller D. & Thompson A.
(2003b). A study of the mechanisms of normal-appearing white matter damage in multiple
sclerosis using diffusion tensor imaging: Evidence of Wallerian degeneration. Journal of
Neurology 250(3):287–292.

Clayden J., Bastin M. & Storkey A. (2006a). Automated assessment of tract similarity in group
diffusion MRI data. In Proceedings of the ISMRM 14th Scientific Meeting & Exhibition, 2742.
International Society for Magnetic Resonance in Medicine.

Clayden J., Bastin M. & Storkey A. (2006b). Improved segmentation reproducibility in group
tractography using a quantitative tract similarity measure. NeuroImage 33(2):482–492.

Clayden J., Marjoram D., Bastin M., Johnstone E. & Lawrie S. (2005). Towards an automated
method for white matter integrity comparison between populations. In Proceedings of the
ESMRMB 22nd Annual Meeting, 508. European Society for Magnetic Resonance in Medicine
and Biology.

Clayden J., Storkey A. & Bastin M. (2007a). A probabilistic model-based approach to consistent
white matter tract segmentation. IEEE Transactions on Medical Imaging 26(11):1555–1561.

Clayden J., Zhang S., Correia S. & Laidlaw D. (2007b). Fine-grained comparison of anisotropy
differences between groups of white matter tracts. In Proceedings of the ISMRM-ESMRMB
Joint Annual Meeting, 82. International Society for Magnetic Resonance in Medicine.

Concha L., Gross D. & Beaulieu C. (2006). Diffusion tensor imaging demonstrates the evolution
of axonal degeneration after corpus callosotomy. In Proceedings of the ISMRM 14th Scientific
Meeting & Exhibition, 274. International Society for Magnetic Resonance in Medicine.

Conturo T., Lori N., Cull T., Akbudak E., Snyder A., Shimony J., McKinstry R., Burton H. &
Raichle M. (1999). Tracking neuronal fiber pathways in the living human brain. Proceedings
of the National Academy of Sciences of the United States of America 96(18):10,422–10,427.

Conturo T., McKinstry R., Akbudak E. & Robinson B. (1996). Encoding of anisotropic diffusion
with tetrahedral gradients: a general mathematical diffusion formalism and experimental
results. Magnetic Resonance in Medicine 35(3):399–412.
122 Bibliography

Cook P., Alexander D. & Parker G. (2004). Modelling noise-induced fibre-orientation error in
diffusion-tensor MRI. In Proceedings of the IEEE International Symposium on Biomedical Imaging,
pp. 332–335. IEEE.

Corouge I., Fletcher P., Joshi S., Gouttard S. & Gerig G. (2006). Fiber tract-oriented statistics for
quantitative diffusion tensor MRI analysis. Medical Image Analysis 10(5):786–798.

Corouge I., Gouttard S. & Gerig G. (2004). A statistical shape model of individual fiber tracts extracted
from diffusion tensor MRI, vol. 3217 of Lecture Notes in Computer Science. Springer-Verlag.

de Boor C. (1978). A practical guide to splines. No. 27 in Applied Mathematical Sciences Series.
Springer-Verlag.

de Certaines J., Henriksen O., Spisni A., Cortsen M. & Ring P. (1993). In vivo measurements of
proton relaxation times in human brain, liver, and skeletal muscle: a multicenter MRI study.
Magnetic Resonance Imaging 11(6):841–850.

Deary I., Bastin M., Pattie A., Clayden J., Whalley L., Starr J. & Wardlaw J. (2006). White matter
integrity and cognition in childhood and old age. Neurology 66(4):505–512.

Dempster A., Laird N. & Rubin D. (1977). Maximum likelihood from incomplete data via the
EM algorithm. Journal of the Royal Statistical Society, Series B 39(1):1–38.

Ding Z., Gore J. & Anderson A. (2003). Classification and quantification of neuronal fiber
pathways using diffusion tensor MRI. Magnetic Resonance in Medicine 49(4):716–721.

Dirac P. (1958). The principles of quantum mechanics. Oxford University Press, UK, 4 edn.

Edelstein W., Hutchison J., Johnson G. & Redpath T. (1980). Spin warp NMR imaging and
applications to human whole-body imaging. Physics in Medicine and Biology 25(4):751–756.

Einstein A. (1905). [On the movement of small particles suspended in a stationary liquid
demanded by the molecular-kinetic theory of heat]. Annalen der Physik 17:549–560.

Ellis C., Simmons A., Jones D., Bland J., Dawson J., Horsfield M., Williams S. & Leigh P. (1999).
Diffusion tensor MRI assesses corticospinal tract damage in ALS. Neurology 53(5):1051–1058.

Evans A., Collins D., Mills S., Brown E., Kelly R. & Peters T. (1993). 3D statistical neuroanatom-
ical models from 305 MRI volumes. In Nuclear Science Symposium and Medical Imaging
Conference, vol. 3, pp. 1813–1817. IEEE.

ffytche D. & Catani M. (2005). Beyond localization: from hodology to function. Philosophical
Transactions of the Royal Society B: Biological Sciences 360(1456):767–779.

Fick A. (1855). [On diffusion]. Annalen der Physik und Chemie 170(1):59–86.

Fick A. (1995). On liquid diffusion. Journal of Membrane Science 100(1):33–38.

Frank L. (2001). Anisotropy in high angular resolution diffusion-weighted MRI. Magnetic

Resonance in Medicine 45(6):935–939.

Frank L. (2002). Characterization of anisotropy in high angular resolution diffusion-weighted

MRI. Magnetic Resonance in Medicine 47(6):1083–1099.

Friman O., Farnebäck G. & Westin C.F. (2006). A Bayesian approach for stochastic white matter
tractography. IEEE Transactions on Medical Imaging 25(8):965–978.

Friston K., Ashburner J., Frith C., Poline J., Heather J. & Frackowiak R. (1995). Spatial registra-
tion and normalization of images. Human Brain Mapping 3(3):165–189.

Friston K. & Frith C. (1995). Schizophrenia: a disconnection syndrome? Clinical Neuroscience

3(2):89–97.
Bibliography 123

Geman S. & Geman D. (1984). Stochastic relaxation, Gibbs distributions, and the Bayesian
restoration of images. IEEE Transactions on Pattern Analysis and Machine Intelligence 6(6):721–
741.

Geschwind N. (1965a). Disconnexion syndromes in animals and man: Part I. Brain 88(2):237–
294.

Geschwind N. (1965b). Disconnexion syndromes in animals and man: Part II. Brain 88(3):585–
644.

Good C., Johnsrude I., Ashburner J., Henson R., Friston K. & Frackowiak R. (2001). A voxel-
based morphometric study of ageing in 465 normal adult human brains. NeuroImage 14(1):21–
36.

Gray H. (1918). Anatomy of the human body. Lea & Febiger, Philadelphia, 20 edn.

Guye M., Parker G., Symms M., Boulby P., Wheeler-Kingshott C., Salek-Haddadi A., Barker
G. & Duncan J. (2003). Combined functional MRI and tractography to demonstrate the
connectivity of the human primary motor cortex in vivo. NeuroImage 19(4):1349–1360.

Hahn E. (1950). Spin echoes. Physical Review 80(4):580–594.

Hasan K., Parker D. & Alexander A. (2001). Comparison of gradient encoding schemes for
diffusion-tensor MRI. Journal of Magnetic Resonance Imaging 13(5):769–780.

Hastings W. (1970). Monte Carlo sampling methods using Markov chains and their applica-
tions. Biometrika 57(1):97–109.

Head D., Buckner R., Shimony J., Williams L., Akbudak E., Conturo T., McAvoy M., Morris
J. & Snyder A. (2004). Differential vulnerability of anterior white matter in nondemented
aging with minimal acceleration in dementia of the Alzheimer type: evidence from diffusion
tensor imaging. Cerebral Cortex 14(4):410–423.

Healy D., Hendriks H. & Kim P. (1998). Spherical deconvolution. Journal of Multivariate Analysis
67(1):1–22.

Heiervang E., Behrens T., Mackay C., Robson M. & Johansen-Berg H. (2006). Between session
reproducibility and between subject variability of diffusion MR and tractography measures.
NeuroImage 33(3):867–877.

Holmes C., Hoge R., Collins D., Woods R., Toga A. & Evans A. (1998). Enhancement of
MR images using registration for signal averaging. Journal of Computer Assisted Tomography
22(2):324–333.

Horsfield M. & Jones D. (2002). Applications of diffusion-weighted and diffusion tensor MRI
to white matter diseases - a review. NMR in Biomedicine 15(7-8):570–577.

Hosey T., Williams G. & Ansorge R. (2005). Inference of multiple fiber orientations in high
angular resolution diffusion imaging. Magnetic Resonance in Medicine 54:1480–1489.

Hu Q. & Nowinski W. (2003). A rapid algorithm for robust and automatic extraction of the
midsagittal plane of the human cerebrum from neuroimages based on local symmetry and
outlier removal. NeuroImage 20(4):2153–2165.

Huang H., Zhang J., Jiang H., Wakana S., Poetscher L., Miller M., van Zijl P., Hillis A., Wytik
R. & Mori S. (2005). DTI tractography based parcellation of white matter: application to the
mid-sagittal morphology of corpus callosum. NeuroImage 26(1):195–205.

Jansons K. & Alexander D. (2003). Persistent angular structure: new insights from diffusion
magnetic resonance imaging data. Inverse Problems 19(5):1031–1046.

Jaynes E. (2003). Probability theory: The logic of science. Cambridge University Press, UK.
124 Bibliography

Jenkinson M. & Smith S. (2001). A global optimisation method for robust affine registration of
brain images. Medical Image Analysis 5(2):143–156.

Johansen-Berg H., Behrens T., Robson M., Drobnjak I., Rushworth M., Brady J., Smith S.,
Higham D. & Matthews P. (2004). Changes in connectivity profiles define functionally
distinct regions in human medial frontal cortex. Proceedings of the National Academy of Sciences
of the United States of America 101(36):13,335–13,340.

Johansen-Berg H., Behrens T., Sillery E., Ciccarelli O., Thompson A., Smith S. & Matthews P.
(2005). Functional-anatomical validation and individual variation of diffusion tractography-
based segmentation of the human thalamus. Cerebral Cortex 15(1):31–39.

Jones D. (2003). Determining and visualizing uncertainty in estimates of fiber orientation from
diffusion tensor MRI. Magnetic Resonance in Medicine 49(1):7–12.

Jones D. (2004). The effect of gradient sampling schemes on measures derived from diffusion
tensor MRI: a Monte Carlo study. Magnetic Resonance in Medicine 51(4):807–815.

Jones D., Catani M., Pierpaoli C., Reeves S., Shergill S., O’Sullivan M., Golesworthy P., McGuire
P., Horsfield M., Simmons A., Williams S. & Howard R. (2006). Age effects on diffusion
tensor magnetic resonance imaging tractography measures of frontal cortex connections in
schizophrenia. Human Brain Mapping 27(3):230–238.

Jones D., Lythgoe D., Horsfield M., Simmons A., Williams S. & Markus H. (1999). Character-
ization of white matter damage in ischemic leukoaraiosis with diffusion tensor MRI. Stroke
30(2):393–397.

Jones D. & Pierpaoli C. (2005). Confidence mapping in diffusion tensor magnetic resonance
imaging tractography using a bootstrap approach. Magnetic Resonance in Medicine 53(5):1143–
1149.

Jones D., Symms M., Cercignani M. & Howard R. (2005a). The effect of filter size on VBM
analyses of DT-MRI data. NeuroImage 26:546–554.

Jones D., Travis A., Eden G., Pierpaoli C. & Basser P. (2005b). PASTA: Pointwise assessment of
streamline tractography attributes. Magnetic Resonance in Medicine 53(6):1462–1467.

Jönsson C. (1974). Electron diffraction at multiple slits. American Journal of Physics 42(1):4–11.

Kaden E., Knosche T. & Anwander A. (2007). Parametric spherical deconvolution: Inferring
anatomical connectivity using diffusion MR imaging. NeuroImage 37(2):474–488.

Kanaan R., Shergill S., Barker G., Catani M., Ng V., Howard R., McGuire P. & Jones D. (2006).
Tract-specific anisotropy measurements in diffusion tensor imaging. Psychiatry Research:
Neuroimaging 146(1):73–82.

Kingman J. & Taylor S. (1966). Introduction to measure and probability. Cambridge University
Press, UK.

Kinoshita M., Yamada K., Hashimoto N., Kato A., Izumoto S., Baba T., Maruno M., Nishimura
T. & Yoshimine T. (2005). Fiber-tracking does not accurately estimate size of fiber bun-
dle in pathological condition: initial neurosurgical experience using neuronavigation and
subcortical white matter stimulation. NeuroImage 25(2):424–429.

Klingberg T., Vaidya C., Gabrieli J., Moseley M. & Hedehus M. (1999). Myelination and
organization of the frontal white matter in children: a diffusion tensor MRI study. Neuroreport
10(13):2817–2821.

Knight R., Ordidge R., Helpern J., Chopp M., Rodolosi L. & Peck D. (1991). Temporal evolution
of ischemic damage in rat brain measured by proton nuclear magnetic resonance imaging.
Stroke 22(6):802–808.
Bibliography 125

Kochunov P., Thompson P., Lancaster J., Bartzokis G., Smith S., Coyle T., Royall D., Laird A.
& Fox P. (2007). Relationship between white matter fractional anisotropy and other indices
of cerebral health in normal aging: tract-based spatial statistics study of aging. NeuroImage
35(2):478–487.

Kubicki M., Westin C.F., Nestor P., Wible C., Frumin M., Maier S., Kikinis R., Jolesz F., McCar-
ley R. & Shenton M. (2003). Cingulate fasciculus integrity disruption in schizophrenia: a
magnetic resonance diffusion tensor imaging study. Biological Psychiatry 54(11):1171–1180.

Lanzer P., Botvinick E., Schiller N., Crooks L., Arakawa M., Kaufman L., Davis P., Herfkens R.,
Lipton M. & Higgins C. (1984). Cardiac imaging using gated magnetic resonance. Radiology
150(1):121–127.

Lazar M. & Alexander A. (2002). White matter tractography using RandomVector (RAVE) per-
turbation. In Proceedings of the ISMRM 10th Scientific Meeting & Exhibition, p. 539. International
Society for Magnetic Resonance in Medicine.

Lazar M. & Alexander A. (2005). Bootstrap white matter tractography (BOOT-TRAC). Neu-
roImage 24(2):524–532.

Le Bihan D., Breton E., Lallemand D., Grenier P., Cabanis E. & Laval-Jeantet M. (1986). MR
imaging of intravoxel incoherent motions: application to diffusion and perfusion in neuro-
logic disorders. Radiology 161(2):401–407.

Lim K. & Helpern J. (2002). Neuropsychiatric applications of DTI - a review. NMR in Biomedicine
15(7-8):587–593.

Lori N., Conturo T. & Le Bihan D. (2003). Definition of displacement probability and diffu-
sion time in q-space magnetic resonance measurements that use finite-duration diffusion-
encoding gradients. Journal of Magnetic Resonance 165(2):185–195.

MacKay D. (1995). Probable networks and plausible predictions - a review of practical Bayesian
methods for supervised neural networks. Network: Computation in Neural Systems 6(3):469–
505.

MacKay D. (2003). Information theory, inference and learning algorithms. Cambridge University
Press, UK.

Maddah M., Mewes A., Haker S., Grimson W. & Warfield S. (2005). Automated atlas-based
clustering of white matter fiber tracts from DTMRI. In Medical Image Computing and Computer-
Assisted Intervention, vol. 3749 of Lecture Notes in Computer Science, pp. 188–195. Springer-
Verlag.

Makris N., Kennedy D., McInerney S., Sorensen A., Wang R., Caviness V. & Pandya D. (2005).
Segmentation of subcomponents within the superior longitudinal fascicle in humans: a
quantitative, in vivo, DT-MRI study. Cerebral Cortex 15(6):854–869.

Makris N., Papadimitriou G., van der Kouwe A., Kennedy D., Hodge S., Dale A., Benner T.,
Wald L., Wu O., Tuch D., Caviness V., Moore T., Killiany R., Moss M. & Rosene D. (2007).
Frontal connections and cognitive changes in normal aging rhesus monkeys: a DTI study.
Neurobiology of Aging 28(10):1556–1567.

Mansfield P. (1977). Multi-planar image formation using NMR spin echoes. Journal of Physics
C: Solid State Physics 10(3):L55–L58.

Mattiello J., Basser P. & Le Bihan D. (1997). The b matrix in diffusion tensor echo-planar
imaging. Magnetic Resonance in Medicine 37(2):292–300.

McIntosh A., Job D., Moorhead T., Harrison L., Forrester K., Lawrie S. & Johnstone E. (2004).
Voxel-based morphometry of patients with schizophrenia or bipolar disorder and their
unaffected relatives. Biological Psychiatry 56:544–552.
126 Bibliography

Metropolis N., Rosenbluth A., Rosenbluth M., Teller A. & Teller E. (1953). Equation of state
calculations by fast computing machines. Journal of Chemical Physics 21(6):1087–1092.
Mori S., Crain B., Chacko V. & van Zijl P. (1999). Three-dimensional tracking of axonal projec-
tions in the brain by magnetic resonance imaging. Annals of Neurology 45(2):265–269.
Mori S. & van Zijl P. (2002). Fiber tracking: principles and strategies - a technical review. NMR
in Biomedicine 15:468–480.
Mori S., Wakana S., Nagae-Poetscher L. & van Zijl P. (2005). MRI atlas of human white matter.
Elsevier, Amsterdam, The Netherlands.
Morris P. (1986). Nuclear magnetic resonance imaging in medicine and biology. Oxford University
Press, UK.
Moseley M. (2002). Diffusion tensor imaging and aging - a review. NMR in Biomedicine 15(7-
8):553–560.
Moseley M., Kucharczyk J., Asgari H. & Norman D. (1991). Anisotropy in diffusion-weighted
MRI. Magnetic Resonance in Medicine 19(2):321–326.
Muñoz Maniega S., Bastin M., Armitage P., Farrall A., Carpenter T., Hand P., Cvoro V., Rivers
C. & Wardlaw J. (2004). Temporal evolution of water diffusion parameters is different in grey
and white matter in human ischaemic stroke. Journal of Neurology Neurosurgery and Psychiatry
75(12):1714–1718.
Neal R. (1993). Probabilistic inference using Markov chain Monte Carlo methods. Tech. Rep.
CRG-TR-93-1, University of Toronto.
Niewenhuys R. (1996). The human central nervous system: a synopsis and atlas. Springer, New
York, 3 edn.
O’Donnell L. & Westin C.F. (2005). White matter tract clustering and correspondence in pop-
ulations. In Medical Image Computing and Computer-Assisted Intervention, vol. 3749 of Lecture
Notes in Computer Science, pp. 140–147. Springer-Verlag.
O’Sullivan M., Jones D., Summers P., Morris R., Williams S. & Markus H. (2001). Evidence
for cortical "disconnection" as a mechanism of age-related cognitive decline. Neurology
57(4):632–638.
Pajevic S. & Basser P. (2003). Parametric and non-parametric statistical analysis of DT-MRI
data. Journal of Magnetic Resonance 161(1):1–14.
Papadakis N., Xing D., Houston G., Smith J., Smith M., James M., Parsons A., Huang C., Hall L.
& Carpenter T. (1999). A study of rotationally invariant and symmetric indices of diffusion
anisotropy. Magnetic Resonance Imaging 17(6):881–892.
Park H.J., Westin C.F., Kubicki M., Maier S., Niznikiewicz M., Baer A., Frumin M., Kikinis
R., Jolesz F., McCarley R. & Shenton M. (2004). White matter hemisphere asymmetries in
healthy subjects and in schizophrenia: a diffusion tensor MRI study. NeuroImage 23:213–223.
Parker G., Haroon H. & Wheeler-Kingshott C. (2003). A framework for a streamline-based
probabilistic index of connectivity (PICo) using a structural interpretation of MRI diffusion
measurements. Journal of Magnetic Resonance Imaging 18(2):242–254.
Parker G., Stephan K., Barker G., Rowe J., MacManus D., Wheeler-Kingshott C., Ciccarelli O.,
Passingham R., Spinks R., Lemon R. & Turner R. (2002a). 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(4):797–809.
Parker G., Wheeler-Kingshott C. & Barker G. (2002b). Estimating distributed anatomical
connectivity using fast marching methods and diffusion tensor imaging. IEEE Transactions
on Medical Imaging 21(5):505–512.
Bibliography 127

Perrin M., Poupon C., Rieul B., Leroux P., Constantinesco A., Mangin J. & Le Bihan D. (2005).
Validation of q-ball imaging with a diffusion fibre-crossing phantom on a clinical scanner.
Philosophical Transactions of the Royal Society B: Biological Sciences 360(1457):881–891.

Pfefferbaum A., Sullivan E., Hedehus M., Lim K., Adalsteinsson E. & Moseley M. (2000).
Age-related decline in brain white matter anisotropy measured with spatially corrected
echo-planar diffusion tensor imaging. Magnetic Resonance in Medicine 44(2):259–268.

Pierpaoli C. & Basser P. (1996). Toward a quantitative assessment of diffusion anisotropy.

Magnetic Resonance in Medicine 36(6):893–906.

Pipe J. (1999). Motion correction with PROPELLER MRI: application to head motion and
free-breathing cardiac imaging. Magnetic Resonance in Medicine 42(5):963–969.

Poupon C., Clark C., Frouin V., Régis J., Bloch I., Le Bihan D. & Mangin J. (2000). Regularization
of diffusion-based direction maps for the tracking of brain white matter fascicles. NeuroImage
12(2):184–195.

Price G., Cercignani M., Parker G., Altmann D., Barnes T., Barker G., Joyce E. & Ron M. (2007).
Abnormal brain connectivity in first-episode psychosis: a diffusion MRI tractography study
of the corpus callosum. NeuroImage 35(2):458–466.

Pusey E., Lufkin R., Brown R., Solomon M., Stark D., Tarr R. & Hanafee W. (1986). Magnetic
resonance imaging artifacts: mechanism and clinical significance. Radiographics 6(5):891–911.

R Development Core Team (2007). R: A language and environment for statistical computing. R
Foundation for Statistical Computing.

Reese T., Heid O., Weisskoff R. & Wedeen V. (2003). Reduction of eddy-current-induced
distortion in diffusion MRI using a twice-refocused spin echo. Magnetic Resonance in Medicine
49(1):177–182.

Riley K., Hobson M. & Bence S. (2002). Mathematical methods for physics and engineering. Cam-
bridge University Press, UK, 2 edn.

Rouw R. & Scholte H. (2007). Increased structural connectivity in grapheme-color synesthesia.

Nature Neuroscience 10(6):792–797.

Sakaie K. & Lowe M. (2007). An objective method for regularization of fiber orientation
distributions derived from diffusion-weighted MRI. NeuroImage 34(1):169–176.

Schmahmann J., Pandya D., Wang R., Dai G., D’Arceuil H., de Crespigny A. & Wedeen
V. (2007). Association fibre pathways of the brain: parallel observations from diffusion
spectrum imaging and autoradiography. Brain 130(3):630–653.

Sebastian T., Klein P. & Kimia B. (2003). On aligning curves. IEEE Transactions on Pattern
Analysis and Machine Intelligence 25(1):116–125.

Skare S., Hedehus M., Moseley M. & Li T. (2000). Condition number as a measure of noise
performance of diffusion tensor data acquisition schemes with MRI. Journal of Magnetic
Resonance 147:340–352.

Smith S., Jenkinson M., Johansen-Berg H., Rueckert D., Nichols T., Mackay C., Watkins K.,
Ciccarelli O., Cader M., Matthews P. & Behrens T. (2006). Tract-based spatial statistics:
Voxelwise analysis of multi-subject diffusion data. NeuroImage 31(4):1487–1505.

Smith S., Jenkinson M., Woolrich M., Beckmann C., Behrens T., Johansen-Berg H., Bannister P.,
De Luca M., Drobnjak I., Flitney D., Niazy R., Saunders J., Vickers J., Zhang Y., De Stefano
N., Brady J. & Matthews P. (2004). Advances in functional and structural MR image analysis
and implementation as FSL. NeuroImage 23 Suppl 1:S208–S219.
128 Bibliography

Staempfli P., Jaermann T., Crelier G., Kollias S., Valavanis A. & Boesiger P. (2006). Resolving
fiber crossing using advanced fast marching tractography based on diffusion tensor imaging.
NeuroImage 30(1):110–120.
Staempfli P., Reischauer C., Jaermann T., Valavanis A., Kollias S. & Boesiger P. (2008). Combin-
ing fMRI and DTI: A framework for exploring the limits of fMRI-guided DTI fiber tracking
and for verifying DTI-based fiber tractography results. NeuroImage 39(1):119–126.
Stejskal E. (1965). Use of spin echoes in a pulsed magnetic-field gradient to study anisotropic,
restricted diffusion and flow. Journal of Chemical Physics 43(10):3597–3603.
Stejskal E. & Tanner J. (1965). Spin diffusion measurements: spin echoes in the presence of a
time-dependent field gradient. Journal of Chemical Physics 42(1):288–292.
Sullivan E. & Pfefferbaum A. (2006). Diffusion tensor imaging and aging. Neuroscience &
Biobehavioral Reviews 30(6):749–761.
Tournier J.D., Calamante F. & Connelly A. (2007). Robust determination of the fibre orien-
tation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical
deconvolution. NeuroImage 35(4):1459–1472.
Tournier J.D., Calamante F., Gadian D. & Connelly A. (2004). Direct estimation of the fiber ori-
entation density function from diffusion-weighted MRI data using spherical deconvolution.
NeuroImage 23(3):1176–1185.
Tuch D. (2004). Q-ball imaging. Magnetic Resonance in Medicine 52(6):1358–1372.
Tuch D., Reese T., Wiegell M., Makris N., Belliveau J. & Wedeen V. (2002). High angular
resolution diffusion imaging reveals intravoxel white matter fiber heterogeneity. Magnetic
Resonance in Medicine 48(4):577–582.
Tuch D., Reese T., Wiegell M. & Wedeen V. (2003). Diffusion MRI of complex neural architecture.
Neuron 40(5):885–895.
Volkau I., Bhanu Prakash K., Ananthasubramaniam A., Aziz A. & Nowinski W. (2006). Extrac-
tion of the midsagittal plane from morphological neuroimages using the Kullback-Leibler’s
measure. Medical Image Analysis 10(6):863–874.
Wedeen V., Hagmann P., Tseng W.Y., Reese T. & Weisskoff R. (2005). Mapping complex tissue
architecture with diffusion spectrum magnetic resonance imaging. Magnetic Resonance in
Medicine 54(6):1377–1386.

Whitcher B., Tuch D., Wisco J., Sorensen A. & Wang L. (2007). Using the wild bootstrap to
quantify uncertainty in DTI. Human Brain Mapping in press.
Woods R., Grafton S., Watson J., Sicotte N. & Mazziotta J. (1998). Automated image registra-
tion: II. Intersubject validation of linear and nonlinear models. Journal of Computer Assisted
Tomography 22(1):153–165.

Wright I., McGuire P., Poline J., Travere J., Murray R., Frith C., Frackowiak R. & Friston K.
(1995). A voxel-based method for the statistical analysis of gray and white matter density
applied to schizophrenia. NeuroImage 2(4):244–252.
Xue R., van Zijl P., Crain B., Solaiyappan M. & Mori S. (1999). In vivo three-dimensional
reconstruction of rat brain axonal projections by diffusion tensor imaging. Magnetic Resonance
in Medicine 42(6):1123–1127.
Zhang S., Demiralp Ç. & Laidlaw D. (2003). Visualizing diffusion tensor MR images using
streamtubes and streamsurfaces. IEEE Transactions on Visualization and Computer Graphics
9(4):454–462.