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Journal ArticleDOI

Investigating the prevalence of complex fiber configurations in white matter tissue with diffusion magnetic resonance imaging.

01 Nov 2013-Human Brain Mapping (Wiley)-Vol. 34, Iss: 11, pp 2747-2766
TL;DR: More robust estimates of the proportion of affected voxels, the number of fiber orientations within each WM voxel, and the impact on tensor‐derived analyses are provided, using large, high‐quality diffusion‐weighted data sets, with reconstruction parameters optimized specifically for this task.
Abstract: It has long been recognized that the diffusion tensor model is inappropriate to characterize complex fiber architecture, causing tensor-derived measures such as the primary eigenvector and fractional anisotropy to be unreliable or misleading in these regions. There is however still debate about the impact of this problem in practice. A recent study using a Bayesian automatic relevance detection (ARD) multicompartment model suggested that a third of white matter (WM) voxels contain crossing fibers, a value that, whilst already significant, is likely to be an underestimate. The aim of this study is to provide more robust estimates of the proportion of affected voxels, the number of fiber orientations within each WM voxel, and the impact on tensor-derived analyses, using large, high-quality diffusion-weighted data sets, with reconstruction parameters optimized specifically for this task. Two reconstruction algorithms were used: constrained spherical deconvolution (CSD), and the ARD method used in the previous study. We estimate the proportion of WM voxels containing crossing fibers to be ∼90% (using CSD) and 63% (using ARD). Both these values are much higher than previously reported, strongly suggesting that the diffusion tensor model is inadequate in the vast majority of WM regions. This has serious implications for downstream processing applications that depend on this model, particularly tractography, and the interpretation of anisotropy and radial/axial diffusivity measures.

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Citations
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Journal ArticleDOI
TL;DR: The physics of DW-MRI is reviewed, currently preferred methodology is indicated, and the limits of interpretation of its results are explained, with a list of 'Do's and Don'ts' which define good practice in this expanding area of imaging neuroscience.

2,027 citations

Journal ArticleDOI
TL;DR: A post-processing technique for fast denoising of diffusion-weighted MR images is introduced and it is demonstrated that the technique suppresses local signal fluctuations that solely originate from thermal noise rather than from other sources such as anatomical detail.

1,110 citations


Cites background or methods from "Investigating the prevalence of com..."

  • ...Second, the fiber orientations are selected as the distinct peaks of the fODF with an amplitude exceeding a user-defined threshold (Jeurissen et al., 2013)....

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  • ...Finally, probabilistic streamline fiber tractography was performed to investigate the effect of denoising on the tractogram using the MRtrix software package (Jeurissen et al., 2013; Tournier et al., 2012)....

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Journal ArticleDOI
TL;DR: The aim of this study is to incorporate support for multi-shell data into the CSD approach as well as to exploit the unique b-value dependencies of the different tissue types to estimate a multi-tissue ODF.

1,015 citations


Cites background or methods from "Investigating the prevalence of com..."

  • ...It also complicates the interpretation of DTI metrics, which are often suggested for use as surrogate markers of WM ‘integrity’ (Jones, 2010; Vos et al., 2012; Wheeler-Kingshott and Cercignani, 2009; Jeurissen et al., 2013)....

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  • ...First, all unique maxima exceeding a threshold of 0.3 relative to the largest peak were extracted from the fODFs by means of the optimisation procedure described in Jeurissen et al. (2013)....

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  • ...surrogate markers of WM ‘integrity’ (Jones, 2010; Vos et al., 2012; Wheeler-Kingshott and Cercignani, 2009; Jeurissen et al., 2013)....

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Journal ArticleDOI
TL;DR: Results indicate that some of the known false positives associated with tractography algorithms are prevented, such that the biological accuracy of the reconstructions should be improved, provided that state-of-the-art streamlines tractography methods are used.

876 citations


Cites background from "Investigating the prevalence of com..."

  • ...Previous research suggested that at typical DWimaging resolutions, around one-third of white matter voxels in the brain contain such complex architecture (Behrens et al., 2007); however,more recent evidence indicates that this figuremay be as high as 90% (Jeurissen et al., 2012)....

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  • ..., 2007); however,more recent evidence indicates that this figuremay be as high as 90% (Jeurissen et al., 2012)....

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Journal ArticleDOI
TL;DR: Direct comparison between functional task-related and anatomical structural connectivity, presented here for the first time in TBI patients, links two powerful approaches to map the patterns of brain connectivity that may underlie behavioral deficits in brain-injured patients.
Abstract: Despite an increasing amount of specific correlation studies between structural and functional connectivity, there is still a need for combined studies, especially in pathological conditions. Impairments of brain white matter (WM) and diffuse axonal injuries are commonly suspected to be responsible for the disconnection hypothesis in traumatic brain injury (TBI) patients. Moreover, our previous research on TBI patients shows a strong relationship between abnormalities in topological organization of brain networks and behavioral deficits. In this study, we combined task-related functional connectivity (using event-related fMRI) with structural connectivity (derived from fiber tractography using diffusion MRI data) estimates in the same participants (17 adults with TBI and 16 controls), allowing for direct comparison between graph metrics of the different imaging modalities. Connectivity matrices were computed covering the switching motor network, which includes the basal ganglia, anterior cingulate cortex/supplementary motor area, and anterior insula/inferior frontal gyrus. The edges constituting this network consisted of the partial correlations between the fMRI time series from each node of the switching motor network. The interregional anatomical connections between the switching-related areas were determined using the fiber tractography results. We found that graph metrics and hubs obtained showed no agreement in both groups. The topological properties of brain functional networks could not be solely accounted for by the properties of the underlying structural networks. However, combining complementary information from both imaging modalities could improve accuracy in prediction of switching performance. Direct comparison between functional task-related and anatomical structural connectivity, presented here for the first time in TBI patients, links two powerful approaches to map the patterns of brain connectivity that may underlie behavioral deficits in brain-injured patients.

466 citations


Cites background from "Investigating the prevalence of com..."

  • ...…to noise, and the tensor model is unable to recover multiple diffusion orientations in single voxels, making it impossible to reconstruct tracts passing through brain regions with complex fiber architecture, also referred to as “crossing fibers” (Tournier et al., 2011; Jeurissen et al., 2013)....

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References
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Journal ArticleDOI
TL;DR: In this article, a derivation of the effect of a time-dependent magnetic field gradient on the spin-echo experiment, particularly in the presence of spin diffusion, is given.
Abstract: A derivation is given of the effect of a time‐dependent magnetic field gradient on the spin‐echo experiment, particularly in the presence of spin diffusion. There are several reasons for preferring certain kinds of time‐dependent magnetic field gradients to the more usual steady gradient. If the gradient is reduced during the rf pulses, H1 need not be particularly large; if the gradient is small at the time of the echo, the echo will be broad and its amplitude easy to measure. Both of these relaxations of restrictions on the measurement of diffusion coefficients by the spin‐echo technique serve to extend its range of applicability. Furthermore, a pulsed gradient can be recommended when it is critical to define the precise time period over which diffusion is being measured.The theoretical expression derived has been verified experimentally for several choices of time dependent magnetic field gradient. An apparatus is described suitable for the production of pulsed gradients with amplitudes as large as 100 ...

7,781 citations


"Investigating the prevalence of com..." refers methods in this paper

  • ...Diffusion-weighted (DW) magnetic resonance imaging (MRI) is a unique noninvasive method for probing tissue microstructure in vivo, based on the random thermal motion of water molecules [Stejskal and Tanner, 1965]....

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Journal ArticleDOI
TL;DR: Once Deff is estimated from a series of NMR pulsed-gradient, spin-echo experiments, a tissue's three orthotropic axes can be determined and the effective diffusivities along these orthotropic directions are the eigenvalues of Deff.

5,641 citations

Journal ArticleDOI
TL;DR: The diagonal and off-diagonal elements of the effective self-diffusion tensor, Deff, are related to the echo intensity in an NMR spin-echo experiment.

3,645 citations

Journal ArticleDOI
TL;DR: The software consists of a collection of algorithms that are commonly used to solve medical image registration problems, and allows the user to quickly configure, test, and compare different registration methods for a specific application.
Abstract: Medical image registration is an important task in medical image processing. It refers to the process of aligning data sets, possibly from different modalities (e.g., magnetic resonance and computed tomography), different time points (e.g., follow-up scans), and/or different subjects (in case of population studies). A large number of methods for image registration are described in the literature. Unfortunately, there is not one method that works for all applications. We have therefore developed elastix, a publicly available computer program for intensity-based medical image registration. The software consists of a collection of algorithms that are commonly used to solve medical image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. The command-line interface enables automated processing of large numbers of data sets, by means of scripting. The usage of elastix for comparing different registration methods is illustrated with three example experiments, in which individual components of the registration method are varied.

3,444 citations


"Investigating the prevalence of com..." refers methods in this paper

  • ...Next, the T1-weighted image was registered to the FA image using 3D nonrigid b-spline-based registration with Mattes mutual information as the similarity measure [Klein et al., 2010; Mattes et al., 2001] (Fig....

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Journal ArticleDOI
Behrens Tej.1, H J Berg1, Saad Jbabdi1, Rushworth Mfs.1, Mark W. Woolrich1 
TL;DR: It is shown that multi-fibre tractography offers significant advantages in sensitivity when tracking non-dominant fibre populations, but does not dramatically change tractography results for the dominant pathways.

3,315 citations