MGH–USC Human Connectome Project datasets with ultra-high b-value diffusion MRI

Fan, Qiuyun; Witzel, Thomas; Nummenmaa, Aapo; Dijk, Koene R. A. Van; Horn, John D. Van; Drews, Monika; Somerville, Leah H.; Sheridan, Margaret A.; Santillana, Rosario M.; Snyder, Jenna; Hedden, Trey; Shaw, Emily; Hollinshead, Marisa O.; Renvall, Ville; Zanzonico, Roberta; Keil, Boris; Cauley, Stephen F.; Polimeni, Jon̈athan R.; Tisdall, M. Dylan; Buckner, Randy L.; Wedeen, Van J.; Wald, Lawrence L.; Toga, Arthur W.; Rosen, Bruce R.

doi:10.1016/j.neuroimage.2015.08.075

Cited by 215 publications

(159 citation statements)

References 33 publications

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“…DTI has been used extensively in the central nervous system . High angular resolution diffusion MRI combined with simultaneous multislice imaging using parallel imaging reconstruction has become a major imaging technique in human brain studies .…”

Section: Discussionmentioning

confidence: 99%

Diffusion tractography of the rat knee at microscopic resolution

Wang

Mirando

Cofer

et al. 2019

Magnetic Resonance in Med

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Purpose To evaluate whole knee joint tractography, including articular cartilage, ligaments, meniscus, and growth plate using diffusion tensor imaging (DTI) at microscopic resolution. Methods Three rat knee joints were scanned using a modified 3D diffusion‐weighted spin echo pulse sequence with 90‐ and 45‐μm isotropic spatial resolution at 9.4T. The b values varied from 250 to 1250 s/mm2 with 4 times undersampling in phase directions. Fractional anisotropy (FA) and mean diffusivity (MD) were compared at different spatial resolution and b values. Tractography was evaluated at multiple b values and angular resolutions in different connective tissues, and compared with conventional histology. The mean tract length and tract volume in various types of tissues were also quantified. Results DTI metrics (FA and MD) showed consistent quantitative results at 90‐ and 45‐μm isotropic spatial resolutions. Tractography of various connective tissues was found to be sensitive to the spatial resolution, angular resolution, and diffusion weightings. Higher spatial resolution (45 μm) supported tracking the cartilage collagen fiber tracts from the superficial zone to the deep zone, in a continuous and smooth progression in the transitional zone. Fiber length and fiber volume in the growth plate were strongly dependent on angular resolution and b values, whereas tractography in ligaments was found to be less dependent on spatial resolution. Conclusion High spatial and angular resolution DTI and diffusion tractography can be valuable for knee joint research because of its visualization capacity for collagen fiber orientations and quantitative evaluation of tissue’s microscopic properties.

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Section: Discussionmentioning

confidence: 99%

Diffusion tractography of the rat knee at microscopic resolution

Wang

Mirando

Cofer

et al. 2019

Magnetic Resonance in Med

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“…For each fascicle direction, the DW‐MRI signal was independently simulated for a gamma distribution,

Γ (shape, scale)

, of parallel cylinders diameter, with a fixed distinct mean diameter per fascicle of

α = 2.44 μ m

(

Γ_{shape} = 5.3316, Γ_{scale} = 1.0242 \times 10^{- 7}

, Camino substrate AbR1a ), and

α = 6.88 μ m

(

Γ_{shape} = 5.3316, Γ_{scale} = 2.0484 \times 10^{- 7}

, Camino substrate AbD1a ) [Alexander et al, ; Auría et al, ; Assaf et al, ; Hall and Alexander, ; Liewald et al, ]. The simulated DW‐MRI images were generated with the in vivo MGH‐USC Human Connectome Project (HCP) imaging protocol (552 volumes, b ‐values up to

10, 000 s / {mm}^{2}

δ = 12.9 ms, Δ = 21.8 ms

) [Fan et al, ], using the Camino [Hall and Alexander, ] Monte‐Carlo diffusion simulator. The simulated signal was contaminated with Rician noise [Gudbjartsson and Patz, ] at signal to noise ratio (SNR) 10, 20, and 30.…”

Section: Methodsmentioning

confidence: 99%

AxTract: Toward microstructure informed tractography

Girard

Daducci

Petit

et al. 2017

Human Brain Mapping

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Diffusion-weighted (DW) magnetic resonance imaging (MRI) tractography has become the tool of choice to probe the human brain's white matter in vivo. However, tractography algorithms produce a large number of erroneous streamlines (false positives), largely due to complex ambiguous tissue configurations. Moreover, the relationship between the resulting streamlines and the underlying white matter microstructure characteristics remains poorly understood. In this work, we introduce a new approach to simultaneously reconstruct white matter fascicles and characterize the apparent distribution of axon diameters within fascicles. To achieve this, our method, AxTract, takes full advantage of the recent development DW-MRI microstructure acquisition, modelling and reconstruction techniques. This enables AxTract to separate parallel fascicles with different microstructure characteristics, hence reducing ambiguities in areas of complex tissue configuration.We report a decrease in the incidence of erroneous streamlines compared to the conventional deterministic tractography algorithms on simulated data. We also report an average increase in streamline density over 15 known fascicles of the 34 healthy subjects. Our results suggest that microstructure information improves tractography in crossing areas of the white matter. Moreover, AxTract provides additional microstructure information along the fascicle that can be studied alongside other streamline-based indices. Overall, AxTract provides the means to distinguish and follow white matter fascicles using their microstructure characteristics, bringing new insights into the white matter organization. This is a step forward in microstructure informed tractography, paving the way to a new generation of algorithms able to deal with intricate configurations of white matter fibres and providing quantitative brain connectivity analysis.

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“…This allows for the mapping of white matter trajectories in the human brain and defining the graph structure of region-to-region connectivity [7, 8]; however, while the reliability of diffusion MRI scans has improved substantially by new acquisition approaches [9, 10], the efficiency and accuracy of tractography approaches have recently come into question [11, 12]. Thus, instead of mapping region-to-region connectivity, the concept of the local connectome was proposed as an alternative measure to overcome the limitations of diffusion MRI fiber tracking [11–13].…”

Section: Introductionmentioning

confidence: 99%

Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints

et al. 2016

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Quantifying differences or similarities in connectomes has been a challenge due to the immense complexity of global brain networks. Here we introduce a noninvasive method that uses diffusion MRI to characterize whole-brain white matter architecture as a single local connectome fingerprint that allows for a direct comparison between structural connectomes. In four independently acquired data sets with repeated scans (total N = 213), we show that the local connectome fingerprint is highly specific to an individual, allowing for an accurate self-versus-others classification that achieved 100% accuracy across 17,398 identification tests. The estimated classification error was approximately one thousand times smaller than fingerprints derived from diffusivity-based measures or region-to-region connectivity patterns for repeat scans acquired within 3 months. The local connectome fingerprint also revealed neuroplasticity within an individual reflected as a decreasing trend in self-similarity across time, whereas this change was not observed in the diffusivity measures. Moreover, the local connectome fingerprint can be used as a phenotypic marker, revealing 12.51% similarity between monozygotic twins, 5.14% between dizygotic twins, and 4.51% between none-twin siblings, relative to differences between unrelated subjects. This novel approach opens a new door for probing the influence of pathological, genetic, social, or environmental factors on the unique configuration of the human connectome.

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MGH–USC Human Connectome Project datasets with ultra-high b-value diffusion MRI

Cited by 215 publications

References 33 publications

Diffusion tractography of the rat knee at microscopic resolution

Diffusion tractography of the rat knee at microscopic resolution

AxTract: Toward microstructure informed tractography

Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints

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