Anatomically constrained tractography facilitates biologically plausible fiber reconstruction of the optic radiation in multiple sclerosis

Horbruegger, M.; Loewe, Kristian; Kaufmann, Jörn; Wagner, Markus; Schippling, Sven; Pawlitzki, Marc; Schoenfeld, Mircea Ariel

doi:10.1016/j.nicl.2019.101740

Cited by 22 publications

(21 citation statements)

References 71 publications

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“…For further details of the MR protocol, see the method section of our previous work. 18 The FMRIB software library (FSL; University of Oxford, fsl. fmrib.ox.ac.uk) version 5.0.9 was used for preprocessing.…”

Section: Mri Acquisition and Data Preprocessingmentioning

confidence: 99%

“…For the fiber tracking procedure, we applied the MRtrix3 software package, 31 which we described in our previous work in detail. 18 In short, using dwi2response (with the "dhollander" algorithm for multishell data), 32 we estimated response functions from the preprocessed diffusion-weighted images. These were then used to estimate fiber orientation distributions (FODs) based on 8th order constrained spherical deconvolution (CSD) using dwi2fod.…”

Section: Fiber Tracking Of Ormentioning

confidence: 99%

“…The anatomically constrained tractography (MRtrix/ACT) option was applied, which facilitates biologically plausible fiber reconstruction of the OR in patients with MS than anatomically unconstrained tracking procedures (figure 1). 18 MRtrix/ACT needs a 5tt (5tissue-type) file to stay within anatomically meaningful borders. It was computed from the high resolution MPRAGE image with 5ttgen_fsl using the FSL segmentation tools FIRST and included partitions of CSF, WM, GM, and subcortical GM.…”

Section: Fiber Tracking Of Ormentioning

confidence: 99%

“…[15][16][17] In a recent previous study, we have already documented significant changes in retinal structures and diffusion values within the OR by comparing patients with MS with healthy controls. 18 The aim of our current study was to characterize and quantify long-term structural abnormalities spanning from the retina to the primary visual cortex using OCT and high-resolution conventional and quantitative MRI at 3 T in patients with and without a history of ON.…”

mentioning

confidence: 99%

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MS optic neuritis-induced long-term structural changes within the visual pathway

Pawlitzki

Horbrügger

Loewe

et al. 2020

Neurol Neuroimmunol Neuroinflamm

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BackgroundThe visual pathway is commonly involved in multiple sclerosis (MS), even in its early stages, including clinical episodes of optic neuritis (ON). The long-term structural damage within the visual compartment in patients with ON, however, is yet to be elucidated.ObjectiveOur aim was to characterize visual system structure abnormalities using MRI along with optical coherence tomography (OCT) and pattern-reversal visual evoked potentials (VEPs) depending on a single history of ON.MethodsTwenty-eight patients with clinically definitive MS, either with a history of a single ON (HON) or without such history and normal VEP findings (NON), were included. OCT measures comprised OCT-derived peripapillary retinal nerve fiber layer (RNFL) and macular ganglion cell/inner plexiform layer (GCIPL) thickness. Cortical and global gray and white matter, thalamic, and T2 lesion volumes were assessed using structural MRI. Diffusion-weighted MRI-derived measures included fractional anisotropy (FA), mean (MD), radial (RD), and axial (AD) diffusivity within the optic radiation (OR).ResultsMean (SD) duration after ON was 8.3 (3.7) years. Compared with the NON group, HON patients showed significant RNFL (p = 0.01) and GCIPL thinning (p = 0.002). OR FA (p = 0.014), MD (p = 0.005), RD (p = 0.007), and AD (p = 0.004) were altered compared with NON. Global gray and white as well as other regional gray matter structures did not differ between the 2 groups.ConclusionA single history of ON induces long-term structural damage within the retina and OR suggestive of both retrograde and anterograde neuroaxonal degeneration.

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Section: Mri Acquisition and Data Preprocessingmentioning

confidence: 99%

Section: Fiber Tracking Of Ormentioning

confidence: 99%

Section: Fiber Tracking Of Ormentioning

confidence: 99%

mentioning

confidence: 99%

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MS optic neuritis-induced long-term structural changes within the visual pathway

Pawlitzki

Horbrügger

Loewe

et al. 2020

Neurol Neuroimmunol Neuroinflamm

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“…The order of spherical harmonics is set to 12. Afterwards, a whole-brain tractogram of 10,000 streamlines is generated for each subject by using the anatomically constrained tractography implemented in MRtrix3 with the default parameter setting 37,45 . This number of streamlines is chosen based on the common practice of connectome research and the tolerability of the computational cost.…”

Section: Dataset and Preprocessingmentioning

confidence: 99%

A Measure of Whole-Brain White Matter Topography

Wang¹,

Shi²

2019

Preprint

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The unprecedentedly high-quality large-scale brain imaging datasets, from such as the Human Connectome Project (HCP) and UK-Biobank, provide a unique opportunity for measuring the white matter topography of the human brain. By leveraging the multi-shell diffusion MRI data from the original young adult HCP, we systematically develop a reliable measure of the whole-brain white matter topography, and we coin it topographic vector. As the main result, we find that the three most dominant dimensions of the topographic vectors strongly and linearly correlate with the coordinates of the corresponding streamlines of the whole-brain tractograms. Our results support the earlier prescient hypothesis that brain development follows a "base-plan" established by three (main) chemotactic gradients of early embryogenesis, and they implicate that the whole brain white matter tracts can be represented by vectors of a natural coordinate system. The topographic organisation, or topography, of the brain white matter was first measured using Klingler's brain dissection technique in early post-mortem studies 30 years ago 1 . However, our understanding of it is still limited. We view the topography of brain white matter pathways at two scales: local and global. The local topographic organisation, which is also known as the topographic regularity, has been defined as the preservation of the spatial relationship between neurons in point-to-point or region-toregion axonal connections 2,3 and it has been supported by tracer injection results 4-7 and diffusion magnetic resonance imaging (dMRI) studies 8-11 for various white matter

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A lesion‐aware automated processing framework for clinical stroke magnetic resonance imaging

Bey,

Dhindsa,

Kashyap

et al. 2024

Human Brain Mapping

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Magnetic resonance imaging (MRI) and MRI based computational modelling studies provide insights into severity and recovery of ischemic stroke patients. The presence of brain lesions, however, can heavily distort and impair state‐of‐the‐art processing frameworks due to abnormal intensity values and tissue distortions. In this study, we introduce and validate the novel “Lesion Aware automated Processing Pipeline (LeAPP).” LeAPP automatically processes clinical stroke MRI data while significantly reducing the impact of pathological artefacts on processing outputs such as structural and functional connectomes (SC, FC). This helps to advance the identification of biomarkers for recovery and mechanism‐based intervention planning using MRI as well as computational approaches. We extended existing frameworks, such as the Human Connectome Project (HCP) minimal processing pipeline, introducing correction steps, and implementing and modifying functional and diffusion processing to cope with MRI acquisition protocols more typical for the clinical context. A total of 51 participants (36 patients, 15 age‐matched controls) were processed across four time points for patients (3–5, 30–40, 85–95, 340–380 days after stroke onset) and one time point for controls. We validated performance using artificial lesioned brains (N = 81), derived from healthy brains and informed by real stroke lesions. The quality of reconstructing the ground truth was quantified on whole brain level and for lesion affected and unaffected regions‐of‐interest (ROIs) for brain parcellations and for SCs. Volume based agreement was evaluated using metrics such as dice coefficient, volume difference or ROI center‐of‐gravity distance while SC based agreement was defined as the difference in network metrics (e.g., node strength, clustering coefficient, or centrality). The observed deviations in reconstructed ground truth brain parcellations and structural connectomes from lesioned brains were significantly reduced for LeAPP, compared to the performance of existing pipelines such as HCP minimal processing pipeline. For instance, in the case of lesion affected ROIS we achieved a mean dice coefficient (where a value of one represents total agreement as defined by an exact overlap of both ROIs) of 0.81 with LeAPP, compared to 0.75 for HCP (p < .0001*). Additionally, the average measured ROI distance (where a value of zero represents no difference) for lesion ROIs was 0.87 for LeAPP in contrast to 1.7 for HCP (p < .0001*), indicating an overall superior performance of LeAPP. The pipeline generates standardized output files ready for brain network modelling for instance with The Virtual Brain software. This novel open‐source automated processing framework contributes to reproducible research and provides a robust framework for automated processing of clinical stroke MRI data, supporting the identification of brain network‐based biomarkers of stroke recovery.

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Anatomically constrained tractography facilitates biologically plausible fiber reconstruction of the optic radiation in multiple sclerosis

Cited by 22 publications

References 71 publications

MS optic neuritis-induced long-term structural changes within the visual pathway

MS optic neuritis-induced long-term structural changes within the visual pathway

A Measure of Whole-Brain White Matter Topography

A lesion‐aware automated processing framework for clinical stroke magnetic resonance imaging

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