Comparison of Acute and Chronic Traumatic Brain Injury Using Semi-Automatic Multimodal Segmentation of MR Volumes

Laboratory of Neuro Imaging, University of California, Los Angeles, California 90095, USA.
Journal of neurotrauma (Impact Factor: 3.71). 07/2011; 28(11):2287-306. DOI: 10.1089/neu.2011.1920
Source: PubMed


Although neuroimaging is essential for prompt and proper management of traumatic brain injury (TBI), there is a regrettable and acute lack of robust methods for the visualization and assessment of TBI pathophysiology, especially for of the purpose of improving clinical outcome metrics. Until now, the application of automatic segmentation algorithms to TBI in a clinical setting has remained an elusive goal because existing methods have, for the most part, been insufficiently robust to faithfully capture TBI-related changes in brain anatomy. This article introduces and illustrates the combined use of multimodal TBI segmentation and time point comparison using 3D Slicer, a widely-used software environment whose TBI data processing solutions are openly available. For three representative TBI cases, semi-automatic tissue classification and 3D model generation are performed to perform intra-patient time point comparison of TBI using multimodal volumetrics and clinical atrophy measures. Identification and quantitative assessment of extra- and intra-cortical bleeding, lesions, edema, and diffuse axonal injury are demonstrated. The proposed tools allow cross-correlation of multimodal metrics from structural imaging (e.g., structural volume, atrophy measurements) with clinical outcome variables and other potential factors predictive of recovery. In addition, the workflows described are suitable for TBI clinical practice and patient monitoring, particularly for assessing damage extent and for the measurement of neuroanatomical change over time. With knowledge of general location, extent, and degree of change, such metrics can be associated with clinical measures and subsequently used to suggest viable treatment options.

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Available from: Andrei Irimia,
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    • "Both studies (Strangman et al., 2010; Warner et al., 2010b) identified several structures, including the thalamus and hippocampus that are particularly affected by TBI and are of significant value when predicting clinical outcome. The automatic structural segmentation of MR brain scans of TBI patients remains, however, a difficult endeavour as most existing methods lack robustness towards TBI-related changes in anatomy (Irimia et al., 2011, 2012). In the acute phase contusions, the presence of blood, hydrocephalus and/or oedema can greatly affect the ability to accurately segment a brain. "
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    ABSTRACT: We propose a framework for the robust and fully-automatic segmentation of magnetic resonance (MR) brain images called "Multi-Atlas Label Propagation with Expectation-Maximisation based refinement" (MALP-EM). The presented approach is based on a robust registration approach (MAPER), highly performant label fusion (joint label fusion) and intensity-based label refinement using EM. We further adapt this framework to be applicable for the segmentation of brain images with gross changes in anatomy. We propose to account for consistent registration errors by relaxing anatomical priors obtained by multi-atlas propagation and a weighting scheme to locally combine anatomical atlas priors and intensity-refined posterior probabilities. The method is evaluated on a benchmark dataset used in a recent MICCAI segmentation challenge. In this context we show that MALP-EM is competitive for the segmentation of MR brain scans of healthy adults when compared to state-of-the-art automatic labelling techniques. To demonstrate the versatility of the proposed approach, we employed MALP-EM to segment 125 MR brain images into 134 regions from subjects who had sustained traumatic brain injury (TBI). We employ a protocol to assess segmentation quality if no manual reference labels are available. Based on this protocol, three independent, blinded raters confirmed on 13 MR brain scans with pathology that MALP-EM is superior to established label fusion techniques. We visually confirm the robustness of our segmentation approach on the full cohort and investigate the potential of derived symmetry-based imaging biomarkers that correlate with and predict clinically relevant variables in TBI such as the Marshall Classification (MC) or Glasgow Outcome Score (GOS). Specifically, we show that we are able to stratify TBI patients with favourable outcomes from non-favourable outcomes with 64.7% accuracy using acute-phase MR images and 66.8% accuracy using follow-up MR images. Furthermore, we are able to differentiate subjects with the presence of a mass lesion or midline shift from those with diffuse brain injury with 76.0% accuracy. The thalamus, putamen, pallidum and hippocampus are particularly affected. Their involvement predicts TBI disease progression.
    Medical Image Analysis 02/2015; 21(1):40-58. DOI:10.1016/ · 3.65 Impact Factor
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    • "The WM model is translucent in each brain view to facilitate the visibility of anatomic details obviated in the MR volume slice displayed. See Irimia et al. (2011) for a detailed description of the neuroinformatics methodology used to generate these visualizations. "
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    ABSTRACT: Throughout the past few decades, the ability to treat and rehabilitate traumatic brain injury (TBI) patients has become critically reliant upon the use of neuroimaging to acquire adequate knowledge of injury-related effects upon brain function and recovery. As a result, the need for TBI neuroimaging analysis methods has increased in recent years due to the recognition that spatiotemporal computational analyses of TBI evolution are useful for capturing the effects of TBI dynamics. At the same time, however, the advent of such methods has brought about the need to analyze, manage, and integrate TBI neuroimaging data using informatically inspired approaches which can take full advantage of their large dimensionality and informational complexity. Given this perspective, we here discuss the neuroinformatics challenges for TBI neuroimaging analysis in the context of structural, connectivity, and functional paradigms. Within each of these, the availability of a wide range of neuroimaging modalities can be leveraged to fully understand the heterogeneity of TBI pathology; consequently, large-scale computer hardware resources and next-generation processing software are often required for efficient data storage, management, and analysis of TBI neuroimaging data. However, each of these paradigms poses challenges in the context of informatics such that the ability to address them is critical for augmenting current capabilities to perform neuroimaging analysis of TBI and to improve therapeutic efficacy.
    Frontiers in Neuroinformatics 02/2014; 8:19. DOI:10.3389/fninf.2014.00019 · 3.26 Impact Factor
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    • "White matter (WM), gray matter (GM), cerebrospinal fluid (CSF), cerebellar WM/GM and subcortical structures were segmented in FreeSurfer (FS) [15], and manual correction of tissue labeling errors was performed by three experienced users with training in neuroanatomy. TBI-related lesions were segmented from GRE/SWI/FLAIR volumes as detailed elsewhere [14], skin was segmented from T 1 MRI, and hard bone was segmented from CT. Eyes, muscle, cartilage, mucus, nerves, teeth, and ventriculostomy shunts were segmented from T 1 /T 2 MRI. 3D models and visualizations were created using 3D Slicer ( "
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    ABSTRACT: Objective: To inverse-localize epileptiform cortical electrical activity recorded from severe traumatic brain injury (TBI) patients using electroencephalography (EEG). Methods: Three acute TBI cases were imaged using computed tomography (CT) and multimodal magnetic resonance imaging (MRI). Semi-automatic segmentation was performed to partition the complete TBI head into 25 distinct tissue types, including 6 tissue types accounting for pathology. Segmentations were employed to generate a finite element method model of the head, and EEG activity generators were modeled as dipolar currents distributed over the cortical surface. Results: We demonstrate anatomically faithful localization of EEG generators responsible for epileptiform discharges in severe TBI. By accounting for injury-related tissue conductivity changes, our work offers the most realistic implementation currently available for the inverse estimation of cortical activity in TBI. Conclusion: Whereas standard localization techniques are available for electrical activity mapping in uninjured brains, they are rarely applied to acute TBI. Modern models of TBI-induced pathology can inform the localization of epileptogenic foci, improve surgical efficacy, contribute to the improvement of critical care monitoring and provide guidance for patient-tailored treatment. With approaches such as this, neurosurgeons and neurologists can study brain activity in acute TBI and obtain insights regarding injury effects upon brain metabolism and clinical outcome.
    Clinical Neurology and Neurosurgery 10/2013; · 1.13 Impact Factor
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