Dataset Information

Atlas registration for edema-corrected MRI lesion volume in mouse stroke models.

ABSTRACT: Lesion volume measurements with magnetic resonance imaging are widely used to assess outcome in rodent models of stroke. In this study, we improved a mathematical framework to correct lesion size for edema which is based on manual delineation of the lesion and hemispheres. Furthermore, a novel MATLAB toolbox to register mouse brain MR images to the Allen brain atlas is presented. Its capability to calculate edema-corrected lesion size was compared to the manual approach. Automated image registration performed equally well in in a mouse middle cerebral artery occlusion model (Pearson r = 0.976, p = 2.265e-11). Information encapsulated in the registration was used to generate maps of edema induced tissue volume changes. These showed discrepancies to simplified tissue models underlying the manual approach. The presented techniques provide biologically more meaningful, voxel-wise biomarkers of vasogenic edema after stroke.

SUBMITTER: Koch S

PROVIDER: S-EPMC6360485 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Atlas registration for edema-corrected MRI lesion volume in mouse stroke models.

Koch Stefan S Mueller Susanne S Foddis Marco M Bienert Thomas T von Elverfeldt Dominik D Knab Felix F Farr Tracy D TD Bernard René R Dopatka Monika M Rex André A Dirnagl Ulrich U Harms Christoph C Boehm-Sturm Philipp P

Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism 20170822 2

Lesion volume measurements with magnetic resonance imaging are widely used to assess outcome in rodent models of stroke. In this study, we improved a mathematical framework to correct lesion size for edema which is based on manual delineation of the lesion and hemispheres. Furthermore, a novel MATLAB toolbox to register mouse brain MR images to the Allen brain atlas is presented. Its capability to calculate edema-corrected lesion size was compared to the manual approach. Automated image registra ...[more]

PMID: 28829217

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Project description:INTRODUCTION:Progressive brain atrophy, development of T1-hypointense areas, and T2-fluid-attenuated inversion recovery (FLAIR)-hyperintense lesion formation in multiple sclerosis (MS) are popular volumetric data that are often utilized as clinical outcomes. However, the exact clinical interpretation of these volumetric data has not yet been fully established. METHODS:We enrolled 42 consecutive patients with MS who fulfilled the revised McDonald criteria of 2010. They were followed-up for more than 3 years from onset, and cross-sectional brain volumetry was performed. Patients with no brain lesions were excluded in advance from this study. For the brain volumetric data, we evaluated several parameters including age-adjusted gray-matter volume atrophy, age-adjusted white-matter volume atrophy, and T2-FLAIR lesion volume. The numbers of T1-hypointense and T2-FLAIR-hyperintense areas were also measured along the same timeline. The clinical data pertaining to disease duration, expanded disability status scale (EDSS), and MS severity score (MSSS) at the timing of volumetry were collected. RESULTS:Among the 42 patients with MS and brain lesions, the number of T1-hypointensity (rho = 0.51, p<0.001), gray-matter atrophy (rho = 0.40, p<0.01) and white-matter atrophy (rho = 0.49, p<0.001) correlated with the EDSS. T1-hypointensity count divided by FLAIR lesion volume correlated with the MSSS (rho = 0.60, p<0.001). Meanwhile, counts or volumes of FLAIR-hyperintense lesions were associated only with the times of past relapses, and did not correlate with present neurological disability level or ongoing disease activity. These findings were consistent regardless of the presence of spinal cord lesions. CONCLUSION:Numbers of T1-hypointensities and brain atrophy equally indicated the current neurological disability in MS. The number of T1-hypointensities divided by FLAIR lesion volume represented the clinical severity. The size or number of FLAIR lesions reflected earlier relapses but was not a good indicator of neurological disability or clinical severity.

Project description:BackgroundTwo-dimensional (2D) ultrasound echocardiography is the primary technique used to diagnose congenital heart disease before birth. There is, however, a longstanding need for a reliable form of secondary imaging, particularly in cases when more detailed three-dimensional (3D) vascular imaging is required, or when ultrasound windows are of poor diagnostic quality. Fetal MRI, which is well established for other organ systems, is highly susceptible to fetal movement, particularly for 3D imaging. The objective of this study was to investigate the combination of prenatal MRI with novel, motion-corrected 3D image registration software, as an adjunct to fetal echocardiography in the diagnosis of congenital heart disease.MethodsPregnant women carrying a fetus with known or suspected congenital heart disease were recruited via a tertiary fetal cardiology unit. After initial validation experiments to assess the general reliability of the approach, MRI data were acquired in 85 consecutive fetuses, as overlapping stacks of 2D images. These images were then processed with a bespoke open-source reconstruction algorithm to produce a super-resolution 3D volume of the fetal thorax. These datasets were assessed with measurement comparison with paired 2D ultrasound, structured anatomical assessment of the 2D and 3D data, and contemporaneous, archived clinical fetal MRI reports, which were compared with postnatal findings after delivery.FindingsBetween Oct 8, 2015, and June 30, 2017, 101 patients were referred for MRI, of whom 85 were eligible and had fetal MRI. The mean gestational age at the time of MRI was 32 weeks (range 24-36). High-resolution (0·50-0·75 mm isotropic) 3D datasets of the fetal thorax were generated in all 85 cases. Vascular measurements showed good overall agreement with 2D echocardiography in 51 cases with paired data (intra-class correlation coefficient 0·78, 95% CI 0·68-0·84), with fetal vascular structures more effectively visualised with 3D MRI than with uncorrected 2D MRI (657 [97%] of 680 anatomical areas identified vs 358 [53%] of 680 areas; p<0·0001). When a structure of interest was visualised in both 2D and 3D data (n=358), observers gave a higher diagnostic quality score for 3D data in 321 (90%) of cases, with 37 (10%) scores tied with 2D data, and no lower scores than for 2D data (Wilcoxon signed rank test p<0·0001). Additional anatomical features were described in ten cases, of which all were confirmed postnatally.InterpretationStandard fetal MRI with open-source image processing software is a reliable method of generating high-resolution 3D imaging of the fetal vasculature. The 3D volumes produced show good spatial agreement with ultrasound, and significantly improved visualisation and diagnostic quality compared with source 2D MRI data. This freely available combination requires minimal infrastructure, and provides safe, powerful, and highly complementary imaging of the fetal cardiovascular system.FundingWellcome Trust/EPSRC Centre for Medical Engineering, National Institute for Health Research.

Dataset Information

Atlas registration for edema-corrected MRI lesion volume in mouse stroke models.

Publications

Atlas registration for edema-corrected MRI lesion volume in mouse stroke models.

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