Atlas registration for edema-corrected MRI lesion volume in mouse stroke models.
Ontology highlight
ABSTRACT:
SUBMITTER: Koch S
PROVIDER: S-EPMC6360485 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Accurately mapping brain structures in three-dimensions is critical for an in-depth understanding of brain functions. Using the brain atlas as a hub, mapping detected datasets into a standard brain space enables efficient use of various datasets. However, because of the heterogeneous and nonuniform brain structure characteristics at the cellular level introduced by recently developed high-resolution whole-brain microscopy techniques, it is difficult to apply a single standard to robust registration of various large-volume datasets. In this study, we propose a robust Brain Spatial Mapping Interface (BrainsMapi) to address the registration of large-volume datasets by introducing extracted anatomically invariant regional features and a large-volume data transformation method. By performing validation on model data and biological images, BrainsMapi achieves accurate registration on intramodal, individual, and multimodality datasets and can also complete the registration of large-volume datasets (approximately 20 TB) within 1 day. In addition, it can register and integrate unregistered vectorized datasets into a common brain space. BrainsMapi will facilitate the comparison, reuse and integration of a variety of brain datasets.
| S-EPMC7005806 | biostudies-literature
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.
| S-EPMC7122737 | biostudies-literature
Project description:This series represents samples of multiple myeloma patients with bone lytic lesion by MRI. Keywords = multiple myeloma Keywords = osteolytic lesions Keywords = MRI Keywords = osteoblast Keywords = mesenchymal stem cell Keywords = Wnt signaling Keywords = DKK1 Keywords: other
2004-01-01 | GSE754 | GEO
Project description:BACKGROUND:Two-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. METHODS:Pregnant 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. FINDINGS:Between 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. INTERPRETATION:Standard 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. FUNDING:Wellcome Trust/EPSRC Centre for Medical Engineering, National Institute for Health Research.
| S-EPMC6484696 | biostudies-literature
Project description:This series represents samples of multiple myeloma patients without bone lytic lesion by MRI. Keywords = multiple myeloma Keywords = osteolytic lesions Keywords = MRI Keywords = osteoblast Keywords = mesenchymal stem cell Keywords = Wnt signaling Keywords = DKK1 Keywords: other
2004-01-01 | GSE753 | GEO
Project description:PurposeDevelopment of a freely available stroke population-specific anatomical CT/MRI atlas with a reliable normalisation pipeline for clinical CT.MethodsBy reviewing CT scans in suspected stroke patients and filtering the AIBL MRI database, respectively, we collected 50 normal-for-age CT and MRI scans to build a standard-resolution CT template and a high-resolution MRI template. The latter was manually segmented into anatomical brain regions. We then developed and validated a MRI to CT registration pipeline to align the MRI atlas onto the CT template. Finally, we developed a CT-to-CT-normalisation pipeline and tested its reliability by calculating Dice coefficient (Dice) and Average Hausdorff Distance (AHD) for predefined areas in 100 CT scans from ischaemic stroke patients.ResultsThe resulting CT/MRI templates were age and sex matched to a general stroke population (median age 71.9 years (62.1-80.2), 60% male). Specifically, this accounts for relevant structural changes related to aging, which may affect registration. Applying the validated MRI to CT alignment (Dice > 0.78, Average Hausdorff Distance < 0.59 mm) resulted in our final CT-MRI atlas. The atlas has 52 manually segmented regions and covers the whole brain. The alignment of four cortical and subcortical brain regions with our CT-normalisation pipeline was reliable for small/medium/large infarct lesions (Dice coefficient > 0.5).ConclusionThe newly created CT-MRI brain atlas has the potential to standardise stroke lesion segmentation. Together with the automated normalisation pipeline, it allows analysis of existing and new datasets to improve prediction tools for stroke patients (free download at https://forms.office.com/r/v4t3sWfbKs ).
| S-EPMC9271109 | biostudies-literature
Project description:The myelin content of the cortex changes over the human lifetime and aberrant cortical myelination is associated with diseases such as schizophrenia and multiple sclerosis. Recently magnetic resonance imaging (MRI) techniques have shown potential in differentiating between myeloarchitectonically distinct cortical regions in vivo. Here we introduce a new algorithm for correcting partial volume effects present in mm-scale MRI images which was used to investigate the myelination pattern of the cerebral cortex in 1555 clinically normal subjects using the ratio of T1-weighted (T1w) and T2-weighted (T2w) MRI images. A significant linear cross-sectional age increase in T1w/T2w estimated myelin was detected across an 18 to 35 year age span (highest value of ~ 1%/year compared to mean T1w/T2w myelin value at 18 years). The cortex was divided at mid-thickness and the value of T1w/T2w myelin calculated for the inner and outer layers separately. The increase in T1w/T2w estimated myelin occurs predominantly in the inner layer for most cortical regions. The ratio of the inner and outer layer T1w/T2w myelin was further validated using high-resolution in vivo MRI scans and also a high-resolution MRI scan of a postmortem brain. Additionally, the relationships between cortical thickness, curvature and T1w/T2w estimated myelin were found to be significant, although the relationships varied across the cortex. We discuss these observations as well as limitations of using the T1w/T2w ratio as an estimate of cortical myelin.
| S-EPMC4262571 | biostudies-literature
Project description:In in-utero MRI, motion correction for fetal body and placenta poses a particular challenge due to the presence of local non-rigid transformations of organs caused by bending and stretching. The existing slice-to-volume registration (SVR) reconstruction methods are widely employed for motion correction of fetal brain that undergoes only rigid transformation. However, for reconstruction of fetal body and placenta, rigid registration cannot resolve the issue of misregistrations due to deformable motion, resulting in degradation of features in the reconstructed volume. We propose a Deformable SVR (DSVR), a novel approach for non-rigid motion correction of fetal MRI based on a hierarchical deformable SVR scheme to allow high resolution reconstruction of the fetal body and placenta. Additionally, a robust scheme for structure-based rejection of outliers minimises the impact of registration errors. The improved performance of DSVR in comparison to SVR and patch-to-volume registration (PVR) methods is quantitatively demonstrated in simulated experiments and 20 fetal MRI datasets from 28-31 weeks gestational age (GA) range with varying degree of motion corruption. In addition, we present qualitative evaluation of 100 fetal body cases from 20-34 weeks GA range.
| S-EPMC7116020 | biostudies-literature
Project description:The spatial heterogeneity in the temporal occurrence of pseudo-normalization of MR apparent diffusion coefficient values for ischemic lesions may be related to morphological and functional vascular remodeling. As the area of accelerated pseudo-normalization tends to expand faster and more extensively into the chronic stage, detailed vascular characterization of such areas is necessary. During the subacute stage of transient middle cerebral artery occlusion rat models, the morphological size of the macrovasculature, microvascular vessel size index (VSI), and microvessel density (MVD) were quantified along with functional perfusion measurements of the relative cerebral blood flow (rCBF) and mean transit time (rMTT) of the corresponding areas (33 cases for each parameter). When compared with typical pseudo-normalization lesions, early pseudo-normalization lesions exhibited larger VSI and rCBF (p < 0.001) at reperfusion days 4 and 7, along with reduced MVD and elongated rMTT (p < 0.001) at reperfusion days 1, 4, and 7. The group median VSI and rCBF exhibited a strong positive correlation (r = 0.92), and the corresponding MVD and rMTT showed a negative correlation (r = -0.48). Light sheet fluorescence microscopy images were used to quantitatively validate the corresponding MRI-derived microvascular size, density, and cerebral blood volume.
| S-EPMC8669276 | biostudies-literature
Project description:The Wenzel model, commonly used for predicting the equilibrium contact angle (CA) of drops which penetrate the asperities of a rough surface, does not account for the liquid volume stored in the asperities. Interestingly, many previous experimental and molecular dynamics studies have noted discrepancies between observed CAs and those predicted by the Wenzel model because of this neglected liquid volume. Here, we apply a thermodynamic model to wetting of periodically patterned surfaces to derive a volume-corrected Wenzel equation in the limit of small pattern wavelength (compared to drop size). We show that the corrected equilibrium CA is smaller than that predicted by the Wenzel equation and that the reduction in CA can be significant when the liquid volume within the asperities becomes non-negligible compared to the total droplet volume. In such cases, the corrected CAs agree reasonably well with experimental observations and results of molecular dynamics simulations reported in previous studies.
| S-EPMC7178789 | biostudies-literature