Soliton dynamics in computational anatomy

Computational anatomy (CA) has introduced the idea of anatomical structures being transformed by geodesic deformations on groups of diffeomorphisms. Among these geometric structures, landmarks and image outlines in CA are shown to be singular solutions of a partial differential equation that is called the geodesic EPDiff equation. A recently discovered momentum map for singular solutions of EPDiff yields their canonical Hamiltonian formulation, which in turn provides a complete parameterization of the landmarks by their canonical positions and momenta. The momentum map provides an isomorphism between landmarks (and outlines) for images and singular soliton solutions of the EPDiff equation. This isomorphism suggests a new dynamical paradigm for CA, as well as new data representation.     

Quantifying anatomical shape variations in neurological disorders

We develop a multivariate analysis of brain anatomy to identify the relevant shape deformation patterns and quantify the shape changes that explain corresponding variations in clinical neuropsychological measures. We use kernel Partial Least Squares (PLS) and formulate a regression model in the tangent space of the manifold of diffeomorphisms characterized by deformation momenta. The scalar deformation momenta completely encode the diffeomorphic changes in anatomical shape. In this model, the clinical measures are the response variables, while the anatomical variability is treated as the independent variable. To better understand the “shape—clinical response” relationship, we also control for demographic confounders, such as age, gender, and years of education in our regression model. We evaluate the proposed methodology on the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database using baseline structural MR imaging data and neuropsychological evaluation test scores. We demonstrate the ability of our model to quantify the anatomical deformations in units of clinical response. Our results also demonstrate that the proposed method is generic and generates reliable shape deformations both in terms of the extracted patterns and the amount of shape changes. We found that while the hippocampus and amygdala emerge as mainly responsible for changes in test scores for global measures of dementia and memory function, they are not a determinant factor for executive function. Another critical finding was the appearance of thalamus and putamen as most important regions that relate to executive function. These resulting anatomical regions were consistent with very high confidence irrespective of the size of the population used in the study. This data-driven global analysis of brain anatomy was able to reach similar conclusions as other studies in Alzheimer’s disease based on predefined ROIs, together with the identification of other new patterns of deformation. The proposed methodology thus holds promise for discovering new patterns of shape changes in the human brain that could add to our understanding of disease progression in neurological disorders.     

High resolution MR anatomy of the subthalamic nucleus: imaging at 9.4 T with histological validation

Using conventional MRI the subthalamic nucleus (STN) is not clearly defined. Our objective was to define the anatomy of the STN using 9.4 T MRI of post mortem tissue with histological validation. Spin-echo (SE) and 3D gradient-echo (GE) images were obtained at 9.4 T in 8 post mortem tissue blocks and compared directly with corresponding histological slides prepared with Luxol Fast Blue/Cresyl Violet (LFB/CV) in 4 cases and Perl stain in 3. The variability of the STN anatomy was studied using internal reference points. The anatomy of the STN and surrounding structures was demonstrated in all three anatomical planes using 9.4 T MR images in concordance with LFB/CV stained histological sections. Signal hypointensity was seen in 6/8 cases in the anterior and medial STN that corresponded with regions of more intense Perl staining. There was significant variability in the volume, shape and location of the borders of the STN. Using 9.4 T MRI, the internal signal characteristics and borders of the STN are clearly defined and significant anatomical variability is apparent. Direct visualisation of the STN is possible using high field MRI and this is particularly relevant, given its anatomical variability, for planning deep brain stimulation.     

Computational anatomy and neuropsychiatric disease: probabilistic assessment of variation and statistical inference of group difference, hemispheric asymmetry, and time-dependent change

Three components of computational anatomy (CA) are reviewed in this paper: (i) the computation of large-deformation maps, that is, for any given coordinate system representations of two anatomies, computing the diffeomorphic transformation from one to the other; (ii) the computation of empirical probability laws of anatomical variation between anatomies; and (iii) the construction of inferences regarding neuropsychiatric disease states. CA utilizes spatial-temporal vector field information obtained from large-deformation maps to assess anatomical variabilities and facilitate the detection and quantification of abnormalities of brain structure in subjects with neuropsychiatric disorders. Neuroanatomical structures are divided into two types: subcortical structures-gray matter (GM) volumes enclosed by a single surface-and cortical mantle structures-anatomically distinct portions of the cerebral cortical mantle layered between the white matter (WM) and cerebrospinal fluid (CSF). Because of fundamental differences in the geometry of these two types of structures, image-based large-deformation high-dimensional brain mapping (HDBM-LD) and large-deformation diffeomorphic metric matching (LDDMM) were developed for the study of subcortical structures and labeled cortical mantle distance mapping (LCMDM) was developed for the study of cortical mantle structures. Studies of neuropsychiatric disorders using CA usually require the testing of hypothesized group differences with relatively small numbers of subjects per group. Approaches that increase the power for testing such hypotheses include methods to quantify the shapes of individual structures, relationships between the shapes of related structures (e.g., asymmetry), and changes of shapes over time. Promising preliminary studies employing these approaches to studies of subjects with schizophrenia and very mild to mild Alzheimer's disease (AD) are presented.     

The feasibility of a common stereotactic space for children and adults in fMRI studies of development

The question of whether pediatric and adult neuroimaging data can be analyzed in a common stereotactic space is a critical issue for developmental neuroscience. Two studies were performed to address this question. In Study 1, high-resolution structural MR brain images of 20 children (7-8 years of age) and 20 young adults (18-30 years of age) were transformed to a common space. Overall brain shape was assessed by tracing the outer boundaries of the brains in three orientations, and more local anatomy was assessed by analysis of portions of 10 selected sulci. Small, but consistent, differences in location and variability were observed in specific locations of the sulcal tracings and outer-boundary sections. In Study 2, a computer simulation was used to assess the extent to which the small anatomical differences observed in Study 1 would produce spurious effects in functional imaging data. Results indicate that, assuming a functional resolution of 5 mm in images averaged across subjects, anatomical differences in either variability or location between children and adults of the magnitude obperved in Study 1 would not negatively affect functional image comparisons. We conclude that atlas-transformed brain morphology is relatively consistent between 7- and 8-year-old children and adults at a resolution appropriate to current functional imaging and that the small anatomical differences present do not limit the usefulness of comparing child and adult functional images within a common stereotactic space.     

From macro-scale to micro-scale computational anatomy: a perspective on the next 20 years

This paper gives our perspective on the next two decades of computational anatomy, which has made great strides in the recognition and understanding of human anatomy from conventional clinical images. The results from this field are now used in a variety of medical applications, including quantitative analysis of organ shapes, interventional assistance, surgical navigation, and population analysis. Several anatomical models have also been used in computational anatomy, and these mainly target millimeter-scale shapes. For example, liver-shape models are almost completely modeled at the millimeter scale, and shape variations are described at such scales. Most clinical 3D scanning devices have had just under 1 or 0.5 mm per voxel resolution for over 25 years, and this resolution has not changed drastically in that time. Although Z-axis (head-to-tail direction) resolution has been drastically improved by the introduction of multi-detector CT scanning devices, in-plane resolutions have not changed very much either. When we look at human anatomy, we can see different anatomical structures at different scales. For example, pulmonary blood vessels and lung lobes can be observed in millimeter-scale images. If we take 10-µm-scale images of a lung specimen, the alveoli and bronchiole regions can be located in them. Most work in millimeter-scale computational anatomy has been done by the medical-image analysis community. In the next two decades, we encourage our community to focus on micro-scale computational anatomy. In this perspective paper, we briefly review the achievements of computational anatomy and its impacts on clinical applications; furthermore, we show several possibilities from the viewpoint of microscopic computational anatomy by discussing experimental results from our recent research activities.     

GRAM: A framework for geodesic registration on anatomical manifolds

Medical image registration is a challenging problem, especially when there is large anatomical variation in the anatomies. Geodesic registration methods have been proposed to solve the large deformation registration problem. However, analytically defined geodesic paths may not coincide with biologically plausible paths of registration, since the manifold of diffeomorphisms is immensely broader than the manifold spanned by diffeomorphisms between real anatomies. In this paper, we propose a novel framework for large deformation registration using the learned manifold of anatomical variation in the data. In this framework, a large deformation between two images is decomposed into a series of small deformations along the shortest path on an empirical manifold that represents anatomical variation. Using a manifold learning technique, the major variation of the data can be visualized by a low-dimensional embedding, and the optimal group template is chosen as the geodesic mean on the manifold. We demonstrate the advantages of the proposed framework over direct registration with both simulated and real databases of brain images.     

Anatomical atlas-guided diffuse optical tomography of brain activation

We describe a neuroimaging protocol that utilizes an anatomical atlas of the human head to guide diffuse optical tomography of human brain activation. The protocol is demonstrated by imaging the hemodynamic response to median-nerve stimulation in three healthy subjects, and comparing the images obtained using a head atlas with the images obtained using the subject-specific head anatomy. The results indicate that using the head atlas anatomy it is possible to reconstruct the location of the brain activation to the expected gyrus of the brain, in agreement with the results obtained with the subject-specific head anatomy. The benefits of this novel method derive from eliminating the need for subject-specific head anatomy and thus obviating the need for a subject-specific MRI to improve the anatomical interpretation of diffuse optical tomography images of brain activation.     

Ultrasound of the normal kidney: A sonographic, anatomic and histologic correlation

Technical progress in sonographic equipment providing routinely high resolution images makes it appropriate that some criteria of normality have to be reviewed. In this paper normal sonographic images of the kidney are correlated with anatomy and histology. The effect of aging upon normal anatomical relations and histologic findings is analysed. Special attention is focussed on particular anatomical details as far as they can explain the particular topography or sonographic appearance of some pathologies.     

Developmental pattern of gentamicin kinetics in very low birth weight (VLBW) sick infants

Kinetic studies were carried out in 15 very low birth weight (VLBW) infants during three courses of gentamicin (G) therapy for suspected sepsis. All received two courses but only 6 required a third course. G dosage was 2.0 +/- 0.2 mg/kg/24 h for the first and second course and 2.5 mg/kg/12 h for the third course. G dosage was adjusted to maintain serum peak G concentration of 4-8 micrograms/ml and trough concentration of 0.5-2 micrograms/ml. On the third day of therapy, a 24-hour collection of urine for creatinine (C) and G concentrations was performed in 28 of 36 cases. G clearance and G elimination rate constant were calculated based on chronological age (CA) of less than or equal to 7 (I), 8-30 (II) and greater than or equal to 31 (III) days. The mean BW and GA were 1,002 +/- 206 g and 28.4 +/- 1.5 weeks, respectively. Mean CA for the starting of therapy for each course was the first day, 19 +/- 9 and 68 +/- 26 days of life, respectively. Mean serum G peak and trough concentrations were 5.9 +/- 1.1 and 1.6 +/- 0.6 micrograms/ml for the first; 5.7 +/- 1.2 and 1.3 +/- 0.6 micrograms/ml for the second; 5.1 +/- 0.8 and 1.1 +/- 0.6 micrograms/ml for the third course of therapy. Mean apparent volume of distribution of G were 0.53 +/- 0.10 liter/kg for the first and 0.50 +/- 0.11 liter/kg for the second and third courses. Mean clearances for the three CA groups were 6.4 +/- 1.9; 7.6 +/- 3.2; 24.1 +/- 8.0 ml/min/1.73 m2 for G and 6.4 +/- 2.2; 7.7 +/- 3.1; 23.3 +/- 8.8 for C with serum C of 1.3 +/- 0.4, 1.2 +/- 0.6 and 0.6 +/- 0.4 mg%, respectively. There were no statistically significant differences for serum C, G and C clearance between CA I and II but significant differences were found for the above between CA III vs. CA I and II (p less than 0.005). G clearance closely correlated with C clearance (r = 0.99, p less than 0.001). The elimination rate constant was significantly higher after 30 days of life when CA III is compared to CA I and II or combined (p less than 0.001). This study shows that during the first month of life, VLBW sick infants still have decreased renal function and poor G clearance, therefore, G should be given every 24 h and the dose be adjusted based on individual patient serum G levels.     

Angiography

The clinical usefulness of three dimensional images was widely recognized. The three dimensional digital subtraction angiography (3D-DSA) well demonstrated anatomical structures of cerebral arteries with high special resolution. This 3D observation allowed high quality planning for aneurysmal coil packing and neck clipping. Because of the bony structure and curvy arterial anatomy in the skull base region, 3D-CTA and MRA was sometimes distureved the demonstration of the anatomical relationship adjacent to the aneurysm. However, 3D-DSA not only demonstrated arterial anatomy, but also analyzed of vascular structure, quantifiably. And it was useful in radiation dose reduction by reduction of DSA exposure number. We believe that 3D-DSA should provided useful information for planning of surgical and endovascular treatment in the field of cerebro-vascular disease.     

Self-co-attention neural network for anatomy segmentation in whole breast ultrasound

The automated whole breast ultrasound (AWBUS) is a new breast imaging technique that can depict the whole breast anatomy. To facilitate the reading of AWBUS images and support the breast density estimation, an automatic breast anatomy segmentation method for AWBUS images is proposed in this study. The problem at hand is quite challenging as it needs to address issues of low image quality, ill-defined boundary, large anatomical variation, etc. To address these issues, a new deep learning encoder-decoder segmentation method based on a self-co-attention mechanism is developed. The self-attention mechanism is comprised of spatial and channel attention module (SC) and embedded in the ResNeXt (i.e., Res-SC) block in the encoder path. A non-local context block (NCB) is further incorporated to augment the learning of high-level contextual cues. The decoder path of the proposed method is equipped with the weighted up-sampling block (WUB) to attain class-specific better up-sampling effect. Meanwhile, the co-attention mechanism is also developed to improve the segmentation coherence among two consecutive slices. Extensive experiments are conducted with comparison to several the state-of-the-art deep learning segmentation methods. The experimental results corroborate the effectiveness of the proposed method on the difficult breast anatomy segmentation problem on AWBUS images.     

组织多普勒显像定量分析窦房结功能

目的 评价心动周期中窦房结内机械运动参数（如：加速度）的时空变化规律及其与心脏电兴奋之间的相关性。方法 制作5只犬开胸动物模型,用心内超声探头采集时间顺序窦房结组织多普勒图像,利用计算机图像处理与分析方法获取时间顺序窦房结内组织的加速度定量数据。结果 得到了窦房结兴奋过程中窦房结内心肌运动的加速度－时间曲线,其舒张末期初始加速度的起始时相与同步心电图特定时机（如：P波起始点）对照,二者具有很好的时相相关性。结论 由窦房结内组织多普勒顺序图像中得到的心肌兴奋的加速度－时间曲线及其与心电图时相之间的相关性,提示心内组织多普勒显像技术可用于定量评价窦房结内心肌机械兴奋及其与心肌电兴奋之间的关系。     

Magnetic Resonance Microscopy of the C57BL Mouse Brain

With the rapid progression in gene technologies, transgenic, targeted, and chemically induced mutations in mice are continually created. The major goal of these studies is to understand and characterize the effects of genotype on anatomy, physiology, and behavior and ultimately the role of genotype in development of disease. The demand for imaging techniques with high spatial resolution potential is rising because such imaging tools would expedite anatomical phenotyping in the genetically altered mice. Magnetic resonance microscopy (MRM) is a noninvasive, inherently three-dimensional (3D) imaging technique capable of visualizing several anatomical structures in the small mouse. The 3D nature of MRM also allows for interpretation of complex spatial relationships between substructures, which is important when phenotyping anatomically. The goal of this paper is to systematically describe three major brain regions in the C57BL/6J mouse at microanatomical spatial resolution ranges using in vitro MRM. We explore different MR contrast parameters, voxel sizes, and signal-to-noise ratios to best characterize C57BL/6J mouse brain microstructure by MRM. Further, we compare all MRM images with Nissl-stained brain sections. Major findings were as follows: T2* MR images visualized several gross anatomical regions in the mouse brain but not, for example, subregions within the hippocampus. Diffusion proton stains on the other hand were superior to T2* MR images and delineated many subregions within the hippocampus proper. Finally, contrast enhancement facilitated visualization of hippocampal anatomy on the T2* MR images. The results of this study are part of an ongoing initiative at our Center focused on creating a complete C57BL/6J mouse anatomical 3D image database by MRM.     

Two- and three-dimensional sonographic assessment of the fetal face. 2. Analysis of cleft lip, alveolus and palate.

OBJECTIVES: To describe the sonographic appearance of cleft lip with or without cleft palate (CL +/- P) using two-dimensional and three-dimensional (3D) ultrasound imaging. Also, to evaluate the accuracy of ultrasound to delineate with precision the bony extent of facial clefts, i.e. to differentiate clefts limited to the lips, or extending to the alveolus/premaxilla or the secondary palate. METHODS: This was a retrospective study based on the examination of fetuses diagnosed with an isolated CL +/- P. Cases included were either discovered at systematic screening or referred for further investigation. Clefts were characterized by their precise anatomical location and extent. The defect could include a cleft lip (CL), a cleft alveolus (CA), or a cleft of the secondary palate (CSP). RESULTS: We analyzed 96 cases of CL +/- P. The mean gestational age at examination was 28.2 +/- 4.1 weeks. The sonographic appearance of CL, CA, and CSP was depicted. Strict concordance of the sonographic report with the anatomical defect was present in 84 cases (87.5%). In eight cases, the severity of the cleft was underestimated: three cases of CA, four of CA + CSP and one of CSP were missed. In four cases, the cleft was overestimated as CA was incorrectly suspected. CONCLUSIONS: Systematic screening with sonography to detect prenatally CL +/- P requires the imaging of at least the mid-sagittal and the anterior coronal 'nose-mouth' views. Once the presence of a facial cleft is suspected, the three reference orthogonal planes are imaged in order to characterize the anatomical defect, and for each plane, the serial scans are thoroughly examined. This protocol allows precise delineation of the defect. Inclusion of 3D and 4D ultrasound imaging in the examination protocol allows easier and more rapid screening and more precise evaluation of the different cleft constituents.     

Virtual endoscopy of the cerebral ventricles based on 3-D ultrasonography

Virtual endoscopy enables preoperative surgical planning based on "surgeons' view" information in the individual patient. In neurosurgery, magnetic resonance (MR) images are mainly used for planning of virtual neuroendoscopy (VNE). We studied the feasibility of three-dimensional (3-D) ultrasonography as the imaging modality for VNE in pediatric patients with hydrocephalus. 3-D ultrasonography data sets were obtained through the open anterior fontanelle and analyzed using perspective volume rendering, with delineation of the ventricular system for anatomical details in relation to standard ultrasonography and intraoperative anatomy, during endoscopy in two infants with hydrocephalus. VNE clarified anatomical variants seen on standard ultrasonography images, anticipated ventricular dysmorphia seen during neuroendosopy and enabled a realistic impression of an endoscopic inspection into the ventricular system of the two infants studied. Based on 3-D ultrasonography, VE enables detailed information on ventricular anatomy in pediatric patients for planning of endoscopic interventions.     

A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T

This paper describes the construction of a computational anatomical atlas of the human hippocampus. The atlas is derived from high-resolution 9.4 Tesla MRI of postmortem samples. The main subfields of the hippocampus (cornu ammonis fields CA1, CA2/3; the dentate gyrus; and the vestigial hippocampal sulcus) are labeled in the images manually using a combination of distinguishable image features and geometrical features. A synthetic average image is derived from the MRI of the samples using shape and intensity averaging in the diffeomorphic non-linear registration framework, and a consensus labeling of the template is generated. The agreement of the consensus labeling with manual labeling of each sample is measured, and the effect of aiding registration with landmarks and manually generated mask images is evaluated. The atlas is provided as an online resource with the aim of supporting subfield segmentation in emerging hippocampus imaging and image analysis techniques. An example application examining subfield-level hippocampal atrophy in temporal lobe epilepsy demonstrates the application of the atlas to in vivo studies.     

Computed tomography of the lumbar spine: techniques, normal anatomy, pitfalls, and clinical applications

Normal cross-sectional anatomy and anatomical variants. Detailed line drawings of important features and images from a correlative CT/anatomical study of human cadaver spines will be included. The cross-sectional appearance of deviations from normal anatomy will also be demonstrated. Scanning techniques and methods of image recording. Patient processing efficiency and expeditious data recording and analysis will be stressed. The utility of multiplanar computer reformations will be discussed. Commonly encountered pathological conditions. Examples of intervertebral disc disease, spinal canal and lateral recess stenosis, facet arthropathy, trauma, infections, and neoplasms will be presented. A protocol for the use of intravenous and intrathecal contrast agents will be proposed.