We propose a deep neural network for supervised learning on neuroanatomical shapes. The network directly operates on raw point clouds without the need for mesh processing or the identification of point correspondences, as spatial transformer networks map the data to a canonical space. Instead of relying on hand-crafted shape descriptors, an optimal representation is learned in the end-to-end training stage of the network. The proposed network consists of multiple branches, so that features for multiple structures are learned simultaneously. We demonstrate the performance of our method on two applications: (i) the prediction of Alzheimer’s disease and mild cognitive impairment and (ii) the regression of the brain age. Finally, we visualize the important parts of the anatomy for the prediction by adapting the occlusion method to point clouds.
Several shape representations have previously been used for supervised learning tasks. Spherical harmonics for approximating the hippocampal shape have been proposed in @cite_10 . Shape information has been derived from thickness measurements of the hippocampus from a medial representation @cite_13 . Statistical shape models to detect hippocampal shape changes were proposed by @cite_11 . Multi-resolution shape features with non-Euclidean wavelets were employed for the analysis of cortical thickness @cite_15 . The use of medial axis shape representations was used to compare the brain morphology of autistic and normal populations @cite_3 . Recently, shape representation based on spectral signatures have been introduced to perform age regression and disease prediction @cite_4 @cite_0 .
@cite_4 @cite_10 @cite_3 @cite_0 @cite_15 @cite_13 @cite_11
2017436068 2097440479 2116329629 2413867752 1996576603 2154758450 2155883645
We introduce BrainPrint, a compact and discriminative representation of brain morphology. BrainPrint captures shape information of an ensemble of cortical and subcortical structures by solving the eigenvalue problem of the 2D and 3D Laplace-Beltrami operator on triangular (boundary) and tetrahedral (volumetric) meshes. This discriminative characterization enables new ways to study the similarity between brains; the focus can either be on a specific brain structure of interest or on the overall brain similarity. We highlight four applications for BrainPrint in this article: (i) subject identification, (ii) age and sex prediction, (iii) brain asymmetry analysis, and (iv) potential genetic influences on brain morphology. The properties of BrainPrint require the derivation of new algorithms to account for the heterogeneous mix of brain structures with varying discriminative power. We conduct experiments on three datasets, including over 3000 MRI scans from the ADNI database, 436 MRI scans from the OASIS dataset, and 236 MRI scans from the VETSA twin study. All processing steps for obtaining the compact representation are fully automated, making this processing framework particularly attractive for handling large datasets. We describe a new method to automatically discriminate between patients with Alzheimer's disease (AD) or mild cognitive impairment (MCI) and elderly controls, based on multidimensional classification of hippocampal shape features. This approach uses spherical harmonics (SPHARM) coefficients to model the shape of the hippocampi, which are segmented from magnetic resonance images (MRI) using a fully automatic method that we previously developed. SPHARM coefficients are used as features in a classification procedure based on support vector machines (SVM). The most relevant features for classification are selected using a bagging strategy. We evaluate the accuracy of our method in a group of 23 patients with AD (10 males, 13 females, age+ -standard-deviation (SD)=73+ -6 years, mini-mental score (MMS)=24.4+ -2.8), 23 patients with amnestic MCI (10 males, 13 females, age+ -SD=74+ -8 years, MMS=27.3+ -1.4) and 25 elderly healthy controls (13 males, 12 females, age+ -SD=64+ -8 years), using leave-one-out cross-validation. For AD vs controls, we obtain a correct classification rate of 94 , a sensitivity of 96 , and a specificity of 92 . For MCI vs controls, we obtain a classification rate of 83 , a sensitivity of 83 , and a specificity of 84 . This accuracy is superior to that of hippocampal volumetry and is comparable to recently published SVM-based whole-brain classification methods, which relied on a different strategy. This new method may become a useful tool to assist in the diagnosis of Alzheimer's disease. An important goal of statistical shape analysis is the discrimination between populations of objects, exploring group differences in morphology not explained by standard volumetric analysis. Certain applications additionally require analysis of objects in their embedding context by joint statistical analysis of sets of interrelated objects. In this paper, we present a framework for discriminant analysis of populations of 3-D multi-object sets. In view of the driving medical applications, a skelet al object parametrization of shape is chosen since it naturally encodes thickening, bending and twisting. In a multi-object setting, we not only consider a joint analysis of sets of shapes but also must take into account differences in pose. Statistics on features of medial descriptions and pose parameters, which include rotational frames and distances, uses a Riemannian symmetric space instead of the standard Euclidean metric. Our choice of discriminant method is the distance weighted discriminant (DWD) because of its generalization ability in high dimensional, low sample size settings. Joint analysis of 10 subcortical brain structures in a pediatric autism study demonstrates that multi-object analysis of shape results in a better group discrimination than pose, and that the combination of pose and shape performs better than shape alone. Finally, given a discriminating axis of shape and pose, we can visualize the differences between the populations. With the increasing prevalence of Alzheimer's disease, research focuses on the early computer-aided diagnosis of dementia with the goal to understand the disease process, determine risk and preserving factors, and explore preventive therapies. By now, large amounts of data from multi-site studies have been made available for developing, training, and evaluating automated classifiers. Yet, their translation to the clinic remains challenging, in part due to their limited generalizability across different datasets. In this work, we describe a compact classification approach that mitigates overfitting by regularizing the multinomial regression with the mixed l1 l2 norm. We combine volume, thickness, and anatomical shape features from MRI scans to characterize neuroanatomy for the three-class classification of Alzheimer's disease, mild cognitive impairment and healthy controls. We demonstrate high classification accuracy via independent evaluation within the scope of the CADDementia challenge. We, furthermore, demonstrate that variations between source and target datasets can substantially influence classification accuracy. The main contribution of this work addresses this problem by proposing an approach for supervised domain adaptation based on instance weighting. Integration of this method into our classifier allows us to assess different strategies for domain adaptation. Our results demonstrate (i) that training on only the target training set yields better results than the naive combination (union) of source and target training sets, and (ii) that domain adaptation with instance weighting yields the best classification results, especially if only a small training component of the target dataset is available. These insights imply that successful deployment of systems for computer-aided diagnostics to the clinic depends not only on accurate classifiers that avoid overfitting, but also on a dedicated domain adaptation strategy. Abstract Statistical analysis on arbitrary surface meshes such as the cortical surface is an important approach to understanding brain diseases such as Alzheimer's disease (AD). Surface analysis may be able to identify specific cortical patterns that relate to certain disease characteristics or exhibit differences between groups. Our goal in this paper is to make group analysis of signals on surfaces more sensitive. To do this, we derive multi-scale shape descriptors that characterize the signal around each mesh vertex, i.e., its local context, at varying levels of resolution. In order to define such a shape descriptor, we make use of recent results from harmonic analysis that extend traditional continuous wavelet theory from the Euclidean to a non-Euclidean setting (i.e., a graph, mesh or network). Using this descriptor, we conduct experiments on two different datasets, the Alzheimer's Disease NeuroImaging Initiative (ADNI) data and images acquired at the Wisconsin Alzheimer's Disease Research Center (W-ADRC), focusing on individuals labeled as having Alzheimer's disease (AD), mild cognitive impairment (MCI) and healthy controls. In particular, we contrast traditional univariate methods with our multi-resolution approach which show increased sensitivity and improved statistical power to detect a group-level effects. We also provide an open source implementation. Abstract The hippocampus is involved at the onset of the neuropathological pathways leading to Alzheimer's disease (AD). Individuals with mild cognitive impairment (MCI) are at increased risk of AD. Hippocampal volume has been shown to predict which MCI subjects will convert to AD. Our aim in the present study was to produce a fully automated prognostic procedure, scalable to high throughput clinical and research applications, for the prediction of MCI conversion to AD using 3D hippocampal morphology. We used an automated analysis for the extraction and mapping of the hippocampus from structural magnetic resonance scans to extract 3D hippocampal shape morphology, and we then applied machine learning classification to predict conversion from MCI to AD. We investigated the accuracy of prediction in 103 MCI subjects (mean age 74.1 years) from the longitudinal AddNeuroMed study. Our model correctly predicted MCI conversion to dementia within a year at an accuracy of 80 (sensitivity 77 , specificity 80 ), a performance which is competitive with previous predictive models dependent on manual measurements. Categorization of MCI subjects based on hippocampal morphology revealed more rapid cognitive deterioration in MMSE scores ( p p The hippocampus is affected at an early stage in the development of Alzheimer's disease (AD). With the use of structural magnetic resonance (MR) imaging, we can investigate the effect of AD on the morphology of the hippocampus. The hippocampal shape variations among a population can be usually described using statistical shape models (SSMs). Conventional SSMs model the modes of variations among the population via principal component analysis (PCA). Although these modes are representative of variations within the training data, they are not necessarily discriminative on labeled data or relevant to the differences between the subpopulations. We use the shape descriptors from SSM as features to classify AD from normal control (NC) cases. In this study, a Hotelling's T2 test is performed to select a subset of landmarks which are used in PCA. The resulting variation modes are used as predictors of AD from NC. The discrimination ability of these predictors is evaluated in terms of their classification performances with bagged support vector machines (SVMs). Restricting the model to landmarks with better separation between AD and NC increases the discrimination power of SSM. The predictors extracted on the subregions also showed stronger correlation with the memory-related measurements such as Logical Memory, Auditory Verbal Learning Test (AVLT) and the memory subscores of Alzheimer Disease Assessment Scale (ADAS).