When processing large medical imaging studies, adopting high performance grid computing resources rapidly becomes important. We recently presented a "medical image processing-as-a-service" grid framework that offers promise in utilizing the Apache Hadoop ecosystem and HBase for data colocation by moving computation close to medical image storage. However, the framework has not yet proven to be easy to use in a heterogeneous hardware environment. Furthermore, the system has not yet validated when considering variety of multi-level analysis in medical imaging. Our target design criteria are (1) improving the framework’s performance in a heterogeneous cluster, (2) performing population based summary statistics on large datasets, and (3) introducing a table design scheme for rapid NoSQL query. In this paper, we present a heuristic backend interface application program interface (API) design for Hadoop and HBase for Medical Image Processing (HadoopBase-MIP). The API includes: Upload, Retrieve, Remove, Load balancer (for heterogeneous cluster) and MapReduce templates. A dataset summary statistic model is discussed and implemented by MapReduce paradigm. We introduce a HBase table scheme for fast data query to better utilize the MapReduce model. Briefly, 5153 T1 images were retrieved from a university secure, shared web database and used to empirically access an in-house grid with 224 heterogeneous CPU cores. Three empirical experiments results are presented and discussed: (1) load balancer wall-time improvement of 1.5-fold compared with a framework with built-in data allocation strategy, (2) a summary statistic model is empirically verified on grid framework and is compared with the cluster when deployed with a standard Sun Grid Engine (SGE), which reduces 8-fold of wall clock time and 14-fold of resource time, and (3) the proposed HBase table scheme improves MapReduce computation with 7 fold reduction of wall time compare with a naïve scheme when datasets are relative small. The source code and interfaces have been made publicly available.
Sulcal depth is an important marker of brain anatomy in neuroscience/neurological function. Previously, sulcal depth has been explored at the region-of-interest (ROI) level to increase statistical sensitivity to group differences. In this paper, we present a fully automated method that enables inferences of ROI properties from a sulcal region- focused perspective consisting of two main components: 1) sulcal depth computation and 2) sulcal curve-based refined ROIs. In conventional statistical analysis, the average sulcal depth measurements are employed in several ROIs of the cortical surface. However, taking the average sulcal depth over the full ROI blurs overall sulcal depth measurements which may result in reduced sensitivity to detect sulcal depth changes in neurological and psychiatric disorders. To overcome such a blurring effect, we focus on sulcal fundic regions in each ROI by filtering out other gyral regions. Consequently, the proposed method results in more sensitive to group differences than a traditional ROI approach. In the experiment, we focused on a cortical morphological analysis to sulcal depth reduction in schizophrenia with a comparison to the normal healthy control group. We show that the proposed method is more sensitivity to abnormalities of sulcal depth in schizophrenia; sulcal depth is significantly smaller in most cortical lobes in schizophrenia compared to healthy controls (p < 0.05).
Abdominal image segmentation is a challenging, yet important clinical problem. Variations in body size, position, and relative organ positions greatly complicate the segmentation process. Historically, multi-atlas methods have achieved leading results across imaging modalities and anatomical targets. However, deep learning is rapidly overtaking classical approaches for image segmentation. Recently, Zhou et al. showed that fully convolutional networks produce excellent results in abdominal organ segmentation of computed tomography (CT) scans. Yet, deep learning approaches have not been applied to whole abdomen magnetic resonance imaging (MRI) segmentation. Herein, we evaluate the applicability of an existing fully convolutional neural network (FCNN) designed for CT imaging to segment abdominal organs on T2 weighted (T2w) MRI’s with two examples. In the primary example, we compare a classical multi-atlas approach with FCNN on forty-five T2w MRI’s acquired from splenomegaly patients with five organs labeled (liver, spleen, left kidney, right kidney, and stomach). Thirty-six images were used for training while nine were used for testing. The FCNN resulted in a Dice similarity coefficient (DSC) of 0.930 in spleens, 0.730 in left kidneys, 0.780 in right kidneys, 0.913 in livers, and 0.556 in stomachs. The performance measures for livers, spleens, right kidneys, and stomachs were significantly better than multi-atlas (p < 0.05, Wilcoxon rank-sum test). In a secondary example, we compare the multi-atlas approach with FCNN on 138 distinct T2w MRI’s with manually labeled pancreases (one label). On the pancreas dataset, the FCNN resulted in a median DSC of 0.691 in pancreases versus 0.287 for multi-atlas. The results are highly promising given relatively limited training data and without specific training of the FCNN model and illustrate the potential of deep learning approaches to transcend imaging modalities. 1
The choice of surface template plays an important role in cross-sectional subject analyses involving cortical brain surfaces because there is a tendency toward registration bias given variations in inter-individual and inter-group sulcal and gyral patterns. In order to account for the bias and spatial smoothing, we propose a feature-based unbiased average template surface. In contrast to prior approaches, we factor in the sample population covariance and assign weights based on feature information to minimize the influence of covariance in the sampled population. The mean surface is computed by applying the weights obtained from an inverse covariance matrix, which guarantees that multiple representations from similar groups (e.g., involving imaging, demographic, diagnosis information) are down-weighted to yield an unbiased mean in feature space. Results are validated by applying this approach in two different applications. For evaluation, the proposed unbiased weighted surface mean is compared with un-weighted means both qualitatively and quantitatively (mean squared error and absolute relative distance of both the means with baseline). In first application, we validated the stability of the proposed optimal mean on a scan-rescan reproducibility dataset by incrementally adding duplicate subjects. In the second application, we used clinical research data to evaluate the difference between the weighted and unweighted mean when different number of subjects were included in control versus schizophrenia groups. In both cases, the proposed method achieved greater stability that indicated reduced impacts of sampling bias. The weighted mean is built based on covariance information in feature space as opposed to spatial location, thus making this a generic approach to be applicable to any feature of interest.
We present a group-wise shape correspondence method for analyzing variable and complex objects in a population study. The proposed method begins with the standard spherical harmonics (SPHARM) point distribution models (PDM) with their spherical mappings. In case of complex and variable objects, the equal area spherical mapping based SPHARM correspondence is imperfect. For such objects, we present here a novel group-wise correspondence. As an example dataset, we use 12 second mandibular molars representing 6 living or fossil euarchontan species. To improve initial correspondence of the SPHARM-PDM representation, we first apply a rigid transformation on each subject using five well-known landmarks (molar cusps). We further enhance the correspondence by optimizing landmarks (local) and multidimensional geometric property (global) over each subject with spherical harmonic representation. The resulting average shape model better captures sharp landmark representation in quantitative evaluation as well as a nice separation of different species compared with that of the SPHARM-PDM method.
High Angular Resolution Diffusion Imaging (HARDI) models are used to capture complex intra-voxel microarchitectures. The magnetic resonance imaging sequences that are sensitized to diffusion are often highly accelerated and prone to motion, physiologic, and imaging artifacts. In diffusion tensor imaging, robust statistical approaches have been shown to greatly reduce these adverse factors without human intervention. Similar approaches would be possible with HARDI methods, but robust versions of each distinct HARDI approach would be necessary. To avoid the computational and pragmatic burdens of creating individual robust HARDI analysis variants, we propose a robust outlier imputation model to mitigate outliers prior to traditional HARDI analysis. This model uses a weighted spherical harmonic fit of diffusion weighted magnetic resonance imaging scans to estimate the values which had been corrupted during acquisition to restore them. Briefly, spherical harmonics of 6th order were used to generate basis function which were weighted by diffusion signal for detection of outliers. For validation, a single healthy volunteer was scanned for a single session comprising of two scans one without head movement and the other with deliberate head movement at a b-value of 3000 s/mm2 with 64 diffusion weighted directions with a single b0 (5 averages) per scan. The deliberate motion from the volunteer created natural artifacts in the acquisition of one of the scans. The imputation model shows reduction in root mean squared error of the raw signal intensities and improvement for the HARDI method Q-ball in terms of the Angular Correlation Coefficient. The results reveal that there is quantitative and qualitative improvement. The proposed model can be used as general pre-processing model before implementing any HARDI model in general to restore the artifacts which are created because of the outlier diffusion signal in certain gradient volumes.
The recognition of sulcal regions on the cortical surface is an important task to shape analysis and landmark detection. However, it is challenging especially in a complex, rough human cortex. In this paper, we focus on the extraction of sulcal curves from the human cortical surface. The previous sulcal extraction methods are time-consuming in practice and often have a difficulty to delineate curves correctly along the sulcal regions in the presence of significant noise. Our pipeline is summarized in two main steps: 1) We extract candidate sulcal points spread over the sulcal regions. We further reduce the size of the candidate points by applying a line simplification method. 2) Since the candidate points are potentially located away from the exact valley regions, we propose a novel approach to connect candidate sulcal points so as to obtain a set of complete curves (line segments). We have shown in experiment that our method achieves high computational efficiency, improved robustness to noise, and high reliability in a test-retest situation as compared to a well-known existing method.
We propose a novel multi-atlas segmentation method that employs a group-wise image registration method for the brain segmentation on rodent magnetic resonance (MR) images. The core element of the proposed segmentation is the use of a particle-guided image registration method that extends the concept of particle correspondence into the volumetric image domain. The registration method performs a group-wise image registration that simultaneously registers a set of images toward the space defined by the average of particles. The particle-guided image registration method is robust with low signal-to-noise ratio images as well as differing sizes and shapes observed in the developing rodent brain. Also, the use of an implicit common reference frame can prevent potential bias induced by the use of a single template in the segmentation process. We show that the use of a particle guided-image registration method can be naturally extended to a novel multi-atlas segmentation method and improves the registration method to explicitly use the provided template labels as an additional constraint. In the experiment, we show that our segmentation algorithm provides more accuracy with multi-atlas label fusion and stability against pair-wise image registration. The comparison with previous group-wise registration method is provided as well.
In this work, we present a novel cortical correspondence method with application to the macaque brain. The correspondence method is based on sulcal curve constraints on a spherical deformable registration using spherical harmonics to parameterize the spherical deformation. Starting from structural MR images, we first apply existing preprocessing steps: brain tissue segmentation using the Automatic Brain Classification tool (ABC), as well as cortical surface reconstruction and spherical parametrization of the cortical surface via Constrained Laplacian-based Automated Segmentation with Proximities (CLASP). Then, initial correspondence between two cortical surfaces is automatically determined by a curve labeling method using sulcal landmarks extracted along sulcal fundic regions. Since the initial correspondence is limited to sulcal regions, we use spherical harmonics to extrapolate and regularize this correspondence to the entire cortical surface. To further improve the correspondence, we compute a spherical registration that optimizes the spherical harmonic parameterized deformation using a metric that incorporates the error over the sulcal landmarks as well as the normalized cross correlation of sulcal depth maps over the whole cortical surface. For evaluation, a normal 18-months-old macaque brain (for both left and right hemispheres) was matched to a prior macaque brain template with 9 manually labeled, major sulcal curves. The results show successful registration using the proposed registration approach. Evaluation results for optimal parameter settings are presented as well.