Automated template-based brain localization and extraction for fetal brain MRI reconstruction.

Most fetal brain MRI reconstruction algorithms rely only on brain tissue-relevant voxels of low-resolution (LR) images to enhance the quality of inter-slice motion correction and image reconstruction. Consequently the fetal brain needs to be localized and extracted as a first step, which is usually a laborious and time consuming manual or semi-automatic task. We have proposed in this work to use age-matched template images as prior knowledge to automatize brain localization and extraction. This has been achieved through a novel automatic brain localization and extraction method based on robust template-to-slice block matching and deformable slice-to-template registration. Our template-based approach has also enabled the reconstruction of fetal brain images in standard radiological anatomical planes in a common coordinate space. We have integrated this approach into our new reconstruction pipeline that involves intensity normalization, inter-slice motion correction, and super-resolution (SR) reconstruction. To this end we have adopted a novel approach based on projection of every slice of the LR brain masks into the template space using a fusion strategy. This has enabled the refinement of brain masks in the LR images at each motion correction iteration. The overall brain localization and extraction algorithm has shown to produce brain masks that are very close to manually drawn brain masks, showing an average Dice overlap measure of 94.5%. We have also demonstrated that adopting a slice-to-template registration and propagation of the brain mask slice-by-slice leads to a significant improvement in brain extraction performance compared to global rigid brain extraction and consequently in the quality of the final reconstructed images. Ratings performed by two expert observers show that the proposed pipeline can achieve similar reconstruction quality to reference reconstruction based on manual slice-by-slice brain extraction. The proposed brain mask refinement and reconstruction method has shown to provide promising results in automatic fetal brain MRI segmentation and volumetry in 26 fetuses with gestational age range of 23 to 38 weeks.

Spatially constrained incoherent motion method improves diffusion-weighted MRI signal decay analysis in the liver and spleen.

PURPOSE: To evaluate the effect of the spatially constrained incoherent motion (SCIM) method on improving the precision and robustness of fast and slow diffusion parameter estimates from diffusion-weighted MRI in liver and spleen in comparison to the independent voxel-wise intravoxel incoherent motion (IVIM) model. METHODS: We collected diffusion-weighted MRI (DW-MRI) data of 29 subjects (5 healthy subjects and 24 patients with Crohn's disease in the ileum). We evaluated parameters estimates' robustness against different combinations of b-values (i.e., 4 b-values and 7 b-values) by comparing the variance of the estimates obtained with the SCIM and the independent voxel-wise IVIM model. We also evaluated the improvement in the precision of parameter estimates by comparing the coefficient of variation (CV) of the SCIM parameter estimates to that of the IVIM. RESULTS: The SCIM method was more robust compared to IVIM (up to 70% in liver and spleen) for different combinations of b-values. Also, the CV values of the parameter estimations using the SCIM method were significantly lower compared to repeated acquisition and signal averaging estimated using IVIM, especially for the fast diffusion parameter in liver (CVIV IM = 46.61 ± 11.22, CVSCIM = 16.85 ± 2.160, p < 0.001) and spleen (CVIV IM = 95.15 ± 19.82, CVSCIM = 52.55 ± 1.91, p < 0.001). CONCLUSIONS: The SCIM method characterizes fast and slow diffusion more precisely compared to the independent voxel-wise IVIM model fitting in the liver and spleen.

Passive fMRI mapping of language function for pediatric epilepsy surgical planning: validation using Wada, ECS, and FMAER.

In this study we validate passive language fMRI protocols designed for clinical application in pediatric epilepsy surgical planning as they do not require overt participation from patients. We introduced a set of quality checks that assess reliability of noninvasive fMRI mappings utilized for clinical purposes. We initially compared two fMRI language mapping paradigms, one active in nature (requiring participation from the patient) and the other passive in nature (requiring no participation from the patient). Group-level analysis in a healthy control cohort demonstrated similar activation of the putative language centers of the brain in the inferior frontal (IFG) and temporoparietal (TPG) regions. Additionally, we showed that passive language fMRI produced more left-lateralized activation in TPG (LI=+0.45) compared to the active task; with similarly robust left-lateralized IFG (LI=+0.24) activations using the passive task. We validated our recommended fMRI mapping protocols in a cohort of 15 pediatric epilepsy patients by direct comparison against the invasive clinical gold-standards. We found that language-specific TPG activation by fMRI agreed to within 9.2mm to subdural localizations by invasive functional mapping in the same patients, and language dominance by fMRI agreed with Wada test results at 80% congruency in TPG and 73% congruency in IFG. Lastly, we tested the recommended passive language fMRI protocols in a cohort of very young patients and confirmed reliable language-specific activation patterns in that challenging cohort. We concluded that language activation maps can be reliably achieved using the passive language fMRI protocols we proposed even in very young (average 7.5 years old) or sedated pediatric epilepsy patients.

Electrode localization for planning surgical resection of the epileptogenic zone in pediatric epilepsy.

PURPOSE: In planning for a potentially curative resection of the epileptogenic zone in patients with pediatric epilepsy, invasive monitoring with intracranial EEG is often used to localize the seizure onset zone and eloquent cortex. A precise understanding of the location of subdural strip and grid electrodes on the brain surface, and of depth electrodes in the brain in relationship to eloquent areas is expected to facilitate pre-surgical planning. METHODS: We developed a novel algorithm for the alignment of intracranial electrodes, extracted from post-operative CT, with pre-operative MRI. Our goal was to develop a method of achieving highly accurate localization of subdural and depth electrodes, in order to facilitate surgical planning. Specifically, we created a patient-specific 3D geometric model of the cortical surface from automatic segmentation of a pre-operative MRI, automatically segmented electrodes from post-operative CT, and projected each set of electrodes onto the brain surface after alignment of the CT to the MRI. Also, we produced critical visualization of anatomical landmarks, e.g., vasculature, gyri, sulci, lesions, or eloquent cortical areas, which enables the epilepsy surgery team to accurately estimate the distance between the electrodes and the anatomical landmarks, which might help for better assessment of risks and benefits of surgical resection. RESULTS: Electrode localization accuracy was measured using knowledge of the position of placement from 2D intra-operative photographs in ten consecutive subjects who underwent intracranial EEG for pediatric epilepsy. Average spatial accuracy of localization was 1.31 ± 0.69 mm for all 385 visible electrodes in the photos. CONCLUSIONS: In comparison with previously reported approaches, our algorithm is able to achieve more accurate alignment of strip and grid electrodes with minimal user input. Unlike manual alignment procedures, our algorithm achieves excellent alignment without time-consuming and difficult judgements from an operator.

Visualization of shape motions in shape space.

Analysis of dynamic object deformations such as cardiac motion is of great importance, especially when there is a necessity to visualize and compare the deformation behavior across subjects. However, there is a lack of effective techniques for comparative visualization and assessment of a collection of motion data due to its 4-dimensional nature, i.e., timely varying three-dimensional shapes. From the geometric point of view, the motion change can be considered as a function defined on the 2D manifold of the surface. This paper presents a novel classification and visualization method based on a medial surface shape space, in which two novel shape descriptors are defined, for discriminating normal and abnormal human heart deformations as well as localizing the abnormal motion regions. In our medial surface shape space, the geodesic distance connecting two points in the space measures the similarity between their corresponding medial surfaces, which can quantify the similarity and disparity of the 3D heart motions. Furthermore, the novel descriptors can effectively localize the inconsistently deforming myopathic regions on the left ventricle. An easy visualization of heart motion sequences on the projected space allows users to distinguish the deformation differences. Our experimental results on both synthetic and real imaging data show that this method can automatically classify the healthy and myopathic subjects and accurately detect myopathic regions on the left ventricle, which outperforms other conventional cardiac diagnostic methods.

Segmentation of cell nuclei in heterogeneous microscopy images: a reshapable templates approach.

Histological tissue images typically exhibit very sophisticated spatial color patterns. It is of great clinical importance to extract qualitative and quantitative information from these images. As an ad hoc solution, various unsupervised approaches address the object detection and segmentation problem which are suitable for limited classes of histology images. In this paper, we propose a general purpose localization and segmentation method which utilizes reshapable templates. The method combines both pixel- and object-level features for detecting regions of interest. Segmentation is carried out in two levels including both the coarse and fine ones. A set of simple-shaped templates is used for coarse segmentation. A content based template reshaping algorithm is proposed for fine segmentation of target objects. Experimentation was done using a publicly available image data set which contains 7931 manually labeled cells of heterogeneous histology images. The experiments have demonstrated acceptable level of detection and segmentation results for the proposed approach (precision=0.904, recall=0.870 and Zijdenbos similarity index=73%). Thus, the prototype software developed based on proposed method can be considered as a potential tool for pathologists in clinical process.

Colon segmentation for prepless virtual colonoscopy.

A novel segmentation framework for a prepless virtual colonoscopy (VC) is presented, which reduces the necessity for colon cleansing before the CT scan. The patient is injected rectally with a water-soluble iodinated contrast medium using manual insufflators and a small rectal catheter. Compared to the air-based contrast medium, this technique can better preserve the color lumen and reduce the partial volume effect. However, the contrast medium, together with the fecal materials and air, makes colon wall segmentation challenging. Our solution makes no assumptions about the shape, size, and location of the fecal material in the colon. This generality allows us to label the fecal material accurately and extract the colon wall reliably. The accuracy of our technique has been verified on 60 human subjects. Compared with current VC technologies, our method is shown to be better in terms of both sensitivity and specificity. Further, in our experiments, the accuracy of the technique was comparable to that of optical colonoscopy results.

Comparative analysis of quasi-conformal deformations in shape space.

A novel approach based on the shape space concept is proposed to classify quasi-conformal deformations of 3D models. A new metric on the quotient space of meshes is introduced to capture changes of the curvature at each vertex of a simplicial complex during deformation. Then, the deformation curve is obtained by calculating the geodesic curve connecting two shapes in the shape space manifold. In order to compare the deformations, the deformation curves are first transferred to the same part of shape space. And then, the Multi-Dimensional Scaling method is employed to eliminate the redundant dimensions facilitating easy comparison of the deformations. To evaluate our method, some synthetic datasets and 23 datasets of gated images of the left heart ventricle during one heartbeat have been examined. Our experiments show that the algorithm can effectively classify normal and abnormal left heart ventricle deformations in shape space.

Web-based interactive 2D/3D medical image processing and visualization software.

There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies.