The subarachnoid space is a layer in the meninges that surrounds the brain and is filled with trabeculae and cerebrospinal fluid. Quantifying the volume and thickness of the subarachnoid space is of interest in order to study the pathogenesis of neurodegenerative diseases and compare with healthy subjects. We present an automatic method to reconstruct the subarachnoid space with subvoxel accuracy using a nested deformable model. The method initializes the deformable model using the convex hull of the union of the outer surfaces of the cerebrum, cerebellum and brainstem. A region force is derived from the subject’s T1-weighted and T2-weighted MRI to drive the deformable model to the outer surface of the subarachnoid space. The proposed method is compared to a semi-automatic delineation from the subject’s T2-weighted MRI and an existing multi-atlas-based method. A small pilot study comparing the volume and thickness measurements in a set of age-matched subjects with normal pressure hydrocephalus and healthy controls is presented to show the efficacy of the proposed method.
The falx cerebri and tentorium cerebelli are dural structures found in the brain. Due to the roles both structures play in constraining brain motion, the falx and tentorium must be identified and included in finite element models of the head to accurately predict brain dynamics during injury events. To date there has been very little research work on automatically segmenting these two structures, which is understandable given that their 1) thin structure challenges the resolution limits of in vivo 3D imaging, and 2) contrast with respect to surrounding tissue is low in standard magnetic resonance imaging. An automatic segmentation algorithm to find the falx and tentorium which uses the results of a multi-atlas segmentation and cortical reconstruction algorithm is proposed. Gray matter labels are used to find the location of the falx and tentorium. The proposed algorithm is applied to five datasets with manual delineations. 3D visualizations of the final results are provided, and Hausdorff distance (HD) and mean surface distance (MSD) is calculated to quantify the accuracy of the proposed method. For the falx, the mean HD is 43.84 voxels and the mean MSD is 2.78 voxels, with the largest errors occurring at the frontal inferior falx boundary. For the tentorium, the mean HD is 14.50 voxels and mean MSD is 1.38 voxels.
Automatic thalamus segmentation is useful to track changes in thalamic volume over time. In this work, we introduce a task-driven dictionary learning framework to find the optimal dictionary given a set of eleven features obtained from T1-weighted MRI and diffusion tensor imaging. In this dictionary learning framework, a linear classifier is designed concurrently to classify voxels as belonging to the thalamus or non-thalamus class. Morphological post-processing is applied to produce the final thalamus segmentation. Due to the uneven size of the training data samples for the non-thalamus and thalamus classes, a non-uniform sampling scheme is pro- posed to train the classifier to better discriminate between the two classes around the boundary of the thalamus. Experiments are conducted on data collected from 22 subjects with manually delineated ground truth. The experimental results are promising in terms of improvements in the Dice coefficient of the thalamus segmentation overstate-of-the-art atlas-based thalamus segmentation algorithms.
Segmentation of the thalamus and thalamic nuclei is useful to quantify volumetric changes from neurodegenerative diseases. Most thalamus segmentation algorithms only use T1-weighted magnetic resonance images and current thalamic parcellation methods require manual interaction. Smaller nuclei, such as the lateral and medial geniculates, are challenging to locate due to their small size. We propose an automated segmentation algorithm using a set of features derived from diffusion tensor image (DTI) and thalamic nuclei location priors. After extracting features, a hierarchical random forest classifier is trained to locate the thalamus. A second random forest classifies thalamus voxels as belonging to one of six thalamic nuclei classes. The proposed algorithm was tested using a leave-one-out cross validation scheme and compared with state-of-the-art algorithms. The proposed algorithm has a higher Dice score compared to other methods for the whole thalamus and several nuclei.
Block-transform lossy image compression is the most widely-used approach for compressing and storing images or video. A novel algorithm to restore highly compressed images with greater image quality is proposed. Since many block-transform coefficients are reduced to zero after quantization, the compressed image restoration problem can be treated as a sparse reconstruction problem where the original image is reconstructed based on sparse, degraded measurements in the form of highly quantized block-transform coefficients. The sparse reconstruction problem is solved by minimizing a homotopic regularized function, subject to data fidelity in the block-transform domain. Experimental results using compressed natural images at di erent levels of compression show improved performance by using the proposed algorithm compared to other methods.