Title: Brain structure segmentation using multiple MRI pulse sequences
Abstract: Medical image segmentation is the process of delineating anatomical structures of interest in images. Automatic segmentation algorithms applied to brain magnetic resonance images (MRI) allow for the processing of large volumes of data for the study of neurodegenerative diseases. Widely-used segmentation software packages only require T1-weighted (T1-w) MRI and segment cortical and subcortical structures, but are unable to segment structures that do not appear in T1-w MRI. Other MRI pulse sequences have properties that allow for the segmentation of structures that are invisible (or barely discernible) in T1-w MRI.
In this dissertation, three novel medical image segmentation algorithms are proposed to segment the following structures of interest: the thalamus; the falx and tentorium; and the meninges. The common theme that connects these segmentation algorithms is that they use information from multiple MRI pulse sequences because the structures they target are nearly invisible in T1-w MRI. Segmentation of these structures is used in the study of neurodegenerative diseases such as multiple sclerosis and for the development of computational models of the brain for the study of traumatic brain injury.
Our automatic thalamus and thalamic nuclei segmentation algorithm extracts features from T1-w MRI, T2-w MRI, and diffusion tensor imaging (DTI) to train a random forest classifier. Using a leave-one-out cross-validation on nine subjects, our algorithm achieves mean Dice coefficients of 0.897 and 0.902 for the left and right thalami, respectively, which are higher Dice scores than the three state-of-art methods we compared against.
Our falx and tentorium segmentation algorithm uses T1-w MRI and susceptibility-weighted imaging (SWI) to register multiple atlases and fuse their boundary points to generate a subject-specific falx and tentorium. Our method is compared against single-atlas approaches and achieves the lowest mean surface distance of 0.86 mm and 0.99 mm to a manually delineated falx and tentorium, respectively.
Our meninges reconstruction algorithm uses T1-w MRI, T2-w MRI, and a synthetic computed tomography (CT) image generated via convolutional neural network to find two layers of the meninges: the subarachnoid space and dura mater. We compare our method with other brain extraction and intracranial volume estimation algorithms. Our method produces a subarachnoid space segmentation with a mean Dice score of 0.991, which is comparable to the top-performing state-of-art method, and produces a dura mater segmentation with a mean Dice score of 0.983, which is the highest among the compared methods.