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Browsing by Author "Efird, Cory"

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    Automatic deep learning segmentation of the hippocampus on high resolution diffusion MRI and its application to the healthy lifespan
    (2024) Efird, Cory; Neumann, Samuel; Solar, Kevin; Beaulieu, Christian; Cobzas, Dana; Miller, Dylan
    Diffusion tensor imaging (DTI) can provide unique contrast and insight into microstructural changes with age or disease of the hippocampus, although it is difficult to measure the hippocampus because of its comparatively small size, location, and shape. This has been markedly improved by the advent of a clinically feasible 1-mm isotropic resolution 6-min DTI protocol at 3 T of the hippocampus with limited brain coverage of 20 axial-oblique slices aligned along its long axis. However, manual segmentation is too laborious for large population studies, and it cannot be automatically segmented directly on the diffusion images using traditional T1 or T2 image-based methods because of the limited brain coverage and different contrast. An automatic method is proposed here that segments the hippocampus directly on high-resolution diffusion images based on an extension of well-known deep learning architectures like UNet and UNet++ by including additional dense residual connections. The method was trained on 100 healthy participants with previously performed manual segmentation on the 1-mm DTI, then evaluated on typical healthy participants (n = 53), yielding an excellent voxel overlap with a Dice score of ~ 0.90 with manual segmentation; notably, this was comparable with the inter-rater reliability of manually delineating the hippocampus on diffusion magnetic resonance imaging (MRI) (Dice score of 0.86). This method also generalized to a different DTI protocol with 36% fewer acquisitions. It was further validated by showing similar age trajectories of volumes, fractional anisotropy, and mean diffusivity from manual segmentations in one cohort (n = 153, age 5–74 years) with automatic segmentations from a second cohort without manual segmentations (n = 354, age 5–90 years). Automated high-resolution diffusion MRI segmentation of the hippocampus will facilitate large cohort analyses and, in future research, needs to be evaluated on patient groups.
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    Creative, interdisciplinary undergraduate research: an educational cell biology video game designed by students for students
    (2020) Sperano, Isabelle; Shaw, Ross W.; Andruchow, Robert; Cobzas, Dana; Efird, Cory; Brookwell, Brian; Deng, William
    In a three-year, practice-based, creative research project, the team designed a video game for undergraduate biology students that aimed to find the right balance between educational content and entertainment. The project involved 7 faculty members and 14 undergraduate students from biological science, design, computer science, and music. This nontraditional approach to research was attractive to students. Working on an interdisciplinary practice-based research project required strategies related to timeline, recruitment, funding, team management, and mentoring. Although this project was time-consuming and full of challenges, it created meaningful learning experiences not only for students but also for faculty members.
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    Hippocampus segmentation on high resolution dffusion MRI
    (2021) Efird, Cory; Neumann, Samuel; Solar, Kevin G.; Beaulieu, Christian; Cobzas, Dana
    We introduce the first hippocampus segmentation method for a novel high resolution (1×1×1mm3) diffusion tensor imaging (DTI) protocol acquired in 5.5 minutes at 3T. A new augmentation technique uses subsets of the DTI dataset to create mean diffusion weighted images (DWI) with plausible noise and contrast variations. The augmented DWI along with fractional anisotropy (FA) and mean diffusivity (MD) maps are used as inputs to a powerful convolutional neural network architecture. The method is evaluated for robustness using a second diffusion protocol.
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    A UNet pipeline for segmentation of new MS lesions
    (2021) Efird, Cory; Miller, Dylan; Cobzas, Dana
    A pipeline for the second multiple sclerosis segmentation challenge (MSSEG-2) hosted by MICCAI is proposed. Two FLAIR images taken at different time-points are used as a multi-channel input to a 3D CNN to detect new lesions. Patch sampling strategies are adopted to keep the input volume shape manageable in terms of memory requirements. To further improve results, multiple models and patch orientations are ensembled. Performance is evaluated against nn-UNet.