Evaluation of atlas-based segmentation of hippocampi in healthy humans

Introduction and aim: Region of interest (ROI)-based functional magnetic resonance imaging (fMRI) data analysis relies on extracting signals from a specific area which is presumed to be involved in the brain activity being studied. The hippocampus is of interest in many functional connectivity studies for example in epilepsy as it plays an important role in epileptogenesis. In this context, ROI may be defined using different techniques. Our study aims at evaluating the spatial correspondence of hippocampal ROIs obtained using three brain atlases with hippocampal ROI obtained using an automatic segmentation algorithm dedicated to the hippocampus. Material and methods: High-resolution volumetric T1-weighted MR images of 18 healthy volunteers (five females) were acquired on a 3T scanner. Individual ROIs for both hippocampi of each subject were segmented from the MR images using an automatic hippocampus and amygdala segmentation software called SACHA providing the gold standard ROI for comparison with the atlas-derived results. For each subject, hippocampal ROIs were also obtained using three brain atlases: PickAtlas available as a commonly used software toolbox; automated anatomical labeling (AAL) atlas included as a subset of ROI into PickAtlas toolbox and a frequency-based brain atlas by Hammers et al. The levels of agreement between the SACHA results and those obtained using the atlases were assessed based on quantitative indices measuring volume differences and spatial overlap. The comparison was performed in standard Montreal Neurological Institute space, the registration being obtained with SPM5 (http://www.fil.ion.ucl.ac.uk/spm/). Results: The mean volumetric error across all subjects was 73% for hippocampal ROIs derived from AAL atlas; 20% in case of ROIs derived from the Hammers atlas and 107% for ROIs derived from PickAtlas. The mean false-positive and false-negative classification rates were 60% and 10% respectively for the AAL atlas; 16% and 32% for the Hammers atlas and 6% and 72% for the PickAtlas. Conclusion: Though atlas-based ROI definition may be convenient, the resulting ROIs may be poor representations of the hippocampus in some studies critical to under- or oversampling. Performance of the AAL atlas was inferior to that of the Hammers atlas. Hippocampal ROIs derived from PickAtlas are highly significantly smaller, and this results in the worst performance out of three atlases. It is advisable that the defined ROIs should be verified with knowledge of neuroanatomy before using it for further data analysis

EchoFusion: Tracking and Reconstruction of Objects in 4D Freehand Ultrasound Imaging without External Trackers

Ultrasound (US) is the most widely used fetal imaging technique. However, US images have limited capture range, and suffer from view dependent artefacts such as acoustic shadows. Compounding of overlapping 3D US acquisitions into a high-resolution volume can extend the field of view and remove image artefacts, which is useful for retrospective analysis including population based studies. However, such volume reconstructions require information about relative transformations between probe positions from which the individual volumes were acquired. In prenatal US scans, the fetus can move independently from the mother, making external trackers such as electromagnetic or optical tracking unable to track the motion between probe position and the moving fetus. We provide a novel methodology for image-based tracking and volume reconstruction by combining recent advances in deep learning and simultaneous localisation and mapping (SLAM). Tracking semantics are established through the use of a Residual 3D U-Net and the output is fed to the SLAM algorithm. As a proof of concept, experiments are conducted on US volumes taken from a whole body fetal phantom, and from the heads of real fetuses. For the fetal head segmentation, we also introduce a novel weak annotation approach to minimise the required manual effort for ground truth annotation. We evaluate our method qualitatively, and quantitatively with respect to tissue discrimination accuracy and tracking robustness.Comment: MICCAI Workshop on Perinatal, Preterm and Paediatric Image analysis (PIPPI), 201

Placental Flattening via Volumetric Parameterization

We present a volumetric mesh-based algorithm for flattening the placenta to a canonical template to enable effective visualization of local anatomy and function. Monitoring placental function in vivo promises to support pregnancy assessment and to improve care outcomes. We aim to alleviate visualization and interpretation challenges presented by the shape of the placenta when it is attached to the curved uterine wall. To do so, we flatten the volumetric mesh that captures placental shape to resemble the well-studied ex vivo shape. We formulate our method as a map from the in vivo shape to a flattened template that minimizes the symmetric Dirichlet energy to control distortion throughout the volume. Local injectivity is enforced via constrained line search during gradient descent. We evaluate the proposed method on 28 placenta shapes extracted from MRI images in a clinical study of placental function. We achieve sub-voxel accuracy in mapping the boundary of the placenta to the template while successfully controlling distortion throughout the volume. We illustrate how the resulting mapping of the placenta enhances visualization of placental anatomy and function. Our code is freely available at https://github.com/mabulnaga/placenta-flattening .Comment: MICCAI 201

Evaluation of local and global atrophy measurement techniques with simulated Alzheimer's disease data

The main goal of this work was to evaluate several well-known methods which provide global (BSI and SIENA) or local (Jacobian integration) estimates of atrophy in brain structures using Magnetic Resonance images. For that purpose, we have generated realistic simulated Alzheimer's disease images in which volume changes are modelled with a Finite Element thermoelastic model, which mimic the patterns of change obtained from a cohort of 19 real controls and 27 probable Alzheimer's disease patients. SIENA and BSI results correlate very well with gold standard data (BSI mean absolute error <0.29%; SIENA <0.44%). Jacobian integration was guided by both fluid and FFD-based registration techniques and resulting deformation fields and associated Jacobians were compared, region by region, with gold standard ones. The FFD registration technique provided more satisfactory results than the fluid one. Mean absolute error differences between volume changes given by the FFD-based technique and the gold standard were: sulcal CSF <2.49%; lateral ventricles 2.25%; brain <0.36%; hippocampi <0.42%

Structural abnormalities in cortical volume, thickness, and surface area in 22q11.2 microdeletion syndrome: Relationship with psychotic symptoms.

Introduction22q11.2 deletion syndrome (22q11DS) represents one of the largest known genetic risk factors for psychosis, yet the neurobiological mechanisms underlying symptom development are not well understood. Here we conducted a cross-sectional study of 22q11DS to decompose cortical volume into its constituent parts, cortical thickness (CT) and surface area (SA), which are believed to have distinct neurodevelopmental origins.MethodsHigh-resolution T1-weighted scans were collected on 65 participants (31 22q11DS, 34 demographically comparable typically developing controls, 10-25&nbsp;years old). Measures of cortical volume, CT, and SA were extracted from regions of interest using the FreeSurfer image analysis suite. Group differences and age-related trajectories in these structures, as well as their association with psychotic symptomatology, were assessed.ResultsRelative to controls, 22q11DS participants showed bilateral volumetric reductions in the inferior temporal cortex, fusiform gyrus, anterior cingulate, superior parietal cortex, and cuneus, which were driven by decreased SA in these regions. 22q11DS participants also had increased volumes, driven by increased CT, in bilateral insula regions. 22q11DS youth had increased CT in frontal regions, particularly middle frontal and medial orbitofrontal cortices. A pattern of age-associated cortical thinning was observed in typically developing controls in brain regions associated with visual and sensory information-processing (i.e., left pericalcarine cortex and fusiform gyrus, right lingual and postcentral cortices). However, this relationship was disrupted in 22q11DS participants. Finally, correlational analyses revealed that increased CT in right medial orbitofrontal cortex was associated with increased positive symptom severity in 22q11DS.ConclusionDifferential disruptions of CT and SA in distinct cortical regions in 22q11DS may indicate abnormalities in distinct developmental neural processes. Further, neuroanatomic abnormalities in medial frontal brain structures disproportionately affected in idiopathic schizophrenia were associated with psychotic symptom severity in 22q11DS youth, suggesting that disrupted biological processes in these cortical regions may underlie development of psychotic symptoms, both in 22q11DS and in the broader population

Accuracy assessment of global and local atrophy measurement techniques with realistic simulated longitudinal data

The main goal of this work was to assess the accuracy of several well-known methods which provide global (BSI and SIENA) or local (Jacobian integration) estimates of longitudinal atrophy in brain structures using Magnetic Resonance images. For that purpose, we have generated realistic simulated images which mimic the patterns of change obtained from a cohort of 19 real controls and 27 probable Alzheimer's disease patients. SIENA and BSI results correlate very well with gold standard data (BSI mean absolute error < 0.29%; SIENA < 0.44%). Jacobian integration was guided by both fluid and FFD-based registration techniques and resulting deformation fields and associated Jacobians were compared, region by region, with gold standard ones. The FFD registration technique provided more satisfactory results than the fluid one. Mean absolute error differences between volume changes given by the FFD-based technique and the gold standard were: sulcal CSF < 2.49%; lateral ventricles < 2.25%; brain < 0.36%; hippocampi < 1.42%

Structural brain complexity and cognitive decline in late life : A longitudinal study in the Aberdeen 1936 Birth Cohort

Copyright © 2014 Elsevier Inc. All rights reserved.Peer reviewedPostprin