Building a Surface Atlas of Hippocampal Subfields from MRI Scans using FreeSurfer, FIRST and SPHARM

The hippocampus is widely studied with neuroimaging techniques given its importance in learning and memory and its potential as a biomarker for brain disorders such as Alzheimer's disease and epilepsy. However, its complex folding anatomy often presents analytical challenges. In particular, the critical hippocampal subfield information is usually ignored by hippocampal registration in detailed morphometric studies. Such an approach is thus inadequate to accurately characterize hippocampal morphometry and effectively identify hippocampal structural changes related to different conditions. To bridge this gap, we present our initial effort towards building a computational framework for subfield-guided hippocampal morphometry. This initial effort is focused on surface-based morphometry and aims to build a surface atlas of hippocampal subfields. Using the FreeSurfer software package, we obtain valuable hippocampal subfield information. Using the FIRST software package, we extract reliable hippocampal surface information. Using SPHARM, we develop an approach to create an atlas by mapping interpolated subfield information onto an average surface. The empirical result using ADNI data demonstrates the promise and good reproducibility of the proposed method

Automated Segmentation of Hippocampal Subfields From Ultra-High Resolution In Vivo MRI

Recent developments in MRI data acquisition technology are starting to yield images that show anatomical features of the hippocampal formation at an unprecedented level of detail, providing the basis for hippocampal subfield measurement. However, a fundamental bottleneck in MRI studies of the hippocampus at the subfield level is that they currently depend on manual segmentation, a laborious process that severely limits the amount of data that can be analyzed. In this article, we present a computational method for segmenting the hippocampal subfields in ultra-high resolution MRI data in a fully automated fashion. Using Bayesian inference, we use a statistical model of image formation around the hippocampal area to obtain automated segmentations. We validate the proposed technique by comparing its segmentations to corresponding manual delineations in ultra-high resolution MRI scans of 10 individuals, and show that automated volume measurements of the larger subfields correlate well with manual volume estimates. Unlike manual segmentations, our automated technique is fully reproducible, and fast enough to enable routine analysis of the hippocampal subfields in large imaging studies.National Institutes of Health (U.S.) (NIH NCRR; Grant number: P41-RR14075)National Institutes of Health (U.S.) (Grant R01 RR16594-01A1)National Institutes of Health (U.S.) (Grant NAC P41-RR13218)Biomedical Informatics Research Network (BIRN002)Biomedical Informatics Research Network (U24 RR021382)National Institute of Biomedical Imaging and Bioengineering (U.S.) (R01 EB001550)National Institute of Biomedical Imaging and Bioengineering (U.S.) (R01EB006758)National Institute of Biomedical Imaging and Bioengineering (U.S.) (NAMIC U54-EB005149)National Institute of Neurological Disorders and Stroke (U.S.) (R01 NS052585-01)National Institute of Neurological Disorders and Stroke (U.S.) (R01 NS051826)Mental Illness and Neuroscience Discovery (MIND) InstituteEllison Medical Foundation (Autism & Dyslexia Project

FKBP5 Modulates Attention Bias for Threat: Associations with Hippocampal Function and Morphology

Context: The FKBP5 gene product regulates glucocorticoid receptor (GR) sensitivity and hypothalamicpituitary‐adrenal axis functioning, and has been associated with a number of stress‐related psychiatric disorders. The study of intermediate phenotypes, such as emotion‐processing biases and their neural substrates, provides a way to clarify the mechanisms by which FKBP5 dysregulation mediates psychopathology risk. Objective: To examine whether allelic variations for a putatively functional SNP associated with FKBP5 gene regulation (rs1360780) would relate differentially to attentional bias for threat; this was measured through behavioral response on a dot probe task and hippocampal activation during task performance. Morphological substrates of differential hippocampal response were also measured. Design: Cross-sectional study examining associations between genotype, behavioral response and neural response (using fMRI) on the dot probe; Voxel-based morphometry (VBM), global and local shape analyses were used to measure structural differences in hippocampi between genotype groups

HIPS: A new hippocampus subfield segmentation method

[EN] The importance of the hippocampus in the study of several neurodegenerative diseases such as Alzheimer's disease makes it a structure of great interest in neuroimaging. However, few segmentation methods have been proposed to measure its subfields due to its complex structure and the lack of high resolution magnetic resonance (MR) data. In this work, we present a new pipeline for automatic hippocampus subfield segmentation using two available hippocampus subfield delineation protocols that can work with both high and standard resolution data. The proposed method is based on multi-atlas label fusion technology that benefits from a novel multi-contrast patch match search process (using high resolution T1-weighted and T2-weighted images). The proposed method also includes as post-processing a new neural network-based error correction step to minimize systematic segmentation errors. The method has been evaluated on both high and standard resolution images and compared to other state-of-the-art methods showing better results in terms of accuracy and execution time.This research was supported by Spanish UPV2016-0099 and TIN2013-43457-R grants from UPV and the Ministerio de Economia y Competitividad. This study has been carried out with financial support from the French State, managed by the French National Research Agency (ANR) in the frame of the Investments for the future Program IdEx Bordeaux (ANR-10-IDEX-03-02, HL-MRI Project), Cluster of excellence CPU and TRAIL (HR-DTI ANR-10-LABX-57) and the CNRS multidisciplinary project "Defi imag'In". We also want to thank Javier Juan Albarracin for his valuable contribution to the development of this method.Romero Gómez, JE.; Coupe, P.; Manjón Herrera, JV. (2017). HIPS: A new hippocampus subfield segmentation method. NeuroImage. 163:286-295. https://doi.org/10.1016/j.neuroimage.2017.09.049S28629516

Uso de la resonancia magnética y la tomografía computarizada en diagnóstico postmortem

Introduction: Given the heterogeneous nature, the inherent complexity to the activity of expertise in legal medicine, the expert (a professional in medicine or related areas) should make the best use of the technical and technological tools available for this. The imaging, which refers to the set of techniques that allow getting images of the human body for clinical or scientific purposes in any of its techniques, has a powerful support tool to establish facts or technical evidence in the legal field. Objective: To analyze the use of magnetic resonance imaging and computed tomography scan in postmortem diagnosis. Methodology: The search for information was carried out in the PubMed, Science Direct, Springer Journal databases and the Google Scholar search engine, by using the terms "X-ray Computed Tomography", "Magnetic Resonance Spectroscopy", "Autopsy", and "Legal Medicine" including articles published from 2008 to 2015. Results: A magnetic resonance imaging is useful for a detailed study of soft tissues and organs, while a computed tomography scan allows identifying fractures, calcifications, implants, and traumas. Conclusions: In the reports found in the literature search, regarding the use of nuclear magnetic resonance imaging and computed tomography scan in postmortem cases which were named after the genesis of the trauma, a correlation was found between the use of the image and the correct expert diagnosis at autopsy. [Najar-Céspedes AP, Fuentes-Martínez EDJ. The Use of Magnetic Resonance Imaging and Computed Tomography Scans in Postmortem Diagnosis. MedUNAB 2017; 20(2): 190-200].Introducción: Ante la naturaleza heterogénea, complejidad inherente de la actividad de peritaje en medicina legal, el perito (profesional de la medicina o áreas afines) debe hacer el mejor uso de las herramientas técnicas y tecnológicas de las cuales disponga. La imagenología, referente al conjunto de las técnicas que permiten obtener imágenes del cuerpo humano con fines clínicos o científicos, en cualquiera de sus técnicas, reviste una potente herramienta de apoyo estableciendo hechos o pruebas técnicas en el campo legal. Objetivo: Analizar el uso de la resonancia magnética y la tomografía computarizada en el diagnóstico postmortem. Metodología: Se realizó búsqueda de información en las bases de datos PubMed, Science Direct, Springer Journal y en el motor de búsqueda Google Académico, usando los términos “Tomografía Computarizada por Rayos X”, “Espectroscopía de Resonancia Magnética”, “Autopsia” y “Medicina Legal” publicados en el periodo 2008-2015. Resultados: La resonancia magnética es útil para el estudio detallado de tejidos blandos y órganos, mientras que la tomografía computarizada permite la identificación de fracturas, calcificaciones, implantes y traumas. Conclusiones: En los reportes hallados en la búsqueda bibliográfica, en cuanto al uso de la resonancia magnética nuclear y la tomografía computarizada en casos postmortem, nombrados por la génesis del trauma, se halló correlación entre la utilización de la imagen y el correcto diagnóstico pericial en la autopsia. [Najar-Céspedes AP, Fuentes-Martínez EDJ. Uso de la resonancia magnética y la tomografía computarizada en diagnóstico postmortem. MedUNAB 2017; 20(2): 190-200]

Representations of recent and remote autobiographical memories in hippocampal subfields.

The hippocampus has long been implicated in supporting autobiographical memories, but little is known about how they are instantiated in hippocampal subfields. Using high resolution functional MRI combined with multi-voxel pattern analysis we found it was possible to detect representations of specific autobiographical memories in individual hippocampal subfields. Moreover, while subfields in the anterior hippocampus contained information about both recent (two weeks old) and remote (ten years old) autobiographical memories, posterior CA3 and DG only contained information about the remote memories. Thus, the hippocampal subfields are differentially involved in the representation of recent and remote autobiographical memories during vivid recall. © 2013 Wiley Periodicals, Inc

Key clinical benefits of neuroimaging at 7 T

The growing interest in ultra-high field MRI, with more than 35.000 MR examinations already performed at 7 T, is related to improved clinical results with regard to morphological as well as functional and metabolic capabilities. Since the signal-to-noise ratio increases with the field strength of the MR scanner, the most evident application at 7 T is to gain higher spatial resolution in the brain compared to 3 T. Of specific clinical interest for neuro applications is the cerebral cortex at 7 T, for the detection of changes in cortical structure, like the visualization of cortical microinfarcts and cortical plaques in Multiple Sclerosis. In imaging of the hippocampus, even subfields of the internal hippocampal anatomy and pathology may be visualized with excellent spatial resolution. Using Susceptibility Weighted Imaging, the plaque-vessel relationship and iron accumulations in Multiple Sclerosis can be visualized, which may provide a prognostic factor of disease. Vascular imaging is a highly promising field for 7 T which is dealt with in a separate dedicated article in this special issue. The static and dynamic blood oxygenation level-dependent contrast also increases with the field strength, which significantly improves the accuracy of pre-surgical evaluation of vital brain areas before tumor removal. Improvement in acquisition and hardware technology have also resulted in an increasing number of MR spectroscopic imaging studies in patients at 7 T. More recent parallel imaging and short-TR acquisition approaches have overcome the limitations of scan time and spatial resolution, thereby allowing imaging matrix sizes of up to 128×128. The benefits of these acquisition approaches for investigation of brain tumors and Multiple Sclerosis have been shown recently. Together, these possibilities demonstrate the feasibility and advantages of conducting routine diagnostic imaging and clinical research at 7 T

Unravelling The Subfields Of The Hippocampal Head Using 7-Tesla Structural MRI

Probing the functions of human hippocampal subfields is a promising area of research in cognitive neuroscience. However, defining subfield borders in Magnetic Resonance Imaging (MRI) is challenging. Here, we present a user-guided, semi-automated protocol for segmenting hippocampal subfields on T2-weighted images obtained with 7-Tesla MRI. The protocol takes advantage of extant knowledge about regularities in hippocampal morphology and ontogeny that have not been systematically considered in prior related work. An image feature known as the hippocampal ‘dark band’ facilitates tracking of subfield continuities, allowing for unfolding and segmentation of convoluted hippocampal tissue. Initial results suggest that this protocol offers sufficient precision and flexibility to accommodate inter-individual differences in morphology and produces segmentations that have improved accuracy and detail compared to other prominent protocols, with similar inter-rater reliability. We anticipate that this protocol will allow for improved anatomical precision in future research on hippocampal subfields in health and neurological disease

The Role of the Nucleus Pulposus in Human Intervertebral Disc Mechanical Function Quantified by Mechanical Loading and Non-Invasive Imaging

The intervertebral disc performs the mechanical roles of supporting loads, permitting motion, and dissipating energy. Disc degeneration affects a large portion of the population, reduces the jointâ??s effectiveness, and is strongly implicated as a cause of low back pain. Degeneration is an irreversible process that manifests early within the centralized nucleus pulposus and subsequently affects other disc components. An incomplete understanding of the role of the nucleus pulposus and how alterations in nucleus function affect disc mechanics has hindered successful development of disc degeneration treatment. The objective of this dissertation was to evaluate the mechanical contributions of the nucleus pulposus to intervertebral disc function in compressive loading. In cyclic loading experiments, it was determined that removal of the nucleus pulposus via nucleotomy caused acute changes to the discâ??s mechanical response such as a decrease in compressive stiffness with an accompanying increase in compressive strain. These changes correspond to hypermobility, which alters overall spinal mechanics and may impact low back pain via altered motion throughout the spinal column. In addition to these acute changes, nucleotomy also decreased the fluid-flow related effects of cyclic compressive loading. Filing the void left by nucleotomy with a hydrogel implant preserved the creep response of the discs. A procedure for creating disc strain templates, which describe average disc strain, from MR images taken before and after loading was developed to non-invasively measure internal disc strains that result from compression loading. In mildly-degenerate human discs, removal of the nucleus increased axial strain throughout the annulus fibrosus, consistent with the existing literature stating that the nucleus plays a significant role in supporting compressive loads. Removal of the nucleus also unevenly altered the distribution of circumferential and radial strains within the annulus. Nucleotomy caused substantially higher circumferential strain in the posterolateral region, which may increase the risk of annular tears. The novel tools developed in this work and the experimental results can be utilized to further understand the mechanical role of the nucleus pulposus on intervertebral disc function, how that role changes with degeneration, and to design and treatments that restore disc mechanics