Functional MRI Core Facility

功能性核磁共振核心设施

• 批准号: 8557114
• 负责人: Peter Bandettini
• 金额: $ 392.11万
• 依托单位: NATIONAL INSTITUTE OF MENTAL HEALTH
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8557114
• 关键词: Acceleration; Address; Algorithms; Anatomy; Archives; Back; Basic Science; Biological Markers; Boxing; Brain; Brain imaging; Budgets; Childhood; Classification; Climate Controls; Clinical; Clinical Sciences; Collaborations; Communication; Communities; Consult; Core Facility; Custom; Data; Data Set; Data Storage and Retrieval; Devices; Diffusion; Disease; Dura Mater; Echo-Planar Imaging; Education; Effectiveness; Electronics; Employee; Ensure; Environmental Hazards; Experimental Designs; Eye; Fees; Floor; Focus Groups; Frequencies; Functional Imaging; Functional Magnetic Resonance Imaging; Galvanic Skin Response; Generations; Goals; Hour; Housing; Human; Human Resources; Image; Individual; Information Technology; Institutes; Joystick; Laboratories; Lamivudine; Longitudinal Studies; MRI Scans; Magnetic Resonance Imaging; Maintenance; Maps; Measurement; Measures; Meta-Analysis; Methods; Mission; Modeling; Monitor; Morphologic artifacts; National Heart, Lung, and Blood Institute; National Institute of Mental Health; National Institute of Neurological Disorders and Stroke; National Institute on Alcohol Abuse and Alcoholism; National Institute on Deafness and Other Communication Disorders; Neurosciences; Noise; Notification; Nuclear Magnetic Resonance; Paper; Participant; Performance; Phase; Physiologic pulse; Policies; Positioning Attribute; Principal Investigator; Procedures; Process; Protocols documentation; Publications; Qi; Radio; Research; Research Infrastructure; Research Personnel; Research Support; Resolution; Resources; Retrieval; Running; Scanning; Schedule; Scientist; Security; Services; Signal Transduction; Site; Specialist; Speed; Stimulus; Study Subject; Surface; System; Systematic Bias; Techniques; Technology; Temperature; Thick; Time; Tissues; Training; Translating; United States National Institutes of Health; Update; Weight; Work; Writing; base; clinically relevant; gray matter; image archival system; image reconstruction; improved; indexing; meetings; neuroimaging; novel; open source; operation; research study; response; square foot; symposium; web site

Space Utilization: The Functional MRI Facility (FMRIF) currently occupies approximately 4800 sq. ft of space, divided between the scanner bays, control rooms and electronics/machine rooms for 3TA, 3TB, 3TC, 3TD, and 7T MRI scanners located within the NMR center and office space on the second floor above the NMR center in the FMRIF/SFIM suite (approximately 1400 sq ft total, including shared conference space). Staff: The FMRIF staff (currently 15 full time employees) consist of: the facility director, four staff scientists to keep the scanners running, eight MRI technologists, an information technology (IT) specialist, and an administrative lab manager. The functional MRI facility supports the research of over 30 Principal Investigators which translates to over 300 researchers overall. Over 70 research protocols are active and making use of FMRIF scanners. Each scanner has scheduled operating hours of 105 hours per week. Since the year 2000 until Sep 2012, a total of 802 (79 papers in just the last year) publications have made use of the core facility. The total is divided among 537 for NIMH, 213 from NINDS, and 62 from the other institutes). These papers have been cited 50,507 times for a combined h-index of 114. This year, we have continued to increase the overall utility of the fMRI core facility. As we adjust our personnel to accommodate some budget cuts, we continue to increase efficiency and availability of cutting edge fMRI and MRI scanning capability. In particular the quality and depth of our specific collaborations with users has increased. To increase the effectiveness of our technologists, we have re-assigned Dr. Vinai Roopchansingh to the position of Technical Laboratory Manager to oversee their day to day operations and serve as the interface between the core staff scientists and the technologists and users on a day to day basis. B IT accomplishments (mostly from Adam Thomas and Sean Marrett): - All of the data collected on FMRIF scanners since approximately 2004 -- more than 20 TB has been transferred from off-line tape storage to on-line disk archive, vastly reducing time and effort needed for retrieval and potential meta-analysis of MRI data from years past. We have also eliminated the Intelerad Image archiving system and replaced it with an simple searchable system built by an in-house developer (Joe Naegele). This will eliminate the $15k/year support fees previously paid to Intelerad. - All computing and storage infrastructure has been moved from shared space in the MR machine room (with vulnerability to power loss and environmental hazards) to a dedicated custom-build computing facility owned by and shared with NINDS. This state-of-the-art server room is fully compliant with all NIH and HHS mandated policies and procedures for data storage. It has been built with temperature and climate control, UPS backup, and card key access, and security cameras; all of which can be monitored remotely and set to trigger notification alarms to the appropriate staff. This will dramatically increase the reliability and security of all FMRIF servers and data. - All scanner data access to scanner data as well as access to the FMRIF web site is now authenticated via the NIH single sign on system. This is convenient for users in that they have only one password to remember. It also ensure that access passwords are regularly changed, that access to FMRIF resource is terminated immediately when researchers end their time at NIH, and provides a centrally accessible audit trail for access to all FMRIF resources. Stimulus/user interface accomplishments (Sean Marrett and Adam Thomas): - New eye tracking system has been developed and debugged on 3T-C which can be used for pediatric studies (in collaboration with LBC and SIN/GCAP) - New audio system with active noise cancellation has been installed for 7T - New high-speed back projection systems for 3TD has been installed. 7T accomplishments: - A cortical surface model extraction and post-processing procedures developed for 7T (with Souheil Inati ) - Single trial FMRI studies on 7T ( with Souheil, Chris Baker and Dwight Kravitz) takes advantage of increased signal/noise available on 7T to use individual responses from large number (750+) of stimuli which are presented to subject only once. This presents opportunity for novel experimental designs for single-subject studies (e.g. for biomarkers of disease in individuals). Specific Staff Scientist Accomplishments: Souheil Inati: - Discovered an artifact in FMRI images acquired with acceleration and reconstructed with the GRAPPA algorithm on the Siemens scanners. This artifact resulted in substantially reduced temporal signal to noise ratio and was due to a previously unknown interaction between the acquisition of accelerated echo planar imaging and parallel imaging reconstruction. The product Siemens pulse sequence was modified and a Works in Progress package was released by Siemens implementing this fix. This is a collaboration with Lalith Talagala from NINDS, Peter Kellman from NHLBI, and Sunil Patil from Siemens. - Implemented a method for improving the registration between functional images (gradient-echo EPI) and anatomical images. The method required the implementation of a pulse sequence, image reconstruction, and synthetic image generation. The pulse sequence was implemented on the Siemens scanner. The image reconstruction and synthetic image generation was implemented in collaboration the Gadgetron, an open-source image reconstruction framework written by Michael Hansen in NHLBI. I am now working with Vinai Roopchansingh on an implementation on the GE scanners. This is a collaboration with Pablo Velasco from NYU. - Implemented a pulse sequence to measure the B1 (flip angle) distribution in the brain on the Siemens scanner. This measurement will allow us to remove a systematic bias in T1 maps generated from multiple flip angle GRE scans. This is a key component of longitudinal and multi-site anatomical imaging protocols. This is a collaboration with Qi Duan from NINDS and Govind Nair from NINDS. - Developed a high-resolution 3T anatomical imaging battery for longitudinal studies on the Siemens scanner consisting of optimized protocols with multiple contrasts. This is a collaboration with Govind Nair from NINDS. Began work on developing analysis methods based on these type of data for tissue classification and segmentation with Ziad Saad from NIMH. - Modified the Siemens product spin-echo DWI pulse sequence to collect images of alternate phase encode polarity. This reverses the geometric distortions inherent in EPI and allows for substantially increased accuracy in registration of diffusion images to anatomical images. - Developed and implemented a new algorithm for combining MR images form multiple receiver coils. This significantly improves imaging with multiple receiver coils in situations where the phase of the image is important (SWI, flow, etc.). This is a collaboration with Peter Kellman and Michael Hansen in NHLBI. Working with Sunil Patil from Siemens on incorporating into the Siemens product. Wenming Luh: - We have made available the multi-echo MPRAGE T1 weighted pulse sequence. MPRAGE is performed routinely to obtain T1-weighted 3D brain images with high spatial resolution and tissue contrast for accessing gray matter thickness and anatomical landmarks. The multi-echo version allows better discerning of dura and cortical gray matter to estimate gray matter thickness more accurately. - We have started to provide the multi-echo echo-planar image pulse sequence to the community. This technique can differentiate BOLD and non-BOLD signal in a functional MRI dataset and is effective in minimizing unwanted fluctuations.

空间利用率： 功能性 MRI 设施 (FMRIF) 目前占据约 4800 平方英尺的空间，分为位于 NMR 中心内的 3TA、3TB、3TC、3TD 和 7T MRI 扫描仪的扫描仪隔间、控制室和电子/机器房以及 FMRIF/SFIM 套件中 NMR 中心上方二楼的办公空间（总共约 1400 平方英尺， 包括共享会议空间）。 职员： FMRIF 工作人员（目前有 15 名全职员工）包括：设施主管、四名负责保持扫描仪运行的科学家、八名 MRI 技术人员、一名信息技术 (IT) 专家和一名实验室行政经理。 功能性 MRI 设施支持 30 多名首席研究员的研究，总共有 300 多名研究人员。超过 70 个研究方案正在使用 FMRIF 扫描仪。每台扫描仪的预定运行时间为每周 105 小时。 自 2000 年至 2012 年 9 月，共有 802 篇出版物（仅去年就有 79 篇论文）使用了该核心设施。总数分为 NIMH 的 537 个、NINDS 的 213 个以及其他机构的 62 个。这些论文已被引用 50,507 次，综合 h 指数为 114。 今年，我们继续提高功能磁共振成像核心设施的整体利用率。在我们调整人员以适应一些预算削减的同时，我们继续提高尖端 fMRI 和 MRI 扫描能力的效率和可用性。特别是我们与用户的具体合作的质量和深度都得到了提高。为了提高技术人员的效率，我们重新任命 Vinai Roopchansingh 博士担任技术实验室经理，负责监督他们的日常运营，并充当核心员工科学家与技术人员和用户之间的日常联络人。乙 IT 成就（主要来自 Adam Thomas 和 Sean Marrett）： - 大约自 2004 年以来在 FMRIF 扫描仪上收集的所有数据 - 超过 20 TB 的数据已从离线磁带存储转移到在线磁盘存档，大大减少了对过去几年的 MRI 数据进行检索和潜在元分析所需的时间和精力。我们还取消了 Intelerad 图像存档系统，并将其替换为由内部开发人员 (Joe Naegele) 构建的简单的可搜索系统。这将消除之前支付给 Intelerad 的 15,000 美元/年的支持费。 - 所有计算和存储基础设施已从 MR 机房的共享空间（易受断电和环境危害影响）转移到 NINDS 拥有并与 NINDS 共享的专用定制计算设施。这个最先进的服务器机房完全符合 NIH 和 HHS 规定的数据存储政策和程序。它配备了温度和气候控制、UPS 备份、卡钥匙访问和安全摄像头；所有这些都可以远程监控并设置为向适当的工作人员触发通知警报。 这将显着提高所有 FMRIF 服务器和数据的可靠性和安全性。 - 所有扫描仪数据对扫描仪数据的访问以及对 FMRIF 网站的访问现在均通过 NIH 单点登录系统进行身份验证。这对于用户来说很方便，因为他们只需记住一个密码。它还确保定期更改访问密码，当研究人员在 NIH 工作结束时立即终止对 FMRIF 资源的访问，并为访问所有 FMRIF 资源提供可集中访问的审计跟踪。 刺激/用户界面成就（Sean Marrett 和 Adam Thomas）： - 已在3T-C上开发并调试了新的眼动追踪系统，可用于儿科研究（与LBC和SIN/GCAP合作） - 7T 安装了具有主动降噪功能的新音频系统 - 已安装新的 3TD 高速背投系统。 7T成就： - 为 7T 开发的皮质表面模型提取和后处理程序（与 Souheil Inati 一起） - 7T 的单次试验 FMRI 研究（与 Souheil、Chris Baker 和 Dwight Kravitz 合作）利用 7T 上增加的信号/噪声来使用来自大量（750+）刺激的个体反应，这些刺激仅向受试者呈现一次。这为单受试者研究（例如个体疾病生物标志物）的新颖实验设计提供了机会。 专职科学家的具体成就： 苏海尔·伊纳蒂： - 在西门子扫描仪上通过加速采集并使用 GRAPPA 算法重建的 FMRI 图像中发现了伪影。 这种伪影导致时间信噪比大幅降低，这是由于加速回波平面成像采集和并行成像重建之间以前未知的相互作用所致。 西门子产品脉冲序列已被修改，并且西门子发布了 Works in Progress 包来实施此修复。这是与 NINDS 的 Lalith Talagala、NHLBI 的 Peter Kellman 和西门子的 Sunil Patil 的合作。 - 实施了一种改进功能图像（梯度回波 EPI）和解剖图像之间配准的方法。 该方法需要执行脉冲序列、图像重建和合成图像生成。 脉冲序列在西门子扫描仪上实现。 图像重建和合成图像生成是与 Gadgetron 合作实现的，Gadgetron 是由 NHLBI 的 Michael Hansen 编写的开源图像重建框架。 我现在正在与 Vinai Roopchansingh 合作在 GE 扫描仪上实施。 这是与纽约大学的 Pablo Velasco 的合作。 - 在西门子扫描仪上实施脉冲序列来测量大脑中的 B1（翻转角）分布。 该测量将使我们能够消除由多个翻转角 GRE 扫描生成的 T1 地图中的系统偏差。 这是纵向和多部位解剖成像协议的关键组成部分。 这是与 NINDS 的 Qi Duan 和 NINDS 的 Govind Nair 的合作。 - 开发了高分辨率 3T 解剖成像电池，用于在西门子扫描仪上进行纵向研究，包括具有多种对比度的优化协议。 这是与 NINDS 的 Govind Nair 的合作。 开始与 NIMH 的 Ziad Saad 一起开发基于此类数据的分析方法，用于组织分类和分割。 - 修改了西门子产品自旋回波 DWI 脉冲序列以收集交替相位编码极性的图像。 这扭转了 EPI 固有的几何畸变，并大大提高了扩散图像与解剖图像的配准精度。 - 开发并实施了一种新算法，用于组合来自多个接收器线圈的 MR 图像。 在图像相位很重要的情况下（SWI、流量等），这可以显着改善多个接收线圈的成像效果。 这是与 NHLBI 的 Peter Kellman 和 Michael Hansen 的合作。 与西门子的 Sunil Patil 合作，将其纳入西门子产品中。 陆文明： - 我们已经提供了多回波 MPRAGE T1 加权脉冲序列。常规执行 MPRAGE 以获得具有高空间分辨率和组织对比度的 T1 加权 3D 脑图像，以获取灰质厚度和解剖标志。多回波版本可以更好地辨别硬脑膜和皮质灰质，从而更准确地估计灰质厚度。 - 我们已经开始向社区提供多回波平面回波图像脉冲序列。该技术可以区分功能 MRI 数据集中的 BOLD 和非 BOLD 信号，并能有效减少不必要的波动。