The University of Washington Integrated Brain Imaging Center (IBIC) is a research resource center located in the Department of Radiology, adjacent to the Diagnostic Imaging Sciences Center (DISC) and its research-dedicated 3T MRI system. This space is designed for facilitate interaction and to support interdisciplinary projects involving human MR imaging, cognitive neuroscience and medicine campus wide. IBIC is directed by Thomas J. Grabowski, Jr., MD, Professor of Radiology and Neurology.
IBIC Core personnel have extensive expertise in cognitive neuroscience, clinical neuroscience, neuroradiology, image processing, general and imaging statistics, computer science, MRI physics, biophysics, and electrophysiology. The core personnel comprise faculty investigators with physical presence at IBIC and support staff with IBIC direct support. Several members leverage additional support from the closely related Diagnostic Imaging Sciences Center (DISC) and the Neuroimaging Core of the Center on Human Disability and Development (for the benefit of CHDD-affiliated investigators). IBIC Core personnel are physically present in the IBIC programmatic space, make their expertise available in collaborative project design meetings with new and established investigators, and participate in the IBIC scientific interest groups.
IBIC space enables and encourages multidisciplinary interaction. It is located in the UW Medical Center AA and RR wing basement and includes core personnel offices; a team collaboration room featuring Mediascape; an open-architecture image processing laboratory with eight workstations including spaces for short-term or “touch-down” users; a multipurpose conference room and overflow image processing space; an information technology room; an EEG suite with control and acquisition rooms; and a mock scanner. The space is essentially contiguous with the MR Research Lab and its Philips 3T Achieva scanner. IBIC computer servers and network-attached storage are located in the 3T scanner equipment room. Additional office space and a legacy EEG suite are located in the Portage Bay Building.
IBIC has established a number of scientific interest groups (SIGs), which meet in IBIC space, optionally with a concurrent virtual meeting using GoToMeeting rendezvous software. The SIGs are a means of disseminating expertise, increasing IBIC's visibility, and catalyzing new projects in areas of strategic interest. Meeting formats differ across groups, but include research talks, visiting speakers, works in progress, presentation rehearsals, software demonstration, and journal club exercises. Recorded meetings are archived for access in Windows media file format on the IBIC wiki site.
Language and Imaging Interest Group
Functional Connectivity Interest Group (Resting Working Group)
DIG-IT (Developers Interest Group for Imaging Technologies)
Information Technology Interest Group
Magnetic Resonance Imaging Acquisition Interest Group
Multivoxel Pattern Analysis Interest Group
Diffusion Tensor Imaging Interest Group
Integration of Electrophysiology and Imaging Interest Group
Aging and Neurodegenerative Disease Interest Group
Neurodevelopmental Interest Group
Educational Resource Interest Group
Data Acquisition Resources
Magnetic resonance imaging
IBIC is in the immediate proximity of the research-dedicated 3T Philips Achieva scanner of the Diagnostic Imaging Sciences Center directed by Dr. Kenneth Maravilla. The Directors of IBIC and DISC meet weekly, and IBIC and DISC cooperate closely. The scanner is jointly administered by the Departments of Radiology and Psychology. A Committee of 3T Directors comprised of 4 members of each department, including Drs. Maravilla and Grabowski meets monthly. Pilot scanner time is available through both departments, and cooperatively administered by the Directors. Under this mechanism, IBIC has access to 10% of the prime time scanning hours for meritorious unfunded pilot work. DISC and IBIC share IT personnel and an MR physicist (Christopher Gatenby). Consulting meetings prior to initiation of new projects typically include members of IBIC and DISC to optimize both acquisition protocol and experimental design.
DISC provides support for a range of IBIC imaging protocols. A set of standard head coils, including both 8- and 32-channel SENSE head coils are supplemented by custom-built coils developed in house by the Electronics/RF Coil Laboratory directed by Cecil Hayes, Ph.D. Pearltec Crania systems in both adult and child sizes are routinely employed to comfortably stabilize the head inside the coil. A computer equipped with E-Prime, Presentation, and PsychToolbox implemented in Matlab controls delivery of auditory, visual, and olfactory stimuli and recording of button box responses in functional imaging experiments. Additional hardware and software is available for recording physiological signals (e.g., heart rate, respiration, ECG), vocal responses, pen stroke responses, and eye movements.
IBIC has an EEG/ERP Laboratory that includes an Electrogeodesics 128 channel EEG system in a sound proofed and electromagnetically shielded room. Ancillary equipment includes a PC for running the E-Prime or Presentation paradigm delivery package, a ten channel BIOPAC system for recording autonomic activity. Source localization packages include BESA and EMSE. In an adjacent room, there is a photogrammetry device for 3D-registration of EEG electrode positions for the purpose of coregistration with MRI and source localization.
IBIC has a Brain Products in-magnet EEG system designed to support simultaneous fMRI-EEG acquisition. The system consists of a BrainAmp MRplus MRI-compatible 64-channel digital system together with the sync box for gradient clock synchronization, amplifiers, and a range of EEG caps.
A mock scanner, constructed by the CHDD Instrument Development Lab to replicate the dimensions and appearance of the 3T Achieva, is housed in the IBIC space. The mock scanner allows for participant desensitization to the scanner environment and is fitted with a blank 32-channel head coil. A stimulus presentation computer running E-prime, Presentation, Inquisit, and PsychoPy paradigm presentation software and attached button boxes allow experimental tasks to be transacted in the mock scanner just as they are in the 3T Achieva. A trakSTAR tracker from Ascension Technology Corporation with a MoTrak console allows for continuous monitoring of head position and training to reduce head motion.
IBIC and DISC share a participant preparation, testing, and consent room, including a computer running E-Prime, Presentation, Inquisit, and PsychoPy.
Pilot Project Resources
IBIC is committed to developing new research projects on the Upper and Medical campuses at the University of Washington. IBIC primarily supports research development using a collaborative model. IBIC allies closely with DISC to provide integrated support for pilot studies, i.e. acquisition, analysis, and training. Support for pilot work is facilitated by the Radiology Department's commitment of pilot scanning hours to IBIC and its commitment to a component of personnel effort. Pilot studies are governed by policy set by the 3T Directors, are generally limited to 10 hours scanner time, and are available for testing a unique idea, developing a new technique, obtaining preliminary data for a grant submission, and in some training circumstances. It is not intended to provide a means for conducting a full-scale study without funding. IBIC also supports studies using a service model.
Computer Hardware Resources
Linux Computing Cluster
Six HP dual Quad-core Xeon Z800 workstations (two with Intel® Xeon® E5530 2.40 GHz 8MB/1066 QC CPU, four with Intel® Xeon® E5630 2.53 GHz 12MB/1066 QC CPU) each with 24GB RAM, 1.5 TB of local hard disk storage, NVidia Quadro FX3800 graphics, are clustered with Sun Grid Engine as a 48-core computing cluster.
Two additional HP dual Quad-core Xeon Z800 workstations (Intel® Xeon® E5630 2.53 GHz 12MB/1066 QC CPU) each with 24GB RAM, 1.5 TB of local hard disk storage, NVidia Quadro FX3800 graphics, are dedicated to individual developers and project groups.
One final HP dual Quad-core Xeon Z800 workstation (Intel® Xeon® E5630 2.53 GHz 12MB/1066 QC CPU) with 72GB RAM, 9.0 TB hard disk space, NVidia Quadro FX3800 graphics, is dedicated to internal development and memory-intensive processing.
All resources are linked with 1 Gb Ethernet, with 10 Gb bandwidth connectivity to two Network Attached Storage (NAS) systems through a dedicated 24 port DLink switch.
The computing cluster workstations support IBIC developers and research scientists developing software and designing/scripting analysis pipelines.
Four Dell PowerEdge servers (each with dual Quad-core Intel® Xeon® E5430 2.66 GHz 12MB/1333) are available for shared projects with the Chaovalitwongse lab.
In addition, a 36-core (AMD Opteron Processor 4180) “condominium cluster” running Sun Grid Engine, administered by IBIC for the Seattle Longitudinal Study, is available for shared use.
Seven Dell Precision T1500 workstations Quad-core Intel® Core™ i5-760 (2.80 GHz 8MB with 8GB RAM, 1.5 TB of local hard disk storage, NVIDIA Quadro FX380 graphics), fourteen Dell Precision T1600 workstations Quad-core Intel® Xeon® E3-1225 workstations (3.10 GHz, 6M with 8GB RAM, 1.5 TB of local hard disk storage, NVIDIA Quadro NVS300), and one Dell Precision T1650 workstation Quad-Core Intel® Xeon® E3-1225 v2 (3.2GHz, 8M, with 8GB RAM, 1.0 TB of local hard disk storage, NVIDIA Quadro 410), all with dual 24 inch LCD monitors, are used at the desktop by individual researchers developing scripts and analysis pipelines.
“ivan” Workstation (Interoperable and Virtualized Analysis of Neuroimages)
One Dell Precision T1600 Quad-core Intel® Xeon® E3-1225 workstation (3.10 GHz, 6M with 8GB RAM, 1.5 TB of local hard disk storage), is available for non-core affiliates of IBIC. It is the preferred platform for converting Enhanced DICOM to NIFTI, and runs the common IBIC workstation image processing application software.
Central Virtualized Environment
IBIC has a virtual desktop interface (VDI) server system implementing virtualization of an interoperable image processing environment (IVAN: Interoperable and Virtualized Analysis for Neuroimaging). The hardware is comprised of three Sun Fire X4170 (two with 8 cores / 8GB RAM, one with 16 cores and 24 GB RAM), and three Sun Fire X4270 servers (each 16 cores with 48 GB RAM).
Two of the servers run Ubuntu Linux 10.04 and the common IBIC workstation image processing application software. Users are authenticated via a web browser Session Manager and presented with the Ulteo Open Virtual Desktop (http://www.ulteo.com). The system is authenticated with UW netid using Shibboleth. UW netids are sponsored by IBIC for users external to the University of Washington.
Virtualization reduces load on IT personnel, ensures efficient use of computing resources, and facilitates dissemination. The overriding advantage is the meta-issue of standardization and tracking of the processing environment, the related issues of stability of the build across investigators, labs, and contexts, and "version control" of the environment.
PACSsoft, a DICOM image archive, and Bioscribe, an overarching research metadata database, manage image data sets related to individual participants and to specified research studies as well as any text-based and graphical data (such as medical histories, medication information, physiological measurements, etc.) associated with the study. Bioscribe allows complete storage, integrity, data security, and HIPAA compliance of research data from the various projects. This powerful system is designed to support multicenter research projects where the central coordinating site would be located at UW. The system has a 4 TB capacity.
XNAT is an open-source eXtensible Neuroimaging Archive Toolkit developed by the NRG at Washington University in Saint Louis. This imaging informatics platform provides the functionality of the combination PACSsoft and Bioscribe systems and adds support for pipeline processing. In addition XNAT has a large and growing user community. XNAT is hosted on an HP ProLiant DL 380p Generation 8 server with 20TB of storage (12.7 TB RAID 6). The XNAT system is the successor to PACSsoft / Bioscribe and is being used for all ongoing and new studies.
High-performance network attached storage is provided by two Sun model 7310 NAS controllers each with a J4400 SAS ARRAY of 24 X1TB 7200RPM SATA HDDs. The disk arrays are configured as Single Parity Mirrored. This NAS system has privileged bandwidth to the compute cluster (10Gbit).
IBIC also also a secondary network attached storage system (Thecus N16000) providing 16 x 3TB in a RAID6 configuration. This system has 10 Gb bandwidth to the UW network.
IBIC also has access to a 50 Tb capacity extensible central data repository in the Department of Radiology, University District Building, funded by an NIH S10 grant (PI: Minoshima).
PACSsoft and Bioscribe, XNAT, the Confluence wiki server, and the MR lab scheduling tool are backed up nightly using Tivoli Storage Manager via a campuswide service.
The IBIC web site is www.ibic.washington.edu. IBIC-wide web resources are collectively managed with enterprise wiki software (Atlassian Confluence). The URL is www.ibic.washington.edu/wiki. Confluence was chosen for a what-you-see-is-what-you-get quality that minimizes barriers to the user.
Image Processing Software
IBIC has a wide range of image processing software platforms for functional, diffusion and structural image processing, which are maintained in a standardized Ubuntu 10.04 operating environment disc image across all IBIC desktop workstations.
The IBIC cluster nodes are running the newest version of image processing software on a standardized Ubuntu 12.04 operating environment disk image (“Evolution”).
The image processing software tools include FSL, SPM8, FreeSurfer, BioImage Suite, AIR, Brains3, tal_programs, MRIcron, ANTS, R, and many others, as well as general purpose scientific analysis software: MATLAB, and Python libraries. Custom software is also described below.
IBIC has developed a standard pipeline for semi-automated processing of resting state fMRI data and will be developing additional pipelines for analysis of DTI and task-based fMRI consistent with IBIC’s established best practices for acquisition and analyses. These pipelines integrate the best available tools from standard packages (e.g., FSL, FreeSurfer, Brains3) with custom software tools and defined manual quality control checkpoints to ensure the highest possible data quality from every scan.
Brainvox is an interactive 3D anatomic and multimodal visualization and interactive analysis package supported by NINDS Program Project NS19632, on which Dr. Grabowski has been an investigator for 16 years.
I/OWA (Input-Output time aWare Architecture) is software supporting a streaming data processing model for "time-aware" fMRI and ancillary data acquisition and analysis. I/OWA provides generalized support for event-related design, and support for interactive fMRI paradigms and applications to impaired subjects. I/OWA was developed under NIBIB R33 EB001484, R21 EB004316.
IBIC is dedicated to strengthening the broader neuroscience community at the University of Washington by making cognitive neuroscience methods accessible to faculty and students in related fields, in the schools of Medicine, Arts & Sciences, and Engineering. IBIC provides both formal and informal instruction to scientists interested in incorporating cognitive neuroscience methods into their work. Through a joint effort with the Psychology Department, IBIC offers an annual course in the acquisition, analysis, and interpretation of fMRI data. Lectures and other course materials are made available to the broader community on the IBIC wiki. Individual researchers are encouraged to pair with an IBIC scientist for collaborative analysis of early projects, fostering deeper understanding through hands-on experience. Core members and affiliates have the opportunity to further expand their knowledge base through access to IBIC’s library of texts on cognitive neuroscience, neurology, radiology, and computer science.