IBIC is a research resource Center, and the focus of a multidisciplinary community mutually invested in those resources. Our resources currently include the following:
Expert effort/time is the key resource of IBIC or any imaging sciences laboratatory. IBIC Core personnel have extensive expertise in cognitive neuroscience, clinical neuroscience, neuroradiology, image processing, imaging statistics, computer science, MRI and PET imaging modalities, and electrophysiology. The core personnel comprise investigators with physical presence at IBIC and support staff with IBIC direct support. Several leverage additional support from the closely related Diagnostic Imaging Sciences Center (DISC) and the Neuroimaging Core of the Center on Human Disability and Development (CHDD).
Programmatic space assigned to IBIC is a substantial token of departmental and institutional commitment to the Center. IBIC space is located in the UW Medical Center AA and RR wing basement. Additional space is located in the Old Fisheries building The space enables and encourages multidisciplinary interaction. The space is essentially contiguous and includes offices, multipurpose interaction space, and a central image processing lab. It is also in contiguity with the MR Research Lab and its Philips 3T Achieva scanner.
IBIC currently occupies about 1250 square feet in UWMC, including offices (AA036, AA010J, AA010M, RR014A-C) in UWMC, a small conference room, and a multipurpose meeting and image processing space currently under renovation. Approximately 2000 square feet of additional space is committed to IBIC for availability by Feb, 2011, as current occupants transition to other locations.
IBIC EEG, psychophysiology, and mock scanner are housed in three additional rooms comprising 500 square feet in the Old Fisheries Building. In addition, three offices for IT and administrative personnel are shared by DISC/IBIC, and the 3T scanner equipment room of DISC also serves a IBIC computer server space.
MR imaging acquisition resources
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. 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. Grabowski and Maravilla, 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. IBIC also receives considerable in-kind assistance from DISC, especially in regard to expertise in MR physics, parameterization of pulse sequences, and instrumentation in the scanner. Consulting meetings prior to initiation of any new projects include members of IBIC and DISC to optimize both acquisition protocol and experimental design. The Directors of IBIC and DISC meet weekly.
As part of the I/OWA project, and in cooperation with the Instrument Development Laboratory of the Center on Human Disability and Development (CHDD), we are installing a National Instruments data acquistion card, linked by a LabView module, to the I/OWA software package. This system will allow the acquisition of data from up to 32 analog and 48 digital channels simultaneously, with sampling rates up to 20 kHz. This will enable investigators to acquire concurrent channels of data (respiration, pulse, GSR, capnometry, etc) and conveniently map all data in time onto the acquired images.
CHDD and IBIC jointly maintain a mock scanner, constructed by the CHDD Instrument Development Lab, available for paradigm development, subject densensitization, and training for reduction of head motion.
Finally, the University of Washington Department of Neurology has recently recruited Dr. Edward Novotny, a pediatric epileptologist and imaging scientist. Dr. Novotny interacts with IBIC extensively, and will bring a capability for simultaneous EEG/fMRI for studies of physiologic correlates of ictal events. This resource will be available to IBIC.
IBIC has an EEG/ERP Laboratory that includes an Electrogeodesics 128 channel EEG system in a sound proofed and electromagnetically shielded room. Ancillary equipment include a PC for running the EPrime 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.
Pilot project resources
IBIC is committed to developing as a research resource serving Upper and Medical campuses at the University of Washington. IBIC allies closely with DISC to provide integrated support for pilot studies, i.e. acquisition, analysis, and training. IBIC primarily supports research development using a collaborative model. 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.
Philosophy behind the collaborative model
How to go about conducting a collaborative pilot study with IBIC
Collaborative model vs. service model?IT resources
PACSoft is a DICOM image archive searcher and Bioscribe is an overarching research metadata database that manages image data sets related to individual subjects 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. A 50 Tb extensible central data repository for research studies, Department of Radiology is currently being constructed.
Linux computing cluster
Seven HP Quad-core Xeon-based Z800 workstations with FX3800 graphics, dual monitors are clustered with Sun Grid Engine. All resources are linked with 1 Gb ethernet. The cluster supports IBIC developers and research scientists developing software and designing/scripting analysis pipelines.
Image Processing Software
IBIC has a wide range of image processing software platforms for functional and structural image processing, including FSL, SPM5, FreeSurfer, BioImage Suite, AIR, as well as general purpose scientific analysis software: Matlab, Python. Custom software is also described below.
Center-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. This resource is managed by Qingyan Guan.
Central virtualized environment (under development)
IBIC is currently implementing central virtualization of an interoperable image processing environment, i.e. a system for abstraction of the operating system from the physical characteristics of the computers we use. Virtualization enables the IBIC image processing environment to be "stamped" on machines with different computing hardware (client virtualization) or else run on a server (central virtualization) that distributes its resources flexibly to support multiple virtual machines for local or remote users interfacing with "thin clients". Virtualization reduces load on IT personnel, ensures efficient use of computing resources, and facilitates dissemination. For IBIC, the overriding advantage is the meta-issue of standardization and tracking of the processing environment, and the related issues of stability of the build across investigators, labs, contexts; and "version control" of the environment. For example, older processing pipeline versions can be recalled as virtual machines.
IBIC will continue to develop and enhance two custom software packages brought by Dr. Grabowski from the University of Iowa. *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. Modularization of Brainvox, and its extension to support multidimensional data browsing are being contemplated.
I/OWA 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. Both qualities are key for applications to impaired subjects. Further, IBIC will extend I/OWA to real-time data analysis, and for emerging modalities such as magnetic source MRI (msMRI, cf Xue et al in press, Xiong et al 2003). I/OWA was developed under NIBIB R33 EB001484, R21 EB004316, and an R03 funding proposal for software enhancement and dissemination via NITRC is pending.
Educational and training resources