BIAD Facilities & Equipment
The Biomedical Image Analysis Division (BIAD) broadly supports each of the RII’s other divisions through scientific research, image processing and data management services.
BIAD supports a broad range of research projects at the Research Imaging Institute (RII) through four sections that focus on:
System Administration Section
BIAD servers are virtual servers, running inside UT Health San Antonio’s Advanced Data Center (ADC). Data storage is provided by IMS’s Isilon network storage. We also collaborate with / have access to Biggs GENIE and TACC.
Data Analysis Section
BIAD uses several many analytical software packages for image analysis and statistical parametric mapping. One in particular is the FMRIB Software Library (FSL)from Oxford. We also use MATLAB and a variety of toolboxes.
AFNI is used for processing, analyzing, and displaying functional MRI data. NIfTI-1 and NIfTI-2 facilitate inter-operation of functional MRI data analysis software packages. Other programs used are IMAGEJ and CMR42 for cardiac image analysis. MR spectra are processed and fitted using the java-based MR processing framework, jMRUI 5.0.
Database R&D Section
The Research Data Archive includes all the biomedical images and auxiliary data required for analyzing RII data. BIAD supports this data archive with the XNAT database package designed for medical imaging, developed at Washington University.
…The BIAD also manages the image archive system, giving investigators direct access to the image database through XNAT, an open source imaging informatics platform, developed at Washington University. Using the XNAT interface, data can be previewed before archiving and downloaded to investigators laboratory computers from the database in a choice of several image formats. XNAT is an NIH-supported data-storing system specifically developed for archiving and shared access of imaging data. The Biomedical Imaging Analysis Division of the Research Imaging Institute (under Dr. Jack Lancaster) is a developer of NIH/XNAT software tools, most recently for web-based viewing tools. The RII archives all imaging data acquired on its scanners (PET, MRI and MRS) in project-specific folders in its XNAT-format archives on UT-managed, HIPAA-compliant servers with automated off-site backup servers. This system is accessed via web-browser interface with password protection, allowing investigators ready but secure access to their data from any location. This system also allows ready but secure sharing of data by authorizing other users through the XNAT user-management system. Access control is managed by the RII, but determined by the PI of each project. RII/MRIC scientists and engineers have a long-standing and continuous track record for developing innovative imaging and data analysis methods for acquiring and interpreting data from a variety of modalities.
BIAD also supports the BrainMap database, which contains content-indexed results of several thousand publications within the brain mapping literature and facilitates rapid meta-analysis.
…BrainMap’s data is managed with Oracle Database Enterprise Edition, a commercial database management system. BrainMap’s database resides on a Linux workstation at the Research Imaging Institute, UTHSCSA, San Antonio, TX. Oracle WebLogic Server hosts the intermediary software, written in Java, that communicates between the client software and the database. BrainMap client software is written using the Java programming language and the targeted computer systems are PC, Macintosh, and UNIX. The use of Java makes updating and distributing these applications simpler for both developers and users. BrainMap’s™ database is publicly accessed through three interfaces: BrainMap™ Scribe (Windows, Macintosh, UNIX), BrainMap™ Sleuth (Windows, Macintosh, UNIX) and BrainMap™ Web (web-based application). All interfaces access BrainMap’s™ database via the network using TCP/IP, even when operated within the RII intranet
Software R&D Section
In addition to the third party analysis software, we also develop our own software. Image processing developments have been integrated into Mango, our image viewer and editor. For more information about the software packages that we have developed, see Resources/Software.
BrainMap apps for meta-analysis.
Also, Talairach Client, icbm2tal, BrainVisa Morphology, etc.