Research Software

RII Software

Software Standards

The Biomedical Image Analysis Division (BIAD) supports data analysis, and software/database research and development. BIAD faculty and staff develop and publish validations of image processing tools and methods. Through the BIAD, investigators have access to specialized software to for conducting complex data analyses and visualizations. Image-processing software is customized in-house for a variety of research protocols and imaging systems, allowing investigators to experiment with unique image forms. Software packages used for image analysis and statistical parametric mapping for fMRI studies include FSL software along with FDT (FMRIB’s Diffusion Toolbox) from the FMRIB Software Library (FSL, Oxford, UK). 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.

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

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.

An extremely versatile stimulus presentation software called E-Prime (Psychology Software Tools, Inc.) is also being used to present audio and video stimuli. E-Prime is a graphical experiment generator for the Windows 95/98/ME environment. E-Prime consists of a suite of applications to design, generate, run, collect data, edit and analyze the data. E-Prime includes: 1) a graphical environment allowing visual selection and specification of experimental functions; 2) a comprehensive scripting language; 3) data management and analysis tools. E-Prime is also capable of sending a signal through the printer or serial ports for interfacing with external devices. Thus, E-Prime can be used to trigger an event (e.g., signal an external device such as a pulse generator to begin and/or stop pulse sequences) or notify an external device of an event (e.g., in order to mark the event in the data collected by the external device).