University of Oregon

Personal tools

Computing Infrastructure

The Center has a number of resources available to support research activities. These include desktop computers, printers and scanners in our Imaging Data Analysis area and 18 terabytes of storage on our file server. There are also a number of network-accessible machines which run a variety of neuroimaging analysis programs. These machines are organized into a compute grid under Son of Grid Engine.

Data Collection and Experiment Support

The Lewis Center has many amenities to support your research. Sensory modalities include visual and auditory, other modalities may be accomplished with equipment particular to the experiment. Data collection includes coded responses through the participant button boxes and video and audio recording. Other types of data can be collected as needed. These include participant physiological metrics and eye tracking.

MR Console Room

This is where all scanning and associated data collection takes place. For stimulus presentation we maintain a main iMac which can boot to Windows, Linux and OS X Yosemite. Software installed includes:

  • Psychopy
  • MATLAB
  • Psychtoolbox

Other software can be installed to accommodate your research needs.

Data collected during scan sessions can be backed up by our tape backup system. See the Data Backups section below for information on how to enable this.

Simulator Room

The simulator room houses our mock scanner and is equipped with stimulus presentation and data collection equipment equivalent to the Console Room iMac. Further details on the mock scanner and associated equipment can be found here.

Imaging Data Analysis Room

The Imaging Data Analysis (IDA) Room houses four workstations for use by researchers for data processing or other work. Three of these computers dual-boot into Ubuntu Linux and Windows 8.1, the fourth is an iMac running Yosemite.

This room can also be booked for interviews or experiments with participants or as a waiting room.

Interview Room

The Interview Room may be used for participant interviews, training and debriefing. It is equipped with an iMac that may be used for any purpose to support your research.

Servers

Bordeaux

Bordeaux is our file server and is available for connections via SSH/SFTP and SMB/CIFS (Windows networking). Current capacity is 40 terabytes.

Data in researcher home directories and the central DICOM repository is backed up nightly.

Printers and Scanners

HP LaserJet 8150

This is a high-volume device loaded with Letter and Legal stock, and can print directly to envelopes.

HP ScanJet 5490c

A flatbed scanner directly connected to IDA workstation 3. HP does not support this scanner under Windows 8.1, however, it is supported under Ubuntu Linux. You can gain access to scanning capabilities with the xsane program.

The Processing of Data

FSL versions 4.x.x and later provide excellent support for grid computing through tight integration with Sun Grid Engine. To take advantage of this, we maintain a set of machines for grid processing.

Oregon Neuroscience Grid

Our main grid is known as the Oregon Neuroscience Grid (ONG) and consists of twelve compute nodes. Each is equipped with a quad-core Intel Core i7 950 processor and 24 GB of RAM. Log on to danbo.uoregon.edu to set up and launch your jobs.

Data Backups

All DICOM data in the central repository is backed up using a policy designed for a high degree of recoverability. Even so, you are encouraged to make copies of your DICOM data on your own devices for archiving purposes.

Participant response data produced during scan sessions can also be backed up by our backup system. The /Users/Shared/Data directory is synchronized with the backup server each night, so if your presentation program writes to that directory, our backup system will capture your data.

As a courtesy to researchers, all home directories are included in our backup schedule. This helps protect research data and analysis results. In general, such data is retained for one year should a researcher need to recover a file or folder that has been inadvertently removed.