Facilities and Equipment
The Lane Neuroimaging Laboratory is located on the first floor of the new addition to the Department of Psychiatry at the University of Wisconsin – Madison. It houses a GE 3T scanner for structural and functional brain imaging, an MRI simulator room, an MRI preparation room for pre- and post-scan behavioral measures, image processing areas with extensive computing facilities, and a conference room and office space. All rooms at the Lane Laboratory as well as at remote labs across the campus are networked together and connect to the Internet.
The Laboratory contains GE’s most advanced scanner the 3.0 Tesla Discovery MR750 . It is faster and provides greater image clarity than previous scanners. Researchers and clinicians can obtain images that were previously unimaginable.
GE’s EPIC software can be used to customize neuroimaging research. Stimulus Presentation can be delivered by using an advanced fiber optic goggle system (Avotec). The fiber optic goggles are interfaced with SensoMotoric Instruments eye-tracking system (sampling rate of 50 Hz). This eye-tracking system yields four different analyses: percentage analysis, pictorial analysis, order of object vs. time, and pupil diameter vs. time.
MRI auditory stimulus is presented using a pneumatic headphone system (Avotec). All auditory stimuli are presented through a digital equalizer that is optimized for tone and clarity.
Stabilizing patients to minimize head movement is critical for MRI studies. The lab has two head stabilizing methods: vacuum pillow and foam inserts.
Collection of peripheral, physiological measures in the MRI are done using the Biopac MP150 system. The MP150 system provides high resolution (16 bit), variable sample rates for analog and calculation channels, 16 analog inputs and two analog outputs, digital I/O lines (automatically control other TTL level equipment), and 16 online calculation channels. The MP150 System provides high-speed acquisition (400 kHz aggregate), and Ethernet connectivity. Controlling the Biopac is the software, AcqKnowledge. This software is an interactive program that lets lab members instantly view, measure, analyze, and transform the incoming data.
The ability to collect both cardiac and respiration activity (sampling rate of 1000 Hz) is possible through the manufacturers standard software.
Stimulus presentation is controlled by E-Prime software (Psychology Software Tools Inc.). The fMRI data are uploaded as DICOM files and preprocessed to correct for rigid body motion and image distortion caused by magnetic field inhomogeneity. Several software packages are available for analysis of fMRI data, including SPM99/SPM2/SPM5, SnPM, AFNI, fmristat, FSL, BrainVoyager, MedX, and VoxBo. Morphometric measurements can use AIR, FSL, Freesurfer, or SPM99/2 for coregistration. Both Freesurfer and in-house tools perform manual coregistration (BrainSqueezer) and distortion-based morphometry (DBM) measurements. Manual ROI drawing can use AFNI or an in-house tool (BrainMaker), automated ROI identification can be performed with Freesurfer. Talairach coordinates can be investigated using the Talairach Daemon. Diffusion Tensor Imaging (DTI) uses in-house software for analysis and display. Cortical flatmaps can be created using BrainVoyager.
Image Display is available through a variety of display programs, including AFNI, SPM99/SPM2, BrainVoyager, FSL, Freesurfer, Spamalize, MedX, LORETA, BESA, and VoxBo.
To acclimate patients to the unique environment of the MRI scanner the lab houses a simulation room. This room has a MRI simulator (non-magnetic) that provides the feel of an actual MRI scanner. It is complete with a moving table, lighting, fans, Avotec fiber optic goggle system, and auditory system with two control computers. This room is used to introduce subjects to the identical experimental procedures that they will experience in the actual scanner. This is done to help ensure subject comfort and data quality.
The HERI MRI computing network is located in a temperature controlled secure location at the Department of Psychiatry. All servers and SAN equipment are on generator backed circuits, with UPS to provide power during cutovers. Authentication is provided by Microsoft Active Directory the Department of Psychiatry’s existing authentication schema.
The authentication and file server is Dell 2970 2U server with six 1TB SATA hard drives in a RAID5 configuration. It has 16GB of RAM and two 2.5 GHz processors with 4 processing cores each. Two Broadcom network interfaces aggregated in an 802.3ad link aggregate for 2 Gb/s of total user throughput. Connection to the san will is through 4 Broadcom iSCSI adapters, also aggregated for 4 Gb/s of throughput. This sever will also provide alternative operating system access by way of virtualized environments using Microsoft Windows Server 2008 Datacenter with Hyper-V with hardware virtualization enabled.
The application server is an Apple Xserve with two 4core Intel Xeon processors at 2.5 GHz. It has 8 Gigs of RAM and is equipped with 4 Intel network interface ports. One port is dedicated to a private network for communication with the MRI machine itself. One port will provide user access at 1 Gb/s and two 1GB/s ports proved 802.3ad aggregated access to the SAN.
MRI and Simulator workstations are Dell Optiplex 760 with 2 GB RAM and 3.0 GHz processors with 4 computing cores each. Startech PCI and PCI-ex serial and parallel cards have been installed to complement the existing USB, serial, and parallel connections. They are further equipped with flash media adaptors allowing the make use of SD, MMC and other card formats for data transfer as well.
Facility workstations are comprised of Apple 24 inch iMac computers with 2 GB Ram and 2.6 GHz processors. Using bootcamp, they run either OSX or Windows Vista. The Vista partition is further accessible using Vmware Fusion in OSX as a virtual machine. Vmware Fusion also allows access to other operating systems as necessary. Network printers include a Sharp digital MX2600N color photocopier and numerous HP LaserJet printers.
The SAN comprised of 4 HP DL185 2U chassis with twelve 1TB SATA hard drives. Access to the storage is mediated and controlled by an HP Server running LeftHand Networks SAN/IQ software for management. Initial storage capacity will be 48 TB of raw storage, and 24-36 TB of usable redundant storage. Online disk to disk backup provided by a Sun X4540 48TB 64GB file server
Access to a wide variety of data analysis software is available throughout the lab. Most software packages are installed on every applicable computer in the lab. The following programming languages are actively used and supported: C/C++, Java, Perl, Python, Tcl, IDL (Research Systems Inc.), and Matlab (MathWorks). Standard office-related software packages are ubiquitous, including Microsoft Office, Adobe Photoshop / Illustrator / Acrobat, webpage editors, web browsers, email programs, etc. We use standard software for writing to CD/RW media.