LCNI resources and
instructions for researchers:
LCNI houses a 3T Siemens Allegra (head only) MRI system and a range of
image processing facilities. We provide a full range of supporting
equipment, software, and expertise, from coil development to
statistical analysis.
In addition to the systems outlined below, we are able to accomodate
most
research specific equipment.
MRI system
MRI system equipment
3T Siemens Allegra, Siemens
NUMARIS/4, syngo MR 2004 A
proton and multi-nuclear
spectroscopy capabilities
specialty coils and coil
development
Requirements for research use of MRI system
safety certification
human subject approval
informed consent
magnet time reservation
Seimens dedicated image processing workstation
(Leonardo)
Setting up for scanning
Subject preparation instructions
MRI system peripheral equipment
Visual
stimuli equipment and overview
Projection instructions
Auditory stimuli equipment and overview
Sound system instructions
Eye tracker
equipment and overview
Eye tracker
instructions
Subject
response equipment and instructions
Physiological monitoring equipment and instructions
Simulator equipment and overview
Simulator instructions
Data handling and archive
The Center's primary data storage is held on a Sunfire
V880 machine with 500 gigabytes of disk storage in a RAID 5
configuration. Data backups to a robotic tape array are performed each
evening, and archive tapes are regularly moved to an offsite location.
Raw data from the MRI system is typically placed into research group
folders by the center's MRI technologist. All raw data is in a DICOM
format. No subject names are embedded in these files, and all data
privacy is maintained. The Center also maintains a confidential key
linking a human subject identification number with any personal
information.
Instructions
Accessing your files in
research group folders
File/directory conversion and renaming with MRIConvert
Software
stimulus
Presentation ( Neurobehavioral Systems
)
data acquisition
MRI system software: Siemens
NUMARIS/4, syngo MR 2004 A
many sequence types available:
structural, angio, functional, DTI, spectroscopy, etc.
ASL eyetracker acquisition and analysis
data handling, file conversion
eFilm ( Merge eFilm )
MRIConvert ,
LCNI
data analysis
BrainVoyager ( Brain Innovation )
Using BrainVoyager
Importing data into BrainVoyager
Basic
processing using BrainVoyager
FSL
(http://www.fmrib.ox.ac.uk/fsl/ )
ASL eyetracker analysis
data visualization
MRIcro
Space
, LCNI
general
Photoshop,
AutoCad,
etc.
other other common software tools, links to
SPM
AFNI
Free medical image conversion,
viewing, visualization and image analysis programs: idoimaging.com
Computational resources
The Center maintains a number of single and dual-processor
workstations running a variety of operating systems, including Windows
2000, Windows XP, Solaris, Linux, and Mac OS X. These machines are
equipped with software for tasks ranging from email to MR spectroscopy.
The Center also has available a 16-processor SMP cluster with 32
gigabytes of RAM for performing compute-intensive tasks. Center staff
can assist in scheduling time on the cluster for processing or special
development projects.
The Center's network connections are also made available to researcher
laptops via wired and wireless protocols.
Other equipment
Additional equipment is also available for use within the
Center. This equipment includes color and black & white printers,
document scanners with optical character recognition software, digital
cameras that can be used to document special equipment setups and
configurations, a variety of digital media for storing and transferring
data, and presentation equipment.
Reference materials
The Center's conference room houses a small library of
reference texts relevant to NMR and MRI.
Current paper journals include:
Human Brain Mapping
Journal of Magnetic Resonance Imaging
Magnetic Resonance in Medicine
NeuroImage
Radiology