Facilities and Resources
From CNI Wiki
Facilities and Resources
The Stanford Center for Cognitive and Neurobiological Imaging (CNI, http://cni.stanford.edu/), a shared facility dedicated to research and teaching, opened in 2011. The center director is Prof. Brian Wandell, with Prof. Anthony Wagner as co-director, Dr. Robert Dougherty as Research Director, and Dr. Laima Baltusis as the Facility Manager. The CNI supports scientific investigations into the brain that make rigorous connections between neuroscience and society. The CNI mission is to (1) Support neuroscience discovery for enhancing society, (2) Develop and disseminate cognitive and neurobiological imaging methods and (3) Create a structured, safe, and innovative environment for human neuroscience research.
The CNI is equipped with a 3T GE Discovery 750 MR system and and EGI 256-channel MR-compatible EEG system. It is maintained by a dedicated staff who oversee daily operations and maintenance. The CNI is a GE research partner and is supported by an MR Physicist from GE who is dedicated to the center. Further MR Physics support is provided by Dr. Hua Wu, a full-time MR Physicist on staff at the CNI, as well as collaborations with the Stanford Magnetic Resonance Systems Research Lab (MRSRL). In addition to the basic imaging equipment, the CNI has a wide array of state-of-the-art peripheral equipment.
The system is equipped with a standard 8-channel head coil from GE and several coils by NOVA Medical Inc that improve the SNR, including a 32 channel brain array (dimensions: 18.5 cm wide, 21 cm high) for collection of MRI images of the whole brain, and a 16 channel visual array for fMRI of visual cortex (dimensions: 18.5 wide, 10 cm high).
Visual display of stimuli during scan is achieved through one of three systems: A 30 inch diagonal (76 cm, 16:10 aspect ratio) flat panel display built by Resonance Technology, a 47" 3D display by Resonance Technology which provides the ability to easily present different stimuli to each eye, and a data projector that provides a brighter stimulus with a larger field of view than the possible with the LCD displays. Eye movements can be tracked using an MR-compatible SR Research EyeLink 1000 with remote optics.
Auditory stimuli can be presented by low-profile MR-compatible headphones from Resonance Technology or through a custom system that uses bone-conduction transducers.
For collecting subject responses, we have a modular response box system (fORP 932) from Current Designs. This system allows users to swap out various response devices. The output from any of these devices is available from the fORP box via USB keyboard emulation. We have confirmed that the fORP 932 USB interface is polled at 1kHz, allowing response time measurement with 1 millisecond resolution.The response devices that we currently have include a scroll-wheel device, bimanual button boxes, a 5-button response pad, a joystick, and a 4-button stick-style response device.
MRI Simulator (mock scanner): The MRI simulator (Psychology Software Tools, Inc.) is designed to parallel the experience an individual will encounter during an actual MRI scan. The simulator consists of a 12-foot mock scanner with 6-foot tapered bore, motorized table, head coil, head stabilizer system, visual and auditory presentation systems, and equipment for monitoring the subject's response to the training procedure. Two speakers are placed within the bore in order to deliver simulated MR gradient sounds to the subject. Behavior analysis and therapy techniques are used to counter conditioned fear or anxiety experienced in response to the imaging equipment and procedures. In brief, this process involves careful control of the salient stimuli in the imaging environment, systematic gradual exposure to the equipment, personnel and sensations involved in image acquisition. The simulator apparatus is housed in a separate room within the CNI facility.
The simulator allows researchers to train subjects to inhibit body motion during scanning. Typically, the subject will to listen to music, hear a story or watch a movie during the training. This "entertainment" serves as both distraction and immediate reinforcement for inhibiting movement. If the subject exceeds a pre-set movement criterion, the entertainment is automatically interrupted for a brief interval to provide a contingent consequence for body motion. The entertainment resumes when movement is again inhibited below the established criterion. The movement criterion can be adjusted according to the subject's current ability and gradually made more stringent as training progresses. The entire training process usually can be accomplished in one to three 30 minute sessions.
Data collected at the CNI are archived in a permanent database using the Neurobiological Image Management System (NIMS), an open source project developed by the CNI team. NIMS stores and organizes the raw data from the MR scanner as well as physiological measurements from the subject (synchronized with the MR data). NIMS allows data to be shared within the CNI community, in accordance with regulations set forth by the Stanford IRB and the usage policies that apply to each investigator. NIMS is secure, using Stanford's WebAuth authentication system. NIMS also does several automated data preprocessing steps, including DICOM-to-NIFTI conversion, reconstruction of raw k-space data, calculation of regressors from physiological recordings, and generation of automated quality assurance reports. NIMS is built upon a state-of-the art, enterprise-grade platform, including a 100TB ZFS file server running FreeBSD, with nightly off-site data replication to a secondary file server housed at Stanford's Tier 2 grade data center. The data preprocessing is handled by two Linux compute servers: one 16-core server with 384GB of RAM, and a 32-core server with 768GB of RAM. A dedicated web server delivers the NIMS web interface. All machines are interconnected through gigabit ethernet, supplemented with 10Gb links for bandwidth-intensive connections. The entire platform is administered by a professional system administrator.