Facilities: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities, pertinent




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FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities, pertinent capabilities, relative proximity, and extent of availability to the project. If research involving Select Agent(s) will occur at any performance site(s), the biocontainment resources available at each site should be described. Under “Other,” identify support services such as machine shop, electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.


Center for Brain Science Neuroimaging Facilities
Waiting and Consenting Rooms

The entrance to the Neuroimaging Facility is comprised of a spacious and comfortable main waiting room with a reception desk. Adjacent to the main waiting room is a separate waiting/play room for children. Another adjacent room is used exclusively for screening and consenting to ensure the privacy of our participants.
Behavioral Testing Rooms

Three rooms for behavioral testing are located outside the scanner suite. One of the rooms is equipped with an infrared eye tracking system and pupil measurement apparatus (EyeLink 1000 Plus, SR Research Ltd., Ottawa, Ontario, Canada) and a system for physiological monitoring (MP150, Biopac Systems, Goleta, CA) allowing for time-locking of stimuli, responses, and eye movement/pupillary data.

Six additional behavioral testing rooms are located at the entrance to the 2nd floor office space and provide quiet and controlled environments for piloting and developing behavioral paradigms.
3.0T Siemens Prisma MRI Scanner Suite

In August 2015, the CBS Neuroimaging Facility upgrade its 3.0 Tesla Siemens MAGNETOM Trio MRI scanner to the state-of-the-art 3.0 Tesla Siemens MAGNETOM Prisma whole-body MRI system. The Prisma MRI system has significant hardware advances and novel capabilities unavailable on other systems. This scanner has a short-bore (2m) magnet, a fast gradient system that provides high-speed structural and functional imaging, and a 64-receiver channel data acquisition system for parallel imaging with acceleration factors up to four-fold, permitting increased temporal resolution and reduced geometric distortions in functional MRI scans. The gradient rise time (200 T/m/s on all three gradient axes simultaneously) and peak gradient strength (80 mT/m per axis), and duty cycle are the most powerful specifications in the industry for whole-body systems (double the current standard gradient strength for advanced human MRI systems). Other novel features include a parallel transmit array to allow B1 shimming, zoomed image field-of-view selection, and selective excitation, all of which improve image uniformity and help to reduce image acquisition time; an all-digital RF chain between the control room and the magnet, which significantly improves RF stability and image SNR; enhanced parallel-receive array hardware, including a 64-channel head/neck array modified to improve subject comfort, increase their vision from the coil, and designed to permit simultaneous EEG or other external equipment, while increasing image SNR over the previous 32-channel coil design used on the former Siemens Trio MRI scanner; modern image reconstruction hardware optimized for rapid reconstruction of images requiring computationally intensive steps, allowing novel image acquisitions to display results in real-time rather than minutes/hours later or require manual offline reconstruction.

The Siemens 64-channel head/neck receive-array coil further enhances image SNR especially for functional MRI, with its significantly improved peripheral image SNR, generally corresponding to the cortex of the human brain. The 64-channel coil for the Prisma system has been designed to permit greater subject comfort with an increased visual field of view for the subjects, and greater accessibility for peripheral equipment including not only eye-tracking cameras, but for equipment that goes inside the coil, such as simultaneous EEG, transcranial direct current stimulation or transcranial magnetic stimulation. An improved 32-channel head receive-array coil and a 20-channel coil are also available.

The Siemens Prisma system is capable of EPI, second order shimming, CINE, MR angiography, diffusion and perfusion studies, and spectroscopy. The sequences available are matched to those of the MGH/HST Athinoula A. Martinos Center for Biomedical Imaging through a Master Research Agreement with Siemens. The MRI Suite also contains (1) a rear projection system, as well as a goggle system with eye-tracking camera (NordicNeuroLab Inc., Miwaukee, WI), for visual presentation; (2) an S14 fMRI Compatible Insert Earphones system (Sensimetrics Corporation, Malden, MA) and a NordicNeuroLab AudioSystem for auditory stimulation; (3) a Biopac MP150 for somatosensory stimulation and physiological monitoring; (4) ergonomic subject response devices; and (5) an EyeLink 1000 fiber-optic eye-tracking system (SR Research, Ottawa, Ontario, Canada). A changing room, keyed storage lockers, and two restrooms are available to participants immediately adjacent to the scanner suite. A dedicated double-locked storage room down the hall from the scanner maintains copies of consent and MRI screening documentation.
Mock Scanner

An MRI simulator or “mock scanner” simulates the real MRI scanner and introduces research subjects, including normal and clinical populations, children and adults, to the scanning environment. The simulator can also be used to develop and test experimental paradigms, and to quickly train new researchers, minimizing the use of costly scanner time for set-up and training. Adjacent to our 3T scanner, the mock scanner (NordicNeuroLab) has a bore diameter of 22” (56cm) (the height from the table to the top of bore is 16.5” (42 cm)), and utilizes a simulated head coil assembly with mounted mirror system.  The simulator is equipped with a sliding patient table, realistic in-bore fans and lighting, and a sound system that mimics the vibrations and pulse sequence noises of an MR imager. The experimental setup includes headphones and rear-mounted monitor for auditory and visual stimulus presentation. Two five-key button box response units are identical to those in the MRI scanner. There is also a system to detect head movement (a small chip containing an accelerometer) and provide biofeedback in the form of interruption of the video presentation. This is useful for training subjects, particularly children, to remain still in the scanner. A comfortable observation area allows family members or caregivers to view the procedure from inside the mock scanner room and cheerful decorations make the space welcoming for children.

Trans-Cranial Magnetic Stimulation

A state-of-the-art system for transcranial magnetic stimulation (TMS) is sited in a room immediately adjacent to the MRI scanner. This location allows subjects to be scanned, TMS applied, and rescanned in rapid succession. The system includes (1) a MagPro X100 with MagOption Magnetic Stimulator; (2) a Cool-B65 A/P (active/placebo for double-blinded studies) dynamic cooled butterfly coil, which is optimized for high repetition rates and long pulse trains, as well as (3) a C-B60 Butterfly Coil; (4) Coil cooler; and (5) an MEP (Motor Evoked Potentials) Monitor, 1 channel EMG amplifier for determination of Motor Threshold (MagVenture, Atlanta GA). A Brainsight 2 Neuronavigation System (Rogue Research, Montreal, Canada) is used to position the TMS coil to target specific brain areas. This technology uses procedures developed for pre-surgical planning. Markers on the coil are imaged with cameras and positioned based on the subject’s own anatomy. An LCD monitor is available for stimulus presentation and software is available for precise time locking of the task paradigm to stimulus presentation.
Computer Facilities

The Neuroimaging IT infrastructure consists of over 15 Linux workstations. In addition a high performance compute cluster is available as part of the larger FAS Research Computing infrastructure. Computing is isolated through virtual hosting within the larger computing environment and is scalable in real time to hundreds of processors if required. The center also leverages storage from the Research Computing group, which hosts multiple Petabytes for the sciences. The storage infrastructure provides multi-site redundancy as well as data replication. All of the center’s workstation, compute, and storage are hosted on a separate, secure network at Harvard University, a private RFC1918 compliant network isolated from the rest of the university through layers of access controls consistent with the Universities security policies. Only vetted users are given accounts. User passwords are always encrypted when traversing the network and host authentication is performed via Kerberos. The only external entry points to the network are via an SSH gateway and Virtual Private Network (VPN) connection requiring two factor authentication. The SSH Gateway only allows access from select hosts at the Martinos Center for Biomedical Imaging at MGH. Connectivity to the cluster and storage is provided via 10G links on an enterprise class Cisco 6509 switch. Oversight is provided by FAS Research Computing, a team of 15+ full-time technical professionals (http://rc.fas.harvard.edu). Available software includes MATLAB (The MathWorks, Natick, MA), SPM, AFNI, FSL Tools, and Analyze (Mayo Clinic, Rochester, Minnesota). Significant internal software development for image and data analysis as well as informatics (e.g., XNAT) is ongoing using HTML, C, C++, Java, FORTRAN, Pascal, Perl and TCL/TK.
Neuroengineering Core

The Center for Brain Science supports a Neuroengineering Core that is available to the Neuroimaging staff and investigators. The Neuroengineering Core consists of two full-time engineers and a Fabrication Laboratory with extensive machine and electronics equipment. Services provided by the Neuroengineering Core include (1) designing and fabricating novel scientific equipment, (2) encouraging the development of technical skills among researchers, (3) facilitating the transfer of existing technologies between laboratories, (4) consulting on equipment purchasing decisions, and (5) assisting with equipment setup. Recent examples of custom fabrication for the Neuroimaging Facilty include the development of a motion detection system for the mock scanner to provide feedback to children and training participants about head motion, fabrication of magnet-compatible ergonomic button boxes for behavioral response acquisition within the MRI scanner, and a trigger/response input device to allow precise time locking for task-based fMRI paradigms.

Conference Room and Common Space

Additional resources include (1) a small conference room for 10 to 15 people outside the scanner suite equipped for video presentation (e.g., for MRI training video viewing), (2) a computer work room adjacent to the scanner equipped with Linux workstations for image viewing and data processing, (3) copiers and other general office equipment, and (4) a kitchen/break room for coffee etc.



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