Overview
The MR Research Center (MRRC) is a state of the art facility located on the 8th floor of Presbyterian University Hospital (PUH) with a satellite facility in Biological Science Tower 3 (BST3) located 5 min. walk from the MRRC, a University of Pittsburgh Building. The MRRC at PUH houses and operates three 3T Siemens Prisma systems and a 7T Siemens Terra.X system. The BST3 building houses another 7T human whole body Siemens system.
Equipment Inventory Summary
Available Sequences
| Sequence (Developer) | Prisma 1 VE11C |
Prisma 2 VE11C |
Prisma 3 VE11E |
| SMS EPI (Siemens) | ✓ | ✓ | ✓ |
| SMS EPI (CMRR) | ✓ | ✓ | ✓ |
| SMS EPI (ABCD) | ✓ | ✓ | ✓ |
| vNAV T1MPRAGE/T2SPACE (ABCD) | ✓ | ✓ | ✓ |
| RESOLVE | ✓ | ✓ | ✓ |
| ZOOMit | ✓ | ✓ | ✓ |
| ASL/pCASL (Siemens/Wang/Kim) | ✓ | ✓ | ✓ |
| Single Voxel Spectroscopy (e.g., MEGA-PRESS) | ✓ | ✓ | ✓ |
| Multi-nuclear Spectroscopy | ✓ | ||
| RSI (Pang) | ✓ | ✓ | ✓ |
| Neuromelanin (Moon) | ✓ | ✓ | ✓ |
| Online T1/T2 mapping w/ B1 correction | ✓ | ||
| SyngoTWIST dynamic contrast angiogram | ✓ | ||
| TRUST (Lu) | ✓ |
Coils
| Compatible with: | ||||
| Coils | Quantity | Prisma 1 | Prisma 2 | Prisma 3 |
| 20-channel head coil | 3 | ✓ | ✓ | ✓ |
| 32-channel head coil | 2 | ✓ | ✓ | ✓ |
| 64-channel head and neck coil | 3 | ✓ | ✓ | ✓ |
| 8-channel flexible coil (small/large) | 3 | ✓ | ✓ | ✓ |
| Knee coil | 2 | ✓ | ✓ | ✓ |
| Shoulder coil (small/large) | 1 | ✓ | ✓ | ✓ |
| 1H/31P coil | 1 | ✓ | ||
| mMR-specific body coil | 1 | |||
| Spine coil | 4 | ✓ | ✓ | ✓ |
Software and Other Equipment
| Compatible with: | |||||
| Software/Equipment | Quantity | Prisma 1 | Prisma 2 | Prisma 3 | |
| Contrast Injector for Dynamic Contrast Enhancement | 2 | ✓ | |||
| Stimulus Presentation Windows PC | 4 | ✓ | ✓ | ✓ | |
| Matlab | 4 | ✓ | ✓ | ✓ | |
| ePrime 1 | 1 | ||||
| ePrime 2 | 4 | ✓ | ✓ | ✓ | |
| ePrime 3 | 3 | ✓ | ✓ | ✓ | |
| Celeritas FORS (Fiber Optic Response System) Gloves/Buttons | 3 | ✓ | ✓ | ✓ | |
| Celeritas FORS (Fiber Optic Response System) Joystick | 2 | ✓ | ✓ | ||
| Avotec Projector (1024x768) | 3 | ✓ | ✓ | ✓ | |
| Psychology Software Tools Projector (1024x768) | 1 | ||||
| Avotec Silent Scan Audio System | 4 | ✓ | ✓ | ✓ | |
| Avotec Eye Tracking System | 3 | ✓ | ✓ | ✓ | |
| SR Research Eye Tracking System | 2 | ✓ | ✓ | ||
| ASL Eye Tracking System | 1 | ||||
| Fiber Optic Mouse by NAtA Technologies | 3 | ✓ | ✓ | ✓ | |
Phantoms
- small ADNI for 64ch coil (qty: 1)
- ADNI for 20ch coil (qty: 2)
- FBIRN (qty: 3)
- bullet (qty: 3)
- Siemens ball (qty: 2 sets)
- ACR for mMR(qty: 1)
- small bullet for mMR (qty: 6)
- traditional ACR (qty: 1)
Detailed Equipment Descriptions
The following text may be useful for grant submissions:
7T Human Systems
Terra.X: The Siemens Terra.X 7T system is currently being installed in the 8th floor PUH facility. Research scanning will be available in May 2025. The system has 32 independent receive channels and 8 independent transmit channels. The 8Tx32Rx Head coil is a 1H (proton) RF-coil with 8 transmit and 32 receive channels used for head applications usable in the 8ch pTx Mode. The system has a hardware adaptor to connect single Tx local RF coils to the pTx system, combining the 8Tx channels to a single channel. We will have access to the following coils: 8Tx32Rx 1H head coil (Nova Medical), 16Tx head coil (RRI), 1Tx28Rx knee coil (QED), and coils designed by the 7TBRP. A high order shim (RRI) will be available. The system is multinuclear imaging capable (13C, 19F, 23Na, 31P). Visual stimulus presentation will be supported by the Cambridge Research Systems BOLD screen, a 32" UHD monitor. Gradient strength = 135 mT/m at 250 T/m/s. Bore diameter = 60cm. Max weight = 400 pounds.
BST 7T: The 7T Siemens whole body human system was installed in 2007 and has 32 independent receive channels, and 8 independent transmit channels. A variety of transceiver arrays including 8x1 8x2 and 16x1 (coils per row x rows) are available for 1H studies. The coils with greater than 8 channels are supported by a set of configurable 8->16 channel splitters. The 8x2 transceiver array includes an integrated eye tracking and mirror system within the RF coil shell for stimulus presentation. A double frequency (1H/31P) 8x1 transceiver array is also available. A very high order shim insert (Resonance Research Inc., all 2nd-4th degree shims + 4 5th degree shims) is available to support MRSI and EPI based imaging. The system is equipped with 10A power supplies and dynamic updating (100us switching time). In December of 2016, the 7T system was upgraded to Step 2.3. In Fall 2024, the 7T system was updated to the 7Tplus platform. This system is located at BST3. Click here for more information about bioengineering-specific equipment for the 7T system. Max weight = 250 pounds.
3T Prisma 1
This system was installed in March of 2016, and is a 64-channel system equipped with Connectome level gradients operating at 80mT/m. The Prisma system features new electronics, with the first stage of mix down located at the RF coil interface and the RF amplifiers mounted to the magnet. The system is equipped with an fMRI paradigm presentation system for functional studies. The system is equipped with a 64 channel head and neck receive only array and a variety of standard RF coils for imaging of the spine and body. The system is equipped with an fMRI paradigm presentation system for functional studies including E-Prime for stimulus presentation, an Avotec MR compatible video projector, Celeritas response gloves, an Avotec eye tracking system and an Avotec audio system with low profile headphones. The system can perform 1H spectroscopy but is not currently capable of multinuclear MR spectroscopy. This system is located at PUH. Prisma 1 has the largest control room and is partiularly well-suited for large study teams and studies requiring auxillary machines/equipment. Bore diameter = 60cm. Max circumference = 188.5 cm or 6'2". Max weight = 550 pounds.3T Prisma 2
This system was installed in January of 2018, and is a 128-channel system equipped with Connectome level gradients operating at 80mT/m. The Prisma system features new electronics, with the first stage of mix down located at the RF coil interface and the RF amplifiers mounted to the magnet. The system is equipped with 32 and 64 channel head and neck receive only arrays and a variety of standard RF coils for imaging of the spine and body. The system is equipped with an fMRI paradigm presentation system for functional studies including E-Prime for stimulus presentation, an Avotec MR compatible video projector, Celeritas response gloves, an Avotec eye tracking system and an Avotec audio system with low profile headphones. The system can perform 1H spectroscopy and multinuclear MR spectroscopy. This system is located at PUH. Bore diameter = 60cm. Max circumference = 188.5 cm or 6'2". Max weight = 550 pounds.3T Prisma 3
This system was installed in June of 2020, and is a 64-channel system equipped with Connectome level gradients operating at 80mT/m. The Prisma system features new electronics, with the first stage of mix down located at the RF coil interface and the RF amplifiers mounted to the magnet. The system is equipped with 32 and 64 channel head and neck receive only arrays and a variety of standard RF coils for imaging of the spine and body. The system is equipped with an fMRI paradigm presentation system for functional studies including E-Prime for stimulus presentation, an Avotec MR compatible video projector, Celeritas response gloves, an Avotec eye tracking system and an Avotec audio system with low profile headphones. The system can perform 1H spectroscopy but is not currently capable of multinuclear MR spectroscopy. This system is located at PUH. Bore diameter = 60cm. Max circumference = 188.5 cm or 6'2". Max weight = 550 pounds.Other Resources
The MRRC has an electronics machine shop for fabrication and repairs of support equipment. A decommissioned 3T Trio and PST head motion tracker is available for acclimating subjects to the magnet environment. All three Prisma scanners have an associated locker/changing room and practice room equipped with ePrime computer for training participants on experimental paradigms. The MRRC has a shared consenting room and procedure room (a hospital-style room typically used to install IVs by studies that require contrast).Computing, Networking, and Data Transfer
As of Summer 2024, the MRRC is pilot testing an on-premises (i.e., cloud-free) instance of flywheel.io's XNAT-like data management software that we hope to eventually offer to the center’s users. Flywheel is a modern web and command line interface for MR imaging ingestion, curation, and provenance tracking. Flywheel can match input pushed directly from the scanner against rules for additional analysis with "gears" (specialized docker containers). The web interface allows a non-expert to upload and/or manually run pipelines. Raw imaging data and gear output can be downloaded from the web, synced to a file-system with the CLI tools, or programmatically accessed with the SDK (python or Matlab). To timely process large batches, Flywheel analysis can be sent to high-performance computing on the MRRC's own compute cluster. For more information, please reach out to the Neuroimaging Processing and Analytics Core Lead, Will Foran.
Three independent, but interconnected, LAN's support the operation of the MRRC, a research network, an administrative network and a scanner network. The computational power for the research network is supplied by multiple server resources. These resources include an eight node linux CPU cluster providing 16 Intel Xeon E5-2690 2.90GHz Eight-Core Processors, 2 TB DDR3-1600 Reg ECC Memory and operating on 6Gb/s Interface Solid State Drives. Another resource is a linux GPU cluster with four Nvidia M2090 GPUs, two Intel Xeon E5-2667 2.90GHz Six-Core Processors, 256GB DDR3-1600 Reg ECC Memory and operating on 6Gb/s Interface Solid State Drives. The MRRC also utilizes a Linux server with Two (2) EPYC 7742 2.25 GHz Sixty-Four-Core 225W Processors, 2048GB DDR4 3200MHz (32 x 64GB Sticks), Two (2) 500GB SSD (Mirror OS), 145TB Enterprise Class Storage dedicated to research faculty and 200TB of online data storage for MRRC users.
Access to the servers is performed through multiple Linux, Macintosh, and Windows workstations. The cluster resources are connected via InfiniBand Switch. All computers on the research network are interconnected by a 1Gb/s LAN. Commercial software for image analysis (AVS, SAGE, IDL, Analyze, MATLAB) as well as freeware packages (FSL, SPM, MIPAV) complements the development of customized software for individual projects. The MRRC's compute infrastructure is supported by a team of experts spanning many technological domains.