Functional MRI Core Facility

Bandettini, Peter

Abstract

Protocol number 93-M-0170, NCT00001360 Space Utilization: The Functional MRI Facility (FMRIF) currently occupies approximately 4800 sq. ft of space, divided between the scanner bays, control rooms and electronics/machine rooms for 3TA, 3TB, 3TC, 3TD, and 7T MRI scanners located within the NMR center and office space on the second floor above the NMR center in the FMRIF/SFIM suite (approximately 1400 sq ft total, including shared conference space). Staff: The FMRIF staff (currently 14 full- time positions) consists of: the facility director, four staff scientists to keep the scanners running, six MRI technologists, an information technology specialist, a programmer, and an administrative laboratory manger. Investigators: The functional MRI facility supports the research of over 30 Principal Investigators translating to over 300 researchers overall. Over 70 research protocols are active and making use of FMRIF scanners. Each scanner has scheduled operating hours of 105 hours per week. Papers published using the core: Since its inception in 2000 until August 2018, a total of 1,147 peer-reviewed publications from intramural investigators have used data acquired in the FMRIF core facility. The total is distributed among 759 papers from NIMH, 287 papers from NINDS, and 101 from the other institutes. These papers have been cited a total of 118,077 times for a combined h-index of 170. In other words, 170 papers using the FMRIF have been cited at least 170 times. Projects of the Staff Scientists in the core: Projects: Staff Scientists working on projects are designated as: Sean Marrett (SM), Vinai Roopchansingh (VR), Andy Derbyshire (AD), and Linqing Li (LL). Other staff are Jan Varada (JV) and Roark Maccado (RM). These projects span subject interface, hardware development and implementation, pulse sequence development, and software and computing development. Pulse Sequence and Scan Protocol Development: AD has been developing new pulse sequences (specifically EPI) to allow finer control of the gradient waveform and acquisition to take advantage of the improved gradient performance and to provide additional fine tuning / calibration with the head gradient system. AD adopted the maintenance of the mcDESPOT suite of MR pulse sequences for the GE Signa platform. We have ported/migrated the sequences (3D fgre and 3D balanced SSFP) to use the current MR750 platform sequence (i.e. DV26R1) as the base sequence. AD developed a variable flip-angle multi-echo EPI sequence to for simultaneous measurement of BOLD fMRI signals and T1 maps was developed as part of a student project (Vincent Mao) during the summer of 2017. The results were presented at ISMRM 2018. AD continued supporting the development of a 3D-EPI sequence for high resolution susceptibility weighted imaging for the detection of MS plaques with a central vein (Danny Reich NINDS). This work involves maintaining pulse sequences for sites in their multi-center initiative, as well as improving the existing sequence e.g. adding multi-dimensional acceleration and motion correction. AD is developing common pulse sequence components to develop standardized (to the limits of the MR hardware) pulse sequences across various MRI platforms. This is analogous to the complementary efforts to employ vendor independent reconstructions LL has been collaborating with Yahui Chai (SFIM) to implement a novel highl resolution blood volume change sensitive approach (DANTE-EPI) to mapping layer-specific activity at 3T and 7T. LL has been collaborating with the MRS core facility to optimize a sequence for accurately measuring T1 and T2 values for metabolites without the need for varying TE. The sequence is called multiple flip angle pulse-driven ratio of longitudinal steady states (MARzss). This work is under consideration for being patented, and is planned to be published shortly. SM collaborated with Grillon group (Torrisi) using high-resolution SMS imaging sequences on the 7T scanner for routine whole brain 1.2mm3 including imaging bed nucleus of stria terminalis (Montreal resting state conference poster) SM collaborated with Laurentius Huber (SFIM) and Joe Murphy-Boesch (FMRIF) on integrating new high-resolution custom array coil from MRCoils for use on our 7T including B1 field characterization and design/debugging of interface. Software and Computing: AD has assisted the data sharing team by helping to identify missing meta-data from GE Dicom MR images. AD provided support for Siemens MR IDEA pulse sequence and ICE reconstruction development by FMRIF users. We maintain virtual machines containing the Siemens VB17A, VD13A, VD13D and VE11C and VE11U environments to support pulse sequence development for the Siemens Skra, Prisma, 7T and incoming Terra scanners. VR has continued his involvement with the ISMRMRD and Gadgetron projects. Over the last year, he has openly made available (in a public GitHub repository) a template ISMRMRD converter that converts data from General Electric scanners into the ISMRMRD format. VR has developed an B0-based distortion correction pipeline using AFNI tools (with guidance and help from Bob Cox). This work was presented as an ISMRM poster this year. VR has taken the AFNI demonstration software for neurofeedback, and re-implemented it using the PsychoPy framework. That is now publicly available here: https://github.com/roopchansinghv/afni-fmrif-neurofeedback-toolbox JV developed a set of python tools for automated BIDS data conversion and archiving software package. This is a complete refactoring and rewrite of our current archiving system to enhance image data security while improving usability so that BIDS can be deployed automatically and also allows searching and querying vast trove of FMRIF neuroimaging data. The source code is available at https://github.com/nih-fmrif/fmrif_tools RM deployed Mac systems for all technologists and Dorian using remote desktop infrastructure and agents. RM upgraded the VMWare virtual infrastructure to take advantage of improved network capabilities. SM installed and debugged a new 7T host to allow for more aggressive high-resolution scanning of humans using faster CPU and expanded storage. JV automated MRI QA for human data collected at FMRIF (still deploying additional storage and compute resources so that this becomes available for all data automatically as it is collected) Subject Interface: SM Installed and tested SR-research eye tracking system on 3TB, in process of designing system for 3TC and 7T projection systems. SM installed a new optoacoustic audio system installed and trained on 3TB and 3TC (Pine group) SM has ongoing projects to acquire and deploy new high quality video projection system on 7T and new high quality audio systems for 3TD and 3TB. Hardware development and implementation: SM worked with Peter Molfese on high density EEG acquisition procedures (256 channel system) using EGI system and training of NIMH technologists and others on new system. AD and SM collaborated with Joelle Sarlls and Lalith Talagala using video-based system for prospective motion correction on 3TD RM restructured 3TD control room and rewired 3TC cabinet. AD is planning for the integration of the high performance head gradient system (Pierpaoli-NIBIB with Brian Rutt - Stanford) with the FMRIF 3TB scanner. The integration will require modifications to the chilled water supply for the system and the gradient electrical connections for the system.