Functional MRI Core Facility

Bandettini, Peter

Abstract

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 employees) consist of: the facility director, three staff scientists to keep the scanners running, six MRI technologists, an information technology specialist, a programmer, a technical laboratory manager, and an administrative laboratory manger. 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. Since the year 2000 until May of 2014, a total of 926 publications have made use of the core facility. The total is divided among 611 for NIMH, 235 from NINDS, and 51 from NICHD, and 29 from NIAAA). These papers have been cited 67,863 times for a combined h-index of 131. This year, we have continued to increase the overall utility of the fMRI core facility. The quality and depth of our specific collaborations with users has increased. We have also been extremely fortunate to have hired Dr. J. Andrew Derbyshire to replace the vacancy left by Dr. Wenming Luh. Dr. Derbyshire brings considerable and unique expertise to the Functional MRI Core Facility as he has pioneered a multitude of fast imaging techniques and has spent many years performing Cardiac MRI development. He has hit the ground running as he's deeply engaged in developing optical-based prospective motion tracking for the scanners. IT accomplishments (mostly from Roark Maccado, Joe Naegele, Souheil Inati, and Sean Marrett): In collaboration with NIH networking infrastructure team: Identified bottlenecks and carried out network access speed analysis throughout imaging center and IRP. Configured and purchased new FMRIF networking infrastructure that will increase access speeds to imaging and central computing cluster from less than 500Mbps to greater than 10Gbps (with IT staff) Optimized backup strategy to ensure faster and more routine tape backups on all critical FMRIF systems. (with IT staff) As member of NIMH bioinformatics committee, advocated for and configured new IRP computing cluster (funded by SD office) that will function as NIMH dedicated--central NIH Biowulf computing cluster. This will improve significantly compute and storage resources available to NIMH and NINDS FMRI imaging community. Imaging/subject interface work: Tested and integrated new prospective motion correction system on 3T-D using high-speeed video tracking of Moire-pattern markers (with Andy Derbyshire and Souheil Inati) Ongoing evaluation of TSNR tradeoffs with multi-band pulse sequences at 7T and 3T. Identified bottleneck in reconstruction at 7T with a GPU based solution that should make this sequence useable with 7T scanner (with Souheil and Dan H) Improved performance of optical-audio delivery system on 7T Evaluated, configured, installed and tested new eye-camera system on 3T-C, pending installation on 3T-A and 3T-D. Established routine high resolution scanning protocol at 7T (1.2mm3) using sinusoidal read-out EPI sequence (with Souheil and Chris Baker group) Improved routine physiological monitoring using GE respiratory belts with Biopac on 7T and established routine GSR recording protocol on 3T-C. Specific Staff Scientist Accomplishments: Souheil Inati: Dr. Inati has continued to be essential for the development of Siemens pulse sequences as well as tools for performing rapid automated image reconstruction, analysis, and off-line storage. He continued the collaboration with Michael Hansen and Peter Kellman of NHLBI on vendor neutral image reconstruction algorithms and infrastructure: 1) a raw data format for MRI (ISMRMRD) and image reconstruction framework (Gadgetron). He has improved on his algorithm for optimal combination of images from multiple receiver coils, substantially increasing its speed and improving overall performance. This algorithm is being considered for incorporation into the image reconstruction pipelines of several vendors. He has developed a new algorithm for reconstructing images from accelerated acquisitions that combines the robustness of GRAPPA with the SNR efficiency of SENSE. He has implemented an image reconstruction pipeline for echo planar imaging (EPI) pulse sequences supporting acceleration (GRAPPA) and multi-echo acquisitions using the Gadgetron image reconstruction framework (see above). This pipeline supports the product EPI pulse sequences from both GE and Siemens, and can be used as a drop-in replacement for the vendors proprietary algorithms in a manner transparent to the user. This is the first step in a major project to produce a set of pulse sequences and image reconstruction algorithms that perform in an identical fashion on the different platforms to enable true multi-platform/multi-site studies. He has continued the collaboration with Daniel Reich and members of his group in NINDS on several projects on high resolution anatomical images of cortical lesions in Multiple Sclerosis. The main effort this year has been focused on the incorporation of high resolution T1 mapping with B1 corrections at 7T. He has continued the collaboration with Peter Bandettinis group in NIMH (Section for Functional Imaging Methods) on the development and validation of denoising methods based on multi-echo EPI. He continued a large scale study using multi-echo fMRI of task and resting state fMRI comparing Autism Spectrum Disorder patients to typically developing normal controls in collaboration with Alex Martin, Steve Gotts, Ziad Saad and Bob Cox of NIMH. Vinai Roopchansingh: Dr. Roopchansingh continues to make himself useful as the interface person between the technologists, users, and staff scientists - an extremely difficult job that he handles with rare skill and dexterity. Below are specifics: - He collaborated with Bandettinis group and Sook Lei Liew on a project to determine how reaction time and training on a motor task interacted with Neuro-feedback performance. - He helped Danny Pine set up a several multi-site collaborations. One involves University of Wisconsin Madison and Vanderbilt, examining neural correlates of pediatric anxiety disorders with task and resting state FMRI, and DTI. The second is with University of Maryland, University of Minnesota, and Oregon, and attempting to look at how attention bias modification therapy changes the neural correlates of attention. - And finally, as part of the NIH CRADA with GE, hes been working with GE scientists, as well as Francois Lalonde, Lalith Talagala and Joelle Sarlls on the GE PROMO software. When we implemented the T1 sequence, he had to enhance it to acquire multi-echo motion-compensated MP-RAGE data. Evaluation of the sequence and its efficacy continues as part of this collaboration. He has organized FMRIF documentation, and has placed it online. He has worked with Joe Naegele and Souheil Inati to implement the reconstruction of our first production sequence running on the Gadgetron (Our sequence is: B0 mapping on the MR-750). Gadgetron is described above. - He has worked extensively with our scientific director and users to maintain and develop the scanner schedule in a fair and transparent manner.