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 15 full time employees) consist of: the facility director, four staff scientists to keep the scanners running, eight MRI technologists, an information technology (IT) specialist, and an administrative lab manager. The functional MRI facility supports the research of over 30 Principal Investigators which translates 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 Sep 2012, a total of 802 (79 papers in just the last year) publications have made use of the core facility. The total is divided among 537 for NIMH, 213 from NINDS, and 62 from the other institutes). These papers have been cited 50,507 times for a combined h-index of 114. This year, we have continued to increase the overall utility of the fMRI core facility. As we adjust our personnel to accommodate some budget cuts, we continue to increase efficiency and availability of cutting edge fMRI and MRI scanning capability. In particular the quality and depth of our specific collaborations with users has increased. To increase the effectiveness of our technologists, we have re-assigned Dr. Vinai Roopchansingh to the position of Technical Laboratory Manager to oversee their day to day operations and serve as the interface between the core staff scientists and the technologists and users on a day to day basis. B IT accomplishments (mostly from Adam Thomas and Sean Marrett): - All of the data collected on FMRIF scanners since approximately 2004 -- more than 20 TB has been transferred from off-line tape storage to on-line disk archive, vastly reducing time and effort needed for retrieval and potential meta-analysis of MRI data from years past. We have also eliminated the Intelerad Image archiving system and replaced it with an simple searchable system built by an in-house developer (Joe Naegele). This will eliminate the $15k/year support fees previously paid to Intelerad. - All computing and storage infrastructure has been moved from shared space in the MR machine room (with vulnerability to power loss and environmental hazards) to a dedicated custom-build computing facility owned by and shared with NINDS. This state-of-the-art server room is fully compliant with all NIH and HHS mandated policies and procedures for data storage. It has been built with temperature and climate control, UPS backup, and card key access, and security cameras;all of which can be monitored remotely and set to trigger notification alarms to the appropriate staff. This will dramatically increase the reliability and security of all FMRIF servers and data. - All scanner data access to scanner data as well as access to the FMRIF web site is now authenticated via the NIH single sign on system. This is convenient for users in that they have only one password to remember. It also ensure that access passwords are regularly changed, that access to FMRIF resource is terminated immediately when researchers end their time at NIH, and provides a centrally accessible audit trail for access to all FMRIF resources. Stimulus/user interface accomplishments (Sean Marrett and Adam Thomas): - New eye tracking system has been developed and debugged on 3T-C which can be used for pediatric studies (in collaboration with LBC and SIN/GCAP) - New audio system with active noise cancellation has been installed for 7T - New high-speed back projection systems for 3TD has been installed. 7T accomplishments: - A cortical surface model extraction and post-processing procedures developed for 7T (with Souheil Inati ) - Single trial FMRI studies on 7T ( with Souheil, Chris Baker and Dwight Kravitz) takes advantage of increased signal/noise available on 7T to use individual responses from large number (750+) of stimuli which are presented to subject only once. This presents opportunity for novel experimental designs for single-subject studies (e.g. for biomarkers of disease in individuals). Specific Staff Scientist Accomplishments: Souheil Inati: - Discovered an artifact in FMRI images acquired with acceleration and reconstructed with the GRAPPA algorithm on the Siemens scanners. This artifact resulted in substantially reduced temporal signal to noise ratio and was due to a previously unknown interaction between the acquisition of accelerated echo planar imaging and parallel imaging reconstruction. The product Siemens pulse sequence was modified and a Works in Progress package was released by Siemens implementing this fix. This is a collaboration with Lalith Talagala from NINDS, Peter Kellman from NHLBI, and Sunil Patil from Siemens. - Implemented a method for improving the registration between functional images (gradient-echo EPI) and anatomical images. The method required the implementation of a pulse sequence, image reconstruction, and synthetic image generation. The pulse sequence was implemented on the Siemens scanner. The image reconstruction and synthetic image generation was implemented in collaboration the Gadgetron, an open-source image reconstruction framework written by Michael Hansen in NHLBI. I am now working with Vinai Roopchansingh on an implementation on the GE scanners. This is a collaboration with Pablo Velasco from NYU. - Implemented a pulse sequence to measure the B1 (flip angle) distribution in the brain on the Siemens scanner. This measurement will allow us to remove a systematic bias in T1 maps generated from multiple flip angle GRE scans. This is a key component of longitudinal and multi-site anatomical imaging protocols. This is a collaboration with Qi Duan from NINDS and Govind Nair from NINDS. - Developed a high-resolution 3T anatomical imaging battery for longitudinal studies on the Siemens scanner consisting of optimized protocols with multiple contrasts. This is a collaboration with Govind Nair from NINDS. Began work on developing analysis methods based on these type of data for tissue classification and segmentation with Ziad Saad from NIMH. - Modified the Siemens product spin-echo DWI pulse sequence to collect images of alternate phase encode polarity. This reverses the geometric distortions inherent in EPI and allows for substantially increased accuracy in registration of diffusion images to anatomical images. - Developed and implemented a new algorithm for combining MR images form multiple receiver coils. This significantly improves imaging with multiple receiver coils in situations where the phase of the image is important (SWI, flow, etc.). This is a collaboration with Peter Kellman and Michael Hansen in NHLBI. Working with Sunil Patil from Siemens on incorporating into the Siemens product. Wenming Luh: - We have made available the multi-echo MPRAGE T1 weighted pulse sequence. MPRAGE is performed routinely to obtain T1-weighted 3D brain images with high spatial resolution and tissue contrast for accessing gray matter thickness and anatomical landmarks. The multi-echo version allows better discerning of dura and cortical gray matter to estimate gray matter thickness more accurately. - We have started to provide the multi-echo echo-planar image pulse sequence to the community. This technique can differentiate BOLD and non-BOLD signal in a functional MRI dataset and is effective in minimizing unwanted fluctuations.