Facilities and Resources

3T MRI Program | MEG | 9.4T MRI Program

The Hoglund Brain Imaging Center (HBIC) occupies a free-standing 11,500 sq. ft. research-based imaging facility on the KUMC campus and provides outstanding imaging capabilities, including magnetic resonance imaging, magnetoencephalolgraphy, electroencephalography, magnetocardiography, and ultrasound, to complement the existing biomedical research community at KUMC and nearby universities. HBIC brings scientists from diverse disciplines such as neurology, neurosurgery, radiology, nephrology, cardiology, psychiatry, psychology, preventive medicine, nursing, physiology, biochemistry, anatomy, medical physics, engineering, and computer science together in a highly collaborative and integrative environment. A further strength of the HBIC is its close proximity to the KU Hospital, providing optimal access for research participants.

The HBIC provides considerable support to investigators through a strong faculty with broad expertise in cognitive neuroscience, neurobiology, biomedical physics, and computing, together with a support team of technologists, nurses, research associates, and research assistants. Through strong collaborations, these individuals assist with study design, collection of data, analysis, and interpretation of results. The HBIC also supports investigators with new technique development, feasibility studies, pilot funding, preparing grant applications and manuscripts, and compliance.

The HBIC carries out investigator-initiated research and research/clinical trials sponsored by public and private agencies. In addition, the HBIC offers an excellent environment for education and training. Students at all levels, both in the clinical and basic sciences, are encouraged to enhance their educational experience by working with state-of-the-art equipment as well as with outstanding faculty. 

3T MRI Program

brooks with scannerThe research program is multidisciplinary including but not limited to collaborations between psychologists, neurologists, physicists, exercise physiologists, physical therapists, and nurses. Ongoing research studies use both structural and functional MRI to study brain responses associated reward processing, decision-making, emotion, motor control, and memory in both children and adults. These studies take advantage of the sophisticated imaging capabilities and data analysis facilities available at Hoglund Brain Imaging Center to examine a wide variety of topic areas and populations including obesity, addiction, Alzheimer's disease, stroke, obsessive compulsive disorder, depression, and autism.

Human Imaging Studies

Magnetic Resonance Imaging System: A 3 Tesla Siemens Skyra MRI scanner funded through a National Institutes of Health High End Instrumentation grant provides a full array of standard and additional features including a variety of clinical MRI and MRS protocols, various head and body receive coils including a 32-channel head coil array.  An AutoAlign option provides an accurate and reproducible positioning of imaging slices in the brain, which ensures reliability of longitudinal studies proposed in this work. The MRI scanner is networked to our XNAT server to provide seamless transfer of MRI data to principal investigators and their research staff for analysis.

 Patient monitoring and physiological recording: An MRI-compatible system (BIOPAC MP150 Data Acquisition and AcqKnowledge software) is used for recording physiological signals including respiration, pulse, and electrodermal activity. These signals are used as input into functional imaging analyses. MRI compatible EMG is also available (BrainVision). Additionally, an MRI compatible pulse oximetry, blood pressure monitoring, and EKG recording system (InVivoMetrics) is synchronized with the scanner to facilitate physiological gating of acquisitions.

Experimental presentation: Experimental presentation and collection software is available on a workstation interfaced to the scanner: E-Prime 2.0 (Psychology Software Tools, Inc., Sharpsburg, PA), Presentation (Neurobehavioral Systems, Inc., Berkeley, CA)


Magnetoencephalography facilities include a 151-Channel whole head biomagnetometer system (CTF/VSM). This unit, which can be operated while a subject is either sitting or supine, consists of SQUID-coupled axial gradiometers arrayed within a helmet shaped cryogenic dewar. The unit is housed within a magnetically and electrically shielded room. System electronics allow for recording of neuromagnetic signals within a bandpass of 0-3000 Hz, with a digitization rate of up to 12KHz. Data can be recorded in both continuous and epoch modes. The system is also capable of recording 64 channels of simultaneous EEG. As needed, EEG channels can also be used to record EOG, ECG, EMG or a galvanic skin response. Associated with the system is a 3D position digitizer (Polhemus) that can be used to define the spatial location of fiduciary points on the head, the positions of EEG electrodes, and the overall head shape.

Fetal Magnetoencephalography (fMEG)

Fetal MEG

Fetal Biomagnetometer/Magnetocardiography: The fetal Biomagnetometer (CTF Systems) is capable of recording data from 83 SQUID sensors. The sensor array is shaped to fit over the gravid maternal abdomen. The hardware interface is identical to the cortical MEG and also operates in a magnetically shielded room equipped with a pneumatic door, a reclining chair designed to ensure a comfortable position for pregnant women (the seat, legs and back supports are adjustable), and a video/audio system that allows monitoring and communication with participants. Hardware (speakers) and software (E-Prime/Presentation) for auditory stimulation are available. Data are pre-processed using CTF software and moved to other software packages for data analysis (EEGLab, QRSTool, Kubios).

Cortical Magnetoencephalography (cMEG)

cMEGThe MEG laboratory is currently supporting a number of studies conducted in collaboration with investigators from several other departments at KUMC and KU, including Neurology, Speech-Language and Hearing, Occupational Therapy, Physical Therapy & Rehabilitation Science, Electrical Engineering, Bioengineering and Linguistics.

The Cortical Biomagnetometer, (CTF system) is capable of recording human magnetoencephalolgraphy (MEG) data from 151 axial gradiometers distributed over the whole cortex. The system uses reference channels for noise cancellation. The electronics system allows for simultaneous EEG recording, EOG/EMG, ADC/DAC and triggers for a wide range of stimuli (visual, auditory, somatosensory, tactile) and a Linux computer for data acquisition, processing and storage. Processing includes amplifying, filtering, sample rate conversion and firmware gradient formation. The biomagnetometer operates in a magnetically shielded room equipped with a pneumatic door, a reclining chair designed to ensure a comfortable position for participants (the seat, legs and back supports are adjustable), a bed for recumbent subjects and a video/audio system that allows monitoring and communication with participants.

Ultrasound scanner (GE Logiq P5): This 2-D ultrasound with the 3.5C Thin Wide Band Convex Probe is capable of imaging the fetus, the fetal heart and recording the location (depth) and orientation of the fetal heart and head. It allows the acquisition and real time transmission of the ultrasound images to the ultrasound acquisition computer.

Electrical Geodesics, Inc (EGI) High Density EEG: The EGI GES 400 series includes the capability for 128 channel infant EEG or 256 channel adult EEG. Geodesic EEG electrodes are evenly spaced over the entire scalp, cheeks and back of the neck, allowing for dense and even sampling at a high spatial resolution. The system includes infant sensor nets that allow for longitudinal studies the first year of life and adult sensor nets. The system is expandable to MRI-compatibility. This system also interfaces with E-prime and Presentation software for evoked and event-related potentials. The system includes Net Station software that provides full acquisition, review and analysis functions with GeoSource source estimation software. The current system is capable of EEG-MEG simultaneous recordings. Data can be processed using Net Station or third party software.


9.4T MRI Program


9.4 Tesla MR System: MR imaging studies are carried out on a 9.4Tesla 31cm horizontal bore Varian/Agilent system that is equipped with three (21cm, 12cm, and 6cm) gradient and shim coil sets that generate maximum gradient amplitudes of 200mT/m and 400mT/m, and 800mT/m respectively. This scanner is optimized for MRI/MRS acquisitions and is ideal for the research activities of the proposed experiments.

Three quadrature coil resonators (140mm, 60mm and 38mm), a surface coil imaging kit, microimaging bay, micropipette rf coil, and sample positioning cradles of various sizes are available for day-to-day operations. An InSightNeuroimaging coil decoupling apparatus is available for studies that require volume transmit/surface coil acquire. A 16cm transmit volume coil and several small surface coils are available. In addition, an inductively coupled coil system designed in-house provides MR microscopy capability on this scanner.

Monitoring and physiological recording: An MR-compatible small animal monitoring and gating system (SA Instruments, Inc., Stony Brook, NY) is used regularly in our studies to monitor the animal vital signs (temperature, ECG, and respiration) and to gate the scanner on the ECG and/or respiratory cycles. The 9.4 T MRI suite is equipped with the following: anesthesia (VMS, Matrx, Inc., Orchard Park, NY), pulsed oximeter (MouseOx, Starr Life Sciences, Oakmont, PA), circulating water heating pad (Polystat temperature controller, Cole-Palmer) and temperature controller (Digi-sense, Cole-Palmer), rodent ventilators (Model 683, Harvard Apparatus and Model 7025, Ugo Basile Biological Apparatus), and MR-compatible syringe pumps (PHD 2000, Harvard Apparatus)

Sample Analysis: The HBIC Sample Analysis Laboratory is equipped with blood chemical analyzer (Micro-Stat Multi-Assay Analyzer - GM7, Analox), blood gas analyzer (Rapidlab 248, Bayer Diagnostics), and capnometer (Capnomac Ultima, Datex Omeda). It also has a sub-80 degree refrigerator to store biological samples.

 Animal welfare and handling  

The Hoglund Brain Imaging Center operates as a clean facility allowing transfer of experimental animals between the KU Laboratory Animal Resources. Animals are housed in the animal housing room, which is maintained by the Laboratory Animal Resources personnel on a daily basis. 

A surgery room is located adjacent to the 9.4T MRI suite and the animal housing room. This room is equipped with stereotaxic surgery platform (Kopf Instruments, Tujunga, CA), VMS anesthesia machine (Matrx, Inc., Orchard Park, NY), active anesthesia scavenging system (Molecular Imaging Products, Bend, OR), surgical microscope, and all instruments needed for minor small animal surgeries. A stereotaxic controlled cortical impact device (Impact One, Leica Microsystems, Buffalo Grove, IL) is available for mouse and rat traumatic brain injury studies. Rapid metabolic fixation is provided by a 4 kW microwave system (model GA5013, Gerling Applied Engineering, Inc., Modesto, CA).

The HBIC animal facility also has 25 sq. ft. of benchtop space available for rodent behavioral testing. It is equipped with a rotorod apparatus (Accuscan Instruments, Columbus, OH), and beam walk apparatus (custom-built, in-house).


Hardware: Shared MacPro, PC, Linux, Unix, and Sun SunBlade 1000, workstations are available for data analysis and interpretation. Additionally, Siemens Syngo.via server and MMWP workstation are available for offline analysis and exploration of MR imaging data.

All computers in the Hoglund Brain Imaging Center (HBIC) are connected to the campus 10 Gigabit Ethernet core network and network file storage. Networked file servers provide constant hardware backups of stored data through mirrored storage systems and daily tape backups are also performed. Weekly tape backups are stored off site for additional protection of research data.  The network is managed by KUMC's Information Resources who provides installation, training, and maintenance on all information systems. The local area network is connected to a switched, 1 Gigabit Ethernet backbone that provides high speed Internet access through the KUMC Internet-2 communication network.

The University of Kansas Medical Center is a member of the Kansas Research and Education Network (KanREN, Inc.) which provides us access to the commodity Internet (Internet 1), Internet 2 via the Great Plains Network (GPN), and connectivity to other Kansas educational/research institutions and Hospitals.

Most recently, the KanREN network was used to create a peering network between the University of Kansas, University of Kansas Medical Center and the School of Medicine Wichita. Setting up the peering network is the first step in providing seamless access to systems used by faculty, staff, students and researchers spanning the campuses including the Advanced Computing Facility (ACF) located at the KU campus.

The Medical Center's centrally managed Data Centers house the infrastructure for our 450+ physical and virtual servers. The data centers also house our Storage Area Network (SAN) and other disk arrays accounting for 190 TB of useable storage along with a 100 Terabyte NAS for researchers to backup their primary research related data.

Magnetic Resonance Imaging data is transferred to and stored on a network server running XNAT (Extensible Neuroimaging Archive Toolkit) developed by Randy Buckner at Harvard University and the Neuroinformatics Research Group at Washington University School of Medicine; Marcus, et al., 2007), an open source imaging informatics platform designed to facilitate management and exploration of imaging and related data, managed by KUMC's Information Resources.

HBIC Image Analysis and Computing Laboratory: The Image Analysis Laboratory is equipped with Unix, PC/Linux, and Mac workstations for data analysis and interpretation. Software includes LabView, E-Prime, Presentation, AFNI, BrainVoyager, LCModel, SAS, Statistica, ImageJ, Matlab, IDL, Analyze GraphPad, Deltagraph, EndNote, Excel, Powerpoint, and Word. The HBIC also has dedicated programmers and staff for managing imaging data and informatics through XNAT, an open source imaging informatics platform designed to facilitate management and exploration of imaging and related data.

The Image Analysis Laboratory also provides a suite of analysis pipelines for functional and structural imaging. These include validated methods for brain volume measurement (Freesurfer), lesion quantification, arterial spin labeling quantification, fat/muscle analysis (ImageJ) as well as functional analysis using AFNI. Other pipelines are under development and personnel are available for establishing customized analyses.


Offices are available for all HBIC faculty and staff within the HBIC building. Each office is equipped with desktop computer (Mac or PC), printer, and network access as described above. All workstations are equipped with EndNote and Microsoft Office Suite (Excel, Powerpoint, and Word).


Clinical space in the HBIC includes a patient waiting area, consultation room, changing suite, patient preparation room, and neuropsychology testing room.  The Center includes space for both human and research activities including offices, changing rooms, patient preparation areas, and consultation rooms.

Examination Room: Also available is a 140 sq ft examination room for clinical procedures adjacent to the MRI and MEG suites. Available procedures include physical examinations, neurological examinations, blood draws and processing, urine sampling, height and weight measurements, balance testing, infusions, providing special diets. The examination room is equipped with general nursing supplies, examination table, phlebotomy chair, refrigerators for patient food and supplies and for samples, and a centrifuge. A full time nurse, Sherry Coleman, is available for nursing care. This examination room is a satellite of the CTSA-funded Frontiers Clinical & Translational Science Unit.

Neuropsychological Testing: A neuropsychological testing room (40 sq ft) is located adjacent to the examination room and scanning facilities. It is equipped with paper and computer-based testing capabilities.


Ancillary services include machine and repair shops, computer support and clinical laboratory services. The clinical laboratory provides all clinical sample testing and analysis including kidney function tests.


Last modified: Oct 14, 2016