mri images
mri and workers

Lane Neuroimaging Lab

Getting Started:

  1. Complete the MRI Acquisition Strategy Request Form (at the bottom of this page) and direct any questions to Ginny Hayes, the Lane Neuroimaging MRI Lab Manager. The information on this form will help our trained staff assist you with the design of your experiment. The research question and experimental design are important aspects to obtaining useful data.
  2. Human Subjects Committee IRB approval is necessary before you can use the MRI at the Health Emotions Research Institute Lane Neuroimaging Lab. HSC/IRB approval can be a lengthy process, therefore it is important to submit your Protocol as soon as possible.  Your proposed Consent Form should include all physiological measures you wish to collect, the ability to run two or three single session pilots to test both your paradigm and equipment, and information about “possible abnormal findings”.

Once you are approved:

  1. Once you have received approval from the IRB, complete the MRI Research Application (at the bottom of this page) and submit it along with your approved Protocol, approved Consent Form(s), and approved Funding/Grant information. You may upload these documents directly to the MRI Research Application below, or submit them to Ginny Hayes, the Lane Neuroimaging MRI Lab Manager. She will organize an MRI Users Committee meeting and notify you by letter of approval for MRI use. No scans or testing will be allowed without the MRI Users Committee approval.
  2.  In addition to Study approval and documentation, it is also necessary for your research lab group members to obtain access to the Lane Neuroimaging MRI Suite. In order for this access to be given, each lab member must submit the following: the MRI Screening Form, verification of completion of the CITI training module(s) required by your IRB, and verification of completion of current HIPAA training. Depending on the medical information provided on the MRI Screening Form, the Surgical Procedure Information Form and/or a Surgical Implant Information Form may also be required. Finally, MRI safety is a serious matter.  All persons involved in your research lab group who will be present during your scans must watch the MRI Safety Video and email Ginny Hayes, the Lane Neuroimaging MRI Lab Manager, that this has been done.
  3. Once you have received your letter for approval from the MRI Users Committee and have completed the safety and access requirements for your research lab staff, you may email Ginny Hayes, the Lane Neuroimaging MRI Lab Manager, to learn about access to the MRI calendar, to discuss time slots for scanning, the equipment available for stimulus and data collection, and your MRI protocol. You may need to schedule time on the MR computer to work with Lane Neuroimaging Lab staff to set up your research protocol on the GE scanning computer, prior to your pilot scan session(s).
  4. The MRI Simulator is available for use if you choose to prepare your subjects with a simulation of an actual MRI scan. Please contact Ginny Hayes the Lane Neuroimaging MRI Lab Manager, for additional information on the Simulator or to schedule its use.

Research Subject Preparation and Documentation:

  1. As you screen and prepare potential research subjects for your MRI study, please go over the Day of Scan Information to educate them about their needed preparation for the scan.
  2. As you screen and prepare potential research subjects for your MRI study, complete the MRI Screening Form. Depending on the medical information provided on the MRI Screening Form, a Surgical Procedure Information Form and/or a Surgical Implant Information Form may also be required.
  3. On the day of your subject’s research scan, you must bring a copy of their MRI Screening Form (and MRI: Surgical Procedure Form and MRI: Surgical Implant Form, if required by their medical information) along with a copy of the signed consent form(s) to the MRI Control Room. All of this documentation will be reviewed and approved by the MRI technologist before you will be allowed to scan. The research subject may not enter the Magnet Room under any circumstances until given permission by the MRI technologist.

How to Schedule:

  1. For instructions on how to view the MRI Scanner and Simulator Calendars for scheduling, please contact Daniel Retzlaff.
  2. When you are able to view the MRI Calendar and have decided what time you would like to reserve for your study, please email your request to: Ginny Hayes, Tracy Patterson-Hegg, and Matt Gabriel. When you are able to view the Simulator Calendar, you may schedule your desired time directly on the Calendar.

Obtaining your data:

When you begin a new study at the Lane Neuroimaging Lab, visit IT to get your account set up and receive instructions on both data acquisition and the processing environment.


mri images and workers

Facilities and Equipment

The Lane Neuroimaging Laboratory is located on the first floor of the Hedberg HealthEmotions Research Institute at the Wisconsin Psychiatric Institute and Clinics building. It houses a GE 3T scanner for structural and functional brain imaging, an MRI simulator room, an MRI preparation room for pre- and post-scan behavioral measures, image processing areas with extensive computing facilities, and a conference room and office space.  All rooms at the Lane Neuroimaging Laboratory as well as at remote labs across the campus are networked together.

MRI Scanner

The Laboratory contains one of GE’s most advanced scanner the  3.0 Tesla Discovery MR750.  It is faster and provides greater image clarity than previous scanners.  Researchers and clinicians can obtain images that were previously unimaginable.

GE’s EPIC software can be used to customize neuroimaging research.  Stimulus Presentation can be delivered by using either an advanced fiber optic goggle system or an LCD projector (both by Avotec).  The fiber optic goggles are interfaced with SensoMotoric Instruments eye-tracking system (sampling rate of 50 Hz). This eye-tracking system yields four different analyses: percentage analysis, pictorial analysis, order of object vs. time, and pupil diameter vs. time.

MRI auditory stimulus is presented using a pneumatic headphone system (Avotec). All auditory stimuli are presented through a digital equalizer that is optimized for tone and clarity.

Stabilizing patients to minimize head movement is critical for MRI studies.  The lab has two head stabilizing methods: vacuum pillow and foam inserts.

Collection of peripheral, physiological measures in the MRI are done using the Biopac MP160 system.  The MP160 system provides high resolution, variable sample rates for analog and calculation channels, 16 analog inputs and two analog outputs, and 16 online calculation channels.  The MP160 System provides high-speed acquisition (400 kHz aggregate), and Ethernet connectivity.  Controlling the Biopac is the software, AcqKnowledge.  This software is an interactive program that lets lab members instantly view, measure, analyze, and transform the incoming data.

The ability to collect both cardiac and respiration activity (sampling rate of 100 Hz and 25 Hz, respectively) is possible through the manufacturers standard software.

Stimulus presentation is controlled by E-Prime, Matlab, and NBS Presentation. Real-time monitoring of the image quality and subject motion is available via both FIRMM and AFNI. Morphometric measurements can use AFNI, FSL, Freesurfer, or SPM for coregistration. Both Freesurfer and in-house tools perform manual coregistration (BrainSqueezer) and distortion-based morphometry (DBM) measurements. Manual ROI drawing can use AFNI or an in-house tool (BrainMaker), automated ROI identification can be performed with Freesurfer. Talairach coordinates can be investigated using the Talairach Daemon. Diffusion Tensor Imaging (DTI) uses in-house software for analysis and display. Cortical flatmaps can be created using BrainVoyager.

Image Display is available through a variety of display programs, including AFNI, SPM, BrainVoyager, FSL, Freesurfer, Spamalize, MedX, LORETA, and BESA.

mri with patient

MRI Simulator

To acclimate research subjects to the MRI’s unique environment, the Lab provides an MRI Simulator.  This MRI Simulator (non-magnetic) provides the experience and feel of an actual MRI scanner.  The Simulator includes a moving table, lighting, fans, a stimulus projector system, and an auditory system with two control computers.  The Simulator is used to introduce research subjects to the experimental procedures similar to what they will experience in the actual scanner, helping to ensure subject comfort and data quality.

child in mri

Computer Facilities

The HERI MRI computing network is split between two geographic locations: the local datacenter within the WISPIC building, and the datacenter at the Medical Foundation Centennial Building (MFCB). Both datacenters are secure and access controlled. All servers and storage equipment are on generator backed circuits, with UPS to provide power during cutovers.

The three processing servers are all Dell PowerEdge R840s. Each server has four Intel Xeon 26-core CPUs with multi-threading, providing 208 effective cores per system; the cores are clocked at 2.0GHz (3.7GHz turbo). In addition, each server has 512GB of RAM. Each server is equipped with 10GB networking for communication with the TrueNAS. Each server is running Ubuntu Linux and is routinely updated with the latest security patches.

The SAN is an iXSystems TrueNAS Z20, which utilizes the ZFS filesystem. The enclosure contains two physical nodes for redundancy, and each connect to the processing servers via 10GB networking. Equipped with dozens of HDDs in RAID 10, the system serves up ~300TB of raw storage. The system is equipped with multiple SSDs, providing both read and write caches for increased performance. Lab volumes are served up to the processing servers via the NFS protocol.

User workstations range from Apple iMacs to PC workstations, the latter usually containing a Linux distribution (typically Ubuntu). Authentication is handled through a redundant LDAP server, with user data being tightly access controlled across both servers and workstations.

Access to a wide variety of data analysis software is available throughout the lab. The following programming languages are actively used and supported: C/C++, Java, Perl, Python, Ruby, and R, among many others. Many industry-standard software suites are available, including Matlab, AFNI, and FreeSurfer; in most cases, any UNIX-compatible software can be installed on-demand to accommodate any use case. Multiple  Standard office-related software packages are ubiquitous, including Microsoft Office and Adobe Photoshop/Illustrator/Acrobat.

mri workers

Faculty and Staff

kalin profile

Ned H. Kalin, MD
Hedberg Professor, Chair, Department of Psychiatry
Director: HealthEmotions Research Institute
Director: Lane Neuroimaging Lab


Rasmus M. Birn, PhD.
Assistant Professor, Physicist
Lane Neuroimaging Lab
Room 110b

Ginny Hayes
Lab Manager
Room 1003
Lane Neuroimaging Lab


Daniel Retzlaff
Network Administrator
Room 110
Lane Neuroimaging Lab

Tracy Patterson-Hegg
MRI Technologist
Room 121
HERI MRI Control Room

Matthew Gabriel
MRI Technologist
Room 121
HERI MRI Control Room

Affiliated Researchers

Andy Alexander, Phd.
Faculty Co-Director, Brain Imaging Core
Associate Professor of Medical Physics & Psychiatry
Director of MR Physics Research, Waisman Laboratory for Brain Imaging and Behavior
Waisman Center
1500 Highland Avenue, Room T135
Madison, WI 53705
(608) 265-8233

rasmus birnRasmus M. Birn, PhD.
Assistant Professor, Psychiatry
HERI room 110b

kalin profileNed H. Kalin, MD
Hedberg Professor, Chair, Psychiatry
Director: HealthEmotions Research Institute
Director: Lane Neuroimaging Lab



Mike Koenigs, PhD
Assistant Professor, Psychiatry
HERI room 1026A


Jonathan Oler, PhD
Associate Scientist, Psychiatry
HERI room 110

David Plante, MD, PhD
Professor, Psychiatry and Sleep Medicine
Wisconsin Sleep

Brad Postle, PhD
Professor, Psychology and Psychiatry
Brogden room 515

Vivek Prabhakaran, MD
Assistant Professor, Neuroradiology and Psychiatry

Giulio Tononi, MD, PhD
Professor, Psychiatry
HERI room 1334

Ryan Herringa, MD, PhD
Assistant Professor, Psychiatry

John Cisler, PhD
Assistant Professor, Psychiatry

Stephanie Jones, PhD
Associate Scientist, Psychiatry
Assistant Director of Compliance and Outreach
Wisconsin Institute for Sleep and Consciousness


headshot Stowe

Zachary Stowe, MD
Professor of Psychiatry
Director, Women’s Mental Health Program



What hours is the MRI available to scan subjects?

The MRI is available for research scans Monday through Friday from 1:00 p.m. to 8:30 p.m. Generally, the MRI is also open two Saturdays a month, from 9:00 a.m. to 5:00 p.m. For further information, contact Ginny Hayes, the Lane Neuroimaging Lab Manager at (608) 265-4019 or by email at

The Simulator is available for use Monday through Friday from 8:00 a.m. to 8:00 p.m. Additional Saturday hours are available on Saturdays when the MRI is open for scanning. For further information, contact Ginny Hayes, the Lane Neuroimaging Lab Manager at (608) 265-4019 or by email at

What are the rates and rules for imaging?

The MRI Scanning fee is $500 per hour for all persons affiliated with the University of Wisconsin System and its Associates. There is a minimum one-hour charge for all scans. Additional time in the same scanning session will be billed in half hour increments.

A Radiology fee of $100 is charged for all over reads.

Once your study is approved, at your request, you will be scheduled for a specific time slot on the MRI calendar. Lab policy is that any time slot cancelled, within one week of the scheduled scan time or less, will be charged the entire session scan fee, unless another investigator requests to use that particular scan time.

When your study is approved, if you need time on the MRI scanner for pilot/testing to evaluate a technique for your study protocol, please contact Ginny Hayes, the Lane Neuroimaging Lab Manager at (608) 265-4019 or by email at, to schedule this time.

Where is the Lane Neuroimaging Lab located?
We are on the main floor of the Hedberg HealthEmotions Building. The entrance is the modern glass addition on the far west end of the Wisconsin Psychiatric Institute & Clinics (WisPIC) building. Our physical address is 6001 Research Park Blvd, Madison, WI 53719.


Where do I park?
There is plenty of free parking in the lot surrounding the building.

Is there a bus stop nearby?
Yes, the West Transfer Point is ½ a block away on Tokay Blvd. and it offers all day service to lines 2, 3, 6, 18, 50, 52, 67, 73; off-peak service to line 51, and peak hour service to lines 11, 12, 28, 55, 56, and 57. Please refer to the City of Madison Metro Schedule for more information.

Contact Us

Lane Neuroimaging Laboratory
HealthEmotions Research Institute
6001 Research Park Blvd.
Madison, WI 53719

If you have a question or if you are interested in participating in one of our numerous research studies, please contact us at 608-265-4019 or

Lane Neuroimaging Lab Forms

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