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Imaging Facilities

Description of the Center's imaging equipment and support labs

Apply to conduct research with the Center as a collaborator or service user



APU (Atlas-guided Photon-migration Utilities) provides utilities for using a structural MRI (from an atlas or any other MRI) to guide the analysis of Near Infra-Red Spectroscopy (NIRS) data. These tools are used in conjunction with Freesurfer and MNE. Detailed information about APU can be found here.

  • Array Sensitivity Metric Software

This reconstruction program runs on the Siemens scanner generating Dicom images of the array SNR computed with the Optimum method (uses noise correlation matix) and Sum of Squares (SoS).  It also generates the noise correlation matrix and G-factors maps.  It uses the method of Peter Kellman for generating SNR in absolute units. E-mail Jonathan Polimeni for download information.

The Freesurfer package is tools for segmentation, surface reconstruction and processing of surface models of the human cerebral cortex. It includes FS-Fast fMRI data analysis tools. (Freesurfer Wiki)

An Open-Source Hardware and Software Platform for Simultaneous Electrophysiology and MRI

HOMER (Hemodynamic Evoked Response) graphical interface for visualization and analysis of Near Infra-Red Spectroscopy (NIRS) data

Software for anatomically and functionally constrained MEG/EEG source modeling

optseq2 is a tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events)

tMCing and Monte Carlo eXtreme (MCX) packages are used to model photon migration through 3D turbid media



A five-day intensive introduction to functional magnetic resonance imaging of the brain

A two-day intensive hands on introduction to functional near-infrared spectroscopy

A two-week hands on introduction to multimodal brain imaging using MR, EEG, MEG and optical techniques

Basic and Advanced training courses for collaborators and service users of the Center's MEG system

A five-day intensive hands-on introduction to the use of FreeSurfer and FSL for analyzing neuroimaging data



Freesurfer MRI data processing software documentation and instruction

MNE software includes a sample data set with a detailed tutorial in the manual

Learn more about how Diffuse Optical Tomography (DOT) is used for functional brain imaging


NITRC Pages (The Neuroimaging Informatics Tools and Resources Clearinghouse)