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PROJECT 1: High-Resolution Anatomical Modeling


Bruce Fischl, PhD Project Leader
Andre Van der Kouwe, PhD Investigator
David Salat, PhD Investigator
Doug Greve, PhD Investigator
Jean Augustinack, PhD Investigator
Koen Van Leemput, PhD Investigator
Bruce Rosen, MD, PhD Investigator
Lilla Zollei, PhD Post-Doctoral Fellow
Allison Stevens, BA Research Assistant
Nick Schmansky, MS Engineer


Project Description

Models of brain structures generated from magnetic resonance imaging (MRI) data have grown in complexity in recent years, evolving from simple representations with few classes, such as gray matter, white matter and cerebrospinal fluid (CSF), into more complex ones representing multiple neural structures separately. This evolution has been possible due to developments in MR data acquisition technology that have yielded finer resolution, higher signal-to-noise ratio (SNR) images and an increasing number of contrast mechanisms. In this project, we will seek to use these higher resolution multi-spectral images to develop a set of tools to fill unmet needs in both MRI and PET image analysis.

Using models and probabilistic information assembled in the previous cycle, we now propose to develop cortical registration and segmentation tools that are explicitly optimal for the alignment and localization of architectonic boundaries across subjects, focusing on cortical area V5/MT.  The surface-based registration utility will then be combined with volumetric intensity information to generate a nonlinear volume warp using a biomechanical model of the brain. This combination will yield a single highly accurate coordinate system applicable across the entire brain. Finally, this coordinate system will be used as initialization for extending the scope and level of detail of our existing segmentation models to explicitly segment bone, air, fat and water for used in MR-based PET attenuation correction. The segmentation will be facilitated by the use of specifically designed sequences incorporating ultra-short TE (UTE) contrast that can directly image bone.



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


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)



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

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

Statistics for fMRI experimentation

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


Electronic Tutorials

Freesurfer MRI data processing software documentation and instruction