Welcome to the CBI

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Research done at the CBI employs a variety of in-vivo imaging techniques to better understand the functions and structures of the human brain. The target of this work is the impact of age and disease processes with a focus on identifying clinically feasible biomarkers.


-Neuropsychological Tests

We often have subjects complete a series of neuropsychological tasks prior to imaging that allows for the monitoring of changes in cognitive function over time. Such tasks include the Mini Mental State Examination (MMSE), Geriatric Depression Scale (GDS), Logical Memory Immediate and Delayed Scores, Part B of the Trailmaking Test, Clock Drawing, the Montreal Cognitive Assessment (MoCA), etc.

-MRI Acquisition

We have the ability to run many different sequences on our 3T MRI including

  • T1 and T2
    • Weighted structural imaging enabling white/grey matter parcellation.
  • FLAIR (FLuid Attenuated Inversion Recovery)
    • T2 weighting with fat saturation to observe cerebellar hyper/hypo intense signals.
  • MRA (Magnetic Resonance Angiography)
    • Visualizing brain vasculature.
  • pCASL (Pseudo Continuous Arterial Spin Labeling)
    • Non invasive form of perfusion imaging.
  • EPI (Echo Planar Imaging)
    • T2* weighted image, used for showing Blood Oxygen Level Dependent (BOLD) signal showing cerebral blood flow in activated regions, at rest or under stimulus.
  • MRS (Magnetic Resonance Spectroscopy)
    • Non imaging technique used to quantify concentrations of metabolites in tissue.
  • Diffusion (HARDI,DTI,DKI)
    • T2 weighted imaging that enables viewing of water molecules diffusion in the brain.
  • SWI (Susceptibility Weighted Imaging)
    • Technique that looks at venous behavior in the brain which can show bleeding and areas of iron deposits.
  • QSM (Quantitative Susceptibility Mapping)
    • QSM utilizes phase images, solves the magnetic field to susceptibility source inverse problem, and generates a three-dimensional susceptibility distribution. Potential QSM applications include standardized quantitative stratification of cerebral microbleeds, neuroinflammation, abnormal iron concentrations and neurodegenerative diseases.

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  • T2 Weighted Image

  • T1 Weighted Image

  • Processed HARDI tractography

  • Quantitative Susceptibility Mapping (QSM)

  • Processed fMRI

  • MR Angiography


Default mode network (DMN) analysis in multiple populations (fMRI) – The default mode network is a group of brain regions that seem to show lower levels of activity when we are engaged in a particular task like paying attention, but higher levels of activity when we are awake and not involved in any specific tasks, thus the network activates by default when a person is not involved in a task. We use the DMN to look into the overall function of the brain and how it can be affected by neurodegenerative disorders.   

White matter based tract analysis (HARDI, DKI, DTI) – Basic principle of diffusion weighted imaging is the microscopic motion of water molecules. Water molecules shift between tissue compartment through several different ways, this includes osmosis, membrane permeability, and active transport. High angular resolution diffusion imaging (HARDI) can measure the diffusion of water in the brain along any number of preset vectors.  We use this tract analysis to quantify degeneration of white matter tracts in the control vs case brains.




We use a variety of analysis packages to analyze MRI data.

  • fMRI
    • FSL , FreeSurfer
  • Structural
    • FreeSurfer, Hippocampal subfield parcellation
  • Diffusion
    • We use both deterministic and probabilistic tractography to explore white matter integrity in multiple populations (DSI Studio, TRACULA)
    • Investigating neurite orientation dispersion density index in multiple populations (NODDI)



Publications from our Lab members

Multimodal MR-imaging reveals large-scale structural and functional connectivity changes in profound early blindness

Corinna M. Bauer, Gabriella V. Hirsch, Lauren Zajac,Bang-Bon Koo, Olivier Collignon, and Lotfi B. Merabet. 2017 , PLOS One.

Retained executive abilities in mild cognitive impairment are associated with increased white matter network connectivity
Danielle C. Farrar & Asim Z. Mian & Andrew E. Budson & Mark B. Moss &
Bang Bon Koo & Ronald J. Killiany for the Alzheimer’s Disease Neuroimaging Initiative. 2018 , European Radiology.

Abnormal white matter tractography of visual pathways detected by high-angular-resolution diffusion imaging (HARDI) corresponds to visual dysfunction in cortical/ cerebral visual impairment
Corinna M. Bauer, PhD, Gena Heidary, MD, PhD, Bang-Bon Koo, PhD, Ronald J. Killiany, PhD, Peter Bex, PhD and Lotfi B. Merabet, OD, PhD. 2014 , J AAPOS.

Seed Location Impacts Whole-Brain Structural Network Comparisons between Healthy Elderly and Individuals with Alzheimer’s Disease
Lauren Zajac , Bang-Bon Koo, Corinna M. Bauer, Ron Killiany and Behalf of the Alzheimer’s Disease Neuroimaging Initiative. 2017 , Brain Sciences

Age-related changes in structural connectivity are improved using subject-specific thresholding
Corinna M. Bauer, Lauren E. Zajac, Bang-Bon Koo, Ronald J. Killiany, Lotfi B. Merabet. 2017 , J Neuroscience