Neuroimaging Processing :
Overview, Limitations,
pitfalls, etc. etc.
Neuroimaging

Neuroimaging includes the use of various techniques to either directly or
indirectly image the structure or function of the brain.

Structural neuroimaging deals with the structure of the brain (e.g. shows
contrast between different tissues: cerebrospinal fluid, grey matter, white
matter).

Functional neuroimaging is used to indirectly measure brain function
(e.g. neural activity)

Molecular neuroimaging measures biological processes in the brain at
the molecular and cellular level.
Malhi et al. 2007
MRI acquisition
MRI Basics
Water = H2O
Each Hydrogen = one proton
Protons Spin
Generates detectable signal in externally
applied magnetic field: that is, it causes
protons to precess at a frequency
proportional to the strength of the
magnetic field – the ‘resonant’ frequency
Water Content of
GM 70%
WM 85%
Blood 93%
Hydrogen Atom
PROTON
Magnetic Resonance Imaging (MRI)
Magnetic Resonance Imaging (MRI)
Excitation

Radio frequency (RF) pulse is applied at the
precession frequency (Lamour Frequency)

Sending an RF pulse at Lamour freq, particular
amplitude and length of time – possible to flip the
net magnetism 90° - perpendicular to Magnetic
Field (B0)
Relaxation

T1-weighted is the time it takes for the protons to relax
to B0

Not all protons bound by their molecules in same way,
dependant on tissue type
Preprocessing: Structural MRI
Volume/Thickness/Surface Area/Curvature ….
Structural MRI
Region of Interest (ROI)
Voxel based morphometry (SPM/FSL)
Surface based morphometry (FreeSurfer)
Structural MRI
Region of Interest (ROI)
Voxel based morphometry (SPM/FSL)
Surface based morphometry (FreeSurfer)
Volume
Structural MRI
Region of Interest (ROI)
Voxel based morphometry (SPM/FSL)
Surface based morphometry (FreeSurfer)
Thickness
Left
Surface Area
Curvature
Gyrification
Right
Region of Interest
What can we measure in a
Region of Interest (ROI)?
Total volume
Shape
Average diffusion
Average blood flow
Average level of Glutamate
Average Dopamine levels
Region of Interest
Manual v Automated
Caudate
Manual v FS
ICC 0.95
Hippocampus
Manual v FS
ICC 0.79
52% Volume
Difference
What’s the problem with ROI?
FreeSurfer
Manual
Region of Interest
Volume
Temporal lobe epilepsy patients (TLE) v Healthy controls (HC)
HC
TLE
Manual
HC
TLE
FreeSurfer
Voxel-based Mophometry
Statistical Parametric Mapping
(SPM)
FMRIB Software Library
(FSL)
No a priori hypothesis
Volume Change
Chronic Schizophrenia patients
after Clozapine treatment for 6
months < Healthy Controls
(FDR correction p<0.05)
Voxel-based Mophometry
Original
MNI Brain
Segmentation
Normalisation
Modulation
Smoothing
VBM - Limitations
Accuracy of the spatial normalisation
Regular SPM uses 1000 parameters – just fits overall shape of
the brain - mis-registrations
Deformation-based morphometry (e.g. DARTEL)
– deformation field is analysed
Grey matter matched with grey matter – doesn't’t indicate
whether sulci/gyri are aligned
FreeSurfer
The cortex
Volume, thickness or surface area?
Volume = surface area * thickness
Volume, thickness & surface area
Related but don’t necessarily track each other ....
Morphometry Differences between Young, Elderly and Mild
Alzheimer’s in entorhinal cortex. *p<0.05
Dickerson et al.2007
Cortical Curvature
Temporal Lobe Epilepsy (MR-negative)
Cortical curvature abnormality in the ipsilateral temporal
lobe - Not explained by volume or thickness
Possible surrogate marker for malformations of cortical
development
Ronan et al. 2011
FreeSurfer
Cortical Reconstruction
Cortical Analysis - cortical
thickness, surface are, volume,
cortical folding and curvature
Cortical and sub-cortical
segmentation
Surfaces: White and Pial
Surface Model
•
•
•
•
Mesh (“Finite Element”)
Vertex = point of 6 triangles
XYZ at each vertex
Triangles/Surface Element ~
150,000
• Area, Curvature, Thickness,
Volume at each vertex
Cortical Thickness
• Distance between white
and pial surfaces
• One value per vertex
mm
white/gray surface
pial surface
Curvature (Radial)
• Circle tangent to surface
at each vertex
• Curvature measure is
1/radius of circle
• One value per vertex
• Signed (sulcus/gyrus)
Inter-subject registration
subject 1
subject 2
subject 3
subject 4
• Gyrus-to-Gyrus and
Sulcus-to-Sulcus
• Some minor folding
patterns won’t line up
Template
• Atlas registration is
probabilistic, most
variable regions get less
weight.
• Done automatically in
recon-all
Query Design Estimate Contrast - QDEC
Average brain
Advantages of FreeSurfer
Analysis of separate components of volume – thickness and
surface area
Geometry is used for inter-subject registration (major sulcal
and gyral patterns)
2-D surface smoothing versus 3-D volume
smoothing – more biologically meaningful
Temporal Lobe Epilepsy (MTS)
Regular VBM
- Volume
DBM
- Volume/Shape
FreeSurfer
- Cortical Thinning
Temporal Lobe Epilepsy (MR-negative)
Volume
Deformation/
Shape
Cortical
Thinning
Use FreeSurfer
Be Happy
Diffusion Tensor Imaging (DTI)
Diffusion MRI
White Matter Organisation
Diffusion Tensor Imaging (DTI)
λ1
λ3
λ2
Eigenvectors: the 3 directions
Eigenvalues: the rate of diffusion, λ1, λ2 and λ3
Apparent diffusion Coefficient (Mean diffusivity)
= average of λ1, λ2 and λ3
Direction of least
resistance to water
diffusion, λ1
Tractography
Tractography
Tractography
Cortical Spinal Tract
Voxel-based Morphometry for dMRI
Issues with regular VBM analysis
Not-perfect alignment
Smoothing - arbitrary
Tract-based Spatial Statistics
Smith et al. 2006 – FMRIB
Fractional Anisotropy (FA) map
DTI-TK with TBSS
High level warping using all the tensor information for better alignment
DTI and
Schizophrenia
Widespread FA reduction in
Schizophrenia versus controls
DeCC neuroimaging

MDD = 153

HC = 153

Matched age and gender

Gaussian Process Classifier

LOOCV

Accuracy = 59%