Neuroimaging processing overview limitations pitfalls etc etc
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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.

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Neuroimaging processing overview limitations pitfalls etc etc

Neuroimaging Processing :Overview, Limitations, pitfalls, etc. etc.


Neuroimaging

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.


Neuroimaging processing overview limitations pitfalls etc etc

Malhi et al. 2007


Mri acquisition

MRI acquisition


Mri basics

Hydrogen Atom

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%

PROTON


Magnetic resonance imaging mri

Magnetic Resonance Imaging (MRI)


Magnetic resonance imaging mri1

Magnetic Resonance Imaging (MRI)

Excitation

  • Radio frequency (RF) pulse is applied at the precession frequency (Lamour Frequency)

  • Sending an RF pulse at Lamourfreq, 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

Preprocessing: Structural MRI

Volume/Thickness/Surface Area/Curvature ….


Structural mri

Structural MRI

  • Region of Interest (ROI)

  • Voxel based morphometry (SPM/FSL)

  • Surface based morphometry (FreeSurfer)


Structural mri1

Structural MRI

  • Region of Interest (ROI)

  • Voxel based morphometry (SPM/FSL)

  • Surface based morphometry (FreeSurfer)

Volume


Structural mri2

Structural MRI

  • Region of Interest (ROI)

  • Voxel based morphometry (SPM/FSL)

  • Surface based morphometry (FreeSurfer)

Thickness

Surface Area

Curvature

Gyrification

Left

Right


Neuroimaging processing overview limitations pitfalls etc etc

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


Neuroimaging processing overview limitations pitfalls etc etc

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

What’s the problem with ROI?

FreeSurfer

Manual


Region of interest

Region of Interest

  • Temporal lobe epilepsy patients (TLE) v Healthy controls (HC)

Volume

Manual

FreeSurfer

HC

TLE

HC

TLE


Voxel based mophometry

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 mophometry1

Voxel-based Mophometry

Segmentation

Normalisation

Modulation

Smoothing

Original

MNI Brain


Vbm limitations

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

FreeSurfer

  • The cortex

    • Volume, thickness or surface area?

    • Volume = surface area * thickness


Volume thickness surface area

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

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


Freesurfer1

FreeSurfer

  • Cortical Reconstruction

  • Cortical Analysis - cortical thickness, surface are, volume, cortical folding and curvature

  • Cortical and sub-cortical segmentation


Neuroimaging processing overview limitations pitfalls etc etc

Surfaces: White and Pial


Surface model

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

Cortical Thickness

pial surface

  • Distance between white and pial surfaces

  • One value per vertex

mm

white/gray surface


Curvature radial

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

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

  • Atlas registration is probabilistic, most variable regions get less weight.

  • Done automatically in recon-all

Template


Neuroimaging processing overview limitations pitfalls etc etc

Query Design Estimate Contrast - QDEC

Average brain


Advantages of freesurfer

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

Temporal Lobe Epilepsy (MTS)

Regular VBM

- Volume

DBM

- Volume/Shape

FreeSurfer

- Cortical Thinning


Temporal lobe epilepsy mr negative

Temporal Lobe Epilepsy (MR-negative)

Volume

Deformation/

Shape

Cortical Thinning


Neuroimaging processing overview limitations pitfalls etc etc

Use FreeSurfer

Be Happy


Diffusion mri

Diffusion MRI

Diffusion Tensor Imaging (DTI)

White Matter Organisation


Diffusion tensor imaging dti

Diffusion Tensor Imaging (DTI)


Neuroimaging processing overview limitations pitfalls etc etc

Measuring Anisotropy

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


Neuroimaging processing overview limitations pitfalls etc etc

Tractography


Neuroimaging processing overview limitations pitfalls etc etc

Tractography


Neuroimaging processing overview limitations pitfalls etc etc

Tractography

Cortical Spinal Tract


Voxel based morphometry for dmri

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

DTI and Schizophrenia

Widespread FA reduction in Schizophrenia versus controls


Decc neuroimaging

DeCC neuroimaging

  • MDD = 153

  • HC = 153

  • Matched age and gender

  • Gaussian Process Classifier

  • LOOCV

  • Accuracy = 59%


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