Neuroimaging processing overview limitations pitfalls etc etc
Download
1 / 44

Neuroimaging Processing : Overview , Limitations , pitfalls, etc . etc. - PowerPoint PPT Presentation


  • 123 Views
  • Uploaded on

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.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Neuroimaging Processing : Overview , Limitations , pitfalls, etc . etc.' - teleri


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
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.


Malhi et al. 2007



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 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


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



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



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


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


Use FreeSurfer

Be Happy


Diffusion mri
Diffusion MRI

Diffusion Tensor Imaging (DTI)

White Matter Organisation



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




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%


ad