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

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Presentation on theme: "Neuroimaging Processing : Overview, Limitations, pitfalls, etc. etc."— Presentation transcript:

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

2 Neuroimaging Neuroimaging includes the use of various techniques to either directly or indirectly image the structure or function of the brain. 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). 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) 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. Molecular neuroimaging measures biological processes in the brain at the molecular and cellular level.

3 Malhi et al. 2007

4 MRI acquisition

5 MRI Basics Water = H 2 O 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

6 Magnetic Resonance Imaging (MRI)

7 Excitation Radio frequency (RF) pulse is applied at the precession frequency (Lamour Frequency) 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) 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 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 Not all protons bound by their molecules in same way, dependant on tissue type

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9 Preprocessing: Structural MRI Volume/Thickness/Surface Area/Curvature ….

10 Structural MRI Region of Interest (ROI) Voxel based morphometry (SPM/FSL) Surface based morphometry (FreeSurfer)

11 Structural MRI Region of Interest (ROI) Voxel based morphometry (SPM/FSL) Surface based morphometry (FreeSurfer) Volume

12 Structural MRI Region of Interest (ROI) Voxel based morphometry (SPM/FSL) Surface based morphometry (FreeSurfer) Left Right Thickness Surface Area Curvature Gyrification

13 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

14 Manual v Automated Caudate Hippocampus Manual v FS ICC 0.79 52% Volume Difference Manual v FS ICC 0.95

15 What’s the problem with ROI? FreeSurfer Manual

16 Region of Interest Temporal lobe epilepsy patients (TLE) v Healthy controls (HC) Manual FreeSurfer TLEHCTLEHC Volume

17 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)

18 Voxel-based Mophometry MNI Brain Original SegmentationNormalisationModulationSmoothing

19 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

20 FreeSurfer The cortex Volume, thickness or surface area? Volume = surface area * thickness

21 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

22 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

23 FreeSurfer Cortical Reconstruction Cortical Analysis - cortical thickness, surface are, volume, cortical folding and curvature Cortical and sub-cortical segmentation

24 Surfaces: White and Pial

25 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

26 Cortical Thickness white/gray surface pial surface Distance between white and pial surfaces One value per vertex mm

27 Curvature (Radial) Circle tangent to surface at each vertex Curvature measure is 1/radius of circle One value per vertex Signed (sulcus/gyrus)

28 Inter-subject registration subject 1subject 2subject 3subject 4 Template 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

29 Query Design Estimate Contrast - QDEC Average brain

30 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 smoothing – more biologically meaningful

31 Temporal Lobe Epilepsy (MTS) Regular VBM - Volume DBM - Volume/Shape FreeSurfer - Cortical Thinning

32 Temporal Lobe Epilepsy (MR-negative) Volume Deformation/ Shape Cortical Thinning

33 Use FreeSurfer Be Happy

34 Diffusion MRI White Matter Organisation Diffusion Tensor Imaging (DTI)

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36 Direction of least resistance to water diffusion, λ1 Eigenvectors: the 3 directions Eigenvalues: the rate of diffusion, λ1, λ2 and λ3 Apparent diffusion Coefficient (Mean diffusivity) = average of λ1, λ2 and λ3 λ1λ1 λ3λ3 λ2λ2

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39 Tractography

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41 Cortical Spinal Tract

42 Voxel-based Morphometry for dMRI Issues with regular VBM analysis Not-perfect alignment Smoothing - arbitrary Fractional Anisotropy (FA) map Tract-based Spatial Statistics Smith et al. 2006 – FMRIB DTI-TK with TBSS High level warping using all the tensor information for better alignment

43 DTI and Schizophrenia Widespread FA reduction in Schizophrenia versus controls

44 DeCC neuroimaging MDD = 153 MDD = 153 HC = 153 HC = 153 Matched age and gender Matched age and gender Gaussian Process Classifier Gaussian Process Classifier LOOCV LOOCV Accuracy = 59% Accuracy = 59%


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