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Fibre Tracking: From Raw Fibre Tracking: From Raw Images ToImages To
Tract VisualisationTract Visualisation
T.R. Barrick
St. George’s Hospital Medical School, London, United Kingdom.
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IntroductionIntroduction
Diffusion Tensor Magnetic Resonance
Imaging has recently emerged as the
technique of choice for representation of
white matter pathways of the human
brain in vivo
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Objectives Objectives
To show how Diffusion Tensor Images
(DTIs) are generated from Diffusion
Weighted Images (DWIs)
To demonstrate how freely available
software may be used to visualise
coloured images and tractography results
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OverviewOverview
Section 1: Computing the DTI
Section 2: Visualising Coloured
Images
Section 3: Streamline Tractography
Section 4: Visualising Tractograms
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Section 1: Computing The Section 1: Computing The Diffusion Tensor Diffusion Tensor
Brownian motion
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Random, translational motion
Water DiffusionWater Diffusion
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Diffusion CharacteristicsDiffusion Characteristics
In a large structure the self diffusion of
water is more or less free (isotropy)
In small structures such as axons the
diffusion is restricted in some directions
more than others (anisotropy)
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Diffusion Coefficient (Diffusion Coefficient (DD))
Diffusion is a time dependent processDiffusion is a time dependent process
Molecules diffuse further from their starting point as Molecules diffuse further from their starting point as
time increasestime increases
Units of Units of DD are mm are mm22 s s-1-1
DD is temperature dependent is temperature dependent
DD depends species under consideration depends species under consideration
Water at 37Water at 37°°C; C; DD = 3.0 x 10 = 3.0 x 10-3-3 mm mm22 s s-1-1
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Diffusion-WeightingDiffusion-Weighting
Make pulse sequence sensitive to diffusionMake pulse sequence sensitive to diffusion
Add additional gradients into sequenceAdd additional gradients into sequence
Spins move in gradient – phase changesSpins move in gradient – phase changes
These gradients cause signal dephasingThese gradients cause signal dephasing
Results in signal lossResults in signal loss
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Diffusion Gradients: Stejskal-Diffusion Gradients: Stejskal-Tanner SequenceTanner Sequence
90° 180° echo
RF
gradient
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Diffusion Sensitivity: Diffusion Sensitivity: bb value value
Amount of diffusion sensitivity is called the Amount of diffusion sensitivity is called the bb
valuevalue
bb value depends on the gradient strength, value depends on the gradient strength, GG, ,
duration duration and separation and separation
3δ/ΔγGδb 2
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Diffusion-Weighted Images (DWI)
increasing increasing bb factor factor
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Diffusion-Weighted Images (DWI)Diffusion-Weighted Images (DWI)
Signal loss is proportional to Signal loss is proportional to bb and and DD
S(0)S(0) is signal without gradients and is signal without gradients and S(b)S(b) is is
signal with gradientssignal with gradients
bD0S
bSln
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Diffusion Tensor Imaging Diffusion Tensor Imaging (DTI)(DTI)
Acquire DWI sensitised in at least 6
different directions
(x,y,0), (x,0,z), (0,y,z), (-x,y,0), (-x,0,z),
(0,-y,z))
Plus image without diffusion
weighting (T2)
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Possible Diffusion Tensor Possible Diffusion Tensor Image AcquisitionImage Acquisition
1.5T GE Signa MRI (max field 22 mT m-1)
Diffusion-weighted axial EPI
– b=1000 s mm-2
– 12 directions
– 4 averages
Voxel size: 2.5mm2.5mm2.8mm
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Computation of the DTIComputation of the DTI
Subject DWIs coregistered to image without
diffusion weighting (Haselgrove and Moore, 1996)
General linear model used to compute D at
each voxel
– Uses observed diffusion weightings and the b-
matrix of diffusion sensitisation (Basser et al., 1996)
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Diffusion Tensor ImagingDiffusion Tensor Imaging
Provides a full description of the second
order diffusion tensor,
zzyzxz
yzyyxy
xzxyxx
DDD
DDD
DDD
D
At each voxel, D is then diagonalised
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Diffusion Tensor ImagingDiffusion Tensor Imaging
Eigenvalues and eigenvectors of D
correspond to principal diffusivities and
principal diffusion directions
Necessarily 3 eigenvalues,
– Principal diffusivities 1, 2, and 3.
– Invariant under rotation.
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Diffusion Tensor ImagingDiffusion Tensor Imaging
For each eigenvalue the corresponding
diffusion direction is given by the
eigenvector, v1, v2, and v3.
Direction of principal diffusivity is
eigenvector corresponding to largest
eigenvalue (diffusivity).
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Diffusion Tensor Orientation Diffusion Tensor Orientation and Shapeand Shape
Prolate, 1 >> 2 3
Oblate, 1 2 >> 3
Spherical, 1 2 3
3
3
2
1
v1
Anisotropic Isotropic
Disc
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Invariant Diffusion Measures: Invariant Diffusion Measures: Mean DiffusivityMean Diffusivity
Apparent Diffusion Coefficient (ADC)
Quantitative Quantitative Bright pixels - high diffusionBright pixels - high diffusion
Uniform across WMUniform across WM
Typical WM values; Typical WM values;
ADC = 0.8 x 10ADC = 0.8 x 10-3-3 mm mm2 2 ss-1-1
3/D 21app
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Diffusion Anisotropy
ADCx ADCy ADCz
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Invariant Diffusion Measures: Invariant Diffusion Measures: Fractional AnisotropyFractional Anisotropy
Fractional anisotropy (Basser et al., 1996)(Basser et al., 1996)
Quantitative, visualizes WMQuantitative, visualizes WM
Bright pixels - high anisotropyBright pixels - high anisotropyData Range 0 to 1
(isotropic to anisotropic)
.
DDD
2
3FA
23
22
21
2app3
2app2
2app1
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Section 2: Visualising Section 2: Visualising Coloured ImagesColoured Images
mri3dX – Krish Singh, Aston University
Home page:
– http://www.aston.ac.uk/lhs/staff/singhkd/mri
3dX/index.shtml
Allows visualisation of:
– 24 bit RGB images (shade files, *.shd)
– Analyze format images (*.hdr, *.img)
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Visualising Coloured ImagesVisualising Coloured Images
24 bit RGB images
– 3 stacked 8 bit volumes (each 256×256×N)
– Order: Red, Green, Blue
– No header
N.B. Due to the *.shd file’s lack of a
header an image with identical height must
be loaded prior to loading the *.shd file
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mri3dX Environmentmri3dX EnvironmentMain Window
Sagittal Coronal Axial
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Principal Diffusion DirectionPrincipal Diffusion Direction
Right-left
Anterior-posterior
Superior-inferior
Red = | vx |Green = | vy |Blue = | vz |
Direction Encoded Colour map (DEC)
Pajevic and Pierpaoli, 1999
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Diffusion Tensor ShapeDiffusion Tensor Shape
Red = 1/1 = 1Green = 2/1
Blue = 3/1
Shape Encoded Colour map (SEC)
Prolate
Oblate (Disc)
Sphere
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Section 3: Streamline Section 3: Streamline TractographyTractography
Attempt to ‘connect’ voxels on basis of Attempt to ‘connect’ voxels on basis of
directional similarity of coincident eigenvectorsdirectional similarity of coincident eigenvectors
Mori et al.,Mori et al.,Ann Neurol 1999Ann Neurol 1999
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Streamline TractographyStreamline Tractography
Tracts generated from DTI
Define step vector length,
e.g. t = 1.0 mm
Define tract termination criteria
Fractional anisotropy, e.g. FA < 0.1
Angle between consecutive
eigenvectors, e.g. angle > 45°
Basser et al., 2000Mori et al., 1999
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Streamline TractographyStreamline Tractography
Tracts computed in orthograde and
retrograde directions from initial seeds
By using multiple seed points white
matter structures are extracted
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Tractography AlgorithmTractography Algorithm
Readtensor
Seed Point
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Diagonalisetensor
Readtensor
Seed Point
Tractography AlgorithmTractography Algorithm
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Diagonalisetensor
Readtensor
Seed Point
FA <threshold?
Tractography AlgorithmTractography Algorithm
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NO
Diagonalisetensor
Readtensor
Seed Point
FA <threshold?
Angle >threshold?
Basser et al., 1999Mori et al., 1999
Tractography AlgorithmTractography Algorithm
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NO
Diagonalisetensor
Readtensor
Seed Point
Step distance, t, along principal
eigenvector
FA <threshold?
Angle >threshold?
NO
Basser et al., 1999Mori et al., 1999
Tractography AlgorithmTractography Algorithm
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NOInterpolate tensor field
Diagonalisetensor
Readtensor
Seed Point
Step distance, t, along principal
eigenvector
FA <threshold?
Angle >threshold?
NO
Basser et al., 1999Mori et al., 1999
Tractography AlgorithmTractography Algorithm
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YES
NOInterpolate tensor field
Diagonalisetensor
Readtensor
Seed Point
Step distance, t, along principal
eigenvector
FA <threshold?
Angle >threshold?
YES
NO
Outputtract
vectors
Basser et al., 2000Mori et al., 1999
Tractography AlgorithmTractography Algorithm
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Section 4: Visualising Section 4: Visualising TractogramsTractograms
GeomView - interactive 3D viewing
program for Unix and Linux (openGL)
View and manipulate 3D objects
Allows rotation, translation, zooming
Geometry Center, University of
Minnesota, USA (1992-1996).
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Although the Geometry Center closed in
1998, GeomView is still available and
continues to evolve
Home page – http://www.geomview.org/
Download from:
– http://www.geomview.org/download/
GeomViewGeomView
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GeomView EnvironmentGeomView Environment
Main Window Tool Bar Camera Window
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GeomView File FormatGeomView File Format
Documentation available online
GeomView input file format:
– Object Oriented Graphics Library
(OOGL)
– OOGL files may be either text (ASCII) or
binary files
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VECT File FormatVECT File Format
VECT is an OOGL format that allows
visualisation of vectors or strings of
vectors in GeomView
– Number of vectors (steps) in tractogram (N)
– Start (s) and end (e) points for each vector
– RGB colour (c) for each vector
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VECT File FormatVECT File Format
The conventional suffix for VECT files is
‘*.vect’.
The files must have the following
syntax:
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VECT File FormatVECT File Format
VECT
#edges (N) #vertices (N×2) #colours (N)
#vertices per edge (i.e. 2, N times)
#colours for each vector (i.e. 1, N times)
N×2 vertices: N×6 floats, s(x,y,z), e(x,y,z)
N vector colours: N×4 floats, R G B A)
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VECT File FormatVECT File FormatExample 1: Drawing two vectors
– N = 2
– Edge 1 (2 vertices v1 = (1 0 0), v2 = (0 1 0))
– Edge 2 (2 vertices v1 = (0 1 0), v2 = (0 0 1))
– Colours (absolute value DEC)
For Edge 1 (R G B A) = (1 1 0 1)
For Edge 2 (R G B A) = (0 1 1 1)
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VECT File FormatVECT File FormatExample 1: Drawing two vectors
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Visualising TractogramsVisualising TractogramsExample 2: Corticospinal pathway
e Patient: Biopsy proven
right temporal
glioblastoma
ROIs in Brodmann
Area 6 and through
the base of the
corticospinal tractClark et al., 2003
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Visualising TractogramsVisualising TractogramsExample 2: Corticospinal pathway
Seed regions of
interest drawn using…
mriCro – Chris
Rorden, Nottingham
University Home page:
–http://www.psychology.nottingham.ac.uk/staff/cr1/mricro.html
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Visualising TractogramsVisualising TractogramsExample 2: Corticospinal pathway
– Streamline tractography (Basser et al., 2000)
– Angle threshold: 45°
– FA threshold: 0.1
– Vector length: 2.0mm
– Whole brain tractography
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Visualising TractogramsVisualising TractogramsExample 2: Corticospinal pathway
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CQUAD File FormatCQUAD File Format
CQUAD is an OOGL format that allows
visualisation of coloured quadrilaterals
in GeomView
– Positions of the 4 vertices
– RGB colour for each of the 4 vertices
For visualisation of image slices in
GeomView
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CQUAD File FormatCQUAD File Format
The conventional suffix for CQUAD files
is ‘*.cquad’.
The files must have the following
syntax:
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CQUAD File FormatCQUAD File Format
CQUAD
N×4 vertices for N quadrilaterals (each
consisting of N×4, x,y,z coordinates)
Corresponding N×4 vertex colours
(each consisting of N×4 floats, R G B A)
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Visualising Image SlicesVisualising Image Slices
Example 3: Drawing a square– CQUAD
– 4 vertices with associated colours v1 = (1 1 0) c1 = (1 0 0 1)
v2 = (1 -1 0) c2 = (1 0 0 1)
v3 = (-1 -1 0) c3 = (0 1 0 1)
v4 = (-1 1 0) c4 = (0 1 0 1)
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Visualising Image SlicesVisualising Image SlicesExample 3: Drawing a square
Lighting On Lighting Off
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Visualising Image SlicesVisualising Image SlicesExample 4: Constructing an image slice
e
Clark et al., 2003
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Visualising Image SlicesVisualising Image SlicesExample 4: Constructing an image slice
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OFF File FormatOFF File Format
OFF is an OOGL format that allows
visualisation of polygons in GeomView
For visualisation of triangulated
surfaces output from the marching
cubes algorithm (Lorenson and Cline, 1987)
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OFF File FormatOFF File Format
The conventional suffix for OFF files is
‘*.off’.
The files must have the following
syntax:
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OFF File FormatOFF File FormatOFF
#edges #faces (N) #vertices
Vertex positions for face N (N×3 x,y,z coordinates)
For face N,
– #vertices followed by vertex order
– Face colour (4 floats, R G B A)
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OFF File FormatOFF File Format
Example 5: Drawing a triangle
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Visualising SurfacesVisualising Surfaces
Example 6: Constructing a surface
Draw the region of interest
Triangulated surface patch coordinates via
the marching cubes algorithm
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Visualising SurfacesVisualising Surfaces
Example 6: Constructing a surface
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Full VisualisationFull Visualisation
Example 7: Tractogram/Slice/Surface
Clark et al., 2003
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Creating GeomView MoviesCreating GeomView MoviesStage Tools is required
Download:
http://www.geom.uiuc.edu/ soft
ware /download/StageTools.html
Stage Tools includes software for:
– Loading and unloading image objects
– Specifying rotation, translation and
zooming parameters to GeomView objects
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Creating GeomView MoviesCreating GeomView Movies
Movie created inPaint Shop Pro 7
Tiff snapshots output from GeomView
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ConclusionConclusion
Computation of the Diffusion Tensor
from Magnetic Resonance Images has
been described
Freely available software has been
shown to be capable of visualising
coloured images and tractograms