maspack.image.dti

Class DTIVoxel

java.lang.Object

maspack.image.dti.DTIVoxel

All Implemented Interfaces:

java.lang.Cloneable, Clonable

public class DTIVoxel
extends java.lang.Object
implements Clonable

Constructor Summary

Constructors

Constructor and Description
DTIVoxel(double d00, double d11, double d22, double d01, double d02, double d12)

Method Summary

Modifier and Type	Method and Description
DTIVoxel	clone()
double	getAD() Axial diffusivity
SymmetricMatrix3d	getD()
double	getE1()
double	getE2()
double	getE3()
double	getFA() Fractional anisotropy
double	getMD() Mean diffusivity
void	getOrientedPrincipalEigenvector(Vector3d o, Vector3d p) Computes an oriented principal vector, where the orientation is nearest to the provided.
double	getRD() Radial diffusivity
Matrix3d	getV()
void	getV1(Vector3d v1)
void	getV2(Vector3d v2)
void	getV3(Vector3d v3)
void	invalidateEigenvectors()
void	orientEigenvectors(Matrix3d O, Vector3d lambda) Orients eigenvectors to align with the given ordered set, flipping signs if need be, or rotating for repeated eigenvalues.
void	orientPrincipalEigenvector(Vector3d o) Orients principal eigenvector to align with the given vector, flipping or rotating eigenspaces if need be
void	scale(double s) Uniform scaling of diffusion tensor, diffusivity scales with distance-squared
void	scale(double sx, double sy, double sz) Non-uniform scaling of diffusion tensor, e.g.
void	setZero()
void	transform(AffineTransform3d trans) Affine transform of diffusion tensor by performing a change of coordinates and definition of diffusivity tensor in Fick's law
void	transform(RigidTransform3d trans) Rotation of diffusion tensor
void	transformPPD(AffineTransform3d trans) Affine transform of diffusion tensor using Preservation of Principal Direction method of

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DTIVoxel

public DTIVoxel(double d00,
                double d11,
                double d22,
                double d01,
                double d02,
                double d12)

Method Detail

getOrientedPrincipalEigenvector

public void getOrientedPrincipalEigenvector(Vector3d o,
                                            Vector3d p)

Computes an oriented principal vector, where the orientation is nearest to the provided. If the principal eigenvalue is distinct, then simply flips the sign to maximize p.dot(o). Otherwise if it is repeated, finds the vector in the eigenspace (plane or sphere) that is closest to o.

Parameters:

o - orientation to match

p - principal vector

invalidateEigenvectors

public void invalidateEigenvectors()

setZero

public void setZero()

scale

public void scale(double s)

Uniform scaling of diffusion tensor, diffusivity scales with distance-squared

Parameters:

s - scale parameter

scale

public void scale(double sx,
                  double sy,
                  double sz)

Non-uniform scaling of diffusion tensor, e.g. if original image has non-uniform voxel spacing
Uses change of coordinates formula, and definition of diffusion via Fick's law

Parameters:

sx - x-scale

sy - y-scale

sz - z-scale

transform

public void transform(RigidTransform3d trans)

Rotation of diffusion tensor

Parameters:

trans - rotation

transform

public void transform(AffineTransform3d trans)

Affine transform of diffusion tensor by performing a change of coordinates and definition of diffusivity tensor in Fick's law

Parameters:

trans - transform

transformPPD

public void transformPPD(AffineTransform3d trans)

Affine transform of diffusion tensor using Preservation of Principal Direction method of

D. C. Alexander, C. Pierpaoli, P. J. Basser and J. C. Gee, "Spatial transformations of diffusion tensor magnetic resonance images," in IEEE Transactions on Medical Imaging, vol. 20, no. 11, pp. 1131-1139, Nov. 2001. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.160.9369&rep=rep1&type=pdf

Note: this definition is inconsistent with change of coordinates formulation and Fick's law

Parameters:

trans - transform

orientPrincipalEigenvector

public void orientPrincipalEigenvector(Vector3d o)

Orients principal eigenvector to align with the given vector, flipping or rotating eigenspaces if need be

Parameters:

o - orientation vector

orientEigenvectors

public void orientEigenvectors(Matrix3d O,
                               Vector3d lambda)

Orients eigenvectors to align with the given ordered set, flipping signs if need be, or rotating for repeated eigenvalues. Attempts to maximize correlation between provided ordered eigenvectors.

Parameters:

O - ordered eigenvectors

lambda - ordered eigenvalues

getV1

public void getV1(Vector3d v1)

getE1

public double getE1()

getV2

public void getV2(Vector3d v2)

getE2

public double getE2()

getV3

public void getV3(Vector3d v3)

getE3

public double getE3()

getFA

public double getFA()

Fractional anisotropy

Returns:

fractional anisotropy

getMD

public double getMD()

Mean diffusivity

Returns:

mean diffusivity

getRD

public double getRD()

Radial diffusivity

Returns:

radial diffusivity

getAD

public double getAD()

Axial diffusivity

Returns:

axial diffusivity

getV

public Matrix3d getV()

getD

public SymmetricMatrix3d getD()

clone

public DTIVoxel clone()

Specified by:

clone in interface Clonable

Overrides:

clone in class java.lang.Object