mritc (version 0.5-3)

mritc: MRI Tissue Classification Using Various Methods

Description

Conduct the MRI tissue classification using different methods including: the normal mixture model (NMM) fitted by the Expectation-Maximization (EM) algorithm; the hidden Markov normal mixture model (HMNMM) fitted by the Iterated Conditional Mode (ICM) algorithm, the Hidden Markov Random Field EM (HMRFEM) algorithm, or the Bayesian Markov chain Monte Carlo method (MCMC); the partial volume HMNMM fitted by the modified EM (PVHMRFEM) algorithm or the higher resolution HMNMM fitted by the MCMC method (MCMCsub); the HMNMM with both PV and intensity non-uniformity addressed (MCMCsubbias).

Usage

mritc.em(y, prop, mu, sigma, err, maxit, verbose)
   mritc.icm(y, neighbors, blocks, spatialMat, beta, mu, sigma,
             err, maxit, verbose)
   mritc.hmrfem(y, neighbors, blocks, spatialMat, beta, mu, sigma,
                err, maxit, verbose)
   mritc.pvhmrfem(y, neighbors, blocks, spatialMat, beta, mu, sigma,
              err, maxit, verbose)
   mritc.bayes(y, neighbors, blocks, sub, subvox,
               subbias, neighbors.bias, blocks.bias, weineighbors.bias, weights.bias,
               spatialMat, beta, mu, sigma, niter, verbose)
   mritc(intarr, mask, method)

Value

For mritc, it generates an object of class "mritc" which is a list containing the following components:

prob

a matrix, one row per voxel and each column corresponding to the probabilities of being allocated to each component of a normal mixture model.

mu

a vector of estimated means of the normal mixture model.

sigma

a vector of estimated standard deviations of the normal mixture model.

method

the method used for computation.

mask

mask of an brain. Voxels inside it are classified.

Generic functions print.mritc,

summary.mritc, and

plot.mritc are provided.

For others, only prob, mu, and sigma are generated.

Arguments

y

a vector of intensity values of voxels.

prop

a vector of initial estimate of the proportions of different components of a normal mixture model. It can be obtained using the function initOtsu.

mu

a vector of initial estimate of the means of different components of a normal mixture model. It can be obtained using the function initOtsu.

sigma

a vector of initial estimates of the standard deviations of different components of a normal mixture model. It can be obtained using the function initOtsu.

err

relative maximum error(s) used to decide when to stop the iteration. It could be a vector corresponding to the relative maximum errors of the means, standard deviations (for mritc.em, mritc.icm, mritc.hmrfem, and mritc.pvhmrfem), and proportions (for mritc.em) of all components of a normal mixture model. When it is a scalar, all have the same relative maximum error. The default value is 1e-4.

maxit

maximum number of iterations to perform. The default is 200 for mritc.em, 20 for mritc.icm, mritc.hmrfem, and mritc.pvhmrfem.

verbose

logical. If TRUE, then indicate the level of output as the algorithm runs.

neighbors

a matrix of neighbors of voxels. One row per voxel. It can be obtained using the function makeMRIspatial.

blocks

split voxels into different blocks to use the checker-board idea. It can be obtained using the function makeMRIspatial.

spatialMat

a matrix defining the spatial relationship in a Potts model. The default value is diag(1,3) for three components models for mritc.icm, mritc.hmrfem and mritc.bayes when sub is FALSE and matrix(c(2,0,-1,0,2,0,-1,0,2), nrow=3) when sub is TRUE. For mritc.pvhmrfem the default is matrix(c(2, 1, -1, -1, -1, 1, 2, 1, -1, -1, -1, 1, 2, 1, -1, -1, -1, 1, 2, 1, -1, -1, -1, 1, 2), ncol=5).

beta

the parameter 'inverse temperature' of the Potts model. The default value is 0.4 for mritc.icm, 0.5 for mritc.hmrfem, 0.6 for mritc.pvhmrfem. For mritc.bayes, the default is 0.7 when sub is FALSE and 0.3 when sub is TRUE.

sub

logical; if TRUE, use the higher resolution model; otherwise, use the whole voxel method.

subvox

for mritc.bayes, the match up tabel of voxels and their corresponding subvoxels for the higher resolution model. It can be obtained using the function makeMRIspatial. For the whole voxel method, subvox=NULL

subbias

logical; if TRUE, use the model that addresses both the PV and intensity non-uniformity. The default is FALSE.

neighbors.bias

a matrix of neighbors of bias field. One row per voxel. It can be obtained using the function makeMRIspatial. The default is NULL.

blocks.bias

blocks for bias field. It can be obtained using the function makeMRIspatial. The default is NULL.

weineighbors.bias

a vector of sum of weights of neighbors of bias field. One element per voxel. It can be obtained using the function makeMRIspatial. The default is NULL.

weights.bias

a vector of weights of different neighbors of every voxel. It can be obtained using the function makeMRIspatial. The default is NULL.

niter

the number of iterations for mritc.bayes. The default values are 1000 and 100 for with and without bias field correction, respectively. The default values seem to be adequate in many cases.

intarr

a three dimensional array of an MR image.

mask

a mask of the MR image. Voxels with value 1 are inside the brain and value 0 are outside. Focus on voxels within the brain.

method

a string giving the method for MRI tissue classification. It must be one of "EM", "ICM", "HMRFEM", "MCMC", "PVHMRFEM", "MCMCsub", or "MCMCsubbias" corresponding to using the NMM fitted by the EM algorithm; the HMNMM fitted by the ICM algorithm, the HMRFEM algorithm, or the MCMC; the partial volume HMNMM fitted by the PVHMRFEM algorithm; the higher resolution HMNMM fitted by the MCMC; the HMNMN addressing both the PV and intensity non-uniformity. It can be abbreviated. The default is "EM".

Details

The function mritc integrates functions mritc.em, mritc.icm, mritc.hmrfem, mritc.pvhmrfem, and mritc.bayes. It provides a uniform platform with easier usage. The user just need to specify the input MR image, the mask of the image, and the method used. The other parameters are specified automatically as follows. The parameters for the initial estimates of the proportions, means, and standard deviations of the normal mixture model are obtained using the function initOtsu. As to the parameters related to the Potts model, the six neighbor structure is used and then the neighbors, blocks, and subvox are obtained using the function makeMRIspatial. For the bias field correction, the twenty-six neighbor structure is used and then the neighbors.bias, blocks.bias, weineighbors.bias and weights.bias are obtained using the function makeMRIspatial. The other parameters are taken as the default values for each method. The process is reported during iterations.

References

Julian Besag (1986) On the statistical analysis of dirty pictures (with discussion) Journal of the Royal Statistical Society. Series B (Methodological) vol. 48 259-302

Meritxell Bach Cuadra, Leila Cammoun, Torsten Butz, Olivier Cuisenaire, and Jean-Philippe Thiran (2005) Comparison and validation of tissue modelization and statistical classification methods in T1-weighted MR brain images IEEE Transactions on Medical Imaging, vol.24 1548-1565

Dai Feng, Dong Liang, and Luke Tierney (2014) An unified Bayesian hierarchical model for MRI tissue classification Statistics in Medicine vol.33, issue 8 1349-1368

Dai Feng, Luke Tierney, and Vincent Magnotta (2012) MRI tissue classification using high resolution Bayesian hidden Markov normal mixture models Journal of the American Statistical Association, vol.107, no.497 102-119

Dai Feng and Luke Tierney (2011) mritc: A package for MRI tissue classification Journal of Statistical Software, vol.44, no.7 1-20 https://www.jstatsoft.org/v44/i07/

Dai Feng (2008) Bayesian hidden Markov normal mixture models with application to MRI tissue classification Ph. D. Dissertation, The University of Iowa

Yongyue Zhang, Michael Brady, and Stephen Smith (2001) Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm IEEE Transactions on Medical Imaging vol. 20 45-57

Examples

  #Example 1
  T1 <- readMRI(system.file("extdata/t1.rawb.gz", package="mritc"),
                c(91,109,91), format="rawb.gz")
  mask <- readMRI(system.file("extdata/mask.rawb.gz", package="mritc"),
                  c(91,109,91), format="rawb.gz")
  y <- T1[mask==1]
  initial <- initOtsu(y, 2)
  prop <- initial$prop
  mu <- initial$mu
  sigma <- initial$sigma
  tc.em <- mritc.em(y, prop, mu, sigma, verbose=TRUE)
 
  # \donttest{
  mrispatial <- makeMRIspatial(mask, nnei=6, sub=FALSE)
  tc.icm <- mritc.icm(y, mrispatial$neighbors, mrispatial$blocks,
                      mu=mu, sigma=sigma, verbose=TRUE)
  tc.hmrfem <- mritc.hmrfem(y, mrispatial$neighbors, mrispatial$blocks,
                            mu=mu, sigma=sigma, verbose=TRUE)
  tc.pvhmrfem <- mritc.pvhmrfem(y, mrispatial$neighbors, mrispatial$blocks,
                                mu=mu, sigma=sigma, verbose=TRUE)
  tc.mcmc <- mritc.bayes(y, mrispatial$neighbors, mrispatial$blocks,
                         mrispatial$sub, mrispatial$subvox,
                         mu=mu, sigma=sigma, verbose=TRUE)

  mrispatial <- makeMRIspatial(mask, nnei=6, sub=TRUE)
  tc.mcmcsub <- mritc.bayes(y, mrispatial$neighbors, mrispatial$blocks,
                         mrispatial$sub, mrispatial$subvox,
                         mu=mu, sigma=sigma, verbose=TRUE)

  mrispatial26 <- makeMRIspatial(mask, nnei=26, sub=TRUE, bias=TRUE)
  tc.mcmcsubbias <- mritc.bayes(y, mrispatial$neighbors, mrispatial$blocks,
                                mrispatial$sub, mrispatial$subvox,
                                subbias=TRUE, mrispatial26$neighbors,
                                mrispatial26$blocks,mrispatial26$weineighbors,
                                mrispatial26$weights, mu=mu, sigma=sigma, verbose=TRUE)

  # }
  #Example 2
  T1 <- readMRI(system.file("extdata/t1.rawb.gz", package="mritc"),
                c(91,109,91), format="rawb.gz")
  mask <-readMRI(system.file("extdata/mask.rawb.gz", package="mritc"),
                 c(91,109,91), format="rawb.gz")
  tc.icm <- mritc(T1, mask, method="ICM")