ffdGroupEvidenceFFBS {BayesDLMfMRI}

ffdGroupEvidenceFFBS

Description

This function can be used to build activation maps for group task-based fMRI data.

Usage

ffdGroupEvidenceFFBS(
  ffdGroup,
  covariates,
  m0 = 0,
  Cova = 100,
  delta = 0.95,
  S0 = 1,
  n0 = 1,
  N1 = FALSE,
  Nsimu1 = 100,
  Cutpos = 30,
  r1,
  mask,
  Ncores = NULL
)

Arguments

ffdGroup

list of N elements, each being a 4D array (ffdc[i,j,k,t]) that contains the sequence of MRI images related to each of the N subjects in the sample.

covariates

a data frame or matrix whose columns contain the covariates related to the expected BOLD response obtained from the experimental setup

m0

the constant prior mean value for the covariates parameters and common to all voxels within every neighborhood at t=0 (m=0 is the default value when no prior information is available). For the case of available prior information, m0 can be defined as a \(p\times q\) matrix, where \(p\) is the number of columns in the covariates object and \(q\) is the cluster size.

Cova

a positive constant that defines the prior variances for the covariates parameters at t=0 (Cova=100 is the default value when no prior information is available). For the case of available prior information, Cova can be defined as a \(p\times p\) matrix, where \(p\) is the number of columns in the covariates object.

delta

a discount factor related to the evolution variances. Recommended values between 0.85<delta<1. delta=1 will yield results similar to the classical general linear model.

S0

prior covariance structure between pair of voxels within every cluster at t=0. S0=1 is the default value when no prior information is available and defines an \(q\times q\) identity matrix. For the case of available prior information, S0 can be defined as an \(q\times q\) matrix, where \(q\) is the common number of voxels in every cluster.

n0

a positive hyperparameter of the prior distribution for the covariance matrix S0 at \(t=0\) (n1=1 is the default value when no prior information is available). For the case of available prior information, n0 can be set as n0=np, where np is the number of MRI images in the pilot sample.

N1

is the number of images (2<N1<T) from the ffdc array employed in the model fitting. N1=NULL (or equivalently N1=T) is its default value, taking all the images in the ffdc array for the fitting process.

Nsimu1

is the number of simulated on-line trajectories related to the state parameters. These simulated curves are later employed to compute the posterior probability of voxel activation.

Cutpos

a cutpoint time from where the on-line trajectories begin. This parameter value is related to an approximation from a t-student distribution to a normal distribution. Values equal to or greater than 30 are recommended (30<Cutpos1<T).

r1

positive integer number that defines the distance from every voxel with its most distant neighbor. This value determines the size of the cluster. The users can set a range of different r1 values: \(r1 = 0, 1, 2, 3, 4\), which leads to \(q = 1, 7, 19, 27, 33\), where \(q\) is the size of the cluster.

mask

a 3D array that works as a brain of reference (MNI atlas) for the group analysis.

Ncores

a postive integer indicating the number of threads or cores to be used in the computation of the activation maps.

Details

A multivariate dynamic linear model is fitted in the same fashion as at the individual level for every subject in the sample. However, at this stage, the posterior distributions from all the subjects are combined to build a single one, which is then employed to compute the activation evidence maps for the group using the Forward Filtering Backward Sampling (FFBS) algorithm. To deeply understand the method implemented in this package, a reading of (Cardona-Jiménez and de B. Pereira 2021) and (Cardona-Jiménez 2021) is mandatory.

Value

It returns a list of the form [[k]][p,x,y,z], where k defines the type of test (k = 1 for Marginal effect, k = 2 for Joint effect, and k = 3 for Average cluster effect), p represents the column position in the covariates matrix and x,y,z represent the voxel position in the brain image.

References

Cardona-Jiménez J, de B. Pereira CA (2021). “Assessing dynamic effects on a Bayesian matrix-variate dynamic linear model: An application to task-based fMRI data analysis.” Computational Statistics & Data Analysis, 163, 107297. ISSN 0167-9473, doi:10.1016/j.csda.2021.107297, https://www.sciencedirect.com/science/article/pii/S0167947321001316.

Cardona-Jiménez J (2021). “BayesDLMfMRI: Bayesian Matrix-Variate Dynamic Linear Models for Task-based fMRI Modeling in R.” arXiv e-prints, arXiv–2111.

Examples

## Not run: 
# This example can take a long time to run.
DatabaseGroup <- get_example_fMRI_data_group()
data("covariates", package="BayesDLMfMRI")
res <- ffdGroupEvidenceFFBS(ffdGroup = DatabaseGroup, covariates = Covariates, 
                            m0=0, Cova=100, delta = 0.95, 
                            S0 = 1, n0 = 1, N1 = FALSE, Nsimu1 = 100,
                            Cutpos = 30, r1 = 1, mask = MASK, Ncores = 7)
str(res)

## End(Not run)