gammCluster: Run a Generalized Additive Mixed Effects Model on the mean...

In angelgar/voxel: Mass-Univariate Voxelwise Analysis of Medical Imaging Data

Description

This function is able to run a Generalized Additive Mixed Effects Model (GAMM) using the gamm4() function. All clusters or Regions of Interest must be labeled with integers in the mask passed as an argument.

Usage

gammCluster(image, mask, fourdOut = NULL, formula, randomFormula, subjData,
  mc.preschedule = TRUE, ncores = 1, ...)

Arguments

image	Input image of type 'nifti' or vector of path(s) to images. If multiple paths, the script will call mergeNifti() and merge across time.
mask	Input mask of type 'nifti' or path to mask. All clusters must be labeled with integers in the mask passed as an argument
fourdOut	To be passed to mergeNifti, This is the path and file name without the suffix to save the fourd file. Default (NULL) means script won't write out 4D image.
formula	Must be a formula passed to gamm4()
randomFormula	Random effects formula passed to gamm4()
subjData	Dataframe containing all the covariates used for the analysis
mc.preschedule	Argument to be passed to mclapply, whether or not to preschedule the jobs. More info in parallel::mclapply
ncores	Number of cores to use for the analysis
...	Additional arguments passed to gamm4()

Value

Returns list of models fitted to the mean voxel intensity a region or interest.

Examples

image <- oro.nifti::nifti(img = array(1:1600, dim =c(4,4,4,25)))
mask <- oro.nifti::nifti(img = array(c(rep(0,14),1,2), dim = c(4,4,4,1)))
set.seed(1)
covs <- data.frame(x = runif(25), id = rep(1:5,5))
fm1 <- "~ s(x)"
randomFormula <- "~(1|id)"
models <- gammCluster(image, mask, formula = fm1, 
                              randomFormula = randomFormula, subjData = covs, ncores = 1, REML=TRUE)
                              

angelgar/voxel documentation built on Dec. 31, 2019, 3:09 p.m.