gamCluster: Run a Generalized Additive Model on the mean intensity over a...

In neuroconductor-devel-releases/voxel: Mass-Univariate Voxelwise Analysis of Medical Imaging Data

Description

This function is able to run a Generalized Additive Model (GAM) using the mgcv package. All clusters must be labeled with integers in the mask passed as an argument.

Usage

gamCluster(image, mask, fourdOut = NULL, formula, 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 mergeNiftis() 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 gam()
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 gam()

Value

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

Examples

image <- oro.nifti::nifti(img = array(1:1600, dim =c(4,4,4,25)))
mask <- oro.nifti::nifti(img = array(1:4, dim = c(4,4,4,1)))
set.seed(1)
covs <- data.frame(x = runif(25))
fm1 <- "~ s(x)"
models <- gamCluster(image=image, mask=mask, 
              formula=fm1, subjData=covs, ncores = 1, method="REML")

neuroconductor-devel-releases/voxel documentation built on May 6, 2020, 4:31 p.m.