anovalmVoxel: Computes voxelwise analysis of variance (ANOVA) tables for a...

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

Description

This function computes analysis of variance tables for the fitted models after running a Linear Model using the stats::lm() function. The analysis will run in all voxels in the mask and will return the analysis of variance table for each voxel. Please check the stats documentation for further information about specific arguments used in stats::anova.lm(). Multi-model calls are disabled.

Usage

anovalmVoxel(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 all mergeNifti() and merge across time.
mask	Input mask of type 'nifti' or path to mask. Must be a binary mask
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 lm()
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
...	Additional arguments passed to lm()

Value

Returns list of models fitted to each voxel over the masked images passed to function.

Examples

image <- oro.nifti::nifti(img = array(1:1600, dim =c(4,4,4,25)))
mask <- oro.nifti::nifti(img = array(0:1, dim = c(4,4,4,1)))
set.seed(1)
covs <- data.frame(x = runif(25), y=runif(25))
fm1 <- "~ x + y"
models <- anovalmVoxel(image=image, mask=mask,
              formula=fm1, subjData=covs, ncores = 1)

Example output

[1] "Created time series to matrix"
[1] "Created formula list"
[1] "Running test ANOVA"
[1] "Running parallel ANOVAs"
elapsed 
  0.083 
[1] "Parallel ANOVAs Ran"

voxel documentation built on May 1, 2019, 10:26 p.m.