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

Description Usage Arguments Value Examples

View source: R/anovalmVoxel.R

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

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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

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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 June 26, 2018, 5 p.m.