lmVoxel: Run a Linear Model on all voxels of a NIfTI image within a...

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

Description

This function is able to run a Linear Model using the stats package. The analysis will run in all voxels in in the mask and will return the model fit for each voxel.

Usage

lmVoxel(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))
fm1 <- "~ x"
models <- lmVoxel(image=image, mask=mask, 
              formula=fm1, subjData=covs, ncores = 1)

Example output

Loading required package: lmerTest
Loading required package: lme4
Loading required package: Matrix

Attaching package: ‘lmerTest’

The following object is masked from ‘package:lme4’:

    lmer

The following object is masked from ‘package:stats’:

    step

[1] "Created time series to matrix"
[1] "Created formula list"
[1] "Running test model"
[1] "Running parallel models"
elapsed 
  0.045 
[1] "Parallel Models Ran"

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