ANTsR (version 1.0)

simple_voxel_based_analysis: Perform voxel-based population analysis between two groups.

Description

Student's t-test performed at each voxel within a specified mask region to determine difference between a control group and an experimental group.

Usage

simple_voxel_based_analysis <- function( dimensionality = 3, imageFileNames = c(), predictors,
  formula, testType = c( "lm", "student.t", "wilcox" ), maskFileName = "", outputPrefix = "./ANTsR" )

Arguments

dimensionality

Dimension of images.

imageFileNames

List of image files.

testType

A value of 'lm', 'student.t', or 'wilcox'. The latter two test types are assumed to be two-sampled parametric and non-parametric, respectively.

predictors

A simple vector or single column matrix or data frame specifying sample membership for student.t or wilcox testing. For the 'lm' option, a data frame must be specified whose column names match the specified formula.

formula

Used with the 'lm' option for more sophisticated modeling.

maskFileName

File name of mask defining the region over which testing is performed (foreground voxel != 0, background voxel = 0)

outputPrefix

Output directory and prefix to prepend to the resulting image file names (t-value image, "one minus" p-value image, and "one minus" (false discovery rate) corrected p-value image.

Value

None.

Examples

# NOT RUN {
# Get the image files
controlFileNames <- list.files( path = "./example_images/", pattern =
  glob2rx( "phantomtemplate_CONTROL*" ), full.names = TRUE, recursive = FALSE )
experimentalFileNames <- list.files( path = "./example_images/", pattern =
  glob2rx( "phantomtemplate_EXP*" ), full.names = TRUE, recursive = FALSE )

images <- c( controlFileNames, experimentalFileNames )
diagnosis <- c( rep( 1, length( controlFileNames ) ), rep( 0, length( experimentalFileNames ) ) )
age <- runif( length( diagnosis ), 25, 30 )
outputPath <- "./test_output/"

prefix <- "ANTsR_t.test_"
simple_voxel_based_analysis( dimensionality = 2, imageFileNames = images,
  predictors = data.frame( diagnosis ),
  maskFileName = "./example_images/phantomtemplate_mask.nii.gz",
  outputPrefix = paste( outputPath, prefix, sep = '' ), testType = 'student.t' )

prefix <- "ANTsR_wilcox_"
simple_voxel_based_analysis( dimensionality = 2, imageFileNames = images,
  predictors = data.frame( diagnosis ),
  maskFileName = "./example_images/phantomtemplate_mask.nii.gz",
  outputPrefix = paste( outputPath, prefix, sep = '' ), testType = 'wilcox' )

prefix <- "ANTsR_lm_"
simple_voxel_based_analysis( dimensionality = 2, imageFileNames = images,
  predictors = data.frame( cbind( diagnosis, age ) ), formula = as.formula( value ~ 1 + diagnosis + age ),
  maskFileName = "./example_images/phantomtemplate_mask.nii.gz",
  outputPrefix = paste( outputPath, prefix, sep = '' ), testType = 'lm' )
# }