simple_voxel_based_analysis¶

purpose:

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” )

examples:

# 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' )

ANTsR 0.0.0 documentation

simple_voxel_based_analysis

simple_voxel_based_analysis¶