simple_roi_analysis: Perform ROI population analysis between two groups.

In stnava/itkImageR: Examples using Rcpp to interface R and ITK

Description

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

Usage

roiResults <- simple_roi_analysis( dimensionality = 3, controlFileNames = c(),
  experimentalFileNames = c(), roiLabelsFileName = "" )

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

Value

list consisting of unique roi labels, t-values, and p-values.

Author(s)

Tustison NJ

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/"

roiResults.ttest <- simple_roi_analysis( dimensionality = 2, imageFileNames = images,
  predictors = data.frame( diagnosis ),
  roiLabelsFileName = "./example_images/phantomtemplate_roi_labels.nii.gz", testType = 'student.t' )

roiResults.wilcox <- simple_roi_analysis( dimensionality = 2, imageFileNames = images,
  predictors = data.frame( diagnosis ),
  roiLabelsFileName = "./example_images/phantomtemplate_roi_labels.nii.gz", testType = 'wilcox' )

roiResults.lm <- simple_roi_analysis( dimensionality = 2, imageFileNames = images,
  predictors = data.frame( cbind( diagnosis, age ) ), formula = as.formula( value ~ 1 + diagnosis + age ),
  roiLabelsFileName = "./example_images/phantomtemplate_roi_labels.nii.gz", testType = 'lm' )

## End(Not run)

stnava/itkImageR documentation built on May 30, 2019, 7:21 p.m.