civet.CreateBrainViewFile: Create a brain view file

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Create a brain view file

Description

Creates a text file that can be loaded into brain-view2

Usage

civet.CreateBrainViewFile(
  dataFile,
  atlasFile,
  atlasVertices,
  outputFileName,
  civetVersion = "1.1.12"
)

Arguments

dataFile	Either the name of a file with atlas labeling or an R array with atlas labeling
atlasFile	Text file with map between atlas labels and numbers
atlasVertices	Text file with map between vertex points and atlas numbers
outputFileName	path to file where output will be saved
civetVersion	Version of CIVET used (Default 1.1.12)

Details

This function will create a txt file that can be loaded into brain-view2, in order to visualize the results from CIVET. This function either accepts a text file or R variable as input. If using an R variable the rows/columns must be labeled with the Atlas Names. The names are then matched to numbers as given by the AtlasFile, and then the numbers are matched to vertices in the AtlasVertexFile.

Examples

## Not run: 
gf = read.csv("~/SubjectTable.csv") 
civet.getAllFilenames(gf,"ID","ABC123","~/CIVET", TRUE, "1.1.12") 
gf = civet.readAllCivetFiles("~/Atlases/AAL/AAL.csv",gf)
civet.CreateBrainViewFile(gf$lobeThickness[1,],
                          "/Atlases/AAL/AAL.csv",
                          "/Atlases/AAL/AAL_atlas_left.txt",
                          "leftLobeThickness.txt")

## End(Not run)

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.