CAT12vextract: CAT12vextract

In VertexWiseR: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal Surface

CAT12vextract

Description

Extracts vertex-wise surface-based measures for each subject from a CAT12 preprocessed directory, resampled to a 32k mesh, and stores them all as a single .RDS file.

Usage

CAT12vextract(
  sdirpath = "./",
  filename,
  measure = "thickness",
  subj_ID = TRUE,
  silent = FALSE,
  VWR_check = TRUE
)

Arguments

sdirpath	A string object containing the path to the CAT12 subjects preprocessed directory. Default is the current working directory ("./").
filename	A string object containing the desired name of the output RDS file. Default is 'CAT12_measure.rds' in the R temporary directory (tempdir()).
measure	A string object containing the name of the measure of interest. Options are 'thickness', 'depth', 'fractaldimension', 'gyrification', and 'toroGI20mm'. Default is 'thickness.'
subj_ID	A logical object to determine whether to return a list object containing both subject ID and data matrix. Subject IDs are assumed to be the top directory names in the sdirpath.
silent	A logical object to determine whether messages will be silenced. Set to 'FALSE' by default
VWR_check	A boolean object specifying whether to check and validate system requirements. Default is TRUE.

Details

The function searches inside the CAT12 preprocessed for 32k meshes (.gii) with the user-selected measure, extracts the data from these files, and organizes the left and right hemisphere vertex data for each subject as rows in a N x 64984 data matrix within a .rds object. Python and reticulate are required as the NiBabel package is used to import .gii files outputted by CAT12.

Value

A .RDSfile with a list containing 1. the list of subject IDs (first element) and 2. a surface data matrix object (second element), or only a data matrix object. The matrix has N subjects x M vertices dimensions and can be readily used by VertexWiseR statistical analysis functions. Each row corresponds to a subject (in the order they are listed in the folder) and contains the left to right hemispheres' vertex-wise values.

Examples

CAT12vextract(sdirpath="./", 
filename='thickness.rds', 
measure='thickness', 
subj_ID = TRUE, 
VWR_check=FALSE)

VertexWiseR documentation built on April 15, 2025, 1:18 a.m.