CAT12vextract
CAT12vextract.RdExtracts 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.
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.
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.