Skip to contents

ASEGvextract

ASEGvextract.Rd

Extracts surface-based measures from ASEG subcortical segmentations in each subject. These must be specifically computed from a FreeSurfer output subjects directory using the python toolbox "subcortexmesh". The function reads through the metrics .vtk files outputted by subcortexmesh, extracts the vertex-wise values, and stores them as a .rds file, merging left and right hemispheres.

Usage

ASEGvextract(
  sdirpath = "./",
  outputdir,
  measure = "thickness",
  roilabel,
  subj_ID = TRUE,
  silent = FALSE,
  VWR_check = TRUE
)

Arguments

sdirpath

A string object containing the path to the 'SubCortexMesh' surface metrics directory, containing surface-based metrics (.vtk files). Default is the current working directory ("./").

outputdir

A string object containing the path of the directory where all ROI RDS files will be stored. Default is 'subcortices' in the R temporary directory (tempdir()).

measure

A string object containing the name of the measure of interest. Options include thickness, and surfarea. Default is thickness.

roilabel

A string object or vector of string objects containing the name(s) of the subcortical region(s) to extract (both hemispheres automatically included when applicable). E.g. "thalamus" or c("thalamus", "caudate"). Default is all regions in sdirpath.

subj_ID

A logical object to determine whether to return a list object containing both subject ID and data matrix.

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 directory containing - for each bilateral subcortical region separately - a .RDS files, each 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. Each matrix has N subjects x M vertices dimensions and can be used readily 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 (if applicable).

Details

The function looks for standard subject folder names (starting "sub-") and surface file names as defined by subcortexmesh (starting "left-","right-", or "brain-Stem"). It requires reticulate and python to read the .vtk files.

Number of vertices in the (bilateral) matrix for each region-of-interest:

  • 2044: accumbens area

  • 3430: amygdala

  • 6940: caudate nuclei

  • 39214: cerebellum

  • 8132: hippocampus

  • 3200: pallidum

  • 8394: putamen

  • 7768: thalamus

  • 7144: ventral diencephalon

  • 9452: brain stem

  • 95718: all aseg ROIs

Examples

ASEGvextract(sdirpath = "subcortexmesh_output_metrics", 
outputdir=paste0(tempdir(), "\\subcortices"), measure="surfarea") 
#> Checking for VertexWiseR system requirements ... 
#> Subcortical meshes could not be found in the set sdirpath.