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SCMvextract

SCMvextract.Rd

Extracts surface-based measures from the python toolbox "SubCortexMesh" in each subject. These can be based on FreeSurfer ASeg or FSL FIRST subcortical segmentations. SCMvextract() reads through the metrics .vtk files outputted by SubCortexMesh (surface_metrics/ directory), extracts the vertex-wise values, and stores them as a .rds file, merging left and right hemispheres when applicable, for each (selected) subcortical region.

Usage

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

ASEGvextract(...)

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()).

template

A string object containing the name of the template segmentation which was used in SubCortexMesh ('fsaverage' or 'fslfirst').

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"). SCMvextract() requires reticulate and python to read the .vtk files.

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

  • fsaverage/fslfirst: ROI

  • 2044/2026: accumbens area

  • 3430/3592: amygdala

  • 6940/7570: caudate nuclei

  • 39214/31466: cerebellum

  • 8132/8244: hippocampus

  • 3200/3548: pallidum

  • 8394/7908: putamen

  • 7768/8542: thalamus

  • 7144/NA: ventral diencephalon

  • 9452/9516: brain stem

  • 95718/82412: all ROIs merged

Examples

SCMvextract(sdirpath = "subcortexmesh_output_metrics", 
outputdir=paste0(tempdir(), "\\subcortices"), template='fsaverage', measure="surfarea") 
#> Checking for VertexWiseR system requirements ... 
#> Checking for Miniconda or Python environment...
#> No system requirements are missing. ✓ 
#> Subcortical meshes could not be found in the set sdirpath.