SURFvextract
SURFvextract.RdExtracts whole-brain vertex-wise surface-based measures for each subject in a 'FreeSurfer' output subjects directory, resamples the data to a common surface template, and stores it as a .rds file. This function requires the 'FreeSurfer' environment to be preset in the unix environment and a 'FreeSurfer' license key.
Usage
SURFvextract(
sdirpath = "./",
filename,
template = "fsaverage5",
measure = "thickness",
subj_ID = TRUE,
fshomepath
)Arguments
- sdirpath
A string object containing the path to the 'FreeSurfer' preprocessed subjects directory. This directory must be the output directory from a FreeSurfer preprocessing recon-all pipeline. Default is the current working directory ("./").
- filename
A string object containing the desired name of the output RDS file. Default is 'brain_measure.rds' in the R temporary directory (tempdir()).
- template
A string object containing the name of surface template (available: 'fsaverage5', 'fsaverage6'). Default is fsaverage5.
- measure
A string object containing the name of the measure of interest. Options are thickness, curv, sulc, area, and volume (for freesurfer 7.4.1 or later). Default is thickness.
- subj_ID
A logical object stating whether to include subject IDs (folder names in the subjects directory) as a first column to the output matrix. Default is TRUE.
- fshomepath
An optional string object containing the path to the FreeSurfer installation directory. This makes sure R accesses FreeSurfer if the system environment variables are not inherited — as would be the case if you are running the function from RStudio.
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 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.
Details
Note that RStudio does not inherit the shell environment variables if it is open from a terminal. In that case, the fshomepath argument needs to be provided. The function runs system shell commands that will produce in the set subjects directory: 1) a sorted list of subjects "sublist.txt"; 2) a link file to the selected surface fsaverage template. 3) left and right hemisphere .mgh maps outputted by 'FreeSurfer' 's mris_preproc.