web/examples/convert_pervertexdata_file.R

In dfsp-spirit/freesurferformats: Read and Write 'FreeSurfer' Neuroimaging File Formats

#!/usr/bin/env Rscript
# Convert a file with per-vertex data to a new format.
#
# To install all required R packages, run from an R session:
#
# R> install.packages("freesurferformats", dependencies = TRUE);
#

library("freesurferformats");


usage_msg <- function() { return(sprintf("USAGE: convert_pervertexdata_file <infile> <outfile>\nExample: convert_pervertexdata_file thickness_overlay.nii.gz new_output_file.gii")); }

args = commandArgs(trailingOnly=TRUE);
if (length(args) != 2) {
    stop(usage_msg());
}

infile = args[1];
outfile = args[2];

if(! file.exists(infile)) { stop(sprintf("Infile %s cannot be read.", infile)); }

cat(sprintf("Converting input per-vertex data file '%s' to target file '%s'...\n", infile, outfile));
pvd = freesurferformats::read.fs.morph(infile);
freesurferformats::write.fs.morph(outfile, pvd);
cat(sprintf("Finished.\n"));