Take a FreeSurfer ASCII format surface and convert to Wavefront .obj, unnecessarily rendering a rainbow-colored surface using rgl ;P

asc-to-obj.R

#!/usr/bin/Rscript
## Josh Moller-Mara
## Take in an .asc file created with mris_convert
## (e.g. mris_convert lh.pial lh.pial.asc)
## and then convert it into a Wavefront OBJ.
## And also unnecessarily render it with rgl :-)
library(rgl)

args <- commandArgs(trailingOnly = TRUE)

## Strings to 3 column numeric matrix
splitex <- function(strings) {
    do.call(rbind, lapply(strsplit(strings, split = " +"), as.numeric))[,1:3]
}


for(file in args) {
    ## Read in lines, filtering out comments
    lines <- grep("^(#.*)?$", readLines(file), value = TRUE, invert = TRUE)

    ## Get the number of vertices and the number of faces
    infos <- as.numeric(unlist(strsplit(lines[1], " ")))
    ## Skip header
    splits <- split(lines, rep(c("Header", "Vertices", "Faces"), times=c(1, infos)))

    ## Convert vertices
    verts <- splitex(splits$Vertices)
    faces <- splitex(splits$Faces) + 1      #Faces have to start at 1

    ## Get a list of all triangles
    triangles <- verts[as.vector(t(faces)),]

    rgl.open()
    rgl.triangles(triangles, color = rainbow(nrow(triangles)))
    play3d(spin3d(axis=c(1,0,0), rpm=60/3), duration=3)
    play3d(spin3d(axis=c(0,0,-1), rpm=60/3), duration=3)

    ## You can't have scientific notation in .obj files
    options(scipen=999)
    vertLines <- paste("v", verts[,1], verts[,2], verts[,3])
    faceLines <- paste("f", faces[,1], faces[,2], faces[,3])

    fileConn <- file(paste0(file, ".obj"))
    writeLines(c(vertLines, faceLines), fileConn)
    close(fileConn)
}