## ----eval = FALSE-------------------------------------------------------------
# library("freesurferformats")
# area <- read.fs.morph(system.file("extdata", "lh.thickness", package = "freesurferformats", mustWork = TRUE))
# thickness <- read.fs.morph(system.file("extdata", "lh.area.gz", package = "freesurferformats", mustWork = TRUE))
# mymorphdata <- area * thickness

## ----eval = FALSE-------------------------------------------------------------
# format1 <- write.fs.morph(tempfile(fileext = "mgz"), mymorphdata)
# format2 <- write.fs.morph(tempfile(fileext = "mgh"), mymorphdata)
# format3 <- write.fs.morph(tempfile(fileext = "curv"), mymorphdata)

## ----eval = FALSE-------------------------------------------------------------
# mgh_outfile <- "mystudy/subject1/mri/shifted_brain.mgz"
# data <- array(data = rep(1L, 256 * 256 * 256), dim = c(256, 256, 256))
# # not exactly a brain, but will do.
# mr_params <- c(2300, 0.1, 2., 900.)
# vox2ras_matrix <- matrix(c(-1, 0, 0, 0, 0, 0, -1, 0, 0, 1, 0, 0, 127.5, -98.6273, 79.0953, 1.000), nrow = 4, byrow = FALSE)
# write.fs.mgh(mgh_outfile, data, vox2ras_matrix = vox2ras_matrix, mr_params = mr_params)

## ----eval = FALSE-------------------------------------------------------------
# some_surface_mask <- rep(1L, 163842)
# some_surface_mask[30000:45000] <- 0L
# write.fs.mgh("regionmask_stored_as_MRI_FLOAT.mgh", as.double(some_surface_mask))

## ----eval = FALSE-------------------------------------------------------------
# data <- rnorm(120000, 2.0, 1.0)
# curvfile <- "mystudy/subject1/surf/lh.random"
# write.fs.curv(curvfile, data)

## ----eval = FALSE-------------------------------------------------------------
# vertices <- matrix(rep(0.3, 15), nrow = 3)
# # 5 vertices
# faces <- matrix(c(1L, 2L, 3L, 2L, 4L, 3L, 4L, 5L, 3L), nrow = 3, byrow = TRUE)
# # 3 faces
# 
# write.fs.surface(tempfile(fileext = "white"), vertices, faces)

## ----eval = FALSE-------------------------------------------------------------
# output_file <- tempfile()
# # generate data
# vertex_indices <- seq(from = 10000, to = 20000)
# # write label to file
# write.fs.label(output_file, vertex_indices)

## ----eval = FALSE-------------------------------------------------------------
# colortable_df <- data.frame(
#   "struct_index" = c(0, 1), "struct_name" = c("struct1", "struct2"),
#   "r" = c(80, 100), "g" = c(50, 40), "b" = c(250, 200), "a" = c(0, 0), stringsAsFactors = FALSE
# )
# output_file <- tempfile(fileext = ".txt")
# write.fs.colortable(output_file, colortable_df)