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Generate volume data from 'MNI' coordinates

Source: R/class_brainatlas.R
voxel_cube.Rd

Generate volume data from 'MNI' coordinates

Usage

add_voxel_cube(
  brain,
  name,
  cube,
  size = c(256, 256, 256),
  trans_mat = NULL,
  trans_space_from = c("model", "scannerRAS"),
  color_format = c("RGBAFormat", "RedFormat")
)

add_nifti(
  brain,
  name,
  path,
  trans_mat = NULL,
  color_format = c("RGBAFormat", "RedFormat"),
  trans_space_from = c("model", "scannerRAS")
)

create_voxel_cube(
  mni_ras,
  value,
  colormap,
  keys = colormap$get_key(value),
  dimension = c(256, 256, 256)
)

Arguments

brain

a 'threeBrain' brain object generated from freesurfer_brain2 or merge_brain. If you have 'rave' package installed, the brain can be generated from rave::rave_brain2

name

the name of voxel cube, only letters, digits and '_' are allowed; other characters will be replaced by '_'

cube

a 3-mode array; see the following example

size

the actual size of the volume, usually dot multiplication of the dimension and voxel size

trans_mat

the transform matrix of the volume. For add_voxel_cube, this matrix should be from data cube geometry model center to world ('tkrRAS') transform. For add_nifti, this matrix is the 'Nifti' 'RAS' to world ('tkrRAS') transform.

trans_space_from

where does trans_mat transform begin; default is from object 'model' space; alternative space is 'scannerRAS', meaning the matrix only transform volume cube from its own 'scannerRAS' to the world space.

color_format

color format for the internal texture. Default is 4-channel 'RGBAFormat'; alternative choice is 'RedFormat', which saves volume data with single red-channel to save space

path

'Nifti' data path

mni_ras

'MNI' 'RAS' coordinates, should be a n-by-3 matrix

value

data values (length n); used if keys is missing

colormap

a color map generated from create_colormap; see voxel_colormap for details

keys

integer color-keys generated from a color map with length of n; alternatively, you could specify value and colormap to generate keys automatically

dimension

volume dimension; default is a 256 x 256 x 256 array cube; must be integers and have length of 3

Value

create_voxel_cube returns a list of cube data and other informations; add_voxel_cube returns the brain object

Examples


# requires N27 brain to be installed
# use `download_N27()` to download template Collins brain


# sample MNI coords
tbl <- read.csv(system.file(
  'sample_data/example_cube.csv', package = 'threeBrain'
))
head(tbl)
#>   X  x   y   z key
#> 1 1 50 -60 -14 215
#> 2 2 62 -22 -22 229
#> 3 3 42 -64  10 209
#> 4 4 36 -60   2 230
#> 5 5 34 -72  10 149
#> 6 6 50 -50   6 229

# load colormap
cmap <- load_colormap(system.file(
  'palettes/datacube2/Mixed.json', package = 'threeBrain'
))

x <- create_voxel_cube(
  mni_ras = tbl[, c('x', 'y', 'z')],
  keys = tbl$key,
  dimension = c(128, 128, 128)
)


n27_path <- file.path(default_template_directory(), "N27")
if( interactive() && dir.exists(n27_path) ) {
  brain <- merge_brain()

  # or add_voxel_cube(brain, 'example', x$cube)
  x$add_to_brain(brain, 'example')

  brain$plot(controllers = list(
    "Voxel Type" = 'example',
    'Right Opacity' = 0.3,
    'Left Opacity' = 0.3,
    'Background Color' = '#000000'
  ), voxel_colormap = cmap)
}