CODEWITHSUNDEEP
rrgl
user3236841
user3236841

Reputation: 1258

R: contour3d add grid to 3D display

I am trying out contour3D on a brain image in the example using brainR at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911196/but I wanted to add a grid to contour 3D.

Here is a reproducible example:

require(brainR)
# Template from MNI152 from McGill
template <- readNIfTI(system.file("MNI152_T1_2mm_brain.nii.gz",
        package="brainR"), reorient=FALSE)
contour3d(template, level = 4500, alpha = 0.1, draw = TRUE)

Now, I would liketo draw a box around the display and a grid for that box. How do I do this? I tried to add a box, but even addbox=T does not seem to do anything? Any suggestions? Many thanks in advance!

Upvotes: 0

Views: 381

Answers (1)

user2554330
user2554330

Reputation: 44957

I'm not sure what you want, but if you want a full box around the display with tick marks and grid lines at the ticks, the code below should do it. I've also changed to alpha = 1 because otherwise I find the grid lines confusing.

require(brainR)
# Template from MNI152 from McGill
template <- readNIfTI(system.file("MNI152_T1_2mm_brain.nii.gz",
                                  package="brainR"), reorient=FALSE)
contour3d(template, level = 4500, alpha = 1, draw = TRUE)
decorate3d()
grid3d(c("x-", "x+", "y-", "y+", "z-", "z+"))

This produces this output after a small rotation:

screenshot

Edited in response to comments:

To display the frame without ticks and numbers, use box3d() instead of decorate3d().

Adding a background colour to the cube can be done with the bbox3d() function. By default it draws only 3 sides of the cube: I find this kind of ugly, but your taste may vary. I prefer to see it with front-facing sides showing; that could be 3, 4, or 5 faces. Here's the code:

require(brainR)
# Template from MNI152 from McGill
template <- readNIfTI(system.file("MNI152_T1_2mm_brain.nii.gz",
                                  package="brainR"), reorient=FALSE)
contour3d(template, level = 4500, alpha = 1, draw = TRUE)
box3d()
grid3d(c("x-", "x+", "y-", "y+", "z-", "z+"))
bbox3d(col="cyan", alpha = c(0.5, 0), shininess = 100,
       draw_front = TRUE, front = "culled")

Here's what you get with the code above:

screenshot

Leave off the last two arguments of the bbox3d call for the 3-side display. It will look the same at this orientation, but will be different as you rotate the display.

Upvotes: 1

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