Plotting

Plotting functionality is provided through Makie.jl recipes. By loading one of the Makie backends (CairoMakie, GLMakie, or WGLMakie), you can use custom functions to visualize FOD (Fiber Orientation Distribution) data.

This tutorial uses CairoMakie for static plots, but GLMakie is recommended for interactive 3D visualization.

Setup

Let's start by loading FOD data from a NIfTI file:

using Tractography
const TG = Tractography

model = TG.TMC(Δt = 0.125f0,
            foddata = TG.FODData((@__DIR__) * "/../../examples/fod-FC.nii.gz"),
            cone = TG.Cone(15f0),
            proba_min = 0.005f0,
            )

TMC with elype Float32
 ├─ Δt = 0.125
 ├─ minimal probability = 0.005
 ├─ cone                = Cone{Float32}(15.0f0)
 ├─ mollifier           = max_mollifier
 ├─ evaluation of SH    = PreComputeAllFOD()
 └─ data : (lmax = 8)

Plotting FODFs

To visualize Fiber Orientation Distribution Functions (FODFs), use the plot_fod! function. See the plot_fod! documentation for details on available keyword arguments.

The following example plots FODFs for a specific region of interest:

using CairoMakie
f, sc = TG.plot_fod(model; n_sphere = 1500, radius = 1., I = 29:31, J = 30:31, K = 2:2);
f

Plotting Streamlines

To visualize tractography streamlines, use the plot_streamlines! function. See the plot_streamlines! documentation for details on available keyword arguments.

The following example creates synthetic streamlines and plots them alongside FODFs:

# Generate synthetic streamlines for demonstration
streamlines = zeros(Float32, 6, 100, 20)
for n = 1:20
    v0 = rand(3) * 15  # Random starting position
    for nt = 1:100
        # Create curved trajectories
        streamlines[1:3, nt, n] .= v0 .+ nt .* [1, 1 + 0.1*rand(), 0]
    end
end

# Create a combined visualization of streamlines and FODFs
f = Figure(backgroundcolor = :white)
lscene = LScene(f[1, 1])
TG.plot_streamlines!(lscene.scene, streamlines[1:3, 1:1:end, :])
TG.plot_fod!(lscene, model; n_sphere = 1500, radius = 1.3, st = 4)
f