Regions of Interest

2024-03-27

Regions of interest

Creating a spherical ROI

In neuroim2 there is basic support for creating regions of interest (ROI). To create a spherical ROI around a central point, we need an existing object of type NeuroVol or NeuroSpace.

To create a spherical region of interest with a 5mm radius around a central voxel at i=20, j=20, k=20, we first read in an image.

      library(neuroim2)        
      file_name <- system.file("extdata", "global_mask.nii", package="neuroim2")
      vol <- read_vol(file_name)

Next, we create a spherical ROI centered around voxel coordinates [20,20,20] with a 5mm radius, filling all values in the ROI with 100.

      sphere <- spherical_roi(vol, c(20,20,20), radius=5, fill=100, use_cpp=FALSE)

#> 
#> 
#> ROIVol 
#>   Size:            11 
#>   Parent Dim:      64 64 25 
#>   Num Data Cols:   1 
#>   Voxel Cen. Mass: 20 20 20

Creating a Spherical ROI around a real-valued coordinate

To create a spherical ROI centered around a real coordinate in millimeters, we need to first convert the real-valued coordinates to a voxel-based coordinate. Suppose our real-world coordinate is at -50, -28, 10 in coordinate space.

    rpoint <- c(-34,-28,10)

Because the function spherical_roi takes a coordinate in voxel units, we need to convert the real-world coordinate (i.e. in millimeter units) to voxel coordinates.