neuroContour {neuroSCC} | R Documentation |
Obtain and save neuroimaging contours from a NIFTI file
Description
This function extracts contours from a neuroimaging NIFTI file where values change according to specified levels.
It processes the NIFTI file with neuroCleaner
to extract structured neuroimaging data, then extracts contours
using contoureR::getContourLines
. These contours serve as input for Triangulation::TriMesh
,
which is used in Simultaneous Confidence Corridors (SCCs) calculations.
While not mandatory, it is highly recommended that the input NIFTI file be pre-processed
such that zero values represent the background and non-zero values represent regions of interest.
The function's default behavior extracts contours at level 0
, which is ideal for well-masked data.
Usage
neuroContour(niftiFile, paramZ = 35, levels = c(0), plotResult = FALSE)
Arguments
niftiFile |
|
paramZ |
|
levels |
|
plotResult |
|
Details
This function extracts contours from a NIFTI file, typically a masked image where background values
are set to zero, and regions of interest contain non-zero values. While users can specify a different
boundary level, the recommended approach is to use levels = 0
for masked data.
The extracted contours are typically used as input to Triangulation::TriMesh
to create
a triangular mesh of the region, which is then used for Simultaneous Confidence Corridors calculations.
Value
A list
of data frames, where each data frame contains the x and y coordinates of a contour.
The first element typically represents the external boundary, while subsequent elements (if present)
represent internal contours or holes. Each data frame has two columns:
-
x
– x-coordinates of the contour points. -
y
– y-coordinates of the contour points.
See Also
getContourLines for the underlying contour extraction.
Triangulation::TriMesh
for the next step in the SCC calculation process.
Examples
# Get the file path for a sample NIfTI file
niftiFile <- system.file("extdata", "syntheticControl1.nii.gz", package = "neuroSCC")
# Extract contours at level 0
contours <- neuroContour(niftiFile, paramZ = 35, levels = 0, plotResult = TRUE)
# Display the first few points of the main contour
head(contours[[1]])