neuroCleaner: Clean and Load Data from NIfTI Neuroimaging Files

Description

Loads a NIfTI-format neuroimaging file and transforms it into a structured data frame, organizing voxel-level information for downstream analysis. This function is the first step in the neuroimaging processing pipeline in neuroSCC, converting raw PET data into a format suitable for functional data analysis. SCCs are later computed using functions from the ImageSCC package, such as ImageSCC::scc.image().

Usage

neuroCleaner(name, demo = NULL, demoRow = 1)

Value

A data frame where each row represents a voxel (3D pixel).

If demographics are provided: the columns include PPT, Group, Sex, Age, z, x, y, and pet.
If demographics are not provided: the columns include z, x, y, and pet.

The pet column contains the PET intensity value at each voxel location.

Arguments

name: character. The full path to the NIfTI file to process.
demo: Optional data.frame containing demographic information. If provided, it should include columns (case-insensitive): PPT, Group, Sex, and Age. If automatic matching via the PPT column fails, the row specified by demoRow is used. Default is NULL.
demoRow: integer. Row to use from the demographic table if automatic matching fails. Default is 1.

Details

The function performs the following steps

Loads the NIfTI file using oro.nifti::readNIfTI().
Converts the 3D image into a tidy data frame.
Adds z, x, and y voxel coordinates.
If demographic data is provided, attempts to match based on PPT (case-insensitive). If no match is found, demoRow is used.

The resulting data frame serves as input for databaseCreator, matrixCreator, and other core functions in the neuroSCC pipeline.

Examples

Run this code

# Load a sample Control NIfTI file
niftiFile <- system.file("extdata", "syntheticControl1.nii.gz", package = "neuroSCC")

# Example Without demographic data
petData <- neuroCleaner(niftiFile)
petData[sample(nrow(petData), 10), ]  # Show 10 random voxels