INTENSITY_RESAMPLING Module
The INTENSITY_RESAMPLING module resamples voxel intensities in a NIfTI image using various methods, including a fixed number of bins, fixed bin width, linear scaling, robust scaling (linear scaling within a percentile range), or z-score normalization. The resampling can be performed on the entire image or only on voxels within a mask specified by the mask_filename option.
Options
The INTENSITY_RESAMPLING module supports the following options:
verbose: Enable or disable verbose mode for more detailed output (default: False).
timer: Enable a timer to record execution time (default: False).
inputFolder: Path to the folder containing the input NIfTI files.
outputFolder: Path to the folder where the resampled images will be saved.
outputFolderSuffix: Adds a suffix to the name of the inputFolder to create the output folder.
image_filename: Specify the filename of the image to read.
mask_filename: Specify the filename of the mask to apply during resampling (optional).
resampled_image_filename: Specify the filename for the output resampled image.
method: Resampling method to apply. Options: binning_number (fixed number of bins), binning_width (fixed bin width), linear_scaling, robust_scaling (linear scaling within a percentile range), or zscore_normalization.
n_bins: Number of bins if method is binning_number (default: 256).
bin_width: Bin width if method is binning_width (default: 25).
min_scaling: Minimum value for scaling if using linear_scaling (default: 0).
max_scaling: Maximum value for scaling if using linear_scaling (default: 1).
lower_bound: Lower percentile bound for robust scaling (default: 2).
upper_bound: Upper percentile bound for robust scaling (default: 98).
log: Path to a log file for saving detailed output information.
new_log_file: Create a new log file, overwriting any existing file with the same name.
skip: Path to a file listing subfolders in inputFolder to exclude from processing.
include: Path to a file listing subfolders in inputFolder to include in processing (all subfolders are included by default).
multiprocessing: Specify the number of CPU cores to use for parallel processing.
suffix_name: Suffix to add to the filename of the resampled image.
Example Usage
The following example demonstrates how to use the INTENSITY_RESAMPLING module:
INTENSITY_RESAMPLING:
{
inputFolder: /path/to/NIFTI_folder
suffix_name: fb256
method: binning_number
n_bins: 256
log: /path/to/logs/intensity_resampling.log
}
In this example:
inputFolder: Specifies the folder containing the NIfTI files to be resampled.
suffix_name: Adds “fb256” as a suffix to the filenames of the resampled data.
method: Sets the resampling method to binning_number, using a fixed number of bins.
n_bins: Sets the number of bins to 256.
log: Specifies the log file path to record processing details.