MASK_THRESHOLDING Module
The MASK_THRESHOLDING module removes voxels from a mask if their intensity falls outside a specified range, allowing for selective masking based on intensity.
Options
The MASK_THRESHOLDING module supports the following options:
verbose: Enable verbose output for more detailed process information (default: False).
timer: Enable a timer to record execution time (default: False).
inputFolder: Path to the folder containing the input images.
outputFolder: Path to save the thresholded mask files.
outputFolderSuffix: Adds a suffix to the inputFolder name to create the output folder.
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.
multiprocessing: Specify the number of CPU cores to use for parallel processing.
image_filename: Name of the image file to read for thresholding.
mask_filename: Name of the mask file to apply the threshold.
suffix_name: Suffix to append to the filename of the new thresholded mask.
min_threshold: Minimum intensity threshold; voxels with lower intensity will be removed from the mask.
max_threshold: Maximum intensity threshold; voxels with higher intensity will be removed from the mask.
Example Usage
The following example demonstrates how to use the MASK_THRESHOLDING module:
MASK_THRESHOLDING:
{
inputFolder: /path/to/NIFTI_folder
image_filename: img.nii.gz
mask_filename: msk.nii.gz
suffix_name: no_fat
min_threshold: 0
log: /path/to/logs/mask_thr.log
}
In this example:
inputFolder: Specifies the folder containing NIfTI files for thresholding.
image_filename and mask_filename: Define the image and mask files to apply the thresholding.
suffix_name: Adds the suffix “no_fat” to the thresholded mask filename.
min_threshold: Sets the minimum voxel intensity to include.
log: Specifies the log file path to record processing details.