RADIOMICS Module

The RADIOMICS module enables the extraction of radiomic features using the PyRadiomics library (https://pyradiomics.readthedocs.io/en/latest/).

Options

The RADIOMICS module can be used with the following options:

• verbose: Enable or disable verbose mode.

• timer: Enable or disable the timer to record execution time.

• inputFolder: Path to the input folder containing images.

• outputFolder: Path to the output folder where radiomics results will be saved.

• outputFolderSuffix: Adds a suffix to the input folder name to create an output folder.

• log: Path to a file for saving logs.

• new_log_file: Create a new log file; if a file with the same name already exists, it will be overwritten.

• skip: Path to a file listing subfolders inside the input folder to exclude from processing.

• multiprocessing: Specify the number of cores to use for parallel processing.

• configs: Path to a radiomics configuration file, which can contain multiple configurations for PyRadiomics. See details in the next section Radiomics Configuration File.

• pyradiomics_config: Specify a PyRadiomics configuration file. Use this instead of configs if multiple configurations are unnecessary or if using PyRadiomics-specific preprocessing options.

• image_filename: Name of the image file used for radiomic analysis.

• mask_filename: Name of the mask (segmentation) file used for radiomic analysis.

• radiomics_filename: Name of the Excel file that will store radiomics results.

• stats_filename: Name of an optional Excel file to store statistics on radiomic features. If not specified, this file will not be created.

• save_at_the_end: Specify whether the Excel file should be created only after processing all patients. Disabled by default, so new lines are added to the Excel file after processing each patient.

Example Usage

Below is an example of how to use the RADIOMICS module:

RADIOMICS:
{
    inputFolder: /path/to/NIFTI_folder
    outputFolder: /path/to/radiomics_results
    image_filename: img_111.nii.gz
    mask_filename: msk_111.nii.gz
    radiomics_filename: radiomics.xlsx
    save_at_the_end: false
    configs: /path/to/radiomics_config_file
    log: /path/to/logs/radiomics.log
}

In this example:

• inputFolder: Specifies the folder containing the NIfTI images for radiomics analysis.

• outputFolder: Directory where radiomics results are stored.

• image_filename: Indicates the name of the image to be analyzed.

• mask_filename: Name of the mask file associated with the image.

• radiomics_filename: Designates the Excel file that will hold radiomics features extracted by PyRadiomics.

• save_at_the_end: If set to false, entries are written to the Excel file immediately after processing each patient.

• configs: Specifies the configuration file for PyRadiomics, allowing customization of feature extraction.

• log: Provides the path to the log file for recording the processing details.

radiomics_multiprocessing.deleteTmp_xlsx(path)

radiomics_multiprocessing.extract_radiomics(patient, inpath, outpath, img_filename, msk_filename, configs, pyrconfigFile, features_df, radiomics_filename, save_xlsx_at_the_end, n_jobs, skip_files, include_files, verbose, log)

radiomics_multiprocessing.gaborFilterImg(img, params, ID, path='~/')

radiomics_multiprocessing.main(argv)

radiomics_multiprocessing.merge_xlsx(path, radiomics_filename)

radiomics_multiprocessing.parse(i)

radiomics_multiprocessing.radiomics_statistics(xlsx_input_file, xlsx_output_file, verbose, log)

radiomics_multiprocessing.read_config_file(config_File, configs, verbose)