CT Scan Analysis Script

Introduction

This Python script is designed for the analysis of noise in CT scan data obtained from DICOM files. The script processes patient-specific DICOM files, extracts relevant information, performs 3D patch analysis on specific rectangle regions, and outputs noise values in Hounsfield Units (HU).

Usage

1. Input and Output Paths:

   • Set the data_path variable to the directory containing patient-specific DICOM files (multiple folders, each with one patient)
   • Set the output_path variable to the desired output directory.

2. Run the Script:

   python noise_calculation_3D.py

Script Overview

Initial Setup:

• Imports necessary libraries and sets up input and output paths.
• Creates output directory if it doesn't exist.

CT Files Extraction:

• Defines a function (CT_files_extract) to extract information from DICOM files.
• Utilizes parallel processing to extract data from all patient directories.

Convert to Hounsfield Units (HU):

• Converts pixel data from DICOM files to Hounsfield Units (HU).

Patch Analysis and Visualization:

• Processes each CT slice, performs patch analysis, and calculates HU values within specific rectangle region.
• Generates visualizations with bounding boxes around regions of interest.

Analysis and Output:

• Outputs key metrics, such as average HU, mean noise, and more, to a text file (output.txt).
• Provides summary statistics and sorted noise values for participants.

Notes:

• The script outputs results to the output_path directory, including visualizations and a text file.
• The script runtime can vary based on the dataset size.