/CT-Scan-Preprocess

This repo gives an example of the general pipeline for preprocessing CT scan

Primary LanguageJupyter NotebookMIT LicenseMIT

CT-Scan-Preprocess

Introduction

This repo gives an example of the general pipeline for preprocessing CT scan in NifTi format.

Requirements

Check requirements.txt for all dependencies To install all dependencies with new environment, run

  • python -m venv <path_new_pyvenv>
  • source <path_new_pyvenv>/bin/activate
  • pip install -r requirements.txt

Files:

  • dcm_display_util.py: contains code for displaying dicom
  • dcm_metadata_util.py: contains code for analyzing meta info for dicom
  • nifti_preprocess_util.py: contains code for preprocessing scans stored with dicom files to nifti format
  • usage_example.ipynb: gives an example on how to use the functions to preprocess one scan.