dcm-classifier 0.6.0rc11

This is a consolidation of work from NAMIC efforts primarily at the University of Iowa.

Introduction

In this work, we developed a robust, easily extensible classification framework that extracts key features from well-characterized DICOM header fields for identifying image modality and acquisition plane. Our tool is crucial for eliminating error-prone human interaction and allowing automatization, increasing imaging applications' reliability and efficiency. We used Random Forrest and Decision Tree algorithms to determine the image modality and orientation. We trained on header meta-data of over 49000 scan volumes from multiple studies and achieved over 99% prediction accuracy on image modality and acquisition plane classification.

This project was supported by several funding sources including:

• UCSF SCOUTS RO1
• NIH-NINDS R01NS114405 and NINDS R01 NS119896
• Botimageai.

Citing

Please reference the manuscript:

Michal Brzus, Cavan J. Riley, Joel Bruss, Aaron Boes, Randall Jones, Hans J. Johnson, "DICOM sequence selection for medical imaging applications," Proc. SPIE 12931, Medical Imaging 2024: Imaging Informatics for Healthcare, Research, and Applications, 12931 (2024)

Instructions

Below are useful commands to start using the tool.

Clone git repo

$ git clone https://github.com/BRAINSia/dcm-classifier.git

Navigate to the cloned repo

$ cd <repo path>

Setup virtual environment

$ python3 -m venv <venv_path> && source <venv_path>/bin/activate

Install required packages

$ pip install -r requirements.txt

Development

$ pip install -r requirements_dev.txt

$ pre-commit install $ pre-commit run -a

Run the script!

python3 classify_study.py -m models/rf_classifier.onnx -d <path_to_dicom_session>

Testing

  pytest
# or to fail on warnings
  python3 -Werror::FutureWarning -m pytest

Coverage Analysis

 coverage run --concurrency=multiprocessing --parallel-mode -m pytest tests --junitxml=tests/pytest.xml
 coverage combine
 coverage report --format=text -m |tee tests/pytest-coverage.txt
 coverage xml -o tests/coverage.xml
 coverage xml -o tests/coverage.xml

Authors

1. Michal Brzus

   github: mbrzus, email: [e-mail]

2. Hans J. Johnson

   github: BRAINSia, email: [e-mail]