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Comp2Comp

License: Apache 2.0 GitHub Workflow Status Documentation Status

Paper | Installation | Basic Usage | Inference Pipelines | Contribute | Citation

Comp2Comp is a library for extracting clinical insights from computed tomography scans.

Installation

git clone https://github.com/StanfordMIMI/Comp2Comp/

# Install script requires Anaconda/Miniconda.
cd Comp2Comp && bin/install.sh

Alternatively, Comp2Comp can be installed with pip:

git clone https://github.com/StanfordMIMI/Comp2Comp/
cd Comp2Comp
conda create -n c2c_env python=3.9
conda activate c2c_env
pip install -e .

For installing on the Apple M1 chip, see these instructions.

Basic Usage

bin/C2C <pipeline_name> -i <path/to/input/folder>

For running on slurm, modify the above commands as follow:

bin/C2C-slurm <pipeline_name> -i <path/to/input/folder>

Inference Pipelines

We have designed Comp2Comp to be highly extensible and to enable the development of complex clinically-relevant applications. We observed that many clinical applications require chaining several machine learning or other computational modules together to generate complex insights. The inference pipeline system is designed to make this easy. Furthermore, we seek to make the code readable and modular, so that the community can easily contribute to the project.

The InferencePipeline class is used to create inference pipelines, which are made up of a sequence of InferenceClass objects. When the InferencePipeline object is called, it sequentially calls the InferenceClasses that were provided to the constructor.

The first argument of the __call__ function of InferenceClass must be the InferencePipeline object. This allows each InferenceClass object to access or set attributes of the InferencePipeline object that can be accessed by the subsequent InferenceClass objects in the pipeline. Each InferenceClass object should return a dictionary where the keys of the dictionary should match the keyword arguments of the subsequent InferenceClass's __call__ function. If an InferenceClass object only sets attributes of the InferencePipeline object but does not return any value, an empty dictionary can be returned.

Below are the inference pipelines currently supported by Comp2Comp.

End-to-End Spine, Muscle, and Adipose Tissue Analysis at T12-L5

Usage

bin/C2C spine_muscle_adipose_tissue -i <path/to/input/folder>
  • input_path should contain a DICOM series or subfolders that contain DICOM series.

Example Output Image

Spine Bone Mineral Density from 3D Trabecular Bone Regions at T12-L5

Usage

bin/C2C spine -i <path/to/input/folder>
  • input_path should contain a DICOM series or subfolders that contain DICOM series.

Example Output Image

Abdominal Aortic Calcification Segmentation

Usage

bin/C2C aortic_calcium -i <path/to/input/folder> -o <path/to/input/folder> --threshold
  • The input path should contain a DICOM series or subfolders that contain DICOM series, or a nifti file.
  • The threshold can be controlled with --threshold and be either an integer HU threshold, "adataptive" or "agatson".
    • If "agatson" is used, agatson score is calculated and the a threshold of 130 HU is used
  • Aortic calcifications are divided into abdominal and thoracic at the T12 level
  • Segmentation masks for aortic calcium, the dilated aorta mask and the T12 seperation plane are saved in ./segmentation_masks/
  • Metrics on an aggregated and individual level for the calcifications are written to .csv files in ./metrics/

Example Output

Statistics on aortic calcifications:
Abdominal:
Total number:            10
Total volume (cm³):      0.161
Mean HU:                 383.3+/-66.4
Median HU:               366.5+/-62.9
Max HU:                  571.9+/-190.6
Mean volume (cm³):       0.016+/-0.020
Median volume (cm³):     0.011
Max volume (cm³):        0.074
Min volume (cm³):        0.002
Threshold (HU):          266.000


Thoracic:
Total number:            1
Total volume (cm³):      0.030
Mean HU:                 378.1+/-0.0
Median HU:               376.0+/-0.0
Max HU:                  538.0+/-0.0
Mean volume (cm³):       0.030+/-0.000
Median volume (cm³):     0.030
Max volume (cm³):        0.030
Min volume (cm³):        0.030
Threshold (HU):          266.000

AAA Segmentation and Maximum Diameter Measurement

Usage

bin/C2C aaa -i <path/to/input/folder>
  • input_path should contain a DICOM series or subfolders that contain DICOM series.

Example Output Image (slice with largest diameter)

Example Output Video Example Output Graph

Contrast Phase Detection

Usage

bin/C2C contrast_phase -i <path/to/input/folder>
  • input_path should contain a DICOM series or subfolders that contain DICOM series.
  • This package has extra dependencies. To install those, run:
cd Comp2Comp
pip install -e '.[contrast_phase]'

3D Analysis of Liver, Spleen, and Pancreas

Usage

bin/C2C liver_spleen_pancreas -i <path/to/input/folder>
  • input_path should contain a DICOM series or subfolders that contain DICOM series.

Example Output Image

Contribute

We welcome all pull requests. If you have any issues, suggestions, or feedback, please open a new issue.

Citation

@article{blankemeier2023comp2comp,
  title={Comp2Comp: Open-Source Body Composition Assessment on Computed Tomography},
  author={Blankemeier, Louis and Desai, Arjun and Chaves, Juan Manuel Zambrano and Wentland, Andrew and Yao, Sally and Reis, Eduardo and Jensen, Malte and Bahl, Bhanushree and Arora, Khushboo and Patel, Bhavik N and others},
  journal={arXiv preprint arXiv:2302.06568},
  year={2023}
}

In addition to Comp2Comp, please consider citing TotalSegmentator:

@article{wasserthal2022totalsegmentator,
  title={TotalSegmentator: robust segmentation of 104 anatomical structures in CT images},
  author={Wasserthal, Jakob and Meyer, Manfred and Breit, Hanns-Christian and Cyriac, Joshy and Yang, Shan and Segeroth, Martin},
  journal={arXiv preprint arXiv:2208.05868},
  year={2022}
}