EchocardiographyQC

Echocardiography Quality Control Utilities

Introduction

This repository contains three Microsoft WINDOWS executable for echocardiography quality control. In some cases, you may have to disable some antivirus software for executing this inference tool

1. dicom-preprocess-1.0.0.exe: Preprocessing tool that takes in DICOMs and outputs JPEG Images and Metadata for dicom-inferrer-1.0.0.exe
2. dicom-inferrer-1.0.0.exe: Inference tool that takes in echocardiography and outputs corresponding quality information.
3. report-viewer-1.0.0.exe: Viewer tool that takes in the output of inference tool for better analysis.

Preprocessing tool

The preprocessing tool, dicom-preprocess-1.0.0.exe is an executable with graphical user interface for extracting DICOM into JPEG images for the inference tool in next step. This tool reads DICOM, masks images, and crops the central region. This tool accepts echocardiography DICOM from four different machines. The mask image file (*.bmp) should be in the same directory as dicom-preprocess-1.0.0.exe

1. Philips CX50
2. Philips EPIQ7C
3. Philips iE33
4. HP SONOS

Usage

First select the source directory and output directory, and then click the Start Preprocessing button. Your directory structures should be as same as SourceDICOM. The tool will only extract DICOM videos and output JPEG images and metadata. Output directory structures will be similar to SourceImages.

Result

After the progress bar is full of color, you'll see the extracted images (Only for video types).

Inference Tool

The inference tool, dicom-inferrer-1.0.0.exe, is an executable with graphical user interface for simple quality inference usage.

Usage

Please turn off the antivirus software to execute inference tool

First select the source directory and output directory, and then click the Start Inference button.

Wait until the progress bar is full of color.

Since the executable only supports CPU inference, it might take a long time if you select all cases for inference. We suggest you to select a single case for inference if you're testing this tool

Input

The source directory should be organized in the following structure (...prefix/patient/series/JPGFiles, see SourceImages as an example). Any directory above case01(included) level in the following figures is acceptable. (or you could directly select the output directory from previous dicom-preprocessing-1.0.0.exe as the input of this tool.)

Inside the series folder, preprocessed images (with .jpg format) from DICOM and metadata text file are required.

The preprocessing steps are

1. Crop the central region of images such that only sector area remains.
2. Mask the cropped image such that only sector area is viewable.

These steps should be easily done with the preprocessing tool that we provided above.

The metadata.txt file includes

Output

The tool would output each series result as a subfolder in output directory named after series ID in input metadata.txt. For each series, CAM results are provided, and the result has been normalized to (-25, 25).

Also, a conf.npy stores the quality information.

Viewer Tool

The viewer tool, report-viewer-1.0.0.exe, is a executable with graphical user interface for viewing inference result.

Usage

Select the source directory and the report directory, which should be as same as those of Inference tool, respectively.

View stats and inference images of patients

After navigating to the patient in the left region, the central region will show each series inference result for this patient. Each column (from left to right) represents:

1. Filename: Filename of the series, which is read from metadata.txt
2. View: Predicted view of the cardiography. The tool shows the predicted view by default, which would be in red color. Other view's quality confidence and prediction confidence can be seen by dragging the list.
3. Avg Prob: Average prediction probability of the view. This number is averaged over the selected cycles(SB column).
4. Avg Conf: Average classification confidence of the view. This number is averaged over the selected cycles(SB column).
5. SD: Standard Deviation of classification confidence of the view.
6. Corr %: The correct percentage of the DICOM video. This value is calculated by correct view prediction frames / total frames.
7. SB: Select which cardiography cycles to be viewed.
8. TB: Select total cardiography cycles to be viewed.

In the right region, the upper block show the original images and the lower block show the inference images.