3D CT Scan Viewer

A graphical user interface (GUI) for viewing 3D CT scans and overlaying ground truth and predicted segmentation masks.

Required Libraries

Install the required libraries using pip:

pip install numpy nibabel PyQt5 matplotlib

How to Use

Here is the updated README to clarify both methods of naming the folders and files:

Prepare Directories

Ensure the following directories exist in the project root:

• CT
• Ground_truth
• Predicted

If they do not exist, the script will create them automatically.

Naming Conventions

You can name your files using one of the following two methods:

1. Numeric Only IDs:

   • CT scans: Place files in the CT directory. Name them as <subject_id>.nii.gz.

     Example:

     CT/
     ├── 001.nii.gz
     ├── 002.nii.gz
     └── 003.nii.gz
     

   • Ground truth segmentations: Place files in the Ground_truth directory. Name them as <subject_id>.nii.gz.

     Example:

     Ground_truth/
     ├── 001.nii.gz
     ├── 002.nii.gz
     └── 003.nii.gz
     

   • Predicted segmentations: Place files in the Predicted directory. Name them as <subject_id>.nii.gz.

     Example:

     Predicted/
     ├── 001.nii.gz
     ├── 002.nii.gz
     └── 003.nii.gz
     

2. Alphanumeric IDs:

   • CT scans: Place files in the CT directory. Name them as <subject_id>.nii.gz.

     Example:

     CT/
     ├── SUB_001.nii.gz
     ├── SUB_002.nii.gz
     └── SUB_003.nii.gz
     

   • Ground truth segmentations: Place files in the Ground_truth directory. Name them as <subject_id>.nii.gz.

     Example:

     Ground_truth/
     ├── SUB_001.nii.gz
     ├── SUB_002.nii.gz
     └── SUB_003.nii.gz
     

   • Predicted segmentations: Place files in the Predicted directory. Name them as <subject_id>.nii.gz.

     Example:

     Predicted/
     ├── SUB_001.nii.gz
     ├── SUB_002.nii.gz
     └── SUB_003.nii.gz
     

Execute the script to start the GUI:

python viewer.py

Using the GUI

• Use the left < and right > arrow buttons to navigate through different subjects. You can use either numeric or alphanumeric IDs for the subjects (e.g., 001, SUB_001).
• Enter the subject ID directly in the input field to load a specific subject.
• View Controls: Switch between axial, coronal, and sagittal views.
• Toggle contour display and adjust contour line width.
• Adjust colors for labels and opacity of overlays.
• Adjust the slider to navigate through slices.
• Change the minimum and maximum intensity values to adjust the CT scan contrast.
• Use the ▶ button to animate through the slices automatically.
• Toggle the overlay of ground truth and predicted segmentation masks using the Toggle Overlay button.
• Plot intensity histogram

Support Us

If you find it helpful, consider supporting us in the following ways:

• ⭐ Star this repository on GitHub.

• 🐦 Follow us on X (Twitter): @AITwinMinds

License

This project is licensed under the MIT License. See the LICENSE file for details.

Contact

For any inquiries, please contact AITwinMinds@gmail.com.