MRI-Vertebrae-Registration

Project Description
Project Structure
Requirements
Folder Structure
Project Team
Project License
Project Acknowledgement
Project Contact

Project Description

This repository is dedicated to the exploration and implementation of deep learning models for image registration of vertebrae, as part of the practical class "Advanced Deep Learning in Medicine". The project focuses initially on the application of Voxelmorph to spine MRI and CT scans.

The primary emphasis lies in training models for intra-modality registration within the same modality (MR). As the project evolves, the scope will extend to cover inter-patient intra-modality registration, specifically targeting MRI sequences such as T1w and T2w.

Project Structure

The development of this project was divided into several key phases:

Literature Review

The initial phase involved an extensive literature review to understand the current landscape of image registration techniques, specifically within the context of MRI scans.

Baseline Model with VoxelMorph

We began by implementing a baseline model using VoxelMorph for intra T1w MRI scans registration. This served as the foundation for further enhancements.

Preprocessing Pipeline

Prior to model development, a robust preprocessing pipeline was crucial. This included techniques to prepare and preprocess MRI scans, ensuring optimal input for subsequent registration models.

Model Progression

The baseline model was progressively refined and expanded to increase complexity. Different strategies were employed to enhance registration accuracy and overall performance. The baseline model was further scaled up to construct a more capable and robust model with expanding network architectures.

Semisupervised Learning

We explored semisupervised learning by incorporating segmentation masks of the vertebrae. This approach leverages additional information to improve the model's understanding of the registration task.

Affine Transformations

To further improve results, we implemented affine transformations. This involved aligning moving and fixed images using transformation matrices, enhancing the overall registration process.

Region of Interest (ROI) Experimentation

In an experimental phase, we focused on using only the Region of Interest (ROI) by identifying the maximum minimum bounding box. This exploration aimed to understand the impact of limiting the registration process to specific regions.

Still a Work in Progress

Currently expermenting with spatially-variant and adaptive regularization. A horizontal comparison with TransMorph is also a work in the future. Based on the previous research, the baseline model had a comparable performance with TransMorph on the same dataset without any other preprocessing.

Requirements

To run the project, follow these steps:

Create a Conda Environment:

conda create --name your_environment_name python=3.8
conda activate your_environment_name

Install Dependencies:

conda install -c simpleitk -c anaconda -c conda-forge nibabel jupyter simpleitk pillow pyparsing matplotlib

Install Python Requirements:
```
pip install -r requirements.txt
```

Folder Structure

.
├── BIDS
├── MRIProcessor.py
├── README.md
├── SegmentationProcessor.py
├── config.ini
├── data
│   ├── numpy
│   │   └── labels.npy
│   ├── preprocessed
│   │   ├── scans
│   │   └── segmentations
│   └── region_of_interest
│       ├── scans
│       └── segmentations
├── main.py
├── requirements.txt
├── utils
│   ├── __init__.py
│   ├── helpers.py
│   └── scripts
│       ├── __init__.py
│       ├── bounding_box_generator.py
│       ├── hyper_search.sh
│       └── hyperparameter_search_visualization.py
└── vxlmorph
    ├── __init__.py
    ├── affine_transformation.py
    ├── generators.py
    ├── model_weights
    ├── scripts
    │   ├── train_baseline.py
    │   ├── train_semisupervised_3d.py
    │   └── train_semisupervised_affine_2d.py
    └── tensorboard

BIDS 📁

The BIDS directory is a versatile package designed to handle BIDS-conform datasets, including CT, MRI, etc. It provides functions for finding, filtering, and searching BIDS families and subjects. For more details, refer to the BIDS README.

vxlmorph 📁

The vxlmorph folder encapsulates tools and subfolders related to working with the Voxelmorph model.

generators.py: This module provides a list of data generators that can generate data in the correct format for Voxelmorph models.
scripts: Contains script files for training and testing various Voxelmorph models.
tensorboard: A directory to store TensorBoard logs of losses and evaluation metrics, which can be visualized later using TensorBoard commands.
model_weights: A directory to store model weights.

Utils 📁

The utils folder contains functionalities that are useful when working on this project.

helpers.py: Defines a set of methods for tasks such as visualizing scans, file handling, etc.

Data 📁

The data directory is intended to store dataset-related files.

MRIProcessor.py

Defines a class MRIProcessor for preprocessing .nii.gz scan files.

SegmentationProcessor.py

Defines a class SegmentationProcessor for preprocessing .nii.gz segmentation files.

Project Team

Supervised by: Robert Graf & Wenqi Huang

Team Members

Name	LinkedIn	Email
Guangyao Quan
Utku Ipek
Anass Ibrahimi

Project License

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

Project Acknowledgement

Special thanks to our supervisor Robert and Wenqi for their continuous support. We would also like to thank all ADLM tutors from the AI in Medicine Lab for their insights and guidance.

Project Contact

Feel free to connect with us on LinkedIn or to drop us an email for any inquiries. We look forward to hearing from you! 🙂

ipekutku/MRI-Vertebrae-Registration