A Hitchhiker's Guide to 3D Medical Image Processing (Preprocessing, Augmentations & DataLoaders)

Toufiq Musah

Keywords: Medical Imaging, 3D, Magnetic Resonance Imaging, Computer Vision

TL;DR: In this article, we will learn the 'what', 'why' and 'how' of 3D medical image processing from basics to preprocessing, and creating the appropriate data loaders.

Abstract:

Transitioning from 2D to 3D medical imaging presents unique challenges for students and early-career researchers entering the field of medical image analysis. While 2D images are often used as introductory material, most real-world clinical data is volumetric. In 'A Hitchhiker’s Guide to 3D Medical Image Processing', a structured introduction to the concepts, tools, and practices involved in working with 3D medical images is provided. We begin by clarifying some fundamental differences between 2D and 3D representations, including voxel spacing and viewing planes, and briefly review major 3D imaging modalities (CT, MRI, PET, Ultrasound) and common file formats (NIfTI, DICOM, NRRD). Building on this, we outline a practical workflow covering preprocessing, augmentations, and DataLoaders.

Medium Article: https://medium.com/@toufiqmusah32/a-hitchhikers-guide-to-3d-medical-image-processing-preprocessing-augmentations-dataloaders-975167d4ffe1

Complimentary Notebook 1: https://medium.com/@toufiqmusah32/introduction-to-torchio-for-3d-mri-processing-preprocessing-transforms-part-1-87947c339400

Complimentary Notebook 2: https://medium.com/@toufiqmusah32/introduction-to-torchio-for-3d-mri-processing-augmentation-transforms-dataloaders-part-2-37272a97ea35

Submission Number: 10