AI Imaging Workshop — Tutorials
Hands-on tutorials for the AI Imaging Workshop (WSUSOM). Work through them in order; each builds on the last. Everything is copy-paste, written for a clinical/ research audience — read the explanation above each command.
| # | Tutorial | Agenda block |
|---|---|---|
| 1 | Environment setup — Miniforge / mamba, imaging packages, Nextflow | 9:30 Python / SLURM |
| 2 | DICOM vs. NIfTI — what's inside a medical image | 10:00 DICOM/NIfTI |
| 3 | Inference with a pretrained nnU-Net | 10:15 CNNs / nnU-Net |
| 4 | AI-powered annotation in ITK-SNAP | 10:45 ITK-SNAP |
| 5 | Training on the WSU grid (SLURM) | 11:00 Training |
| 6 | Writing an AI paper | 11:30 Writing |
Before the workshop: bring a laptop and, if you can, finish Tutorial 1 so your environment is ready. Setup videos: the OpenSpineConsortium channel.
Resources used throughout
- Dataset: https://huggingface.co/datasets/anonymous-mlhc/CTSpinoPelvic1K
- Trained checkpoints: https://huggingface.co/anonymous-mlhc/spinopelvic-seg-checkpoints
- ITK-SNAP: http://www.itksnap.org