Running nnU-Net on custom Dataset

[bhaveshsharma91]

Hello nnU-Net Community,

I am currently working on a university assignment that involves medical image segmentation. I have chosen to work with the HaN-Seg dataset, which focuses on the head and neck organ-at-risk CT and MR segmentation. As I delve into this project, I've encountered a couple of challenges and would greatly appreciate any guidance or advice you can offer.

1. Data Format Compatibility and Dataset JSON Generation

My dataset is in .nddr format. I understand nnU-Net typically works with DICOM, NIfTI, or similar formats for medical imaging.

Is .nddr format supported by nnU-Net? If not, could you recommend the best approach to convert .nddr files into a format compatible with nnU-Net?
Generating dataset.json: I am also trying to figure out how to automatically generate the dataset.json file required by nnU-Net. Any suggestions on tools or scripts that could facilitate this process would be highly beneficial.
2. Utilizing Pretrained Models

Given the specific focus of my project on head and neck organ-at-risk segmentation:

Are there any pretrained models available within the nnU-Net framework that are suitable for this task? If so, could you provide some insights on how to effectively utilize these models for the HaN-Seg dataset?
I am keen on leveraging nnU-Net's capabilities for my project and ensuring that I adhere to best practices in medical image segmentation. Any advice, resources, or examples you could share would be immensely valuable.

Thank you for your time and assistance.

Best regards,
Bhavesh Sharma