Utilities

Repository containing utility scripts for handling various aspects in a DL model training pipeline:

• Conversion to/from BIDS format to nnU-Net or other ecosystem-specific formats;
• Quick-start guides (nnU-Net, ANIMA, MetricsReloaded)
• Template for running inference on NifTI images (a list or dataset) or using nnUNet in packaging/
• compute_metrics/compute_metrics_reloaded.py wrapper script to compute segmentation metrics using MetricsReloaded