changing nnUNet base directories

[idinsmore1]

Hello! Thanks for putting this tool together. I just wanted to bring up a bug that I noticed while testing this repo. I've used nnUNet before, so I placed my data in a different location than U-Mamba/data and changed the default nnUNet_raw/preprocessed/results directories using bash's export command. However, your custom script doesn't reflect those changes when you run any of the nnUNet commands, it still points nnUNet_raw to U-Mamba/data/nnUNet_raw (same with preprocessed and results). Just wanted to bring this to attention if other experienced nnUNet users try this out. Great work on the paper and model!

[ff98li]

Hi,
Thank you for your interest in trying out U-Mamba! The paths to directories of data in U-Mamba are indeed preset to the codebase's data directory U-Mamba/data. This is for preventing conflicts with environment variables set for pre-existing nnUNet instances. However, feel free to customize these paths to fit your setup by modifying the directory paths in umamba/nnunetv2/path.py according to your preferred nnUNet data directories, as in

U-Mamba/umamba/nnunetv2/paths.py

Lines 44 to 48 in 887b3ca

	base = join(os.sep.join(__file__.split(os.sep)[:-3]), 'data')
	# or you can set your own path, e.g., base = '/home/user_name/Documents/U-Mamba/data'
	nnUNet_raw = join(base, 'nnUNet_raw') # os.environ.get('nnUNet_raw')
	nnUNet_preprocessed = join(base, 'nnUNet_preprocessed') # os.environ.get('nnUNet_preprocessed')
	nnUNet_results = join(base, 'nnUNet_results') # os.environ.get('nnUNet_results')

We hope this addresses your concern.

[JunMa11]

We also add a remark on readme. Thanks for pointing out this:)