Perivascular space Identification Nnunet for Generalised Usage (PINGU)

Preprint:
https://arxiv.org/abs/2405.08337

Setup:
1) Set up python environment:
conda env create -f PINGU_env.yml
NOTE: the nnunet code may need to be installed separately with pip. pip install nnunet==1.7.0

2) Download PINGU weights:
DOI: 10.26180/27176523
https://dx.doi.org/10.26180/27176523
https://bridges.monash.edu/articles/dataset/PINGU_Weights/27176523?file=49632888

3) Set up nnUNet with PINGU weights:
import_nnunet.sh
# note, this assumes that the weights zip file is in the same directoru as the import_nnunet script

4) Put T1 images in a single folder. All images must end with _0000.nii.gz (nnUNet constraints, sorry)

5) run PINGU:
run_pingu.sh