Find appropriate threshold for each contrast with deepseg algorithm
- Python 3.7 (miniconda distrib)
- SCT commit 7ed63da96fa13b4446ad636c25692ff69fe4b44f
- Note: This commit is important as it includes specific features on deepseg to enable testing for various thresholds
- Download the spine generic dataset
- Create a parameters.sh file
- Run processing across the DB:
sct_run_batch parameters.sh deepseg_threshold.sh
- Run the Jupyter notebook to find the optimal thresholds for each contrast:
jupyter notebook deepseg_find_threshold.ipynb