deepseg-threshold

Find appropriate threshold for each contrast with deepseg algorithm

Dependencies

• 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

Getting started

• 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