Fix bugs introduced by #501. - Githubissues

Deep-MI / FastSurfer

PyTorch implementation of FastSurferCNN

Apache License 2.0

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Fix bugs introduced by #501. #513

Closed dkuegler closed 5 months ago

dkuegler commented 5 months ago

This PR fixes a couple of bugs introduced in #501. They should have been caught before...

CerebNet/utils/load_config.py

remove unused setup_options
fix typing of yacs.config
fix assignment of cfg.LOG_DIR which cannot be a Path, but must be a string (yacs requirement)

CerebNet/run_prediction.py

fix the path to the checkpoint_paths.yaml file
clean up the imports

FastSurferCNN/utils/parser_defaults.py

remove unwanted commas, they make the value a tuple

FastSurferCNN/run_prediction.py

Fix parameter names in main function
add a try-except block in main
add/fix typing
fix typo in main

recon_surf/N4_bias_correct.py

Formatting (e.g. constants are UPPERCASE)
fix typos
fix incorrect conversion of default "do nothing strings" to Path

doc/overview/OUTPUT_FILES.md

fix the formatting of the tables