Hypothalamus Implementation #459
Merged
+4,251
−58
Commits on Jun 20, 2024
-
without __pycache__ files include HypVINN labels Create Main function for N4 bias correct include fs bin for registration
-
Include copyright statements in Hypvinn files
-
-
-
update run pipeline test fs
-
-
-
clean pipeline, comments, conflicts, functions, etc
add t2 option select automatically processing mode re-strucuture pre-processing remove bias field correction organize bin additions alphabetically Modifications based on merge comments Reimplement run_cmd Change run_cmd for Popen from FastSurferCNN.utils.run_tools Change config files from json to yaml
-
-
-
-
-
-
-
-
-
-
-
-
Update download_checkpoints.py
update network name update download_checkpoints
-
-
-
-
-
-
-
-
Refactor and cleanup of hypvinn
- rename mode "multi" to "t1t2" - reformatting for line length - replace single quotes to double quotes - add typing information - clean up docstrings - replace os.path with pathlib.Path
-
- remove/rename changed filenames - format table HypVINN/config/checkpoint_paths.yaml - add config HypVINN/data_loader/data_utils.py - fix typing and formatting HypVINN/utils/checkpoint.py - fix YAML_DEFAULT HypVINN/utils/mode_config.py - set default values for get_hypvinn_mode HypVINN/inference.py - fix inclusion of ModalityMode HypVINN/run_prediction.py - move HypVINN/run_pipeline.py into run_prediction.py - fix typing, e.g. FileBasedHeader - fix function parameters - add help text to hypo_segfile argument - fix passing of t1_path and t2_path - various other changes
-
- Fix errors in t1t2 mode - Fix qc_snaps argument in run_fastsurfer.sh - Fix reg_mode test in run_fastsurfer.sh
-
-
update model weight (version 1.1) for hypvinn update download script
-
-
Better input handling of the input T2 file
Convert the T2 image to unit8 to save hard disc space for registration - set --uchar for N4_bias_correct.py - `conform.py --no_force_(img_size|vox_size|lia) --t2 <arg>` if --no_biasfield Copy the T2 file to $SUBJECTS_DIR/$SID/mri/orig/T2.001.mgz
-
-
- Added docstring for functions in HypVINN
-
- adding space before colon separating parameter name and type
-
-
-
Add mask_file as a parameter (with default value) for saving instead …
…of a constant Make saving a main thread function instead of a future/task
-
- Fix for bash-3.2 (|& => 2&>1 |) - Add warning if T2 is passed, but biasfield is skipped --no_biasfield
-
- add comment paper vs. retrained weights. - add hypothal module in main README - fix sphinx errors - add an additional message in fix_links to debug errors - add the hypvinn script documentation
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.