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Add a command to convert datasets with aneurysm masks - #28
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The scripts and their configs only worked from a clone. They now live in the package (deepaneseg/cli, deepaneseg/configs) and are installed as commands: deepaneseg-remove-skull, -extract-points, -preprocess, -train, -predict and -evaluate. `pip install git+<repo>` is enough to run them from any folder. configs/ is a package so that Hydra finds it once installed. Existing tests now run the modules instead of the script paths; the Docker image and CI use the commands.
deepaneseg-prepare converts a dataset of scans and aneurysm label
masks, by default in the ADAM challenge layout, to the P????/F.csv/
config.json layout the pipeline reads. Scans and masks are found
with {case} patterns, each mask component becomes a two-point
diameter annotation (the sphere fit used by the evaluation code), and
cases.csv maps patients back to the original cases. Cases with an
empty mask become patients without aneurysm.
youssefassis
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Sep 30, 2026
Add a command to convert datasets with aneurysm masks
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Based on #27 (merge that first; this PR then only shows its own commits).
deepaneseg-prepareconverts a dataset of scans and aneurysm label masks to the pipeline's layout. The defaults match the ADAM challenge; other datasets only need theirscanandmaskpatterns:Each aneurysm becomes a two-point annotation, and
cases.csvmaps patients to the original cases.