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I am using windows, where the local variables are used second, and the npz file in stage 01 is converted by its own method. In the second step (airway/image_processing/remove_all_0_layers.py), "ERROR: No patient data path supplied"
I cannot reproduce the error. What happens if you run the tutorial with airway tutorial? It should create a sample patient, can you then run airway stages 2 --path example? Does that work?
The defaults.yaml file path is set as follows
path: local
paths:
local: /home/anne/Anne/data/airway_vida_test/A2019RR46/
The file structure is
Error content prompts
ERROR: Insufficient count of input/output paths supplied!
Expected 1 output paths and 2 input paths!
Got sys.argv: []
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