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spinalcordtoolbox / manual-correction

Scripts for the manual correction of spinal cord labels
MIT License
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Confusing command for path output #83

Open jcohenadad opened 7 months ago

jcohenadad commented 7 months ago

Based on the wiki:

image

However, it does not. Here's what I've entered:

python ~/code/manual-correction/manual_correction.py -path-img data -path-out data -config config_labels.yml

My input and output path are the same-- i expected the labels to go under derivatives/labels, but instead they are placed at the same level as the input data:

image
valosekj commented 7 months ago

If -path-out is not specified, it is automatically constructed as -path-img + derivatives/labels (L117, L734).

However, if -path-out is provided, the exact path specified by the user is used (i.e., no derivatives/labels is automatically added). IIRC, I implemented this behaviour because sometimes we use other output paths, such as derivatives/labels_soft.

jcohenadad commented 7 months ago

If -path-out is not specified, it is automatically constructed as -path-img + derivatives/labels (L117, L734).

I understand the logic after you explained it, but I don't find it intuitive. If I struggled, other external users will also struggle.