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Set the default value for -path-label to match -path-img #106

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merged 3 commits into from
Dec 16, 2024

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Description

This PR changes the default value for -path-label to match -path-img. Context: #104

The change simplifies the manual_correction.py syntax as used for the SCT course to

manual_correction.py -config qc_fail.yml -path-img output/data_processed/ -path-out data/derivatives/labels

(i.e., we do not need to specify -path-label now, as it is automatically set to -path-img)

How to test this PR

cd ~/code/manual-correction
git fetch
git checkout jv/104-set_path-label_to_path-img
sct_download_data -d sct_course_data -o sct_course_data_2024
cd sct_course_data_2024/multi_subject
chmod +x process_data.sh
sct_run_batch -script process_data.sh -config config.yml -jobs 3
# Note: you can add `exit` to line 115 to run only the contrast-agnostic model on T2w to save time

$SCT_DIR/python/envs/venv_sct/bin/python ~/code/manual-correction/manual_correction.py -config qc_fail.yml -path-img output/data_processed/ -path-out data/derivatives/labels

Resolves: #104

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@sandrinebedard sandrinebedard left a comment

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tested and works! Thanks @valosekj for this change!

@valosekj
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Thank you @sandrinebedard! I tested the PR again myself and it works. --> merging

@valosekj valosekj merged commit a2bb5a5 into main Dec 16, 2024
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@valosekj valosekj deleted the jv/104-set_path-label_to_path-img branch December 16, 2024 15:40
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Set the default value for -path-label to match -path-img
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