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Analyze midsagittal lesion length and width #96

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Analyze midsagittal lesion length and width #96

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Commits on Sep 20, 2024

  1. Add script to segment the spinal cord and lesions from T2w images and… 

    … compute the midsagittal lesion length and width.
    @valosekj
    valosekj committed Sep 20, 2024
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  2. Change logic how to save XLS files produced by sct_analyze_lesion. If… 

    … we use '-ofolder' for sct_analyze_lesion, then QC report fails.
    @valosekj
    valosekj committed Sep 20, 2024
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  3. Remove forgotten '-ofolder ${PATH_RESULTS}/contrast-agnostic' from th… 

    …e previous commit
    @valosekj
    valosekj committed Sep 20, 2024
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  4. Remove 'CUDA_VISIBLE_DEVICES=1 SCT_USE_GPU=1' for the contrast-agnost… 

    …ic model for now

Context: spinalcordtoolbox/spinalcordtoolbox#4633
    @valosekj
    valosekj committed Sep 20, 2024
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  5. Use '-largest 1' to keep only the largest connected component. Context: 

    https://github.com/ivadomed/model_seg_sci/pull/96\#issuecomment-2364121461
    @valosekj
    valosekj committed Sep 20, 2024
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  6. Add README for the midsagittal lesion length and width analysis

    @valosekj
    valosekj committed Sep 20, 2024
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Commits on Sep 21, 2024

  1. Generate sagittal lesion QC report

    @valosekj
    valosekj committed Sep 21, 2024
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Commits on Oct 2, 2024

  1. Remove the CA model because it does not work well on lumbar data with… 

    … metal artifacts

See comments in the following PR for context: #96
    @valosekj
    valosekj committed Oct 2, 2024
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  2. Add 02_read_xls_files.py script to aggregate lesion metrics across su… 

    …bjects
    @valosekj
    valosekj committed Oct 2, 2024
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  3. Include measurements also for GT masks

    @valosekj
    valosekj committed Oct 2, 2024
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  4. Add QC for manual GT

    @valosekj
    valosekj committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. Run sct_analyze_lesion on GT masks before running SCIseg inference. B… 

    …ecause if SCIseg predictions no lesion, it finished with a QC error and GT masks are not analyzed at all
    @valosekj
    valosekj committed Oct 3, 2024
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  2. Add logging to better track number of processed subjects

    @valosekj
    valosekj committed Oct 3, 2024
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  3. Update docstring

    @valosekj
    valosekj committed Oct 3, 2024
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  4. Take into account multiple lesions

    @valosekj
    valosekj committed Oct 3, 2024
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  5. Add script to generate figures

    @valosekj
    valosekj committed Oct 3, 2024
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