Move scripts from utilities to inter-rater_variability
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- rename segment_to_csv.py to rootlets_to_spinal_levels.py - move code from intersect.py to intersect_seg_and_rootlets function - move code from rootlet_to_level.py project_rootlets_to_segmentation function - use SCT Image class instead of nibabel
- segment spinal cord - detect PMJ label - run rootlets_to_spinal_levels.py
…or individual subjects and spinal levels.
…ons into the reference segmentation using STAPLE algorithm
…o slices_level_prediction
…e run for each subject separately
…rater variability
…nter_rater_variablity-PMJ_COV.py
…catter_plot_inter_rater_variability-dice_f1.py
…ew 'inter-rater_variability' folder: - rename scripts to make clear in which order they should be run - update README.md
valosekj
changed the title
utilities folderutilities to inter-rater_variability
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This PR:
segment_to_csv.py, now namedrootlets_to_spinal_levels.py, for details, see this commit messagerun_batch_inter_rater_variability.shscript to perform inter-rater variability analysis; see the script heregenerate_figure_inter_rater_variablity.pyto generate a figure showing the inter-rater variability; see the script heregenerate_scatter_plot_inter_rater_variability.pyto generate a scatter plot for F1 score showing the inter-rater variability; see the script herecombine_segmentations_from_different_raters.pyscript to combine three multi-class (i.e., not binary) segmentations into the reference segmentation using the STAPLE algorithm; see the script hereutilities/dice_y_value_soft.pyscript - see the current script here and list of all commits here