Fixed wrong disc labeling and other minor improvements #1814
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jcohenadad
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zougloub
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Jun 5, 2018
| for iz in range(nz): | ||
| # get 2d slice | ||
| slice = im_seg_labeled.data[:, :, iz] | ||
| # check if at least one voxel is non-zero | ||
| if np.any(slice): | ||
| slice_one = np.copy(slice) | ||
| # set all non-zero values to 1 | ||
| # set all non-zero values to 1 (to compute center of mass) |
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Just curious, why not use center of mass with the original slice?
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if one slice includes part of vertebral level i and i+1, the center of mass will be shifted towards the i+1 level. We don't want that here (i.e. the goal is to be at the center of the cord). Comments added: c7b4b1e
scripts/sct_label_vertebrae.py
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| vertebral_level_previous = np.max(im_seg_labeled.data) | ||
| # loop across z | ||
| vertebral_level_previous = np.max(im_seg_labeled.data) # initialize with the max label value | ||
| # loop across z in the superior direction (i.e. starts with the bottom slice) |
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comments added: c7b4b1e
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Fixes #1812, Fixes #1810