Update spine-generic processing script to SCT 7.3#51
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…rientation (using HOG method).
Add `--include-symmetry` to plot AP and RL symmetry Dice (SCT >= v7.3, sct_process_segmentation -anat) in a rightmost 2x4 column; default keeps the original 2x3 6-metric layout. Add `--intersect-subjects` to restrict comparison to participants present in every -path-SC / -path-canal dataset, and `--dataset-labels` to override legend/filename labels per path. Fix get_vert_indices() to also mask by `dataset` when present, so the same participant_id appearing in multiple datasets does not create a spurious VertLevel transition at the dataset boundary.
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Description
This PR updates the spine-generic processing script (process_data_spine-generic.sh) to SCT 7.3, namely:
sct_process_segmentationuses-discfileinstead of-vertfile.sct_process_segmentationuses-anatflag to compute spinal cord orientation (using HOG method) in order to compute symmetry and quadrants area metrics.Figure
Comparison of the current morphometrics in this repo obtained using SCT v7.1 and newly obtained morphometrics using SCT v7.3 using this PR (that included new AP diameter calculation and symmetry measurements):
Note
With SCT v7.3, we now have also other symmetry measurements. I'm showing only
symmetry_dice_APandsymmetry_dice_RLfor now to keep the figure simple.Note
Symmetry measurements are shown only for v7.3 as SCT v7.1 didn't compute them.
Note
As we updated the AP diameter calculation, we can see differences between 7.1 and 7.3 for AP diameter, AP/RL ratio (formerly named compression ratio), and solidity.
Tagging @jcohenadad, @sandrinebedard, @plbenveniste
Resolves: #40