contour - Evaluate metrics between two sets of contours

This pipeline compares comparable contours (i.e. of the same participant, carotid, object and axial slice) using two metrics:

• the Dice score compares the areas enclosed in the contours. For the wall, the area enclosed by the lumen is not considered.
• the minimal euclidean distance between each point of the first contour (transform) and the second contour (reference). Note that this metric is not symmetric and depends on which contour is the first or second.

Example of lumen contours being compared. In this example the first contour is the blue one and the reference is in red.

Prerequisites

This step relies on the outputs of transform contour.

Running the task

The task can be run with the following command line:

carotid compare centerline TRANSFORM_DIR REFERENCE_DIR OUTPUT_DIR

where:

• TRANSFORM1_DIR (str) is the path to the directory containing the first set of contours.
• TRANSFORM2_DIR (str) is the path to the directory containing the set of contours which are considered as a reference (for example manual annotations).
• OUTPUT_DIR (str) is the path to the directory in which the TSV files compare_contour_dice.tsv and compare_contour_points.tsv will be written.

Outputs

This pipeline writes two TSV files. compare_contour_dice.tsv has the following structure:

participant_id	side	label	object	z	dice_score
Anon450	left	internal	lumen	340	0.95
Anon450	left	internal	lumen	341	0.87
...	...	...	...	...	...
Anon062	right	external	wall	413	0.0

for each contour, only one value is computed.

---

compare_contour_points.tsv has the following structure:

participant_id	side	label	object	z	x	y	deviation	min_distance
Anon450	left	internal	lumen	340	250.5	52.3	0.60	1.1
Anon450	left	internal	lumen	341	249.7	52.1	0.70	1.3
...	...	...	...	...	...	...	...	...
Anon062	right	external	wall	413	626.9	12.5	1.65	0.5

In this file two values exist per point in contours: the deviation is the uncertainty already computed by the transform command. The min_distance is the metrics computed by compare.