Question on comparing individual lesions between two masks based on the cc3d.statistics output. about connected-components-3d

[william-silversmith]

Hi PanosProv,

I'm very glad you are getting a lot of use out of cc3d!

I would start by comparing the centroids (also provided by stats), just because it's easier to manage than with the entire bounding box. Just look for the minimum distance centroids. This won't necessarily be a perfect metric, but it'll get you started. You can use scipy to perform a distance calculation between two collections of points.

https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.cdist.html

The real right way to make this comparison will likely depend on your data, but you can try checking that the number, size, and centroids of the regions are approximately the same. You can also compute e.g. voxel-wise F1 scores by comparing the number of false-positive, false-negative, true-positive, and true-negative voxels for each component. There may be other appropriate metrics you can use too, such as variation of information. However, voxel-wise scores can miss useful connectivity information (something my field deals with). So many years ago, we started using RAND scores, and then even more obscure metrics.

Unfortunately, cc3d only provides basic information and the rest is kind of up to you.