Connected clusters

After creating a binary image, connected clusters thresholding can be used to remove the speckle-like small structures.

Here is an example python script to perform connected clusters thresholding from command line.

1. Download the script.
2. In your command line:

python /path/to/connected_clusters.py /path/to/image.nii.gz -c 100

3. For further options:

python /path/to/connected_clusters.py -h

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TODO: I might add this utility to segmentator. The example script is quite slow but does the job.