nctool is the Neural Network classification or clustering tool that leads you to solving a clustering problem. The majority part in getting a clustering output is played by the data provided to the tool. In case of using nctool you are training a neural network. So, the number of neurons decided will also play some role. Also, setting some of the parameters while moving forward in the nctool app will help you in getting good clusters (if your data is for what you are expecting the clusters).
I am providing you some links to refer in order to use all the parameters of nctool in a productive way. Please refer to the following links:
Hope this helps!