calculate_connectome.sh

[mphook]

I think the script should be edited to skip running the MRtrix connectome command if the csv file already exists. Currently the script looks through all existing connectome files and reruns the matrix, but that is unnecessary as the matrix file will not change between runs. This could help us speed up the calculation so that it only focuses on running new profiles.

[mphook]

I can see why this might not be practical as the matrix can change based on what assignment method you choose. A better solution would be to choose which profile to run instead.

[jessdtate]

we also want to be able to specify a specific ( or list of ) profile