I managed to customize Xubuntu 14.04LTS to be Lin4Neuro-14.04.
For this customization I did the following;
- .desktop files for neuroimaging analysis packages are stored in .local/share/applications
- Neuroimaging.directory is stored in .local/share/desktop-directories.
- Custom icons are stored in ~/.icons
If you look at these files, you will see how you can add your entries to menu.
I keep maintaining Xubuntu 12.04 because I am not certain Connectome mapper works in Xubuntu 14.04. If you want to use Connectome mapper, I recommend to use Lin4Neuro 12.04.