The most simple way would be through the Connectome Mapper interface. Select a base directory, copy the raw data in the appropriate folders and press the "Check input data" button. Once this is done you can configure the different stages as you want. To save the configuration file, go to the menu toolbar -> Configuration -> Save configuration as...
This will create a .ini file with all the required information to run the pipeline. If you use it to process other subjects, remember to change subject specific options, like the path to the custom atlas for example.
The most simple way would be through the Connectome Mapper interface. Select a base directory, copy the raw data in the appropriate folders and press the "Check input data" button. Once this is done you can configure the different stages as you want. To save the configuration file, go to the menu toolbar -> Configuration -> Save configuration as... This will create a .ini file with all the required information to run the pipeline. If you use it to process other subjects, remember to change subject specific options, like the path to the custom atlas for example.