Batching

Creating a batch file with the new Connectome Mapper should be very easy thanks to the simplified command-line arguments:

connectomemapper input_folder config_file

Several possibilities exists, looping over different input folders with the same config file (multiple subjects study), looping over the same input folder with multiple config files (parameter exploration) or running multiple input folders with multiple config files. Batch scripts can be written in any language, example bash script:

 #!/bin/bash   
subjects_folders=(path/to/subject1 path/to/subject2 path/to/subject3)
config_file = path/to/configfile
for subject in "${subjects_folders[@]}"; do
   connectomemapper "${subject}" "${config_file}"
done