makeDirectory(args.outDir, args.force) can be used

Since `FA` is checked right up front, it should be okay to use `args.force` for the following directory creations:
```
    if modalities[0]=='FA':
        # we cannot overwrite outDir, because previous output can be there
        makeDirectory(args.outDir)

        # we cannot overwrite logDir, because previous commands can be there
        makeDirectory(args.logDir)
```