Summary

I've been running into an (admittedly, entirely user-fault) error because I haven't been setting the --atlas flag for the 4S Schaefer 100 atlas properly. But it's been difficult to debug because QSIrecon does run for quite awhile before hitting this error. It would be great if the CLI parser would check to see if the atlas string is valid.

Others have also encountered similar difficulties using custom atlases (see: this post on neurostars), so there could also be a check that the expected atlas path exists.

Next steps

Potentially could be solved with an additional if statement in parse_args i.e. along the lines of:

if atlas not in [list_of_builtin_atlases]:
     if os.path.exists(atlas_path) == False:    
         parser.error("Invalid atlas path") 
     else: 
          parser.error("Invalid atlas string for built in atlas")