--downsamplePaths to N additional channels to downsample to the same coordinate space.
--sort-input-fileIf set to true, the input text file will be sorted using natural sorting. This means that the file paths will be sorted as would be expected by a human and not purely alphabetically
--n-free-cpusThe number of CPU cores on the machine to leave unused by the program to spare resources.
--debugDebug mode. Will increase verbosity of logging and save all intermediate files for diagnosis of software issues.
--save-original-orientationOption to save the registered atlas with the same orientation as the input data.
--atlasflag, followed by the string describing the atlas, e.g.:
--backendflag. The default is
niftyregas that is currently the only option.