Command line tool#

Basic usage#

brainreg /path/to/raw/data /path/to/output/directory -v 5 2 2 --orientation osl


Full command-line arguments are available with brainreg -h


If you have any spaces in your file-path, please enclose it in quotation marks, otherwise brainreg will interpret it as two inputs, separated by a space. i.e. "/path/to/my data" not path/to/my data.



  • Path to the directory of the images. (Can also be a text file pointing to the files)

  • Output directory for all intermediate and final results


You must also specify the orientation and voxel size of your data, see Image definition.

Additional options#

  • -a or --additional Paths to N additional channels to also register to the same coordinate space.

  • --sort-input-file If 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

Misc options#

  • --n-free-cpus The number of CPU cores on the machine to leave unused by the program to spare resources.

  • --debug Debug mode - will increase verbosity of logging and save all intermediate files for diagnosis of software issues.

  • --save-original-orientation Option to save the registered atlas with the same orientation as the input data.

  • --brain_geometry To allow brain sub-volumes to be processed. Currently, the options are full (default, whole brain), hemisphere_l (only the left hemisphere) and hemisphere_r (only the right hemisphere).

  • --pre-processing To specify the preprocessing method used before registration. Currently, the only options are default or skip. Use skip to ensure no preprocessing is performed.


By default, brainreg will use the 25μm version of the Allen Mouse Brain Atlas. To use another atlas (e.g. for another species, or another resolution), you must use the --atlas flag, followed by the string describing the atlas, e.g.:

--atlas allen_mouse_50um


To find out which atlases are available, once brainreg is installed, please run brainglobe list. The name of the resulting atlases is the string to pass with the --atlas flag.

Registration backend#

To change the registration algorithm used, use the --backend flag. The default is niftyreg as that is currently the only option.

Registration options#

To change how the actual registration performs, see Registration parameters