Command line tool#

Basic usage#

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

Hint

Full command-line arguments are available with brainreg -h

Caution

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.

Arguments#

Mandatory#

  • 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

Hint

You must also specify the voxel size using the -v flag (in microns, matching your orientation order) and the orientation using the --orientation flag.

See Image definition for details on how to determine the correct values.

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.

Atlas#

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

Hint

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