brainreg /path/to/raw/data /path/to/output/directory -x 2 -y 2 -z 5
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
--downsample Paths to N additional channels to downsample 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
--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.
By default, brainreg will use the 25um 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.:
To change the registration algorithm used, use the
--backend flag. The default is
niftyreg as that is currently the only option.
If your data does not match the brainglobe default orientation (the origin voxel is the most anterior, superior, left-most voxel, then you must specify the orientation by using the
--orientation flag. What follows must be a string in the bg-space "initials" form, to describe the origin voxel.
If the origin of your data (first, top left voxel) is the most posterior, superior, left part of the brain, then the orientation string would be "psl" (posterior, superior, left), and you would use:
To change how the actual registration performs, see Registration parameters