Command line tool#
brainreg /path/to/raw/data /path/to/output/directory -v 5 2 2 --orientation osl
Full command-line arguments are available with
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.
"/path/to/my data" not
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.
--additionalPaths to N additional channels to also register 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.
--brain_geometryTo 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-processingTo specify the preprocessing method used before registration. Currently, the only options are
skipto 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.:
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
To change the registration algorithm used, use the
--backend flag. The default is
niftyreg as that is
currently the only option.
To change how the actual registration performs, see Registration parameters