amap /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.
--no-save-downsampled Don't save the downsampled brain before filtering.
--registration-config To supply your own, custom registration configuration file
--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.
If your data does not match the NifTI standard orientation (origin is the most ventral, posterior, left voxel), then please see Image orientation to reorient the atlas
To change how the actual registration performs, see Registration parameters
--no-boundaries Do not precompute the outline images (if you don't want to use
To visualise your data, please see Visualisation