User guide

How to register your data to the template

Basic usage

amap /path/to/raw/data /path/to/output/directory -x 2 -y 2 -z 5

Full command-line arguments are available with amap -h

If you have any spaces in your file-path, please enclose it in quotation marks, otherwise amap 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 pixel sizes, see Specifying pixel size

Additional options

  • -d or --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

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.

Input data orientation

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

Registration options

To change how the actual registration performs, see Registration parameters

Visualisation options

  • --no-boundaries Do not precompute the outline images (if you don't want to use amap_vis)


To visualise your data, please see Visualisation