When amap runs, the appropriate reference atlas will be downloaded (if not previously done so). If you would like to download in advance to save time (or if you will not have an internet connection) please use
Currently, the only supported atlas is the Allen reference mouse brain, originally from here. The atlas will download into
In the future, other atlases will be available, and you will be able to choose which is downloaded.
If you want to modify the am amap download, use:
--atlas-install-path Supply a path to download the atlas elsewhere. This
should also update the default
registration.conf file so that the correct
atlas is sourced. Alternatively, use this command to tell amap where an
existing atlas is, to save it being downloaded twice. (Requires 20GB
--atlas download path The path to download the atlas into.
(Requires 1.2GB disk space). Defaults to