Exclusion Regions

ALE offers exclusion regions as a way to disallow certain areas from being used in alignment and (optionally) rendering. Spatial coordinates are expressed in the rendering coordinate system (prior to scaling). In cases where the default transformation is used with the original frame, this is identical to the unscaled original frame coordinate system, taking the upper-left corner to be (0, 0). Frame numbering begins with 0, which represents the original frame.

Rectangular Exclusion

All specified volumes are excluded from alignment (except where they affect the alignment reference image), and are excluded from rendering by default. (See for information on how to ignore exclusion regions.) Exclusion region syntax is as follows:

--ex <args> Exclude a specified volume. <args> are space-delimited horizontal, vertical, and frame limits: <xmin> <xmax> <ymin> <ymax> <fmin> <fmax> Cropping

Cropping excludes the spatial complement of an area over a specified set of frames.

--crop <args> Exclude the spatial complement of an area over a specified set of frames. <args> are: <xmin> <xmax> <ymin> <ymax> <fmin> <fmax>