Workbench Command is a set of command-line tools that can be used to perform simple and complex operations within Connectome Workbench.
The GIFTI format is an established data file format intended for use with surface-based data. It has subtypes for geometry (.surf.gii), continuous data (.func.gii, .shape.gii), and integer label data (.label.gii). The files that contain data, rather than geometry, consist mainly of a 2D array, with one dimension having length equal to the number of vertices in the surface. Label files (.label.gii) also contain a list of integer values that are used in the file, plus a name and a color for each one. In workbench, the files for continuous data are called 'metric files', and .func.gii is usually the preferred extension, but there is no difference in file format between .func.gii and .shape.gii. Geometry files are simply called 'surface files', and must contain only the coordinate and triangle arrays. Notably, other software may put data arrays (the equivalent of a metric file) into the same file as the geometry information. Workbench does not support this kind of combined format, and you must use other tools to separate the data array from the geometry. For the full details of the GIFTI format, see http://www.nitrc.org/projects/gifti/