deformetrica is an alias for python deformetrica.py: the main script of the software, in the src folder, automatically created during the conda installation.
model.xml is an xml file containing the description of the task. It specifies the kind of task which is to be performed (such as estimating a registration, an atlas, ...) as well as some hyperparameters for the objects and the deformations used.
data_set.xml is an xml file containing the paths to the different files to be used during the run.
optimization_parameters.xml contains additional details about the optimization method such as the type (GradientAscent or L-BFGS), the step sizes, when to write the output etc.
Additional arguments in the command line are:
--output=path/to/output/folder used to specify the output directory i.e. where all results are saved.
-v DEBUG: allow to get more printed information about the current computation.
Tutorials and examples are available to demonstrate how the three xml files should be filled. Exhaustive lists of options are given in the user manual.
The Deformetrica applications theoretically rely on a control-points-based instance of the Large Deformation Diffeomorphic Metric Mapping (LDDMM) framework. Find more details on the dedicated wiki page.