Usage

[Installation]

1.) Run reg_stack.py with Python 2.7.X, passing the NiftyReg install directory, the directory containing your images, and a registration window size as command line arguments.

2.) Pass additional Nifty-related arguments (such as the -gpu flag for GPU usage) last--they will find their way into reg_f3d. Keep in mind, though, that the required flags (-ref, -flo, -res, -cpp) are handled automatically. Only optional flags used to tweak the registration algorithm should be passed.

3.) That's it! You should find several new folders alongside your input images folder. 'Result' contains the results of the initial transformations, 'CPP' contains the initial deformation fields, 'averagedCPP' contains a comprehensive deformation field for each image, and 'averagedResult' contains a single resultant image after applying the averaged transformation.

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