This guide is still under construction

Image Registration

Dosma supports image registration using the Elastix and Transformix by creating a wrapper around the standard command-line usage. In addition to multi-threading, Dosma supports true parallel execution when registering multiple volumes to a target.

Elastix/Transformix must be installed and configured on your machine. See the setup guide for more information

To register moving image(s) to a target image, we can use dosma.utils.registration.register:

>>> from dosma.utils.registration import register
>>> out = register(target, moving, "/path/to/elastix/file", "/path/to/save", return_volumes=True)
>>> registered_images = out["volumes"]

To use multiple workers, we can pass the num_workers argument. Note that num_workers parallelizes registration when there are multiple moving images. The true number of parallel processes are equivalent to min(num_workers, len(moving)). To increase the number of threads used per, use num_threads.

To transform moving image(s) using a transformation file, we can use dosma.utils.registration.apply_warp:

>>> from dosma.utils.registration import apply_warp
>>> transformed_image = apply_warp(image, transform="/path/to/transformation/file")

Often we may want to copy the final transformation file produced during registration to transform other volumes:

>>> reg_out = register(target, moving, "/path/to/elastix/file", "/path/to/save", return_volumes=True)
>>> warp_out = apply_warp(other_moving, transform=out_reg["outputs"].transform)