SlicerElastix

This extension makes available Elastix medical image registration toolkit (http://elastix.isi.uu.nl/) available in Slicer.

Installation

Download and install latest stable release or a recent nightly release of 3D Slicer (https://download.slicer.org).
Start 3D Slicer application, open the Extension Manager (menu: View / Extension manager)
Install SlicerElastix extension (in Registration category)

Start 3D Slicer
Load your volumes (for example: switch to SampleData module and load MRBrainTumor1 and MRBrainTumor2 images)
Switch to General registration (Elastix) module (in Registration category)
Select Fixed volume (for example: MRBrainTumor1)
Select Moving volume (this volume will be resampled to match voxels of the Fixed volume; for example: MRBrainTumor2)
Select Preset: generic (all) performs deformable registration; generic rigid (all) performs rigid registration
Select "Create new Volume" for Output volume (this will be the resampled moving volume)
Select "Create new Transform" if later you want to visualize the displacement field or apply the transform to other nodes (points, surfaces, other volumes)
Click Apply button and wait a couple of minutes

To compare Fixed volume with Output volume (registered moving volume): set Fixed volume as Foreground volume in slice viewers and fade between the Output volume and Foreground volume to see how well they are aligned.
To display displacement field: in Transforms module, select the Output transform and in Display section enable visualization in slice and/or 3D views.
To apply transforms to other nodes: use Transforms module (or in Data module / Transform hierarchy tab: drag-and-drop nodes under the Output transform).
To save Output volume or transform, select menu: File / Save.

Click Show database folder in Advanced section, which will open the tolder that contains all registration preset parameter files
Edit the parameter set database file (ElastixParameterSetDatabase.xml) to edit or add a new preset (each ParameterSet element defines one preset)
To modify parameters of a registration step, edit the corresponding .txt parameter file