SlicerElastix

This extension makes available Elastix medical image registration toolkit (https://elastix.lumc.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)

Register two volumes

• 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

Visualize and save results

• 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.

Customize registration parameters

• 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