The FastModelAlign module in SlicerMorph is for 3D model registration. Currently, it perfroms rigid (with or without scaling) and affine registration. The rigid registration involves RANSAC and ICP steps from the downsampled pointclouds derived from 3D models. For more technical implementation details, see the related ALPACA automated landmarking publication.

We provided two partial models of the same mountain beaver skull derived from two separate photogrammetric runs as sample data: partial_photogram_model1.obj is a partial skull with no bottom, and partial_photogram_model2.obj is a partial skull with no top. After installing the SlicerMorph extension, they can be downloaded from the Sample data module: clicking the partial photogrammetry models button under the FastModelAlign tab will download the two sample models to the Slicer cache folder and load them into Slicer automatically (also downloadable here: SlicerMorph sample data. The following tutorial are based on these two sample models.

If using the Sample Data module, the two partial models should be loaded into Slicer automatically. If downloaded manually, drag and drop the downloaded sample models into 3D Slicer. The two models have distinct sizes because no size reference was provided for the two photogrammetric runs.

Switch to the FastModelAlign module. Select partial_photogram_model2 from the Source Model drop-down menu and partial_photogram_model1 from the Target Model drop-down menu. Also create a model from the Output registered model drop-down menu. In this tutorial, the output registered model is named as test_registration. Leave the Skip scaling unchecked. If checked, the source model will not be scaled to approximate the size of the target model.

After the three fields in the Setup source and target models are populated, the Testing pointcloud subsampling and Run rigid registration buttons are enabled.

(Optional) Click Testing pointcloud subsampling button can show the density of the downsampled source and target point clouds. Adjusting the Point density adjustment bar to adjust the number of points in each point cloud. Usually, 4,000 to 6,000 points per point cloud would be optimal.

Click the Run rigid registration button to rigidly register the source partial_photogram_model2 to the target model partial_photogram_model1. If Skip scaling is unchecked, the process first scale the source model to approximate the size of the target model, then rigidly registered the source to the target.After the process is finished, the user specified output model test_registration (red) is generated and represents the source model rigidly registered to the target model (yellow).

After running a rigid registration, the module also generates a scaling matrix node named as partial_photogram_model2_scaling (source model name plus "_scaling") and a rigid registration matrix node named as partial_photogram_model2_rigid (source model name plus "_rigid"), which can be viewed in the data module. This allows users to repeat and visualize the scaling and rigid registration process. The original source model partial_photogram_model2 is unmodified. For tutorials of applying, editing, and visualizng transformation in 3D Slicer, please see the official doc: https://slicer.readthedocs.io/en/latest/user_guide/modules/transforms.html.

Note that the scaling node is nested under the rigid registration node. This is because the module first performs a scaling transformation for the source model, then performs a rigid registration for the scaled source model. This is equivalent to transforming the scaling matrix by the rigid registration matrix (equivalent to generating a similarity transformation for the source model).

To repeat and vidualize the process of rigid registration after scaling, users can drag the original source model partial_photogram_model2.obj (blue) to the scaling node, which has been transformed by the rigid registration node.

Switch to the Transform hierarchy, users can visualize the hierarchical transformation of the source model node, which is first scaled by the scaling node, then rigidly registered by the rigid transformation node.

After running a rigid transformation, the Run affine registration button will be enabled. Click this button will perform an affine deformable transformation for the scaled (if Scaling optin is left unchecked) and rigidly registered source model. Therefore, the user defined output model (test_registration (red)) is then undergone an affine transformation to match with the target (yellow).

After this process, an affine transformation node, named as partial_photogram_model2_affine (source model name plus "_rigid"), is generated based on the scaled and rigidly registered model. The Transform Hiearchy tab in the Data module shows that the scaling node is under the rigid trasnformation node, which is further nested under the affine transformation node partial_photogram_model2_affine.

To repeat and visualize the affine registration, users can drag the original untransformed source model partial_photogram_model2.obj (blue) into the scaling node partial_photogram_model2_scaling for a full sequence of scaling, rigid registration, and affine transformation.

Users can adjust the parameter settings under the Advanced Settings tab before running each registration step. For settings related to ridgid registration, please refer to the ALPACA publication.