View source for Documentation/Nightly/Modules/LandmarkRegistration

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
Author: Steve Pieper, Isomics, Inc.<br>
Contact: Steve Pieper, <email>pieper@isomics.com</email><br>
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|Image:Logo-isomics.png|Isomics, Inc.
|Image:Logo-namic.jpg|NA-MIC
|Image:Logo-nac.jpg|NAC
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Interactive registration and visualization.

[[image:LandmarkRegistration-4.4.png|LandmarkRegistration Module|thumb|500px|left]]

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Examples:
* Use Case 1: Interactively align two volumes
* Use Case 2: Align volumes as pre-processing step for automated registration
* Use Case 3: Visually review results of automated registration

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When you enter the module it will prompt for a fixed and moving volume.  The is trigger the creation of a transformed volume that is a duplicate of the moving volume.  Operations will take place on the "-transformed" volume.

* Parameters: these are the currently selected volumes and can be changed using the "Select Volumes To Register" button.
* Visualization
** Layout: by clicking these buttons you can change what orientations are shown by for each volume.  The order will always be: Fixed first, Moving in the middle, Fixed plus transform blended last.
** Display: select which of the volumes to display
** RevealCursor: creates a 2x2 checkerboard of the bg and fb volumes of a slice view.  Follows mouse.  Note you can also put label maps in fg layer for inspection.
** Controls all fixed/moving slice views
*** Rock: goes back and forth between volumes
*** Flicker: flashes between volumes
** Zoom: synchronous inspection of all slice views
* Landmarks
** Add: puts you in landmark placement mode, and any click in fixed or moving will create a landmark in both volumes (corresponding to named fiducial list).
** Landmarks are monitored so that any movement causes all other viewers to center on that landmark.  Moving a landmark can trigger update of the active registration.
* Registration
** Registration Type: selects what is active
*** Affine Registration: Supports three modes.
**** Rigid: only rotate, translate
**** Similarity: rigid + uniform scale
**** Affine: rotate, translate, non-uniform scale, non-uniform shear
*** ThinPlate Registration
**** Hot Update: recalculate the nonlinear transform at every mouse movement.
**** Export to Grid Transform: create a transform that can be saved/loaded and used with CLIs (thin plate can be used only within the Landmark Registration module).

Note that these transforms work with the transform visualization modes for real-time visualization.

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[[Documentation/4.0/Modules/Transforms|Transforms]]

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N/A

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This module is written in python.  There is a pluggable API for defining new interactive registrations.  Implement a subclass of [https://github.com/pieper/LandmarkRegistration/blob/master/RegistrationLib/RegistrationPlugin.py a RegistrationPlugin] in python.  It can call C++ routines either wrapped in VTK, through SimpleITK, or by calling a CLI.
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