Category:Documentation/4.1/Modules/Registration

This is an introduction to the registration technology which is available in Slicer 4. This page is intended to help you choose the right tool. For detailed information on using a particular module please follow the links to the module's reference page. You will find the most commonly used registration tools in the Modules menu under Registration. Some more specialized and legacy versions you will find only in the "All Modules" submenu. In the Registration menu you will find the default registration tool as General Registration (BRAINS) and all other forms under Specialized. Conceptually it also important to distinguish between the transform and the resampled image. The result of any registration is always at least one of the two, often both. More details on how 3DSlicer handles transforms and resampling can be found here.

We have assembled a library of solutions which you might you to find examples on how to approach your problem. Click here for a listing of examples.

Default Registration Modules

Manual/interactive alignment can be done via the Transforms module, e.g. for initial alignment. See here for a tutorial and example dataset on Manual Registration. This module is under the Registration/Transforms menu, and also accessible via the toolbar .	The BRAINSfit Module performs automated intensity-based image alignment via rigid to affine to nonrigid transforms, with many options such as automated initialization, masking support, resampling. Advanced options allow to control the degree of freedom in sequence from 6 to 12 and beyond. You can find it under the Registration/General Registration (BRAINS) menu.	Nonrigid registration is also provided by the BRAINSfit module. Deformation is controlled via a BSpline control grid of custom size. This can be combined with linear/affine registration steps. Found under Registration/General Registration (BRAINS) menu. An alternative module (found under "All Modules") is BSpline Deformable Registration, an older but efficient module with less control but also some options not avail. in BRAINSfit (histogram bins and warp field output).

Alternative/Specialized Registration Modules

The Fiducial Registration module will align images based on pairs of manually selected fiducial points (rigid and affine). Two sets of fiducials (fiducial lists) are required, forming matching pairs to be aligned. This module is in the Registration/Specialized/Fiducial Registration menu.	The ACPC Transform module is used to orient brain images along predefined anatomical landmarks: (manually defined) fiducials for the inter-hemispheral midline, anterior- and posterior commissure are used to align an image such that these landmarks become vertical and horizontal, respectively. This module is in the Registration/Specialized/ACPC Transform menu.	The BRAINSDemonWarp Module performs automated image warping based on an optic flow mechanism. Deformations here are significantly more "fluid" (i.e. have more DOF and are less constrained) than for the nonrigid BSpline method provided in the general (BRAINS) registration above. This module is in the Registration/Specialized/Demon Registration (BRAINS) menu.
The Expert Automated Registration Module performs rigid, affine and nonrigid registration, based on image intensity similarities. Same basic functionality as BRAINSfit, with a few differences: choice of similarity function, 1 mask image required only for masking (BRAINSfit requires 2 masks), initialization via landmarks. This module is in the All Modules menu.	The Robust Multiresolution Affine Registration module performs robust automated affine image registration employing a multi-resolution scheme. This was designed for robustness rather than speed. It can be particularly useful when direct approaches fail, e.g. due to lack of overlap or a lot of "distracting" image content. This module is in the All Modules menu.