View source for Category:Documentation/Nightly/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. Much of the registration functionality has been streamlined into a [[Documentation/{{documentation/version}}/Modules/BRAINSFit|main module (BRAINSfit)]] and specialized modules. 
Additional specialized and legacy modules 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''.
The basic functionality can be understood as two parts: 1) determine a transform to align one image to another 2) apply this transform to the data. The [[Documentation/{{documentation/version}}/Modules/BRAINSFit|main module (BRAINSfit)]]  does both, but often you may prefer to separate the two steps to have better control over your workflow. Step 1 always produces a '''Transform''', which is visible in the [[Documentation/{{documentation/version}}/Modules/Data|Data module]] and (in the case of linear transforms) can be inspected and edited in the  [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module. Step 2 often, but not always, involves generating a new image by some form of resampling. The exception is the application of linear transforms to images via the ''Harden Transform'' option in the [[Documentation/{{documentation/version}}/Modules/Data|Data module]], which applies the transform by storing it as new orientation info in the image header. <br>
*The [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|'''Slicer Registration Library''']] is a collection of example cases including solutions and step-by-step instructions that demonstrate the use of the Slicer registration tools, strategies and methods for particular image types and registration needs. For examples using older versions of Slicer (3.6 to 4.1) [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable click here].
*[[Documentation/{{documentation/version}}/FAQ|'''Slicer Registration FAQ''']]: answers to the most common questions/problems, including cookbook recipes for common registration steps.
*[[Documentation/{{documentation/version}}/RegistrationVideoTutorials|'''Slicer Registration Training Videos''']]: brief videos/screencasts showing  step-by-step approaches to the most common tasks. Most cases in the  [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Registration Library]] contain screencast videos that show the procedure start-to-finish.
*[[Documentation/{{documentation/version}}/Modules/Resampling|'''Slicer Resampling Overview''']] a summary of how 3DSlicer handles transforms and how image resampling is performed.]] 
The main modules/tools are listed/explained below, to help you find the right tool for the task:
== Default Registration Modules==

{| cellpadding="2" cellspacing="2"  width="1250"
|align="center" |[[Image:Registration_Manual_icon.png| 135px |link=Documentation/{{documentation/version}}/Modules/Transforms]]
|align="center" |[[Image:Registration_Rigid+Affine_icon.png| 135px |link=Documentation/{{documentation/version}}/Modules/BRAINSFit]]
|align="center" |[[Image:Registration_NonRigid_icon.png| 135px |link=Documentation/{{documentation/version}}/Modules/BRAINSFit]]
|-
|Manual/interactive alignment can be done via the [[Documentation/{{documentation/version}}/Modules/Transforms|'''Transforms''' ]] module, e.g. for initial alignment. See [[Slicer3.4:Training#Slicer_3.4_Tutorials| 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 [[Documentation/{{documentation/version}}/Modules/BRAINSFit| '''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  [[Documentation/{{documentation/version}}/Modules/BRAINSFit| '''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  [[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration| '''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).
|-
|align="center" |[[Image:Registration_Resample_icon.png| 135px |link=Documentation/{{documentation/version}}/Modules/BRAINSResample]]
|-
|The [[Documentation/{{documentation/version}}/Modules/BRAINSResample|'''Resample Image (BRAINS)''']] module is used to apply a given transform to a volume, with specific interpolation settings (linear, nearest neighbor, sinc etc).It also permits to add a grid to the image that shows the effects of the transform, particularly useful for visualizing the deformation in nonrigid registration. The  [[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|'''Resample ScalarVectorDWI''']] module (under ''AllModules'') also provides resampling functionality. Note that to resample '''tensor''' images (e.g.DTI) a special  [[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume |'''ResampleDTI''']]  module must be used to correctly apply a transform.
|}

== Alternative/Specialized  Registration Modules ==

<small>
{| cellpadding="2" cellspacing="2"  width="1250"
|align="center" |[[Image:Registration_Fiducial_icon.png|95px|link=Documentation/{{documentation/version}}/Modules/FiducialRegistration]]
|align="center" |[[Image:Registration_ACPC_icon.png|95px |link=Documentation/{{documentation/version}}/Modules/ACPCTransform]]
|align="center" |[[Image:Registration_BRAINSdemonwarp.png|95px|link=Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp]]
|-
|The [[Documentation/{{documentation/version}}/Modules/FiducialRegistration|'''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.<br>An alternative landmark registration tool is also available in the [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|'''Slicer IGT extension''']] as "Fiducial Registration Wizard". 
|The [[Documentation/{{documentation/version}}/Modules/ACPCTransform|'''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 [[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|'''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.
|}
</small>