Category:Documentation/4.1/Modules/Registration - Revision history

JChris.FillionR at 22:11, 31 October 2012

2012-10-31T22:11:16Z

Kikinis at 12:29, 10 May 2012

2012-05-10T12:29:57Z

Meier at 17:11, 20 April 2012

2012-04-20T17:11:13Z

Meier at 16:20, 20 April 2012

2012-04-20T16:20:01Z

Meier at 16:19, 20 April 2012

2012-04-20T16:19:21Z

Meier at 16:15, 20 April 2012

2012-04-20T16:15:39Z

Meier: /* Alternative Registration Modules */

2012-04-20T16:10:15Z

Alternative Registration Modules

Meier: /* Alternative Registration Modules */

2012-04-20T16:04:01Z

Alternative Registration Modules

Meier at 16:02, 20 April 2012

2012-04-20T16:02:48Z

Meier at 16:01, 20 April 2012

2012-04-20T16:01:11Z

@@ Line 2: / Line 2: @@
 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 [[Documentation/4.1/Modules/Resampling|how 3DSlicer handles transforms and resampling can be found here]].
+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 [[Documentation/{{documentation/version}}/Modules/Resampling|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 [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable here] for a listing of examples.
@@ Line 9: / Line 9: @@
 <small>
 {| cellpadding="2" cellspacing="2"  width="1250"
-|align="center" |[[Image:Registration_Manual_icon.png| 135px |link=Documentation/4.1/Modules/Transforms]]
+|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/4.1/Modules/BRAINSFit]]
+|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/4.1/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/4.1/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 .
+|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/4.1/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.
+|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/4.1/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/4.1/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).
+|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).
 |}
 </small>
@@ Line 22: / Line 22: @@
 <small>
 {| cellpadding="2" cellspacing="2"  width="1250"
-|align="center" |[[Image:Registration_Fiducial_icon.png|95px|link=Documentation/4.1/Modules/FiducialRegistration]]
+|align="center" |[[Image:Registration_Fiducial_icon.png|95px|link=Documentation/{{documentation/version}}/Modules/FiducialRegistration]]
-|align="center" |[[Image:Registration_ACPC_icon.png|95px |link=Documentation/4.1/Modules/ACPCTransform]]
+|align="center" |[[Image:Registration_ACPC_icon.png|95px |link=Documentation/{{documentation/version}}/Modules/ACPCTransform]]
-|align="center" |[[Image:Registration_BRAINSdemonwarp.png|95px|link=Documentation/4.1/Modules/BRAINSDemonWarp]]
+|align="center" |[[Image:Registration_BRAINSdemonwarp.png|95px|link=Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp]]
 |-
-|The [[Documentation/4.1/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.
+|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.
-|The [[Documentation/4.1/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/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/4.1/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.
+|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.
 |-
-|align="center" |[[Image:Registration_Rigid+Affine_icon.png|95px|link=Documentation/4.1/Modules/ExpertAutomatedRegistration]]
+|align="center" |[[Image:Registration_Rigid+Affine_icon.png|95px|link=Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration]]
-|align="center" |[[Image:Registration_Multires_icon.png| 95px |link=Documentation/4.1/Modules/MultiResolutionAffineRegistration]]
+|align="center" |[[Image:Registration_Multires_icon.png| 95px |link=Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration]]
 |-
-|The [[Documentation/4.1/Modules/ExpertAutomatedRegistration|'''Expert Automated Registration''']] Module performs rigid, affine and nonrigid registration, based on image intensity similarities. Same basic functionality as [[Documentation/4.1/Modules/BRAINSFit| '''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 [[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|'''Expert Automated Registration''']] Module performs rigid, affine and nonrigid registration, based on image intensity similarities. Same basic functionality as [[Documentation/{{documentation/version}}/Modules/BRAINSFit| '''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 [[Documentation/4.1/Modules/MultiResolutionAffineRegistration|'''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.
+|The [[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|'''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.
 |}
 </small>

@@ Line 3: / Line 3: @@
 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 [[Documentation/4.1/Modules/Resampling|how 3DSlicer handles transforms and resampling can be found here]].
 == Default Registration Modules==
 <small>

@@ Line 15: / Line 15: @@
 |}
 </small>
-== Alternative  Registration Modules ==
+== Alternative/Specialized  Registration Modules ==
 <small>

@@ Line 2: / Line 2: @@
 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 and an overview of [[Documentation/4.1/Modules/Resampling how 3DSlicer handles transforms and resampling can be found here]].
+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 [[Documentation/4.1/Modules/Resampling|how 3DSlicer handles transforms and resampling can be found here]].
 == Default Registration Modules==
 <small>

@@ Line 2: / Line 2: @@
 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.
+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 and an overview of [[Documentation/4.1/Modules/Resampling how 3DSlicer handles transforms and resampling can be found here]].
 == Default Registration Modules==
 <small>

@@ Line 30: / Line 30: @@
 |align="center" |[[Image:Registration_Multires_icon.png| 95px |link=Documentation/4.1/Modules/MultiResolutionAffineRegistration]]
 |-
-|The [[Documentation/4.1/Modules/ExpertAutomatedRegistration|'''Expert Automated Registration''']] Module performs automated image registration, with custom combinations of rigid to affine to nonrigid, based on image intensity similarities. It allows to focus the registration on a region of interest via a label mask. This module is in the '''All Modules''' menu.
+|The [[Documentation/4.1/Modules/ExpertAutomatedRegistration|'''Expert Automated Registration''']] Module performs rigid, affine and nonrigid registration, based on image intensity similarities. Same basic functionality as It allows to focus the registration on a region of interest via a label mask. This module is in the '''All Modules''' menu.
 |The [[Documentation/4.1/Modules/MultiResolutionAffineRegistration|'''Robust Multiresolution Affine Registration''']] module performs robust  automated affine image registration employing a multi-resolution scheme.  This module is in the '''All Modules''' menu.
 |}
 </small>