Modules:RealignVolume-Documentation-3.4 - Revision history

Nicole: /* Source code & documentation */

2010-01-15T22:00:13Z

Source code & documentation

Nicole: /* Quick Tour of Features and Use */

2009-10-06T20:12:01Z

Quick Tour of Features and Use

Nicole: /* Module Description */

2009-10-06T20:10:47Z

Module Description

Marianna at 19:59, 26 May 2009

2009-05-26T19:59:28Z

Kikinis: /* Quick Tour of Features and Use */

2009-04-16T19:30:43Z

Quick Tour of Features and Use

Kikinis: /* Quick Tour of Features and Use */

2009-04-16T18:14:07Z

Quick Tour of Features and Use

Nicole: /* Module Description */

2009-04-14T00:27:41Z

Module Description

Nicole: /* ACPC Transform */

2009-04-14T00:27:15Z

ACPC Transform

Nicole at 00:21, 14 April 2009

2009-04-14T00:21:19Z

Nicole: New page: Return to Slicer 3.4 Documentation NOTOC ===Realign Volume=== Realign Volume {| |GUI |} == General Information == =...

2009-02-25T22:13:27Z

New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Realign Volume=== Realign Volume {| |thumb|280px|GUI |} == General Information == =...

New page

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Realign Volume===
Realign Volume

{|
|[[Image:SlicerRealign-3.4.jpg|thumb|280px|GUI]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Nicole Aucoin: Brigham and Women's Hospital
* Contact: Nicole Aucoin, nicole@bwh.harvard.edu

===Module Description===

Realigns a volume based on a transformation matrix (if output volume is specified). It can make a transform using a list of fiducials. If pass in a transform matrix and an output volume, but no fiducials, applies the transform to the input volume.

== Usage ==

===Examples, Use Cases & Tutorials===

* Useful when can place fiducials in two orthogonal lines in a an image to define the midline and the ACPC line

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Transform panel:''' Calculate a transform from midline and ACPC fiducial lists, or specify a transform.
**ACPC Line: pick a fiducial list from the scene that defines the ACPC line.
**Midline: pick a fiducial list from the scene that defines the midline.
**Output transform: An output transform - load a calculated transform in this node.
* '''Reslice panel:''' Apply transform to volume
** Input transform: An input transform, apply this to the input volume and get the output volume
** Input Volume: The input volume to work upon
** Output Volume: Output realigned volume, optional (if not set, just returns the output transform)
** Reference Volume: Reference volume, optional. If set, use the RAS/IJK transform from this volume instead of the input volume.
**Interpolation Type: Controls the type of interpolation done when reslicing, can be nearest neighbour, linear, or cubic.

== Development ==

===Dependencies===

The fiducials and volumes modules are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source Code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Realign/Realign.xml Realign.xml]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Realign/Realign.cxx Realign.cxx]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Realign/vtkPrincipalAxesAlign.cxx vtkPrincipalAxesAlign.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Realign/vtkPrincipalAxesAlign.h vtkPrincipalAxesAlign.h]

Doxygen documentation:
*[]

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

===References===

@@ Line 39: / Line 39: @@
 * '''Transform panel:''' Calculate a transform from midline and ACPC fiducial lists, and specify an output transform.
-**ACPC Line: pick a fiducial list from the scene that defines the ACPC line.
+**ACPC Line: a fidicual list containing two fiducial points, one at the anterior commissure and one at the posterior commissure. The resulting transform will bring the line connecting them to horizontal to the AP axis.
-**Midline: pick a fiducial list from the scene that defines the midline.
+**Midline: pick a fiducial list from the scene that defines the midline. The midline is a series of points defining the division between the left and right hemispheres of the brain (the mid sagittal plane). The resulting transform will put the output volume with the mid sagittal plane lined up with the AS plane.
 **Output transform: An output transform - load the calculated transform in this node.
 * '''Debug panel:''' Set debugging flag

@@ Line 24: / Line 24: @@
 ===Module Description===
-Calculate a transformation from two input fiducial lists. This transformation can then be applied to a volume using the Resample Scalar/Vector/DWI Volume module.
+Calculate a transformation from two input fiducial lists.
 Note: renamed from RealignVolume.

@@ Line 41: / Line 41: @@
 ** Debug: click to see print outs
-*Use: first create the two fiducial lists, then use the module
+*Use: the order in which the acpc fiducials are picked is not important.
 == Development ==

@@ Line 40: / Line 40: @@
 * '''Debug panel:''' Set debugging flag
 ** Debug: click to see print outs
 == Development ==

← Older revision		Revision as of 00:27, 14 April 2009
Line 23:		Line 23:

	Calculate a transformation from two input fiducial lists. This transformation can then be applied to a volume using the Resample Scalar/Vector/DWI Volume module.		Calculate a transformation from two input fiducial lists. This transformation can then be applied to a volume using the Resample Scalar/Vector/DWI Volume module.
		+
		+	Note: renamed from RealignVolume.

	== Usage ==		== Usage ==

@@ Line 71: / Line 71: @@
 Doxygen documentation:
-*[]
+* [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPrincipalAxesAlign.html vtkPrincipalAxesAlign].
 == More Information ==

@@ Line 1: / Line 1: @@
 [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===ACPC Transform===

@@ Line 1: / Line 1: @@
   [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
-===Realign Volume===
+===ACPC Transform===
-Realign Volume
+ACPC Transform
 {|
-|[[Image:SlicerRealign-3.4.jpg|thumb|280px|GUI]]
+|[[Image:SlicerACPCTransformGUI-3.4.jpg|thumb|280px|GUI]]
 |}
@@ Line 21: / Line 21: @@
 ===Module Description===
-Realigns a volume based on a transformation matrix (if output volume is specified). It can make a transform using a list of fiducials. If pass in a transform matrix and an output volume, but no fiducials, applies the transform to the input volume.
+Calculate a transformation from two input fiducial lists. This transformation can then be applied to a volume using the Resample Scalar/Vector/DWI Volume module.
 == Usage ==
@@ Line 30: / Line 30: @@
 ===Quick Tour of Features and Use===
-* '''Transform panel:''' Calculate a transform from midline and ACPC fiducial lists, or specify a transform.
+* '''Transform panel:''' Calculate a transform from midline and ACPC fiducial lists, and specify an output transform.
 **ACPC Line: pick a fiducial list from the scene that defines the ACPC line.
 **Midline: pick a fiducial list from the scene that defines the midline.
-**Output transform: An output transform - load a calculated transform in this node.
+**Output transform: An output transform - load the calculated transform in this node.
-* '''Reslice panel:''' Apply transform to volume
+* '''Debug panel:''' Set debugging flag
-** Input transform: An input transform, apply this to the input volume and get the output volume
+** Debug: click to see print outs
 == Development ==
@@ Line 47: / Line 42: @@
 ===Dependencies===
-The fiducials and volumes modules are required for this module's use.
+The fiducials module is required for this module's use. The Resample Scalar/Vector/DWI Volume module can be used to apply the transform once it has been calcualted.
 ===Known bugs===

Modules:RealignVolume-Documentation-3.4 - Revision history

Nicole: /* Source code & documentation */

Nicole: /* Quick Tour of Features and Use */

Nicole: /* Module Description */

Marianna at 19:59, 26 May 2009

Kikinis: /* Quick Tour of Features and Use */

Kikinis: /* Quick Tour of Features and Use */

Nicole: /* Module Description */

Nicole: /* ACPC Transform */

Nicole at 00:21, 14 April 2009

Nicole: New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Realign Volume=== Realign Volume {| |GUI |} == General Information == =...

Nicole: New page: Return to Slicer 3.4 Documentation NOTOC ===Realign Volume=== Realign Volume {| |GUI |} == General Information == =...