Projects:RegistrationLibrary:RegLib A01 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:18Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* Registration Library : Using Deformation Field Images */

2011-04-07T16:27:04Z

Registration Library : Using Deformation Field Images

Meier at 16:25, 7 April 2011

2011-04-07T16:25:46Z

Meier: /* Registration Library : Using Grid Images */

2011-03-30T13:42:35Z

Registration Library : Using Grid Images

Meier at 21:55, 25 March 2011

2011-03-25T21:55:06Z

Meier at 21:54, 25 March 2011

2011-03-25T21:54:51Z

Meier at 21:54, 25 March 2011

2011-03-25T21:54:36Z

Meier at 21:53, 25 March 2011

2011-03-25T21:53:27Z

Meier at 21:46, 25 March 2011

2011-03-25T21:46:01Z

Meier at 21:40, 25 March 2011

2011-03-25T21:40:15Z

@@ Line 17: / Line 17: @@
 .Deform
-##go to [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''ResampleScalarVectorDWIVolume''] module (Filtering menu)
+##go to [https://www.slicer.org/wiki/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''ResampleScalarVectorDWIVolume''] module (Filtering menu)
 ##select grid image as input, your target as reference
 ##select "create new volume" from output volume and rename to "grid_deformed" or similar

@@ Line 32: / Line 32: @@
 = Registration Library : Using Deformation Field Images =
-.Build/convert
+'''1.Build/convert'''
 *There is commandline functionality in Slicer to convert a  BSpline ITK transform  file (.tfm) into a deformation field volume. To execute, type (exchange ''/Applications/Slicer3.6.3'' with the path of your Slicer installation):
    /Applications/Slicer3.6.3/Slicer3 --launch /Applications/Slicer3.6.3/lib/Slicer3/Plugins/BSplineToDeformationField --tfm InputBSpline.tfm
@@ Line 46: / Line 46: @@
 ----
-. Visualize
+<br>
 [[Image: RegLib_DefFieldColor.png| Example of 4D displacement field rendered in Slicer. displacements in the  x-, y- and z-direction in red, green and blue color, respectively.]
 *if loaded properly, the 4D volume is rendered in RGB color, with displacements in the  x-, y- and z-direction in red, green and blue color, respectively. RGB mixtures of yellow, cyan and magenta then indicate displacements of similar magnitude in both xy, yz and xz directions, respectively etc.
 *Note that negative displacements (as of v.3.6) are clipped and will all show as black.

← Older revision		Revision as of 16:25, 7 April 2011
Line 30:		Line 30:
	*the grid images have different values for the axial, sagittal and coronal planes to help you distinguish. An orthogonal plane being bent down into an adjacent slice shows up as rings or blobs. You can adjust the window & level values to match the particular plane and thus fade out the distracting other ones. Or you can threshold the grid image to generate labelmaps that contain only 1 set of planes for easier viewing.		*the grid images have different values for the axial, sagittal and coronal planes to help you distinguish. An orthogonal plane being bent down into an adjacent slice shows up as rings or blobs. You can adjust the window & level values to match the particular plane and thus fade out the distracting other ones. Or you can threshold the grid image to generate labelmaps that contain only 1 set of planes for easier viewing.
	*the alternative 4D grid image contain each plane as a separate channel and are loaded as vector images that will show up in color (see figure above) that help distinguish the different directions.		*the alternative 4D grid image contain each plane as a separate channel and are loaded as vector images that will show up in color (see figure above) that help distinguish the different directions.
		+
		+	= Registration Library : Using Deformation Field Images =
		+	1.Build/convert
		+	*There is commandline functionality in Slicer to convert a BSpline ITK transform file (.tfm) into a deformation field volume. To execute, type (exchange ''/Applications/Slicer3.6.3'' with the path of your Slicer installation):
		+	/Applications/Slicer3.6.3/Slicer3 --launch /Applications/Slicer3.6.3/lib/Slicer3/Plugins/BSplineToDeformationField --tfm InputBSpline.tfm
		+	--refImage ReferenceImage.nrrd --defImage Output_DeformationField.nrrd
		+	*for more details try:
		+	/Applications/Slicer3.6.3/Slicer3 --launch /Applications/Slicer3.6.3/lib/Slicer3/Plugins/BSplineToDeformationField --help
		+	*this creates a 4-dimensional (4D) image that contains the displacements of each image point in the x-, y- and z-direction as 3 separate volumes. You can load this image into Slicer and visualize the distribution and values of the deformation field. If loaded as a NRRD "list" image (as of v.3.6.3 there was a problem with loading 4D "vector" NRRD images, so if you have trouble loading, try changing the following line in the NRRD header, e.g. with a text editor:
		+	sizes: 3 256 256 124
		+	space directions: none (0.9375,0,0) (0,0,-0.9375) (0,-1.5,0)
		+	kinds: vector domain domain domain
		+	change the word "vector" to the word "list" and then save and retry loading:
		+	kinds: list domain domain domain
		+
		+	----
		+	2. Visualize
		+	[[Image: RegLib_DefFieldColor.png\| Example of 4D displacement field rendered in Slicer. displacements in the x-, y- and z-direction in red, green and blue color, respectively.]
		+	*if loaded properly, the 4D volume is rendered in RGB color, with displacements in the x-, y- and z-direction in red, green and blue color, respectively. RGB mixtures of yellow, cyan and magenta then indicate displacements of similar magnitude in both xy, yz and xz directions, respectively etc.
		+	*Note that negative displacements (as of v.3.6) are clipped and will all show as black.

@@ Line 6: / Line 6: @@
 ##Load grid image with the desired number of grid points (e.g. ~50% higher than the DOF of the BSpline applied)
 ##Place your target image in background and grid image in foreground
-##Go to ''Volumes'' module / Info tab
+##Go to ''Volumes'' module / ''Info'' tab
 ##select first target and then grid image from ''Active Volume'' menu; for both click on ''Center Volume'' button to match image centers
 ##set fading slider to halfway, so you can see both target and grid image

@@ Line 1: / Line 1: @@
    [[Projects:RegistrationDocumentation|Back to Registration main page]]
    [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]]
-   [[Projects:RegistrationDocumentation:UseCaseInventory:Auxiliary|back to Auxiliary Data collection]]
+   [[Projects:RegistrationDocumentation:UseCaseInventory:Auxiliary|Back to Auxiliary Data collection]]
 = Registration Library : Using Grid Images =
 .Match physical dimensions & position

@@ Line 1: / Line 1: @@
-[[Projects:RegistrationDocumentation|Back to Registration main page]] <br>
+  [[Projects:RegistrationDocumentation|Back to Registration main page]] <br>
-[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
+  [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
 = Registration Library : Using Grid Images =
 .Match physical dimensions & position

← Older revision		Revision as of 21:53, 25 March 2011
Line 1:		Line 1:
		+	[[Projects:RegistrationDocumentation\|Back to Registration main page]] <br>
		+	[[Projects:RegistrationDocumentation:UseCaseInventory\|Back to Registration Use-case Inventory]] <br>
	= Registration Library : Using Grid Images =		= Registration Library : Using Grid Images =
	1.Match physical dimensions & position		1.Match physical dimensions & position

@@ Line 18: / Line 18: @@
 ##select "create new volume" from output volume and rename to "grid_deformed" or similar
 ##under ''Transform Node'' select the nonrigid (BSpline) transformation
 ##leave rest at defaults; click ''Apply''.
 [[Image:BWGrid_overlay_deformed.png|200px|center]]
 [[Image:ColorGrid_overlay_deformed.png|500px|center]]