Slicer3:DTMRI:GeneralDiffusionFramework - Revision history

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

2017-07-10T18:07:30Z

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

Marianna: Protected "Slicer3:DTMRI:GeneralDiffusionFramework" [edit=sysop:move=sysop]

2008-05-22T16:09:13Z

Protected "Slicer3:DTMRI:GeneralDiffusionFramework" [edit=sysop:move=sysop]

Marianna: Unprotected "Slicer3:DTMRI:GeneralDiffusionFramework"

2008-05-19T18:15:19Z

Unprotected "Slicer3:DTMRI:GeneralDiffusionFramework"

Marianna: Replacing page with ''''Note:''' We are migrating this content to the slicer.org domain - The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI:Gener...'

2008-05-19T18:15:09Z

Replacing page with '<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI:Gener...'

Demian at 22:00, 3 July 2007

2007-07-03T22:00:56Z

Raul at 14:42, 29 June 2007

2007-06-29T14:42:13Z

Raul at 03:53, 29 June 2007

2007-06-29T03:53:52Z

Raul: /* MRML Redesign */

2007-06-29T03:51:51Z

MRML Redesign

Raul at 03:49, 29 June 2007

2007-06-29T03:49:40Z

Raul at 03:44, 29 June 2007

2007-06-29T03:44:46Z

← Older revision		Revision as of 18:07, 10 July 2017
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−	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [~~http~~://www.slicer.org/~~slicerWiki/index.php~~/Slicer3:DTMRI:GeneralDiffusionFramework here]</font></big>a	+	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:DTMRI:GeneralDiffusionFramework here]</font></big>a

← Older revision		Revision as of 18:15, 19 May 2008
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−	~~Demian Wassermann, Raul San Jose, Lauren O~~'~~Donnell~~	+	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI:GeneralDiffusionFramework here]</font></big>a
−
−	~~The goal is to define the basic design and data structure specifications~~ to ~~support general diffusion models in~~ the ~~Slicer~~. General diffusion models refer to new ways of approaching diffusion imaging in the brain like the two tensor diffusion model [Sharon et al] and higher order spherical harmonics tensors [Decautox et al]
−
−	~~[[Image:DiffusionTODOList.jpg\|thumb\|300px\|left\|Initial development draft. Authors: Lauren, Demian, Raul]]~~
−
−
−	= ~~MRML Redesign =~~
−	The ~~generalization to general diffusion data models comes through a superclass that generalizes the original behaviour of vtkDiffusionTensorVolumeNode as described in the original design (~~[http://~~wiki~~.~~na-mic~~.org/~~Wiki~~/index.php/Slicer3:DTMRI] ~~and [http:~~//~~wiki.na-mic.org/Wiki/index.php/AHM_2007:Slicer3_Developer_Feedback#DTI])~~
−
−	~~[[Image:DiffusionImagingMRML.png\|thumb\|200px\|right\|MRML class diagram for diffusion imaging]]~~
−	~~This new class, vtkDiffusionImageVolumeNode, is a child of vtkMRMLTensorVolumeNode and abstracts the behaviour related to diffusion imaging. The main members of vtkDiffusionImageVolumeNode are:~~
−	* ID to the Diffusion Weighted Volume Node
−	* ID to the Baseline Image Volume Node
−	* ID to the Mask Image Volume Node.
−
−	As part of this redesign, the handling of IDs to the display node and storage node have been revamped to keep consistency. vtkMRMLVolumeNode is the class that keeps the DisplayNodeID and the subclassess take care of downcasting the node corresponding to that ID to make sure that the DisplayNode is the right one corresponding to the specific VolumeNode
−
−	~~The VolumeDisplayNode hierarchy has been refactored to better support display nodes that rely on glyphs as~~ a display option. A new abstract class, vtkMRMLGlyphedDisplayNode, handles the different glyph properties. This class serves as parent class for vtkMRMLDiffusionTensorVolumeDisplayNode and vtkMRMLVectorVolumeDisplayNode.
−
−	~~= Specifications to encapsulate General Diffusion Data into vtkImageData =~~
−	~~Slicer 3 intrinsic image data representation is a vtkImageData class. This implies important limitations, namely~~
−	* The dimensionality is strictly 3D: the data is supposed to be arranged in a 3D grid and there is not possibilities for further extensions
−	* A specific set of point data attributes are allowed: Scalars, Normals, Vectors and Tensors.
−
−	There is not much we can do about dimensionality. However we can define a convention to be able to store point data attributes beyond the previously commented using new vtkDataArrays in the vtkFieldData.
−	~~Then, our work now is to define a clear convention that allow us to make an unequivocal connection between the vtkDataArray an the representation associated to it.~~
−
−	Each vtkDataArray will be a new array with a predefined name in the vtkFieldData associated to the PointData (or CellData for that sake) of the vtkImageData. The DataArray will be a multicomponent DataArray. The components will have a predefined semantic meaning to encompass different data complexities.
−	~~{\|class="wikitable" style="text-align:center" style="width:75%; height:200px" border="1"~~
−	~~\|+ DataArray name convention~~
−	\|-
−	~~\|'Array Name' \|\| ' Number of Component' \|\| 'Multicomponent Semantic'~~
−	\|-
−	~~\| Scalar~~
−	~~\| 1~~
−	~~\| A standard scalar image~~
−	\|-
−	~~\| RGB~~
−	~~\| 3~~
−	~~\| Color Image. First component is R channel, Second component is the G channel and Thrid component is the B channel~~
−	\|-
−	~~\| Symmetric-Tensor~~
−	~~\| 6~~
−	~~\| A symmetric tensor. The data is arranged as follows: [dxx dxy dxz dyy dyz dzz]~~
−	\|}
−
−	~~= Design to dispaly glyphs =~~
−	~~[[Image:GlyphLogic.png\|thumb\|200px\|right\|Glyph pipeline logic]]~~
−	Glyphs is a common way to represent complex diffusion data that encodes information about the multiple orientation nature of the water diffusion in the brain. Glyphs are polygonal elements that can be associated to every location in the image grid.

← Older revision		Revision as of 22:00, 3 July 2007
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−	Demian ~~Wasserman~~, Raul San Jose, Lauren O'Donnell	+	Demian Wassermann, Raul San Jose, Lauren O'Donnell

	The goal is to define the basic design and data structure specifications to support general diffusion models in the Slicer. General diffusion models refer to new ways of approaching diffusion imaging in the brain like the two tensor diffusion model [Sharon et al] and higher order spherical harmonics tensors [Decautox et al]		The goal is to define the basic design and data structure specifications to support general diffusion models in the Slicer. General diffusion models refer to new ways of approaching diffusion imaging in the brain like the two tensor diffusion model [Sharon et al] and higher order spherical harmonics tensors [Decautox et al]

← Older revision		Revision as of 14:42, 29 June 2007
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	\| A symmetric tensor. The data is arranged as follows: [dxx dxy dxz dyy dyz dzz]		\| A symmetric tensor. The data is arranged as follows: [dxx dxy dxz dyy dyz dzz]
	\|}		\|}
		+
		+	= Design to dispaly glyphs =
		+	[[Image:GlyphLogic.png\|thumb\|200px\|right\|Glyph pipeline logic]]
		+	Glyphs is a common way to represent complex diffusion data that encodes information about the multiple orientation nature of the water diffusion in the brain. Glyphs are polygonal elements that can be associated to every location in the image grid.

@@ Line 1: / Line 1: @@
 Demian Wasserman, Raul San Jose, Lauren O'Donnell
-The goal is the define the basic design and data structure specifications to support general diffusion models in the slicer like two tensor diffusion models and higher order spherical harmonics tensors.
+The goal is to define the basic design and data structure specifications to support general diffusion models in the Slicer. General diffusion models refer to new ways of approaching diffusion imaging in the brain like the two tensor diffusion model [Sharon et al] and higher order spherical harmonics tensors [Decautox et al]
 [[Image:DiffusionTODOList.jpg|thumb|300px|left|Initial development draft. Authors: Lauren, Demian, Raul]]

← Older revision	Revision as of 16:09, 22 May 2008
(No difference)

@@ Line 8: / Line 8: @@
 = MRML Redesign =
 The generalization to general diffusion data models comes through a superclass that generalizes the original behaviour of vtkDiffusionTensorVolumeNode as described in the original design ([http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI] and [http://wiki.na-mic.org/Wiki/index.php/AHM_2007:Slicer3_Developer_Feedback#DTI])
 This new class, vtkDiffusionImageVolumeNode, is a child of vtkMRMLTensorVolumeNode and abstracts the behaviour related to diffusion imaging. The main members of vtkDiffusionImageVolumeNode are:
 * ID to the Diffusion Weighted Volume Node
@@ Line 16: / Line 18: @@
 The VolumeDisplayNode hierarchy has been refactored to better support display nodes that rely on glyphs as a display option. A new abstract class, vtkMRMLGlyphedDisplayNode, handles the different glyph properties. This class serves as parent class for vtkMRMLDiffusionTensorVolumeDisplayNode and vtkMRMLVectorVolumeDisplayNode.
 = Specifications to encapsulate General Diffusion Data into vtkImageData =

← Older revision		Revision as of 03:49, 29 June 2007
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	The VolumeDisplayNode hierarchy has been refactored to better support display nodes that rely on glyphs as a display option. A new abstract class, vtkMRMLGlyphedDisplayNode, handles the different glyph properties. This class serves as parent class for vtkMRMLDiffusionTensorVolumeDisplayNode and vtkMRMLVectorVolumeDisplayNode.		The VolumeDisplayNode hierarchy has been refactored to better support display nodes that rely on glyphs as a display option. A new abstract class, vtkMRMLGlyphedDisplayNode, handles the different glyph properties. This class serves as parent class for vtkMRMLDiffusionTensorVolumeDisplayNode and vtkMRMLVectorVolumeDisplayNode.

−	[[Image:DiffusionImagingMRML.~~svg~~\|thumb\|300px\|left\|MRML class diagram for diffusion imaging. Authors: Lauren, Demian, Raul]]	+	[[Image:DiffusionImagingMRML.png\|thumb\|300px\|left\|MRML class diagram for diffusion imaging. Authors: Lauren, Demian, Raul]]

← Older revision		Revision as of 03:44, 29 June 2007
Line 16:		Line 16:

	The VolumeDisplayNode hierarchy has been refactored to better support display nodes that rely on glyphs as a display option. A new abstract class, vtkMRMLGlyphedDisplayNode, handles the different glyph properties. This class serves as parent class for vtkMRMLDiffusionTensorVolumeDisplayNode and vtkMRMLVectorVolumeDisplayNode.		The VolumeDisplayNode hierarchy has been refactored to better support display nodes that rely on glyphs as a display option. A new abstract class, vtkMRMLGlyphedDisplayNode, handles the different glyph properties. This class serves as parent class for vtkMRMLDiffusionTensorVolumeDisplayNode and vtkMRMLVectorVolumeDisplayNode.
		+
		+	[[Image:DiffusionImagingMRML.svg\|thumb\|300px\|left\|MRML class diagram for diffusion imaging. Authors: Lauren, Demian, Raul]]
		+

	= Specifications to encapsulate General Diffusion Data into vtkImageData =		= Specifications to encapsulate General Diffusion Data into vtkImageData =