Documentation/Labs/Slicer Visualization module - Revision history

JChris.FillionR at 21:33, 21 August 2019

2019-08-21T21:33:42Z

2019-08-21T21:31:43Z

2019-08-21T14:34:39Z

2019-08-21T14:34:12Z

2019-08-15T15:46:17Z

2019-08-15T14:30:30Z

2019-08-15T14:30:18Z

2019-08-15T13:58:25Z

2019-08-14T20:53:09Z

2019-08-14T20:49:41Z

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-<big>'''<big>Overview</big>'''</big>
+{{TOC right}}
 This is a page introducing the Slicer Connectome Visualization project for adding new visualization extensions into 3DSlicer.
@@ Line 11: / Line 13: @@
 Each connection is defined by its strength (visually it represents the thickness of the connection between two nodes) and this value is found in the matrices (edge files).
-<big>'''<big>Goal</big>'''</big><br />
+==Goal==
 Implement two different modules into Slicer:
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-<big>'''<big>Details</big>'''</big><br />
+==Details==
 The user will have the choice between the 2D and the 3D visualization module.

← Older revision		Revision as of 14:34, 21 August 2019
Line 1:		Line 1:
−	~~[[Documentation/Labs#Extension]]~~<big>'''<big>Overview</big>'''</big>	+	<big>'''<big>Overview</big>'''</big>

	This is a page introducing the Slicer Connectome Visualization project for adding new visualization extensions into 3DSlicer.		This is a page introducing the Slicer Connectome Visualization project for adding new visualization extensions into 3DSlicer.

← Older revision		Revision as of 14:34, 21 August 2019
Line 1:		Line 1:
−	<big>'''<big>Overview</big>'''</big>	+	[[Documentation/Labs#Extension]]<big>'''<big>Overview</big>'''</big>

	This is a page introducing the Slicer Connectome Visualization project for adding new visualization extensions into 3DSlicer.		This is a page introducing the Slicer Connectome Visualization project for adding new visualization extensions into 3DSlicer.

@@ Line 36: / Line 36: @@
 * Implement a 3D visualization tool that is faster than BrainNetViewer and CIVILITY (based on Matlab).
 * For each node we could sum the connections and generate 2 files. One disk file (how do I save them on a disk?) and one data structure file (how do I store data in memory?)
-* The 3D visualization module should offer the possibility to rotate around the connectome and zoom for more precision.
+* The 3D visualization module should offer the possibility to rotate around the connectome, add data cursor and zoom for more precision.
 * Impose a minimum strength on the connectome connections

@@ Line 4: / Line 4: @@
 '''''What do we want to visualize?''' <br />''
-Visualizations are based on symmetric and normalized matrices (AAL or Destrieux)) with connectivity values that may be obtained from diffusion connectivity or resting state connectivity studies (region-to-region values).<br />
+Visualizations are based on symmetric and normalized matrices (AAL or Destrieux) with connectivity values that may be obtained from diffusion connectivity or resting state connectivity studies (region-to-region values).<br />
 The matrices represent a graph, where the edges are the connectivity values and the nodes are brain regions.

← Older revision	Revision as of 21:31, 21 August 2019
(No difference)

@@ Line 41: / Line 41: @@
 '''''Features 2D module:'''''
 * Use as much Python as we can (VTK) otherwise C++
-* Implement a 2D spherical graph visualization (may apply Hierarchical Edge Bundling), using matrices
+* Implement a 2D spherical graph visualization (may apply Hierarchical Edge Bundling), using matrices<br />
 * Custom graph view representing the associated matrix and define the connection strength by the opacity of the color <br />

@@ Line 27: / Line 27: @@
 *Volume file
 *Node file (and maybe add and option for the user to be able to edit the node characterization ;for example with labels)
-*Edge file
+*Edge file (could be binary, but we will not impose any constraints on the range)
 The Node file and the Edge file will have to be adaptable formats, that is the reason why we want to use ASCII files.
 The Node file should include information about where the node is located. <br />
 The file extension could either be a Landmark Registration format (existing module in Slicer) or a Jason file (including a node description file (x,y,z coordinates and node color index) and a node magnitude file(with just the size of a node)).
-'''''Features:'''''
+'''''Features 3D module:'''''
 * Python module (using VTK) and maybe C++
 * Implement a 3D visualization tool that is faster than BrainNetViewer and CIVILITY (based on Matlab).
@@ Line 39: / Line 39: @@
 * Impose a minimum strength on the connectome connections
 * Implement a 2D spherical graph visualization (may apply Hierarchical Edge Bundling), using matrices
 * Custom graph view representing the associated matrix and define the connection strength by the opacity of the color <br />
 (possible options: vtkMRMLGraphMarkupNode,vtkSlicerGraphRepresentation3D and associated widget (looking at vtkMRMLMarkupsCurveNode, vtkSlicerCurveRepresentation and vtkSlicerCurveWidget))