Slicer3:DTMRI - Revision history

Alexy at 16:11, 12 August 2008

2008-08-12T16:11:26Z

Alexy at 20:00, 22 May 2008

2008-05-22T20:00:54Z

Marianna: /* Notes on general diffusion framework (ODF/2 tensor) support */

2008-05-19T18:11:01Z

Notes on general diffusion framework (ODF/2 tensor) support

Marianna: 1 revision

2008-05-15T17:59:24Z

1 revision

Alexy at 19:31, 1 April 2008

2008-04-01T19:31:11Z

New page

<flash>file=dti_glyphs.swf|width=800|height=600|quality=best|loop=true|play=true</flash>

= Goals =

* Development of the core infrastructure for DT-MRI processing and visualization.
* Development of the core infrastructure for fiber tracks processing and visualization.
* Integration of new and existing methods and algorithms for DT-MRI processing using the provided infrastructure.
* Porting of the current DT-MRI capabilities existing in Slicer 2.x

= Core infrastructure for DT-MRI processing and visualization, fiber processing and visualization =
* MRML nodes for data representation, storage, and display. MRML nodes store data and the state of Slicer modules.
* Data display and processing logic components.
* GUI components.

== Data Representation ==
MRML nodes for different data representations involved in DTI analysis:
* Diffusion Weighted Images, represented as vtkImageData: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionWeightedVolumeNode.h?view=log vtkMRMLDiffusionWeightedVolumeNode].
* Diffusion Tensor Images, represented as vtkImageData: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionTensorVolumeNode.h?view=log vtkMRMLDiffusionTensorVolumeNode].
* Fiber Bundles, represented as vtkPolyData: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleNode.h?view=log vtkMRMLFiberBundleNode].

==Data Storage and I/O ==
* DWI and DTI I/O: NRRD is the format supported by Slicer3 for storing DWI and DTI images.
** NNRD reader/writer: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkTeem/vtkNRRDReader.h?view=log vtkNRRDReader] and [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkTeem/vtkNRRDWriter.h?view=log vtkNRRDWriter].
** MRML Storage node: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLNRRDStorageNode.h?view=log vtkMRMLNRRDStorageNode].
* Fiber I/O: vtkPolyData has been the format adopted for the description of fibers
** MRML Storage node: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleStorageNode.h?view=log vtkMRMLFiberBundleStorageNode]

== Visualization/Display ==
MRML nodes for DWI, DTI, Tractography data visualization:
* Diffusion Weighted Images: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionWeightedVolumeDisplayNode.h?view=log vtkMRMLDiffusionWeightedVolumeDisplayNode].
* Diffusion Tensor Images: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionTensorVolumeDisplayNode.h?view=log vtkMRMLDiffusionTensorVolumeDisplayNode], and [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionTensorDisplayPropertiesNode.h?view=log vtkMRMLDiffusionTensorDisplayPropertiesNode].
* Fiber Bundles: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleDisplayNode.h?view=log vtkMRMLFiberBundleDisplayNode], [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleLineDisplayNode.h?view=log vtkMRMLFiberBundleLineDisplayNode], [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleTubeDisplayNode.h?view=log vtkMRMLFiberBundleTubeDisplayNode], and [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleGlyphDisplayNode.h?view=log vtkMRMLFiberBundleGlyphDisplayNode].

== Displaying Logic ==
* Visualization pipelines for DTI, DWI volumes, and fiber bundles are incorporated into the corresponding display nodes.
* DWI volumes are displayed as separate components.
* DTI volumes are displayed as computed scalar properties (such as FA, Linear Measure, Color Orientation, etc.)
* Fiber bundles are displayed as lines, tubes, and glyphs with their own properties and colors

== Diffusion Processing Toolbox ==
[http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkTeem vtkTeem-library] provides tools for:
* Tensor estimation
* Computation of scalar measurements from tensor fields
*Fast rendering of tensor fields using glyphs: line, box, ellipsoid
*Fiber Tracking using integration techniques
* Multiple ROI seeding and logic interconnections between ROIs

= DT-MRI processing and visualization Modules =

== Volumes Module ==
* Volume module is capable of loading and saving DWI and DTI images in the NRRD file format
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"|

* Volume Module is capable of displaying DWI image components and DTI images as derived scalar properties
| style="background: #ebeced"|[[Image:Dti-color.jpg|center|300px|Colore DTI]]
| style="background: #ebeced"|DTI volume slices colored by orientaion.
|}
<br>

* Volume Display GUI provides different display controls based on the type of the volume
* Built-in Slicer3 module

== Tractography Module ==
* Tractography Display-Load-Save module is capable of loading and saving fiber tracts in the vtkPolyData file formats.

{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"|

* Tractography Display-Load-Save module is capable of displaying fiber tracts as lines, tubes, and glyphs, all colored by different scalar properties

| style="background: #ebeced"|[[Image:Line-glyph-tracts.jpg|center|300px|fiber bundles]]
| style="background: #ebeced"|Fiber bundles displayed as lines and glyph ellipsoids.
|}
<br>

* Slicer Models module also can be used to load, save, display tracts as lines, but it does not provide tensor data display

* Built-in Slicer3 module

== Tensor Estimation from DWI Module ==
* CLI Module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionTensorEstimation.xml?view=log DiffusionTensorEstimation].
Teem currently provides a clean interface to do this estimation in a voxel by voxel fashion. Collaboration with Gordon Kindlmann for a vtk filter implementation that encapsulates the estimation process ([http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkTeem/vtkTeemEstimateDiffusionTensor.h?view=log vtkTeemEstimateDiffusionTensor]).

== Diffusion Tensor Scalar Measurements Module ==
* CLI Module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionTensorMathematics.xml?view=log DiffusionTensorMathematics].
* Implemented in vtkTeem library [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkTeem/vtkDiffusionTensorMathematics.h?view=log vtkDiffusionTensorMathematics].

== Rician LMMSE Filter Module ==
* CLI Module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/dwiNoiseFilter/dwiNoiseFilter.xml?view=log dwiNoiseFilter].

*Filters a set of diffusion weighted images in the mean squared error sense using a Rician noise model. The noise parameter is automatically estimated.
*Contributed by Santiago Aja Fernandez and Marc Niethammer
*Additional [[Slicer3:Module:Rician_Noise_Removal | Rician filtering module]] provided by Sylvain Gouttard et al

== Tractography ROI Seeding Module ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"|

* Creates fibers passing through a specified ROI
* CLI Module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Tractography/Seeding/Seeding.xml?view=log ROI Seeding].
| style="background: #ebeced"|[[Image:roi_tract.jpg|center|300px|Roi seeding]]
| style="background: #ebeced"|Seeding from ROI example.
|}
<br>

== Tractography Fiducial Seeding Module ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"|

* Creates fibers passing through the specified fiducial points interactively
* Built-in Slicer3 module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Tractography/FiducialSeeding/vtkSlicerTractographyFiducialSeedingGUI.cxx?view=log vtkSlicerTractographyFiducialSeedingGUI.cxx]
| style="background: #ebeced"|[[Image:Fiducial-seeding.jpg|center|300px|fiducial seeding]]
| style="background: #ebeced"|Seeding from fiducials example.
|}
<br>

== Tractography ROI Select Module ==
* Select tracts passing or not passing through ROIs
* CLI Module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Tractography/Editor/ROISelect.xml?view=log ROI Select].

== Stochastic Tractography Filter ==
* CLI Module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/StochasticTractographyFilter/StochasticTractographyFilter.xml?view=log StochasticTractographyFilter].
* Generates a map of connectivity probabilities from a DWI volume.).
* Contributed by Tri Ngo (tringo@gmail.com)

== ROI Tract Filter ==
* CLI Module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/StochasticTractographyFilter/ROITractFilter.xml?view=log ROITractFilter].
* Creates a new tract container containing only tracts which pass through the selected ROI's.
* Contributed by Tri Ngo (tringo@gmail.com)

== Generate Connectivity Map ==
* CLI Module: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/StochasticTractographyFilter/GenerateConnectivityMap.xml?view=log GenerateConnectivityMap].
* Generates a volume where the value of each voxel is the number of fibers which pass through that voxel divided by the total number of sampled fibers. This value can been interpreted as the probability that a particular voxel is connected to the seed ROI by a fiber tract.
* Contributed by Tri Ngo (tringo@gmail.com)

:

= Future development plans =
* Fiber editing: enviroment for manually editing individual fibers/bundles, reassigning of fibers to bundles.
* Fiber Bundle Clustering (Core 1).
* Render glyphs in the 2D slice windows.
* Statistics along fiber tracts (Core 1).
* Quantitative measurement
** Tract-based
** Region of interest-based
* fMRI seeding
* Surgical planning
* DT-MRI segmentation/atlas creation: enviroment for segmentation of DT-MRI fields
* DT-MRI registration: enviroment for registration of DT-MRI fields (possibly via DWI registration -- work done at GE and presented in MICCAI '06).
* Tensor estimation using different methods, namely:
** Least Squares
** Weighted Least Squares
** Non-linear methods
** Maximum Likelihood approach

= Development Screenshots =

[[Image:DtiDevel1.jpg]]

[[Image:DtiDevel2.jpg]]

= Notes on general diffusion framework (ODF/2 tensor) support =
http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI:GeneralDiffusionFramework

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	= Goals =		= Goals =

← Older revision		Revision as of 18:11, 19 May 2008
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−	= Notes on general diffusion framework (ODF/2 tensor) support =	+	[[Slicer3:DTMRI:GeneralDiffusionFramework\|Notes on general diffusion framework (ODF/2 tensor) support]]
−	~~http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI:GeneralDiffusionFramework~~

@@ Line 1: / Line 1: @@
 = Goals =
@@ Line 28: / Line 27: @@
 MRML nodes for DWI, DTI, Tractography data visualization:
 * Diffusion Weighted Images: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionWeightedVolumeDisplayNode.h?view=log vtkMRMLDiffusionWeightedVolumeDisplayNode].
-* Diffusion Tensor Images:  [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionTensorVolumeDisplayNode.h?view=log vtkMRMLDiffusionTensorVolumeDisplayNode], and [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionTensorDisplayPropertiesNode.h?view=log vtkMRMLDiffusionTensorDisplayPropertiesNode].
+* Diffusion Tensor Images:  [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionTensorVolumeDisplayNode.h?view=log vtkMRMLDiffusionTensorVolumeDisplayNode], and [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionTensorDisplayPropertiesNode.h?view=log vtkMRMLDiffusionTensorDisplayPropertiesNode]. There is also [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLDiffusionTensorVolumeSliceDisplayNode.h?view=log vtkMRMLDiffusionTensorVolumeSliceDisplayNode] for displaying tensor glyphs in the 2D slice windows.
 * Fiber Bundles: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleDisplayNode.h?view=log vtkMRMLFiberBundleDisplayNode], [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleLineDisplayNode.h?view=log vtkMRMLFiberBundleLineDisplayNode], [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleTubeDisplayNode.h?view=log vtkMRMLFiberBundleTubeDisplayNode], and [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/MRML/vtkMRMLFiberBundleGlyphDisplayNode.h?view=log vtkMRMLFiberBundleGlyphDisplayNode].
@@ Line 34: / Line 33: @@
 * Visualization pipelines for DTI, DWI volumes, and fiber bundles are incorporated into the corresponding display nodes.
 * DWI volumes are displayed as separate components.
-* DTI volumes are displayed as computed scalar properties (such as FA, Linear Measure, Color Orientation, etc.)
+* DTI volumes are displayed as computed scalar properties (such as FA, Linear Measure, Color Orientation, etc.). Tensor glyphs are displayed in the 2D slice views as well as in the 3D view.
 * Fiber bundles are displayed as lines, tubes, and glyphs with their own properties and colors
@@ Line 54: / Line 53: @@
 * Volume Module is capable of displaying DWI image components and DTI images as derived scalar properties
-| style="background: #ebeced"|[[Image:Dti-color.jpg|center|300px|Colore DTI]]
+| style="background: #ebeced"|[[Image:Dti-color.jpg|center|300px|Colored DTI]]
-| style="background: #ebeced"|DTI volume slices colored by orientaion.
+| style="background: #ebeced"|DTI volume slices colored by orientation.
 |}
 <br>
 * Volume Display GUI provides different display controls based on the type of the volume
@@ Line 146: / Line 153: @@
 * Fiber editing: enviroment for manually editing individual fibers/bundles, reassigning of fibers to bundles.
 * Fiber Bundle Clustering (Core 1).
 * Statistics along fiber tracts (Core 1).
 * Quantitative measurement

← Older revision	Revision as of 17:59, 15 May 2008
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