Slicer Wiki - User contributions [en]

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2017-03-03T06:23:04Z

Grandwork2: /* Extensions by category */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]


== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]
== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]
* [[Documentation/Nightly/Extensions/DatabaseInteractor|Database Interactor]]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T06:19:41Z

Grandwork2:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ScatteredTransform|ScatteredTransform]] 
Acknowledgments:
G. R. Joldes has been funded by Raine Medical Research Foundation through a Raine Priming Grant. 
Author: G. R. Joldes

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

Creates a BSpline transform from a displacement field defined at scattered points by using the Multi-level BSpline interpolation algorithm.


{{documentation/{{documentation/version}}/module-section|Use Cases}}

1. Create a B-Spline transform based on two sets of fiducials.

2. Create a B-Spline transform based on two sets of points read from files.
These files can contain the initial and deform configurations for a biomechanics-based FEM or mesh-free registration.
The resulting B-Spline transform can be used to warp 3D images, a process which is very time consuming if spatial interpolation is performed using the mesh [1]. This module reduces the image warping time from hours to seconds.
{|
|[[Image:ScatteredTransform_displacementField.png|thumb|340px|Brain shift computed using a biomechanics based brain model and FEM. The deformed high resolution pre-operative image (left) is compared to the intra-operative image (right). The pre-operative image has been warped using the B-Spline obtained by applying ScatteredTransform to the original and deformed mesh nodal positions.]]
|[[Image:ScatteredTransform_mesh.jpg|thumb|200px|A section through the brain computational model used to predict the brain shift, showing the ventricles (green) and tumor (red).]]
|}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
|[[Image:ScatteredTransform_panel.png|thumb|560px|Module UI]]
|[[Image:ScatteredTransform_panelAdvanced.png|thumb|560px|Advanced parameters]]
|}
<UL>
Input points:
<LI>Initial landmarks: Ordered list of fiducials in initial position. Select these from the moving image if the resulting transform is used for image registration.</LI>
<LI>Displaced landmarks: Ordered list of fiducials in displaced position. Select these from the fixed image if the resulting transform is used for image registration.</LI>
Input files:
<LI>File with initial point positions: File with coordinates of points in initial position.</LI>
<LI>File with displaced point positions: File with coordinates of points in displaced position.</LI>
<LI>Ignore first value: Ignores first value in each line of the input files (which may be a node number).</LI>
Output transform:
<LI>Slicer BSpline Transform: Slicer transform node for the generated B-Spline transform. NOTE: Only 3D transforms are handled by 3D Slicer!</LI>
Advanced parameters:
<LI>BSpline Transform file: File where to save the transform. Needed for 1D and 2D transforms, as Slicer does not create a transform node for these transforms.</LI>
<LI>Space dimension: The space dimension (1D, 2D or 3D).</LI>
<LI>For use in: Where is the transform going to be used? If the transform is a 3D transform to be used in Slicer, a coordinate transformation (similar to what Slicer does internally) is applied to the coordinates before the transform is computed.(only 3D transforms can be used in Slicer)</LI>
<LI>Invert transform: Inverts the transform. Always done if transform is for use in Slicer.</LI>
<LI>Use linear approximation: Sets the initial B-Spline grid values using a linear approximation of the displacements.</LI>
<LI>B-Spline Grid Spacing: The distance between the BSpline control grid points.</LI>
<LI>Domain computed from input points: Computes the transform domain as the bounding box of the input points.</LI>
<LI>Minimum domain coordinates: The minimum coordinates of the domain (if not computed from input points).</LI>
<LI>Maximum domain coordinates: The maximum coordinates of the domain (if not computed from input points).</LI>
<LI>Tolerance: Absolute tolerance in approximating the transform at the input points.</LI>
<LI>Minimum grid spacing: Minimum grid spacing during grid refinement.</LI>
<LI>Maximum number of levels: Maximum number of levels of B-Spline refinements.</LI>
Output information:
<LI>Residual: Display residual approximation error on successful completion.</LI>
</UL>

{{documentation/{{documentation/version}}/module-section|References}}

1. Joldes GR, Wittek A, Warfield SK, Miller K (2012) "Performing Brain Image Warping Using the Deformation Field Predicted by a Biomechanical Model." In: Nielsen PMF, Miller K, Wittek A, editors. Computational Biomechanics for Medicine: Deformation and Flow: Springer New York. pp. 89-96.


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Extensions]]

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T06:16:47Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T06:14:57Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T06:13:40Z

Grandwork2:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/ScatteredTransform|ScatteredTransform]] 
Acknowledgments:
G. R. Joldes has been funded by Raine Medical Research Foundation through a Raine Priming Grant. 
Author: G. R. Joldes

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

Creates a BSpline transform from a displacement field defined at scattered points by using the Multi-level BSpline interpolation algorithm.


{{documentation/{{documentation/version}}/module-section|Use Cases}}

1. Create a B-Spline transform based on two sets of fiducials.

2. Create a B-Spline transform based on two sets of points read from files.
These files can contain the initial and deform configurations for a biomechanics-based FEM or mesh-free registration.
The resulting B-Spline transform can be used to warp 3D images, a process which is very time consuming if spatial interpolation is performed using the mesh [1].
{|
|[[Image:ScatteredTransform_displacementField.png|thumb|340px|Brain shift computed using a biomechanics based brain model and FEM. The deformed high resolution pre-operative image (left) is compared to the intra-operative image (right). The pre-operative image has been warped using the B-Spline obtained by applying ScatteredTransform to the original and deformed mesh nodal positions.]]
|[[Image:ScatteredTransform_mesh.jpg|thumb|200px|A section through the brain computational model used to predict the brain shift, showing the ventricles (green) and tumor (red).]]
|}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
|[[Image:ScatteredTransform_panel.png|thumb|560px|Module UI]]
|[[Image:ScatteredTransform_panelAdvanced.png|thumb|560px|Advanced parameters]]
|}
<UL>
Input points:
<LI>Initial landmarks: Ordered list of fiducials in initial position. Select these from the moving image if the resulting transform is used for image registration.</LI>
<LI>Displaced landmarks: Ordered list of fiducials in displaced position. Select these from the fixed image if the resulting transform is used for image registration.</LI>
Input files:
<LI>File with initial point positions: File with coordinates of points in initial position.</LI>
<LI>File with displaced point positions: File with coordinates of points in displaced position.</LI>
<LI>Ignore first value: Ignores first value in each line of the input files (which may be a node number).</LI>
Output transform:
<LI>Slicer BSpline Transform: Slicer transform node for the generated B-Spline transform. NOTE: Only 3D transforms are handled by 3D Slicer!</LI>
Advanced parameters:
<LI>BSpline Transform file: File where to save the transform. Needed for 1D and 2D transforms, as Slicer does not create a transform node for these transforms.</LI>
<LI>Space dimension: The space dimension (1D, 2D or 3D).</LI>
<LI>For use in: Where is the transform going to be used? If the transform is a 3D transform to be used in Slicer, a coordinate transformation (similar to what Slicer does internally) is applied to the coordinates before the transform is computed.(only 3D transforms can be used in Slicer)</LI>
<LI>Invert transform: Inverts the transform. Always done if transform is for use in Slicer.</LI>
<LI>Use linear approximation: Sets the initial B-Spline grid values using a linear approximation of the displacements.</LI>
<LI>B-Spline Grid Spacing: The distance between the BSpline control grid points.</LI>
<LI>Domain computed from input points: Computes the transform domain as the bounding box of the input points.</LI>
<LI>Minimum domain coordinates: The minimum coordinates of the domain (if not computed from input points).</LI>
<LI>Maximum domain coordinates: The maximum coordinates of the domain (if not computed from input points).</LI>
<LI>Tolerance: Absolute tolerance in approximating the transform at the input points.</LI>
<LI>Minimum grid spacing: Minimum grid spacing during grid refinement.</LI>
<LI>Maximum number of levels: Maximum number of levels of B-Spline refinements.</LI>
Output information:
<LI>Residual: Display residual approximation error on successful completion.</LI>
</UL>

{{documentation/{{documentation/version}}/module-section|References}}

1. Joldes GR, Wittek A, Warfield SK, Miller K (2012) "Performing Brain Image Warping Using the Deformation Field Predicted by a Biomechanical Model." In: Nielsen PMF, Miller K, Wittek A, editors. Computational Biomechanics for Medicine: Deformation and Flow: Springer New York. pp. 89-96.


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T05:15:28Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:58:50Z

Grandwork2:

File:ScatteredTransform panelAdvanced.png

2017-03-03T04:57:36Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:57:07Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:56:28Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:55:35Z

Grandwork2:

File:ScatteredTransform panel.png

2017-03-03T04:55:02Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:54:19Z

Grandwork2:

File:ScatteredTransform mesh.jpg

2017-03-03T04:45:46Z

Grandwork2: Grandwork2 uploaded a new version of File:ScatteredTransform mesh.jpg

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:43:12Z

Grandwork2:

File:ScatteredTransform mesh.jpg

2017-03-03T04:41:19Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:40:06Z

Grandwork2:

File:ScatteredTransform displacementField.png

2017-03-03T04:36:17Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:35:02Z

Grandwork2:

Documentation/Nightly/Extensions/ScatteredTransform

2017-03-03T04:32:32Z

Grandwork2: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."