Slicer Wiki - User contributions [en]

Documentation/Nightly/Modules/TrackerStabilizer

2015-05-15T21:44:55Z

Lchauvin:

<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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Jayender Jagadeesan, Andras Lasso 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are particularly usefull to track surgical tools, robots, patient motion, etc... . However, data imported in 3D Slicer from these devices are often noisy. To reduce the noise and smoothly control objects, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and uncomfortable to look at. By filtering this raw data, camera motion is smoothed.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
The GUI of the {{documentation/modulename}} module contains 4 elements:
* Input Transform. This is the raw data, usually raw tracker data, represented by a vtkMRMLLinearTransformNode
* Output Transform. This is the filtered transform represented also by a vtkMRMLLinearTransformNode. This node can be created directly from the list
* Filter checkbox. This checkbox turn on/off the filtering
* Smoothing slider. This slider control the smoothing parameter. In the left, smoother, with relatively important delay. In the right, faster (almost no delay), but noisier.
|}
{|
|[[Image:Slicer4-TrackerStabilizer-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
This module is for now only a low-pass filter, but in the futur, several filters would be implemented to let the choice to the user.

Source code: https://github.com/lchauvin/Slicer-TrackerStabilizer


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/TrackerStabilizer

2015-05-15T21:44:33Z

Lchauvin:

<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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Jayender Jagadeesan, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are particularly usefull to track surgical tools, robots, patient motion, etc... . However, data imported in 3D Slicer from these devices are often noisy. To reduce the noise and smoothly control objects, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and uncomfortable to look at. By filtering this raw data, camera motion is smoothed.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
The GUI of the {{documentation/modulename}} module contains 4 elements:
* Input Transform. This is the raw data, usually raw tracker data, represented by a vtkMRMLLinearTransformNode
* Output Transform. This is the filtered transform represented also by a vtkMRMLLinearTransformNode. This node can be created directly from the list
* Filter checkbox. This checkbox turn on/off the filtering
* Smoothing slider. This slider control the smoothing parameter. In the left, smoother, with relatively important delay. In the right, faster (almost no delay), but noisier.
|}
{|
|[[Image:Slicer4-TrackerStabilizer-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
This module is for now only a low-pass filter, but in the futur, several filters would be implemented to let the choice to the user.

Source code: https://github.com/lchauvin/Slicer-TrackerStabilizer


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/PathExplorer

2014-03-28T18:42:55Z

Lchauvin:

<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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin 
Contact: <email> lchauvin@bwh.harvard.edu</email> 
Contributors: Junichi Tokuda, Atsushi Yamada 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} is a Slicer4 module, part of the SlicerIGT extension, designed to facilitate the creation of trajectory. User is able to place some target points and entry points, represented respectively by green and blue fiducials. When one target point and one entry point are selected, user can create a path that connects these two points, using a slicer ruler.
Points (target and entry) could be moved in real-time, using a drag-and-drop on the fiducial, or by specifying coordinates in the entry of the table corresponding to the point to move.
Selecting a trajectory in the list will automatically select in the target and entry tables the corresponding fiducials. Trajectory could be changed at this time by selecting a new target or entry point, and clicking on "Update" button.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} is an interesting tool for needle insertion planning. By defining targets, and entry points, we could evaluate distance between both points, visualize the regions the needle will go through to reach the target. It is also possible to easily evaluate several entry points for a given target to find the most suitable.
{{documentation/modulename}} is interesting in the fact that it allows the user to reslice along the trajectory line, or perpendicular to the line. In the first case, slice plane rotate around the trajectory, in the second case, slice plane is centered on the trajectory and can 'travel' along the line. Use cases of this feature are needle insertion planning for example, to visualize path of the needle and ensure no important structures will be damaged.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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

{|
|[[Image:PathXplorer_Planning.png|thumb|400px|{{documentation/modulename}} Planning Panel ]]
|[[Image:PathXplorer_PathCreation.png|thumb|470px|{{documentation/modulename}} Path Creation Panel ]]
|[[Image:PathXplorer_Visualization.png|thumb|470px|{{documentation/modulename}} Visualization Panel ]]
|}

* Planning Panel
**# Target table
**#* "+" button allows the user to place a new target point by clicking at desired location on 2D or 3D viewers.
**#* "-" button remove the selected line
**#* "Clear" button remove all points in the table
**# Entry table
**#* Same as target table, for entry points
* Path Creation Panel
** Select a target and an entry point
** Click "+" in Path Visualization panel to create a new trajectory
* Visualization Panel
** Select a trajectory
** Click on "Red" to reslice Red viewer with selected trajectory (same for Green and Yellow)
** Text of the button represent the current trajectory reslicing corresponding viewer (e.g. E1T1 reslicing red viewer, E1T2 reslicing yellow viewer, no reslicing for green viewer)
** When selecting a new trajectory previous reslicing values are automatically reloaded
** Choose perpendicular to reslice perpendicular to trajectory, In plane to reslice along the trajectory
** If reslicing perpendicularly, "Distance" value represent distance of the reslicing plane from entry point
** If reslicing in plane, "Angle" represent the angle value of the slice plane from original orientation




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/PathExplorer

2014-03-28T18:14:06Z

Lchauvin:

<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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin 
Contact: <email> lchauvin@bwh.harvard.edu</email> 
Contributors: Junichi Tokuda, Atsushi Yamada 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} is a Slicer4 module designed to facilitate the creation of trajectory. User is able to place some target points and entry points, represented respectively by green and blue fiducials. When one target point and one entry point are selected, user can create a path that connects these two points, using a slicer ruler.
Points (target and entry) could be moved in real-time, using a drag-and-drop on the fiducial, or by specifying coordinates in the entry of the table corresponding to the point to move.
Selecting a trajectory in the list will automatically select in the target and entry tables the corresponding fiducials. Trajectory could be changed at this time by selecting a new target or entry point, and clicking on "Update" button.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} is an interesting tool for needle insertion planning. By defining targets, and entry points, we could evaluate distance between both points, visualize the regions the needle will go through to reach the target. It is also possible to easily evaluate several entry points for a given target to find the most suitable.
{{documentation/modulename}} is interesting in the fact that it allows the user to reslice along the trajectory line, or perpendicular to the line. In the first case, slice plane rotate around the trajectory, in the second case, slice plane is centered on the trajectory and can 'travel' along the line. Use cases of this feature are needle insertion planning for example, to visualize path of the needle and ensure no important structures will be damaged.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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

{|
|[[Image:PathXplorer_Planning.png|thumb|400px|{{documentation/modulename}} Planning Panel ]]
|[[Image:PathXplorer_PathCreation.png|thumb|470px|{{documentation/modulename}} Path Creation Panel ]]
|[[Image:PathXplorer_Visualization.png|thumb|470px|{{documentation/modulename}} Visualization Panel ]]
|}

* Planning Panel
**# Target table
**#* "+" button allows the user to place a new target point by clicking at desired location on 2D or 3D viewers.
**#* "-" button remove the selected line
**#* "Clear" button remove all points in the table
**# Entry table
**#* Same as target table, for entry points
* Path Creation Panel
** Select a target and an entry point
** Click "+" in Path Visualization panel to create a new trajectory
* Visualization Panel
** Select a trajectory
** Click on "Red" to reslice Red viewer with selected trajectory (same for Green and Yellow)
** Text of the button represent the current trajectory reslicing corresponding viewer (e.g. E1T1 reslicing red viewer, E1T2 reslicing yellow viewer, no reslicing for green viewer)
** When selecting a new trajectory previous reslicing values are automatically reloaded
** Choose perpendicular to reslice perpendicular to trajectory, In plane to reslice along the trajectory
** If reslicing perpendicularly, "Distance" value represent distance of the reslicing plane from entry point
** If reslicing in plane, "Angle" represent the angle value of the slice plane from original orientation




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/PathExplorer

2014-03-28T18:13:45Z

Lchauvin:

<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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
Contributors: Junichi Tokuda, Atsushi Yamada 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} is a Slicer4 module designed to facilitate the creation of trajectory. User is able to place some target points and entry points, represented respectively by green and blue fiducials. When one target point and one entry point are selected, user can create a path that connects these two points, using a slicer ruler.
Points (target and entry) could be moved in real-time, using a drag-and-drop on the fiducial, or by specifying coordinates in the entry of the table corresponding to the point to move.
Selecting a trajectory in the list will automatically select in the target and entry tables the corresponding fiducials. Trajectory could be changed at this time by selecting a new target or entry point, and clicking on "Update" button.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} is an interesting tool for needle insertion planning. By defining targets, and entry points, we could evaluate distance between both points, visualize the regions the needle will go through to reach the target. It is also possible to easily evaluate several entry points for a given target to find the most suitable.
{{documentation/modulename}} is interesting in the fact that it allows the user to reslice along the trajectory line, or perpendicular to the line. In the first case, slice plane rotate around the trajectory, in the second case, slice plane is centered on the trajectory and can 'travel' along the line. Use cases of this feature are needle insertion planning for example, to visualize path of the needle and ensure no important structures will be damaged.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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

{|
|[[Image:PathXplorer_Planning.png|thumb|400px|{{documentation/modulename}} Planning Panel ]]
|[[Image:PathXplorer_PathCreation.png|thumb|470px|{{documentation/modulename}} Path Creation Panel ]]
|[[Image:PathXplorer_Visualization.png|thumb|470px|{{documentation/modulename}} Visualization Panel ]]
|}

* Planning Panel
**# Target table
**#* "+" button allows the user to place a new target point by clicking at desired location on 2D or 3D viewers.
**#* "-" button remove the selected line
**#* "Clear" button remove all points in the table
**# Entry table
**#* Same as target table, for entry points
* Path Creation Panel
** Select a target and an entry point
** Click "+" in Path Visualization panel to create a new trajectory
* Visualization Panel
** Select a trajectory
** Click on "Red" to reslice Red viewer with selected trajectory (same for Green and Yellow)
** Text of the button represent the current trajectory reslicing corresponding viewer (e.g. E1T1 reslicing red viewer, E1T2 reslicing yellow viewer, no reslicing for green viewer)
** When selecting a new trajectory previous reslicing values are automatically reloaded
** Choose perpendicular to reslice perpendicular to trajectory, In plane to reslice along the trajectory
** If reslicing perpendicularly, "Distance" value represent distance of the reslicing plane from entry point
** If reslicing in plane, "Angle" represent the angle value of the slice plane from original orientation




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/PathExplorer

2014-03-28T18:13:24Z

Lchauvin:

<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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin 
Contributors: Junichi Tokuda, Atsushi Yamada
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} is a Slicer4 module designed to facilitate the creation of trajectory. User is able to place some target points and entry points, represented respectively by green and blue fiducials. When one target point and one entry point are selected, user can create a path that connects these two points, using a slicer ruler.
Points (target and entry) could be moved in real-time, using a drag-and-drop on the fiducial, or by specifying coordinates in the entry of the table corresponding to the point to move.
Selecting a trajectory in the list will automatically select in the target and entry tables the corresponding fiducials. Trajectory could be changed at this time by selecting a new target or entry point, and clicking on "Update" button.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} is an interesting tool for needle insertion planning. By defining targets, and entry points, we could evaluate distance between both points, visualize the regions the needle will go through to reach the target. It is also possible to easily evaluate several entry points for a given target to find the most suitable.
{{documentation/modulename}} is interesting in the fact that it allows the user to reslice along the trajectory line, or perpendicular to the line. In the first case, slice plane rotate around the trajectory, in the second case, slice plane is centered on the trajectory and can 'travel' along the line. Use cases of this feature are needle insertion planning for example, to visualize path of the needle and ensure no important structures will be damaged.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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

{|
|[[Image:PathXplorer_Planning.png|thumb|400px|{{documentation/modulename}} Planning Panel ]]
|[[Image:PathXplorer_PathCreation.png|thumb|470px|{{documentation/modulename}} Path Creation Panel ]]
|[[Image:PathXplorer_Visualization.png|thumb|470px|{{documentation/modulename}} Visualization Panel ]]
|}

* Planning Panel
**# Target table
**#* "+" button allows the user to place a new target point by clicking at desired location on 2D or 3D viewers.
**#* "-" button remove the selected line
**#* "Clear" button remove all points in the table
**# Entry table
**#* Same as target table, for entry points
* Path Creation Panel
** Select a target and an entry point
** Click "+" in Path Visualization panel to create a new trajectory
* Visualization Panel
** Select a trajectory
** Click on "Red" to reslice Red viewer with selected trajectory (same for Green and Yellow)
** Text of the button represent the current trajectory reslicing corresponding viewer (e.g. E1T1 reslicing red viewer, E1T2 reslicing yellow viewer, no reslicing for green viewer)
** When selecting a new trajectory previous reslicing values are automatically reloaded
** Choose perpendicular to reslice perpendicular to trajectory, In plane to reslice along the trajectory
** If reslicing perpendicularly, "Distance" value represent distance of the reslicing plane from entry point
** If reslicing in plane, "Angle" represent the angle value of the slice plane from original orientation




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Extensions

2014-03-28T18:12:46Z

Lchauvin: /* Cat 2 */

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

Documentation/4.3/Extensions

2014-03-28T18:11:34Z

Lchauvin: /* Cat 2 */

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Xiaojun Chen,Jun Lin,Qiqin Zhan)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Xiaojun Chen,Jiaxi Luo, Ruqing Ye)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)
*[[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

File:PathExplorerIcon.png

2014-01-08T20:53:10Z

Lchauvin:

Documentation/Nightly/Extensions/PathExplorer

2014-01-08T20:50:59Z

Lchauvin: Redirected page to Documentation/Nightly/Modules/PathExplorer

#REDIRECT [[Documentation/Nightly/Modules/PathExplorer]]

{{documentation/{{documentation/version}}/extension-footer}}

Documentation/4.3/Modules/PathPlanner

2014-01-08T18:23:34Z

Lchauvin:

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

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

'''Latest version available [[Documentation/Nightly/Modules/PathExplorer | here]]. Soon PathPlanner will be replace by PathExplorer. PathExplorer will regroup PathPlanner and VisuaLine in a single module, more robust.''' 

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Atsushi Yamada, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} is a Slicer4 module designed to facilitate the creation of trajectory. User is able to place some target points and entry points, represented respectively by green and blue fiducials. When one target point and one entry point are selected, user can create a path that connects these two points, using a slicer ruler.
Points (target and entry) could be moved in real-time, using a drag-and-drop on the fiducial, or by specifying coordinates in the entry of the table corresponding to the point to move.
Selecting a trajectory in the list will automatically select in the target and entry tables the corresponding fiducials. Trajectory could be changed at this time by selecting a new target or entry point, and clicking on "Update" button.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} is an interesting tool for needle insertion planning. By defining targets, and entry points, we could evaluate distance between both points, visualize the regions the needle will go through to reach the target. It is also possible to easily evaluate several entry points for a given target to find the most suitable.
Combine with other extensions like VisuaLine, or VolumeResliceDriver, it is possible to have a more accurate overview of the trajectory in 2D and 3D.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-PathPlanner-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Target table
#* "+" button allows the user to place a new target point by clicking at desired location on 2D or 3D viewers.
#* "-" button remove the selected line
#* "Clear" button remove all points in the table
# Entry table
#* Same as target table, for entry points
# Trajectory table
#* "+" button add a new trajectory with selected target point (on target table) and entry point (on entry table)
#* "-" button remove the selected line in the trajectory table
#* "Update" button, when a trajectory is selected and target or entry point is modify will update the trajectory with the new selected point
#* "Clear" button will remove all lines in trajectory table
# Hierarchy node of target points (first node is automatically created when entering module)
# Hierarchy node of entry points (first node is automatically created when entering module)
# PathPlanner node ( = Hierarchy node) contains all rulers created by the module (first node is automatically created when entering the module)




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
[[Documentation/Nightly/Modules/VisuaLine | VisuaLine]] module allows visualization of trajectories that could be created with {{documentation/modulename}} module.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.3/Modules/PathPlanner

2014-01-08T18:23:21Z

Lchauvin:

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

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

'''Latest version available [[Documentation/Nightly/Modules/PathExplorer | here]]. Soon PathPlanner will be replace by PathXplorer. PathXplorer will regroup PathPlanner and VisuaLine in a single module, more robust.''' 

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Atsushi Yamada, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} is a Slicer4 module designed to facilitate the creation of trajectory. User is able to place some target points and entry points, represented respectively by green and blue fiducials. When one target point and one entry point are selected, user can create a path that connects these two points, using a slicer ruler.
Points (target and entry) could be moved in real-time, using a drag-and-drop on the fiducial, or by specifying coordinates in the entry of the table corresponding to the point to move.
Selecting a trajectory in the list will automatically select in the target and entry tables the corresponding fiducials. Trajectory could be changed at this time by selecting a new target or entry point, and clicking on "Update" button.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} is an interesting tool for needle insertion planning. By defining targets, and entry points, we could evaluate distance between both points, visualize the regions the needle will go through to reach the target. It is also possible to easily evaluate several entry points for a given target to find the most suitable.
Combine with other extensions like VisuaLine, or VolumeResliceDriver, it is possible to have a more accurate overview of the trajectory in 2D and 3D.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-PathPlanner-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Target table
#* "+" button allows the user to place a new target point by clicking at desired location on 2D or 3D viewers.
#* "-" button remove the selected line
#* "Clear" button remove all points in the table
# Entry table
#* Same as target table, for entry points
# Trajectory table
#* "+" button add a new trajectory with selected target point (on target table) and entry point (on entry table)
#* "-" button remove the selected line in the trajectory table
#* "Update" button, when a trajectory is selected and target or entry point is modify will update the trajectory with the new selected point
#* "Clear" button will remove all lines in trajectory table
# Hierarchy node of target points (first node is automatically created when entering module)
# Hierarchy node of entry points (first node is automatically created when entering module)
# PathPlanner node ( = Hierarchy node) contains all rulers created by the module (first node is automatically created when entering the module)




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
[[Documentation/Nightly/Modules/VisuaLine | VisuaLine]] module allows visualization of trajectories that could be created with {{documentation/modulename}} module.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/PathExplorer

2014-01-08T18:21:26Z

Lchauvin: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'

<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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Atsushi Yamada, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} is a Slicer4 module designed to facilitate the creation of trajectory. User is able to place some target points and entry points, represented respectively by green and blue fiducials. When one target point and one entry point are selected, user can create a path that connects these two points, using a slicer ruler.
Points (target and entry) could be moved in real-time, using a drag-and-drop on the fiducial, or by specifying coordinates in the entry of the table corresponding to the point to move.
Selecting a trajectory in the list will automatically select in the target and entry tables the corresponding fiducials. Trajectory could be changed at this time by selecting a new target or entry point, and clicking on "Update" button.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} is an interesting tool for needle insertion planning. By defining targets, and entry points, we could evaluate distance between both points, visualize the regions the needle will go through to reach the target. It is also possible to easily evaluate several entry points for a given target to find the most suitable.
{{documentation/modulename}} is interesting in the fact that it allows the user to reslice along the trajectory line, or perpendicular to the line. In the first case, slice plane rotate around the trajectory, in the second case, slice plane is centered on the trajectory and can 'travel' along the line. Use cases of this feature are needle insertion planning for example, to visualize path of the needle and ensure no important structures will be damaged.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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

{|
|[[Image:PathXplorer_Planning.png|thumb|400px|{{documentation/modulename}} Planning Panel ]]
|[[Image:PathXplorer_PathCreation.png|thumb|470px|{{documentation/modulename}} Path Creation Panel ]]
|[[Image:PathXplorer_Visualization.png|thumb|470px|{{documentation/modulename}} Visualization Panel ]]
|}

* Planning Panel
**# Target table
**#* "+" button allows the user to place a new target point by clicking at desired location on 2D or 3D viewers.
**#* "-" button remove the selected line
**#* "Clear" button remove all points in the table
**# Entry table
**#* Same as target table, for entry points
* Path Creation Panel
** Select a target and an entry point
** Click "+" in Path Visualization panel to create a new trajectory
* Visualization Panel
** Select a trajectory
** Click on "Red" to reslice Red viewer with selected trajectory (same for Green and Yellow)
** Text of the button represent the current trajectory reslicing corresponding viewer (e.g. E1T1 reslicing red viewer, E1T2 reslicing yellow viewer, no reslicing for green viewer)
** When selecting a new trajectory previous reslicing values are automatically reloaded
** Choose perpendicular to reslice perpendicular to trajectory, In plane to reslice along the trajectory
** If reslicing perpendicularly, "Distance" value represent distance of the reslicing plane from entry point
** If reslicing in plane, "Angle" represent the angle value of the slice plane from original orientation




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

File:PathXplorer Visualization.png

2013-08-26T16:22:30Z

Lchauvin:

File:PathXplorer PathCreation.png

2013-08-26T16:19:23Z

Lchauvin:

File:PathXplorer Planning.png

2013-08-26T16:15:17Z

Lchauvin:

File:DiceSimilarityCoefficient.png

2013-06-13T16:42:02Z

Lchauvin:

Documentation/Nightly/Modules/DiceComputation

2013-06-13T16:24:35Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Nobuhiko Hata 
Contributors: Sonia Pujol 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} is capable of calculating the Dice Similarity Coefficient (DSC) between multiple label map images. If the label map images represent '''registered''' segmented structures, the DSC will provide a volumetric alignment between the images. The DSC gives measures of the volumetric overlap between two of the segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment.

If more than 2 label map images are specified as input, the module computes DSCs for all combinations and present results in a NxN matrix, where N is the number of the label map images, with color coding for convenient reading.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} compute DSC to quantitatively compare several '''registered''' segmented volumes. It could be used to compare:
* Several algorithms with ground truth
* Automated segmentation vs manual
* etc...


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-DiceComputation-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Parameters
#* Number of label map images to use for computation
# Label Maps
#* Select labels map images (only label maps could be selected) to use for computation or None
#* Compute Dice coefficient: Press button to start computation
# Results
#* Once computation is over, results will appear in an NxN matrix with color coding
#** Red stripes indicate no label map have been selected (None)
#** Green stripes indicate this is Dice's coefficient of a label map with itself (always 1.0, so not displayed)
#** Values represent Dice's similarity coefficient. The bigger the value is, the greener the background is, in order to quickly find higher matches.




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
* A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

File:Slicer4-DiceComputation-GUI.png

2013-06-12T13:46:18Z

Lchauvin: uploaded a new version of "File:Slicer4-DiceComputation-GUI.png"

Documentation/Nightly/Developers/FAQ/Extensions

2013-06-04T14:42:44Z

Lchauvin:

<noinclude>__TOC__
={{#titleparts: {{PAGENAME}} | | -1 }}=</noinclude><includeonly>
='''Developer FAQ: {{{1}}}'''=
</includeonly>

== What is the Extensions Index ? ==

{{:Documentation/{{documentation/version}}/Developers/Extensions/Index}}

== What is an API Key ? ==

See http://en.wikipedia.org/wiki/Application_programming_interface_key

== How to obtain an API key to submit on the extension server ? ==
{{:Documentation/{{documentation/version}}/Developers/Tutorials/ObtainExtensionServerApiKey}}

== Is --launch flag available for a MacOSX installed Slicer.app ?==

On MacOSx, running Slicer with the --help argument does NOT list the usual launcher related options.

$ ./Slicer.app/Contents/MacOS/Slicer --help
Usage
Slicer [options]

Options
--, --ignore-rest Ignores the rest of the labeled arguments following this flag. (default: false)
-h, --help Display available command line arguments.
[...]
--version Displays version information and exits.

To provide some background information, when generating the package that will be distributed, an application bundle <code>Slicer.app</code> is created. As explained [http://developer.apple.com/library/mac/#documentation/CoreFoundation/Conceptual/CFBundles/Introduction/Introduction.html here], a bundle is a directory with a standardized hierarchical structure that holds executable code and the resources used by that code. It means that since all libraries contained within a bundle are referenced relatively to the location of either the CLI or the Slicer executable, the use of launcher does NOT make sens.

To help fixing-up the libraries, executables and plugins so that they reference each other in a relative way, CMake provides us with the [http://www.cmake.org/cmake/help/v2.8.8/cmake.html#module:BundleUtilities BundleUtilities] module.

This module is used in two situations:
# Fixup of Slicer application itself. See [https://github.com/Slicer/Slicer/blob/master/CMake/SlicerCPack.cmake#L36-68 SlicerCPack.cmake#L36-68] and [https://github.com/Slicer/Slicer/blob/master/CMake/SlicerCPackBundleFixup.cmake.in SlicerCPackBundleFixup.cmake.in]
# Fixup of an extension package. See [https://github.com/Slicer/Slicer/blob/master/CMake/SlicerExtensionCPack.cmake#L126-143 SlicerExtensionCPack.cmake#L126-143] and [https://github.com/Slicer/Slicer/blob/master/CMake/SlicerExtensionCPackBundleFixup.cmake.in SlicerExtensionCPackBundleFixup.cmake.in]

== What is the difference between Documentation/Nightly/Modules and Documentation/Nightly/Extensions ? ==

As suggested by the namespace names:
* All module documentation pages should be located under <code>Documentation/Nightly/Modules</code>
* All extension documentation pages should be located under <code>Documentation/Nightly/Extensions</code>

For example, if an an extension named <code>DoSomethingGreat</code> bundles three modules <code>ModuleA</code>, <code>ModuleB</code> and <code>ModuleC</code>. The following pages should be created:
* <code>Documentation/Nightly/Extensions/DoSomethingGreat</code>
* <code>Documentation/Nightly/Modules/ModuleA</code>
* <code>Documentation/Nightly/Modules/ModuleB</code>
* <code>Documentation/Nightly/Modules/ModuleC</code>

In case your extension bundles only one module, the extension name is expected to match the module name. For example, if your extension is named <code>DoSomethingAwesome</code>, the associated module is expected to be named <code>DoSomethingAwesome</code>. The following pages will then be created:
* <code>Documentation/Nightly/Extensions/DoSomethingAwesome</code>
* <code>Documentation/Nightly/Modules/DoSomethingAwesome</code>
where page <code>Extensions/DoSomethingAwesome</code> redirect to page <code>Modules/DoSomethingAwesome</code>.

To setup a redirection, simply add the following text to page <code>Extensions/DoSomethingAwesome</code>:
<pre>
#REDIRECT [[Documentation/Nightly/Modules/DoSomethingAwesome]]
</pre>
For an example, see [http://www.slicer.org/slicerWiki/index.php?title=Documentation/Nightly/Extensions/SkullStripper&action=edit here]

More details about redirection are available here: http://www.mediawiki.org/wiki/Help:Redirects

== Which URL should be associated with EXTENSION_HOMEPAGE metadata ? ==

Extensions available through the Slicer Extensions Catalog are expected to have a page created under the <code>Nightly</code> documentation namespace. The corresponding URL should be associated with the <code>EXTENSION_HOMEPAGE</code> metadata.

For example:
* <code><nowiki>set(EXTENSION_HOMEPAGE "http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DoSomethingGreat")</nowiki></code>
* <code><nowiki>set(EXTENSION_HOMEPAGE "http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DoSomethingAwesome")</nowiki></code>

Note that this also apply for extension bundling only one module. Indeed, in this case the page will redirect to the appropriate module page. For example: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SkullStripper

== How to rename an extension to add new features ? ==

If you created an extension to perform Task1, but later on, your module is getting more generic and you add some other tasks, the name of your extension might change.
In order to rename, your extension, you should:
* Remove your old extension from the ExtensionsIndex
* Then, submit your extension again (including new features) with a new name

Documentation/Nightly/Modules/DiceComputation

2013-06-03T14:46:31Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module is capable of calculating the Dice Similarity Coefficient (DSC) between several label map images. If the label map images represent '''registered''' segmented structures then the DSC will provide a volumetric alignment between the images. The DSC gives measures of the volumetric overlap between two of the segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment.
{{documentation/modulename}} is a Slicer4 module computing DSC for several label map images, and presenting results in a NxN matrix (where N is number of label map images) with color coding for convenient reading.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} compute DSC to quantitatively compare several '''registered''' segmented volumes. It could be used to compare:
* Several algorithms with ground truth
* Automated segmentation vs manual
* etc...


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-DiceComputation-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Parameters
#* Number of label map images to use for computation
# Label Maps
#* Select labels map images (only label maps could be selected) to use for computation or None
#* Compute Dice coefficient: Press button to start computation
# Results
#* Once computation is over, results will appear in an NxN matrix with color coding
#** Red stripes indicate no label map have been selected (None)
#** Green stripes indicate this is Dice's coefficient of a label map with itself (always 1.0, so not displayed)
#** Values represent Dice's similarity coefficient. The bigger the value is, the greener the background is, in order to quickly find higher matches.




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
* A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/DiceComputation

2013-06-03T14:46:02Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module is capable of calculating the Dice Similarity Coefficient (DSC) between several label map images. If the label map images represent '''registered''' segmented structures then the DSC will provide a volumetric alignment between the images. The DSC gives measures of the volumetric overlap between two of the segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment.
{{documentation/modulename}} is a Slicer4 module computing DSC for several label map images, and presenting results in a NxN matrix (where N is number of label map images) with color coding for convenient reading.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} compute DSC to quantitatively compare several registered segmented volumes. It could be used to compare:
* Several algorithms with ground truth
* Automated segmentation vs manual
* etc...


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-DiceComputation-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Parameters
#* Number of label map images to use for computation
# Label Maps
#* Select labels map images (only label maps could be selected) to use for computation or None
#* Compute Dice coefficient: Press button to start computation
# Results
#* Once computation is over, results will appear in an NxN matrix with color coding
#** Red stripes indicate no label map have been selected (None)
#** Green stripes indicate this is Dice's coefficient of a label map with itself (always 1.0, so not displayed)
#** Values represent Dice's similarity coefficient. The bigger the value is, the greener the background is, in order to quickly find higher matches.




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
* A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/DiceComputation

2013-06-03T14:43:56Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module is capable of calculating the Dice Similarity Coefficient (DSC) between several label map images. If the label map images represent '''registered''' segmented structures then the DSC will provide a volumetric alignment between the images. The DSC gives measures of the volumetric overlap between two of the segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment.
{{documentation/modulename}} is a Slicer4 module computing DSC for several label map images, and presenting results in a NxN matrix (where N is number of label map images) with color coding for convenient reading.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} compute DSC to quantitatively compare several registered segmented volumes. It could be used to compare:
* Several algorithms with ground truth
* Automated segmentation vs manual
* etc...


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-DiceComputation-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Parameters
#* Number of label map images to use for computation
# Label Maps
#* Select labels map images (only label maps could be selected) to use for computation or None
#* Compute Dice coefficient: Press button to start computation
# Results
#* Once computation is over, results will appear in an NxN matrix with color coding
#** Red stripes indicate no label map have been selected (None)
#** Green stripes indicate this is Dice's coefficient of a label map with itself (always 1.0, so not displayed)
#** Values represent Dice's similarity coefficient. The bigger the value is, the greener the background is, in order to quickly find higher matches.




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/DiceComputation

2013-06-03T14:36:50Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module is capable of calculating the Dice Similarity Coefficient (DSC) between several label map images. If the label map images represent '''registered''' segmented structures then the DSC will provide a volumetric alignment between the images. The DSC gives measures of the volumetric overlap between two of the segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment.
{{documentation/modulename}} is a Slicer4 module computing DSC for several label map images, and presenting results in a NxN matrix (where N is number of label map images) with color coding for convenient reading.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} could be useful to quantitatively compare several registered segmented volumes. It could be used to compare several algorithms with ground truth, or automated segmentation vs manual, etc...


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-DiceComputation-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Parameters
#* Number of label map images to use for computation
# Label Maps
#* Select labels map images (only label maps could be selected) to use for computation or None
#* Compute Dice coefficient: Press button to start computation
# Results
#* Once computation is over, results will appear in an NxN matrix with color coding
#** Red stripes indicate no label map have been selected (None)
#** Green stripes indicate this is Dice's coefficient of a label map with itself (always 1.0, so not displayed)
#** Values represent Dice's similarity coefficient. The bigger the value is, the greener the background is, in order to quickly find higher matches.




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Extensions/DiceComputation

2013-05-31T18:56:05Z

Lchauvin: Redirected page to Documentation/Nightly/Modules/DiceComputation

#REDIRECT [[Documentation/Nightly/Modules/DiceComputation]]

{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/DiceComputation

2013-05-31T18:54:55Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
Dice's coefficient is used to measure the similarity of two datasets together. If Dice's coefficient is 1, datasets are identical, is coefficient is 0, datasets are not overlapping at all.
{{documentation/modulename}} is a Slicer4 module designed to compute several Dice's coefficients and display them to immediately visualize results.
Number of label maps used could be adjusted dynamically.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} could be useful to quantitatively compare several label maps. It could be used to compare several algorithms with ground truth, or automated segmentation vs manual.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-DiceComputation-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Parameters
#* Number of label maps to use for computation
# Label Maps
#* Select labels maps (only label maps could be selected) to use for computation or None
#* Compute Dice coefficient: Press button to start computation
# Results
#* Once computation is over, results will appear in an array
#* Red stripes indicate no label map have been selected (None)
#* Green stripes indicate this is Dice's coefficient of a label map with itself (always 1.0, so not displayed)
#* Values represent Dice's similarity coefficient. The bigger the value is, the greener the background is, in order to quickly find higher matches.




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/DiceComputation

2013-05-31T18:51:15Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
Dice's coefficient is used to measure the similarity of two datasets together. If Dice's coefficient is 1, datasets are identical, is coefficient is 0, datasets are not overlapping at all.
{{documentation/modulename}} is a Slicer4 module designed to compute several Dice's coefficients and display them to immediately visualize results.
Number of label maps used could be adjusted dynamically.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} could be useful to quantitatively compare several label maps. It could be used to compare several algorithms with ground truth, or automated segmentation vs manual.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-DiceComputation-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Parameters
#* Number of label maps to use for computation
# Label Maps
#* Select labels maps (only label maps could be selected) to use for computation or None
#* Compute Dice coefficient: Press button to start computation
# Results
#* Once computation is over, results will appear in an array
#* Red stripes indicate no label map have been selected (None)
#* Green stripes indicate this is Dice's coefficient of a label map with itself (always 1.0, so not displayed)
#* Values represent Dice's similarity coefficient. The bigger the value is, the greener the background is, in order to quickly find higher matches.




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
[[Documentation/Nightly/Modules/VisuaLine | VisuaLine]] module allows visualization of trajectories that could be created with {{documentation/modulename}} module.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/DiceComputation

2013-05-31T18:50:53Z

Lchauvin: Created page with ' {{documentation/{{documentation/version}}/module-header}}   {{doc…'

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
Dice's coefficient is used to measure the similarity of two datasets together. If Dice's coefficient is 1, datasets are identical, is coefficient is 0, datasets are not overlapping at all.
{{documentation/modulename}} is a Slicer4 module designed to compute several Dice's coefficients and display them to immediately visualize results.
Number of label maps used could be adjusted dynamically.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/modulename}} could be useful to quantitatively compare several label maps. It could be used to compare several algorithms with ground truth, or automated segmentation vs manual.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|[[Image:Slicer4-DiceComputation-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}
# Parameters
#* Number of label maps to use for computation
# Label Maps
# * Select labels maps (only label maps could be selected) to use for computation or None
# * Compute Dice coefficient: Press button to start computation
# Results
# * Once computation is over, results will appear in an array
# * Red stripes indicate no label map have been selected (None)
# * Green stripes indicate this is Dice's coefficient of a label map with itself (always 1.0, so not displayed)
# * Values represent Dice's similarity coefficient. The bigger the value is, the greener the background is, in order to quickly find higher matches.




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
[[Documentation/Nightly/Modules/VisuaLine | VisuaLine]] module allows visualization of trajectories that could be created with {{documentation/modulename}} module.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

File:Slicer4-DiceComputation-GUI.png

2013-05-31T18:45:57Z

Lchauvin:

Documentation/Nightly/Extensions

2013-05-31T18:34:42Z

Lchauvin: /* Cat 2 */

<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/PatientHierarchy|Patient hierarchy]]
** [[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Deformation field visualizer]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/PathPlanner|PathPlanner]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] (Laurent Chauvin)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)

<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

File:PathPlannerIcon.png

2013-04-15T16:26:53Z

Lchauvin:

File:VisuaLineIcon.png

2013-04-15T16:25:38Z

Lchauvin:

File:Slicer4-PathPlanner-GUI.png

2013-04-09T15:04:27Z

Lchauvin:

File:VisuaLine.png

2013-03-19T16:41:18Z

Lchauvin:

File:Slicer4-VisuaLine-GUI.png

2013-03-18T18:26:06Z

Lchauvin:

File:VisuaLine-GUI.png

2013-03-18T18:24:49Z

Lchauvin:

Documentation/Nightly/Extensions

2013-02-12T16:50:34Z

Lchauvin: /* Cat 2 */

<noinclude>{{:{{FULLPAGENAME}}/Description}}

__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|CARMA]] (Alan Morris)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)

Documentation/4.2/Extensions

2013-02-12T16:50:18Z

Lchauvin: /* Cat 2 */

<noinclude>{{:{{FULLPAGENAME}}/Description}}

__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|CARMA]] (Alan Morris)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
** [[Documentation/{{documentation/version}}/Extensions/LabelToDICOMSEGImport|LabelToDICOMSEGConverter]]
** [[Documentation/{{documentation/version}}/Extensions/DICOMSEGImport|DICOM SEG Import]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|IGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylaward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]] (Sunil Kumar, Dan Marcus, Steve Pieper)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)

Documentation/4.2/Extensions

2013-02-12T16:49:43Z

Lchauvin: /* Cat 2 */

<noinclude>{{:{{FULLPAGENAME}}/Description}}

__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|CARMA]] (Alan Morris)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
** [[Documentation/{{documentation/version}}/Extensions/LabelToDICOMSEGImport|LabelToDICOMSEGConverter]]
** [[Documentation/{{documentation/version}}/Extensions/DICOMSEGImport|DICOM SEG Import]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|IGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylaward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]] (Sunil Kumar, Dan Marcus, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)

Documentation/Nightly/Extensions/TrackerStabilizer

2013-02-12T14:28:43Z

Lchauvin: Redirected page to Documentation/Nightly/Modules/TrackerStabilizer

#REDIRECT [[Documentation/Nightly/Modules/TrackerStabilizer]]

{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/TrackerStabilizer

2013-02-12T14:28:06Z

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Jayender Jagadeesan, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are particularly usefull to track surgical tools, robots, patient motion, etc... . However, data imported in 3D Slicer from these devices are often noisy. To reduce the noise and smoothly control objects, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and uncomfortable to look at. By filtering this raw data, camera motion is smoothed.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
The GUI of the {{documentation/modulename}} module contains 4 elements:
* Input Transform. This is the raw data, usually raw tracker data, represented by a vtkMRMLLinearTransformNode
* Output Transform. This is the filtered transform represented also by a vtkMRMLLinearTransformNode. This node can be created directly from the list
* Filter checkbox. This checkbox turn on/off the filtering
* Smoothing slider. This slider control the smoothing parameter. In the left, smoother, with relatively important delay. In the right, faster (almost no delay), but noisier.
|}
{|
|[[Image:Slicer4-TrackerStabilizer-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
This module is for now only a low-pass filter, but in the futur, several filters would be implemented to let the choice to the user.


{{documentation/{{documentation/version}}/module-footer}}

File:TrackerStabilizer.png

2013-02-11T17:29:28Z

Lchauvin:

Documentation/Nightly/Extensions/TrackerStabilizer

2013-02-11T17:01:37Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Jayender Jagadeesan, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are particularly usefull to track surgical tools, robots, patient motion, etc... . However, data imported in 3D Slicer from these devices are often noisy. To reduce the noise and smoothly control objects, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and uncomfortable to look at. By filtering this raw data, camera motion is smoothed.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
The GUI of the {{documentation/modulename}} module contains 4 elements:
* Input Transform. This is the raw data, usually raw tracker data, represented by a vtkMRMLLinearTransformNode
* Output Transform. This is the filtered transform represented also by a vtkMRMLLinearTransformNode. This node can be created directly from the list
* Filter checkbox. This checkbox turn on/off the filtering
* Smoothing slider. This slider control the smoothing parameter. In the left, smoother, with relatively important delay. In the right, faster (almost no delay), but noisier.
|}
{|
|[[Image:Slicer4-TrackerStabilizer-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
This module is for now only a low-pass filter, but in the futur, several filters would be implemented to let the choice to the user.


{{documentation/{{documentation/version}}/module-footer}}

File:Slicer4-TrackerStabilizer-GUI.png

2013-02-11T17:00:58Z

Lchauvin:

Documentation/Nightly/Extensions/TrackerStabilizer

2013-02-09T05:54:01Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Jayender Jagadeesan, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}

This project is supported by National Institute of Health (5P01CA067165, 5R01CA124377, 5R01CA138586, 2R44DE019322, 7R01CA124377, 5R42CA137886, 8P41EB015898).

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are particularly usefull to track surgical tools, robots, patient motion, etc... . However, data imported in 3D Slicer from these devices are often noisy. To reduce the noise and smoothly control objects, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and uncomfortable to look at. By filtering this raw data, camera motion is smoothed.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
The GUI of the {{documentation/modulename}} module contains 4 elements:
* Input Transform. This is the raw data, usually raw tracker data, represented by a vtkMRMLLinearTransformNode
* Output Transform. This is the filtered transform represented also by a vtkMRMLLinearTransformNode. This node can be created directly from the list
* Filter checkbox. This checkbox turn on/off the filtering
* Smoothing slider. This slider control the smoothing parameter. In the left, smoother, with relatively important delay. In the right, faster (almost no delay), but noisier.
|}
{|
|[[Image:TrackerStabilizer_GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
This module is for now only a low-pass filter, but in the futur, several filters would be implemented to let the choice to the user.


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Extensions/TrackerStabilizer

2013-02-08T04:27:08Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Jayender Jagadeesan, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are really usefull to track surgical tools, robots, patient motion, etc... . However, the data imported in 3D Slicer from these devices are often noisy. In order to reduce this noise and being able to smoothly control some object, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and make it difficult to see what is happening in the scene. By filtering this raw data, we could smooth the camera motion.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
The GUI of the {{documentation/modulename}} module contains 4 elements:
* Input Transform. This is the raw data, usually raw tracker data, represented by a vtkMRMLLinearTransformNode
* Output Transform. This is the filtered transform represented also by a vtkMRMLLinearTransformNode. This node can be created directly from the list
* Filter checkbox. This checkbox turn on/off the filtering
* Smoothing slider. This slider control the smoothing parameter. In the left, really smooth, with quiet important delay. In the right, faster (almost no delay), but noisier.
|}
{|
|[[Image:TrackerStabilizer_GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
This module is for now only a low-pass filter, but in the futur, several filters would be implemented to let the choice to the user.


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Extensions/TrackerStabilizer

2013-02-08T04:26:20Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. 
Author: Laurent Chauvin, Jayender Jagadeesan, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are really usefull to track surgical tools, robots, patient motion, etc... . However, the data imported in 3D Slicer from these devices are often noisy. In order to reduce this noise and being able to smoothly control some object, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and make it difficult to see what is happening in the scene. By filtering this raw data, we could smooth the camera motion.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
The GUI of the {{documentation/modulename}} module contains 4 elements:
* Input Transform. This is the raw data, usually raw tracker data, represented by a vtkMRMLLinearTransformNode
* Output Transform. This is the filtered transform represented also by a vtkMRMLLinearTransformNode. This node can be created directly from the list
* Filter checkbox. This checkbox turn on/off the filtering
* Smoothing slider. This slider control the smoothing parameter. In the left, really smooth, with quiet important delay. In the right, faster (almost no delay), but noisier.
|}
{|
|[[Image:TrackerStabilizer_GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
This module is for now only a low-pass filter, but in the futur, several filters would be implemented to let the user choose.


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Extensions/TrackerStabilizer

2013-02-05T17:12:14Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. This work is supported by P01-CA67165 "Image Guided Therapy" (PI: Ferenc Joelsz) 
Author: Laurent Chauvin, Jayender Jagadeesan, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are really usefull to track surgical tools, robots, patient motion, etc... . However, the data imported in 3D Slicer from these devices are often noisy. In order to reduce this noise and being able to smoothly control some object, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and make it difficult to see what is happening in the scene. By filtering this raw data, we could smooth the camera motion.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
The GUI of the {{documentation/modulename}} module contains 4 elements:
* Input Transform. This is the raw data, usually raw tracker data, represented by a vtkMRMLLinearTransformNode
* Output Transform. This is the filtered transform represented also by a vtkMRMLLinearTransformNode. This node can be created directly from the list
* Filter checkbox. This checkbox turn on/off the filtering
* Smoothing slider. This slider control the smoothing parameter. In the left, really smooth, with quiet important delay. In the right, faster (almost no delay), but noisier.
|}
{|
|[[Image:TrackerStabilizer_GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
|}




{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}
This module is for now only a low-pass filter, but in the futur, several filters would be implemented to let the user choose.


{{documentation/{{documentation/version}}/module-footer}}

File:TrackerStabilizer GUI.png

2013-02-05T17:03:54Z

Lchauvin:

Documentation/Nightly/Extensions/TrackerStabilizer

2013-02-05T17:00:47Z

Lchauvin:

{{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}}
This work is supported by NA-MIC, NCIGT, and the Slicer Community. This work is supported by P01-CA67165 "Image Guided Therapy" (PI: Ferenc Joelsz) 
Author: Laurent Chauvin, Jayender Jagadeesan, Nobuhiko Hata 
Contact: Laurent Chauvin <email> lchauvin@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|ncigt}}|NCIGT
|{{collaborator|logo|spl}}|SPL
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are really usefull to track surgical tools, robots, patient motion, etc... . However, the data imported in 3D Slicer from these devices are often noisy. In order to reduce this noise and being able to smoothly control some object, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and make it difficult to see what is happening in the scene. By filtering this raw data, we could smooth the camera motion.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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



{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


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


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}