NAMIC Wiki - User contributions [en]

File:Demo1-ContourSegmentation1.avi.zip

2010-03-16T05:34:40Z

Karthik:

User:Karthik

2010-03-16T05:33:11Z

Karthik: /* Contour widget polyplane ROI segmentation in 3D */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.zip]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

==== Contour widget polyplane ROI segmentation in 3D ====
* Contour widget polyplane ROI segmentation in 3D based on an extrusion along the viewing ray [[Media:Demo1-ContourSegmentation1.avi.zip]]

=== EM Segmenter ===
EM Segmenter simple example data for segmentation from a T1 MR. [[Media:EMSegmenterT1Example.zip]]

=== Temporary hosting for NAMIC (RemoveMe) ===
[[Image:KarthikMRPhantomWithEndorectalCoilBalloon.jpg]]

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2010-03-16T05:25:19Z

Karthik: /* Contour widget polyplane ROI segmentation in 3D */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.zip]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

==== Contour widget polyplane ROI segmentation in 3D ====
* Contour widget polyplane ROI segmentation in 3D based on an extrusion along the viewing ray [[Media:Demo1-ContourSegmentation1.avi]]

=== EM Segmenter ===
EM Segmenter simple example data for segmentation from a T1 MR. [[Media:EMSegmenterT1Example.zip]]

=== Temporary hosting for NAMIC (RemoveMe) ===
[[Image:KarthikMRPhantomWithEndorectalCoilBalloon.jpg]]

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2010-03-16T05:24:26Z

Karthik: /* VTKEdge */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.zip]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

==== Contour widget polyplane ROI segmentation in 3D ====
* Contour widget polyplane ROI segmentation in 3D based on an extrusion along the viewing ray [[Media:Example.ogg]]

=== EM Segmenter ===
EM Segmenter simple example data for segmentation from a T1 MR. [[Media:EMSegmenterT1Example.zip]]

=== Temporary hosting for NAMIC (RemoveMe) ===
[[Image:KarthikMRPhantomWithEndorectalCoilBalloon.jpg]]

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

Projects:ARRA:miAnnotation

2009-12-31T09:45:23Z

Karthik: /* To Do */

[[Projects:ARRASuplements|Back to Slicer ARRA home page]]
= Aim =
Medical images often contain a wealth of information, such as anatomy and pathology, not explicitly accessible. One way to address this issue is via image annotation and markup. We propose to create a comprehensive framework for annotation and markup within 3D Slicer, enabling users to capture structured information easily. Furthermore, we will develop schemas for saving and recovering this information into and from XNAT, allowing queries of larger data sets of medical scans. This tool will provide clinicians with a relatively simple way to capture information latent in medical scans, and also to select micro-cohorts of medical scans for studying diseases.

= Research Plan =
3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include:
* a rich set of geometric objects for improved visual differentiation between annotations
* markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection
* entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologiesand
* a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT.

We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region.

The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values.

Both modules are accompanied by training materials and documentation to ensure usability.
=Design of Module=
* Current [[Media:AMI-GUI-Design.ppt | GUI ]] outline - [[Media:SlicerAM QtAnnotation.png | Screenhot]] in Slicer
* Suggested [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] outline

=Key Personnel=
60% Kilian Pohl <BR>
95% Yong Zhang

=Events=
* 12/16/09 - 12/17/09 [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]]
* 01/06/10 [[AHM2010:AnnotationBreakout | Break out session]] at AHM 2010

=Progress=
(reverse chronological order, most recent on top)
*01/01/10 Generated a [[Media:SlicerAM QtAnnotation.png | GUI interface]] via QT for the annotation module.
*12/25/09 Created [[ 2010_Winter_Project_Week_mComment | project ]] and organized [[ AHM2010:AnnotationBreakout | break out session ]] at AHM meeting. Coordinated efforts with BWH team in preparation of the meeting.
*12/18/09 Held workshop to integrate AMI into 3D Slicer. Hired Yong Zhang to implement AMI in Slicer.
*12/11/09 [[ Projects:ARRA:SlicerAM_RSNA09Report | Summary ]] of tools demoed at RSNA
*12/04/09 Visited RSNA to review annotation tools by GE, Siemens & Phillips. Connected to caBIG AIM project to see how we can make use of their data scheme
*11/29/09 Created GUI for MarkUp module
*11/20/09 Design MRML Structure of Annotation and MarkUp Module
*11/13/09 Organize [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]] Session
*11/06/09 Designed User Interface , Meet with Julien Finet and Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer
*10/30/09 Participated in Qt-Tcon, Interviewed candidate at Almaden, coordinated efforts with Nicole Aucoin
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal

= To Do =
* Prepare for AHM
** Prepare Break out session
** Define two use cases

== Widget related action items ==

=== Annotations ===
* '''vtkCaptionWidget''': The widget is buggy - the cursor icon seems to suggest a different functionality then what you can do to move the / modify the location of the text . I was only able to move the text by clicking on the lower bar of the text box. Furthermore in TestCaptionWidget.cxx I had to uncomment widget->On(); - so I believe by default it is never tested
* '''vtkBalloonWidget''' : ok
* '''vtkTextWidget''': Font size customization ? Currently the font size scales to the entire text box size. Check with KP on what he needs

=== Measurements ===
* '''vtkSeedWidget''': Custom measurement annotations needed, such as the intensity value
* '''vtkDistanceWidget''' (2D distance widget):
** Instead of displaying measurement along line display it outside with dotted line such as in caption widget
** Measurement should be moved anywhere in the image without obstructing important anatomy
** Distance text font customization (too small to read)
* '''vtkLineWidget2''' (3D distance widget):
** Hard to initialize control points in 3D (difficult to judge behavior)
* '''vtkAngleWidget'''
** vtkAngleRepresentation2D
*** Instead of displaying measurement along line display it outside with dotted line such as in caption widget
*** text font customization (too small to read)
*** Half circle scale customization to create less image obstruction
** vtkAngleRepresentation3D
*** Instead of displaying measurement along line display it outside with dotted line such as in caption widget
*** Widget measurement disappeared as it was placed inside the sphere (Check with KP. This is indeed the intended behaviour)
*** Half circle scale customization to create less image obstruction
* '''vtkBiDimensionalWidget'''
** Instead of displaying measurement along line display it outside with dotted line such as in caption widget
** KP: ''It is strange that the fourth point is set automatically but can be modified later. Once the second control point is set I would just draw a line orthogonal to the one already created . Once the third control point is set the line is fixed and only the length of the line can be changed.''

=== ROI ===
* '''vtkContourWidget''':
** the line is drawn once the control point is set. Instead, the line should always follow the cursor - once the MB is pressed the line is fixed up to this control point
** missing measurement with length of line and region of interest (for closed lines)

Dec-2009-SlicerAIMBrainstorming

2009-12-23T09:51:43Z

Karthik: /* Schedule */

== Current Status of Annotation and MarkUp Modules ==
* Summary of [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] that currently exists in annotation tools of large software vendors (created by Kilian after RSNA visit)
* Suggested design of [[Media:AMI-GUI-Design.ppt | GUI ]] and [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] structure
* [[ Projects:ARRA:SlicerAM | Progress report ]]

== Logistics ==
*Confirmed date: Wednesday and Thursday, '''December 16 (1-5pm) and 17 (9am-1pm), 2009'''
*Location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room
*Tcon Number: (218) 862-1115 Conference ID 348265#

== Goals ==
The purpose of this meeting is to coordinate the efforts of the [[Projects:ARRA:SlicerAM|Markup and Annotation project]] with the development of the fiducial, measurement model, ROI, and LabelDiameterEstimation. Important questions to consider at the meeting are
* What are similarities and differences between the modules ?
* How should we proceed with the development of the three modules ? Should they be totally separate, share a basic framework, or be combined to one ?
* What should be the overall design of the GUI for the three modules?
* What functionality do we need ? What are specific user scenarios we need to address ?
* What Qt functionality do we need in Slicer ?
* Which interaction are inherently 3D and which are best performed on slice views? How to reconcile these in the most logical and productive way.

== Schedule ==
* Wednesday - Dec 16th
** 1:00 Intro: What is the vision of the AIM project (Kilian)
*** A simple user interface such as ClearCanvas
*** A [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] structure that consolidates several existing structures. Furthermore, the structure should be flexible enough to extend to new functionality and work flows
** 1:15 Demo's
*** Measurement and Fiducial (Nicole) [[Media:Annotation_Brainstorming_Mini_Retreat.ppt‎ | PPT]]
*** ROI and LabelDiameterEstimation (Andriy, Alex)
*** MarkUp and Annotation (Kilian)
** 2:15 Annotation and markup widgets in VTK (Karthik)
*** Currently available Annotation and Markup widgets in VTK [http://wiki.na-mic.org/Wiki/images/1/11/VTK-AnnotationAndMarkupWidgets.pdf link].
*** VTK's 3D Widgets in general [http://www.na-mic.org/Wiki/images/b/bb/VTKWidgets2.ppt link]
*** VTK widget gallery [http://www.vtk.org/Wiki/VTK_Widget_Examples link]
*** Tcon: 1 800 704 9804, code: 718324
*** [http://connect.acrobat.com/KitwareDemo Presentation] via Adobe Connection
** 2:35 Current State of Qt in Slicer [http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt presentation]. Julien Finet and Jean-Christophe Fillion-Robin.
*** Tcon: 1 800 704 9804, code: 718324
*** [http://connect.acrobat.com/KitwareDemo Presentation] via Adobe Connection
** 2:55 Break
** 3:15 Discussion Session:Integrate Modules Into One Coherent User Experience
*** Design overall architecture of the three module - possible [[http://wiki.na-mic.org/Wiki/images/d/d5/AMI_MRMLMarkUpNode.ppt MRML ]] structure
*** Create a feature list based on [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] of annotation capabilities of major vendors
*** Create a description of user-experience and target look & feel (current [[Media:AMI-GUI-Design.ppt | design ]])
** 5:00 Happy hour
* Thursday - Dec 17th
** 9:00 Programming
** 12:00 Final Wrap Up over Lunch
** 1:00 Fly home

== Attendance ==
Open to all self-declared Slicer developers:
#Kilian Pohl
#Steve Pieper (by phone on Wednesday afternoon only)
#Nicole Aucoin
#Andriy Fedorov (Wed only)
#Ron Kikinis (Wed only)
#Wendy Plesniak
#Alex Yarmarkovich (probably Wed)
#Julien Finet
#Karthik Krishnan
#Michael Halle

== References ==

* [http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelDiameterEstimation-Documentation-3.5 Slicer LabelDiameterEstimation extension documentation]
* [http://wiki.slicer.org/slicerWiki/index.php/Modules:ExractSubvolumeROI-Documentation-3.5 Slicer ExtractSubvolumeROI module documentation]

File:VTK-AnnotationAndMarkupWidgets.pdf

2009-12-23T09:19:59Z

Karthik: uploaded a new version of "File:VTK-AnnotationAndMarkupWidgets.pdf"

Dec-2009-SlicerAIMBrainstorming

2009-12-14T10:06:49Z

Karthik: /* Schedule */

== Current Status of Annotation and MarkUp Modules ==
* Summary of [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] that currently exists in annotation tools of large software vendors (created by Kilian after RSNA visit)
* Suggested design of GUI and MRML Structure
* [[ Projects:ARRA:SlicerAM | Progress report ]]

== Logistics ==
*Confirmed date: Wednesday and Thursday, '''December 16 (1-5pm) and 17 (9am-1pm), 2009'''
*Location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room
*Tcon Number: (218) 862-1115 Conference ID 348265#

== Goals ==
The purpose of this meeting is to coordinate the efforts of the [[Projects:ARRA:SlicerAM|Markup and Annotation project]] with the development of the fiducial, measurement model, ROI, and LabelDiameterEstimation. Important questions to consider at the meeting are
* What are similarities and differences between the modules ?
* How should we proceed with the development of the three modules ? Should they be totally separate, share a basic framework, or be combined to one ?
* What should be the overall design of the GUI for the three modules?
* What functionality do we need ? What are specific user scenarios we need to address ?
* What Qt functionality do we need in Slicer ?
* Which interaction are inherently 3D and which are best performed on slice views? How to reconcile these in the most logical and productive way.

== Schedule ==
* Wednesday - Dec 16th
** 1:00 Intro: What is the vision of the AIM project (Kilian)
** 1:15 Demo's
*** Measurement and Fiducial (Nicole)
*** ROI and LabelDiameterEstimation (Andriy, Alex)
*** MarkUp and Annotation (Kilian)
** 2:15 Annotation and markup widgets in VTK [http://wiki.na-mic.org/Wiki/images/1/11/VTK-AnnotationAndMarkupWidgets.pdf link]. VTK's 3D Widgets in general [http://www.na-mic.org/Wiki/images/b/bb/VTKWidgets2.ppt link] (Karthik) .
** 2:35 Current State of Qt in Slicer (Julien Finet and Jean-Christophe Fillion-Robin ?)
** 2:55 Break
** 3:15 Discussion Session:Integrate Modules Into One Coherent User Experience
*** Design overall architecture of the three module - possible [http://wiki.na-mic.org/Wiki/images/d/d5/AMI_MRMLMarkUpNode.ppt MRML ] structure
*** Create a feature list
*** Create a description of user-experience and target look & feel
** 5:00 Happy hour
* Thursday - Dec 17th
** 9:00 Programming
** 12:00 Final Wrap Up over Lunch
** 1:00 Fly home

== Attendance ==
Open to all self-declared Slicer developers:
#Kilian Pohl
#Steve Pieper
#Nicole Aucoin
#Andriy Fedorov
#Ron Kikinis (Wed only)
#Wendy Plesniak
#Alex Yarmarkovich (probably Wed)

== Kilian's ToDo ==

== Results ==
TBA

== Time Line ==
TBA

== References ==

* [http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelDiameterEstimation-Documentation-3.5 Slicer LabelDiameterEstimation extension documentation]
* [http://wiki.slicer.org/slicerWiki/index.php/Modules:ExractSubvolumeROI-Documentation-3.5 Slicer ExtractSubvolumeROI module documentation]

Dec-2009-SlicerAIMBrainstorming

2009-12-14T10:06:34Z

Karthik: /* Schedule */

== Current Status of Annotation and MarkUp Modules ==
* Summary of [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] that currently exists in annotation tools of large software vendors (created by Kilian after RSNA visit)
* Suggested design of GUI and MRML Structure
* [[ Projects:ARRA:SlicerAM | Progress report ]]

== Logistics ==
*Confirmed date: Wednesday and Thursday, '''December 16 (1-5pm) and 17 (9am-1pm), 2009'''
*Location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room
*Tcon Number: (218) 862-1115 Conference ID 348265#

== Goals ==
The purpose of this meeting is to coordinate the efforts of the [[Projects:ARRA:SlicerAM|Markup and Annotation project]] with the development of the fiducial, measurement model, ROI, and LabelDiameterEstimation. Important questions to consider at the meeting are
* What are similarities and differences between the modules ?
* How should we proceed with the development of the three modules ? Should they be totally separate, share a basic framework, or be combined to one ?
* What should be the overall design of the GUI for the three modules?
* What functionality do we need ? What are specific user scenarios we need to address ?
* What Qt functionality do we need in Slicer ?
* Which interaction are inherently 3D and which are best performed on slice views? How to reconcile these in the most logical and productive way.

== Schedule ==
* Wednesday - Dec 16th
** 1:00 Intro: What is the vision of the AIM project (Kilian)
** 1:15 Demo's
*** Measurement and Fiducial (Nicole)
*** ROI and LabelDiameterEstimation (Andriy, Alex)
*** MarkUp and Annotation (Kilian)
** 2:15 Annotation and markup widgets in VTK [http://wiki.na-mic.org/Wiki/images/1/11/VTK-AnnotationAndMarkupWidgets.pdf link] VTK's 3D Widgets in general [http://www.na-mic.org/Wiki/images/b/bb/VTKWidgets2.ppt link] (Karthik) .
** 2:35 Current State of Qt in Slicer (Julien Finet and Jean-Christophe Fillion-Robin ?)
** 2:55 Break
** 3:15 Discussion Session:Integrate Modules Into One Coherent User Experience
*** Design overall architecture of the three module - possible [http://wiki.na-mic.org/Wiki/images/d/d5/AMI_MRMLMarkUpNode.ppt MRML ] structure
*** Create a feature list
*** Create a description of user-experience and target look & feel
** 5:00 Happy hour
* Thursday - Dec 17th
** 9:00 Programming
** 12:00 Final Wrap Up over Lunch
** 1:00 Fly home

== Attendance ==
Open to all self-declared Slicer developers:
#Kilian Pohl
#Steve Pieper
#Nicole Aucoin
#Andriy Fedorov
#Ron Kikinis (Wed only)
#Wendy Plesniak
#Alex Yarmarkovich (probably Wed)

== Kilian's ToDo ==

== Results ==
TBA

== Time Line ==
TBA

== References ==

* [http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelDiameterEstimation-Documentation-3.5 Slicer LabelDiameterEstimation extension documentation]
* [http://wiki.slicer.org/slicerWiki/index.php/Modules:ExractSubvolumeROI-Documentation-3.5 Slicer ExtractSubvolumeROI module documentation]

Dec-2009-SlicerAIMBrainstorming

2009-12-14T10:04:25Z

Karthik: /* Schedule */

== Current Status of Annotation and MarkUp Modules ==
* Summary of [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] that currently exists in annotation tools of large software vendors (created by Kilian after RSNA visit)
* Suggested design of GUI and MRML Structure
* [[ Projects:ARRA:SlicerAM | Progress report ]]

== Logistics ==
*Confirmed date: Wednesday and Thursday, '''December 16 (1-5pm) and 17 (9am-1pm), 2009'''
*Location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room
*Tcon Number: (218) 862-1115 Conference ID 348265#

== Goals ==
The purpose of this meeting is to coordinate the efforts of the [[Projects:ARRA:SlicerAM|Markup and Annotation project]] with the development of the fiducial, measurement model, ROI, and LabelDiameterEstimation. Important questions to consider at the meeting are
* What are similarities and differences between the modules ?
* How should we proceed with the development of the three modules ? Should they be totally separate, share a basic framework, or be combined to one ?
* What should be the overall design of the GUI for the three modules?
* What functionality do we need ? What are specific user scenarios we need to address ?
* What Qt functionality do we need in Slicer ?
* Which interaction are inherently 3D and which are best performed on slice views? How to reconcile these in the most logical and productive way.

== Schedule ==
* Wednesday - Dec 16th
** 1:00 Intro: What is the vision of the AIM project (Kilian)
** 1:15 Demo's
*** Measurement and Fiducial (Nicole)
*** ROI and LabelDiameterEstimation (Andriy, Alex)
*** MarkUp and Annotation (Kilian)
** 2:15 Annotation and markup widgets in VTK (Karthik) [http://wiki.na-mic.org/Wiki/images/1/11/VTK-AnnotationAndMarkupWidgets.pdf Presentation]. VTK 3D Widgets [http://www.na-mic.org/Wiki/images/b/bb/VTKWidgets2.ppt Presentation]
** 2:35 Current State of Qt in Slicer (Julien Finet and Jean-Christophe Fillion-Robin ?)
** 2:55 Break
** 3:15 Discussion Session:Integrate Modules Into One Coherent User Experience
*** Design overall architecture of the three module - possible [http://wiki.na-mic.org/Wiki/images/d/d5/AMI_MRMLMarkUpNode.ppt MRML ] structure
*** Create a feature list
*** Create a description of user-experience and target look & feel
** 5:00 Happy hour
* Thursday - Dec 17th
** 9:00 Programming
** 12:00 Final Wrap Up over Lunch
** 1:00 Fly home

== Attendance ==
Open to all self-declared Slicer developers:
#Kilian Pohl
#Steve Pieper
#Nicole Aucoin
#Andriy Fedorov
#Ron Kikinis (Wed only)
#Wendy Plesniak
#Alex Yarmarkovich (probably Wed)

== Kilian's ToDo ==

== Results ==
TBA

== Time Line ==
TBA

== References ==

* [http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelDiameterEstimation-Documentation-3.5 Slicer LabelDiameterEstimation extension documentation]
* [http://wiki.slicer.org/slicerWiki/index.php/Modules:ExractSubvolumeROI-Documentation-3.5 Slicer ExtractSubvolumeROI module documentation]

Dec-2009-SlicerAIMBrainstorming

2009-12-14T09:53:21Z

Karthik: /* Schedule */

== Current Status of Annotation and MarkUp Modules ==
* Summary of [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] that currently exists in annotation tools of large software vendors (created by Kilian after RSNA visit)
* Suggested design of GUI and MRML Structure
* [[ Projects:ARRA:SlicerAM | Progress report ]]

== Logistics ==
*Confirmed date: Wednesday and Thursday, '''December 16 (1-5pm) and 17 (9am-1pm), 2009'''
*Location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room
*Tcon Number: (218) 862-1115 Conference ID 348265#

== Goals ==
The purpose of this meeting is to coordinate the efforts of the [[Projects:ARRA:SlicerAM|Markup and Annotation project]] with the development of the fiducial, measurement model, ROI, and LabelDiameterEstimation. Important questions to consider at the meeting are
* What are similarities and differences between the modules ?
* How should we proceed with the development of the three modules ? Should they be totally separate, share a basic framework, or be combined to one ?
* What should be the overall design of the GUI for the three modules?
* What functionality do we need ? What are specific user scenarios we need to address ?
* What Qt functionality do we need in Slicer ?
* Which interaction are inherently 3D and which are best performed on slice views? How to reconcile these in the most logical and productive way.

== Schedule ==
* Wednesday - Dec 16th
** 1:00 Intro: What is the vision of the AIM project (Kilian)
** 1:15 Demo's
*** Measurement and Fiducial (Nicole)
*** ROI and LabelDiameterEstimation (Andriy, Alex)
*** MarkUp and Annotation (Kilian)
** 2:15 Current State of VTK 3D Widgets (Karthik) [http://wiki.na-mic.org/Wiki/images/1/11/VTK-AnnotationAndMarkupWidgets.pdf Presentation]
** 2:35 Current State of Qt in Slicer (Julien Finet and Jean-Christophe Fillion-Robin ?)
** 2:55 Break
** 3:15 Discussion Session:Integrate Modules Into One Coherent User Experience
*** Design overall architecture of the three module - possible [http://wiki.na-mic.org/Wiki/images/d/d5/AMI_MRMLMarkUpNode.ppt MRML ] structure
*** Create a feature list
*** Create a description of user-experience and target look & feel
** 5:00 Happy hour
* Thursday - Dec 17th
** 9:00 Programming
** 12:00 Final Wrap Up over Lunch
** 1:00 Fly home

== Attendance ==
Open to all self-declared Slicer developers:
#Kilian Pohl
#Steve Pieper
#Nicole Aucoin
#Andriy Fedorov
#Ron Kikinis (Wed only)
#Wendy Plesniak
#Alex Yarmarkovich (probably Wed)

== Kilian's ToDo ==

== Results ==
TBA

== Time Line ==
TBA

== References ==

* [http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelDiameterEstimation-Documentation-3.5 Slicer LabelDiameterEstimation extension documentation]
* [http://wiki.slicer.org/slicerWiki/index.php/Modules:ExractSubvolumeROI-Documentation-3.5 Slicer ExtractSubvolumeROI module documentation]

File:VTK-AnnotationAndMarkupWidgets.pdf

2009-12-14T09:51:54Z

Karthik:

Dec-2009-SlicerAIMBrainstorming

2009-12-14T09:50:34Z

Karthik: /* Schedule */

== Current Status of Annotation and MarkUp Modules ==
* Summary of [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] that currently exists in annotation tools of large software vendors (created by Kilian after RSNA visit)
* Suggested design of GUI and MRML Structure
* [[ Projects:ARRA:SlicerAM | Progress report ]]

== Logistics ==
*Confirmed date: Wednesday and Thursday, '''December 16 (1-5pm) and 17 (9am-1pm), 2009'''
*Location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room
*Tcon Number: (218) 862-1115 Conference ID 348265#

== Goals ==
The purpose of this meeting is to coordinate the efforts of the [[Projects:ARRA:SlicerAM|Markup and Annotation project]] with the development of the fiducial, measurement model, ROI, and LabelDiameterEstimation. Important questions to consider at the meeting are
* What are similarities and differences between the modules ?
* How should we proceed with the development of the three modules ? Should they be totally separate, share a basic framework, or be combined to one ?
* What should be the overall design of the GUI for the three modules?
* What functionality do we need ? What are specific user scenarios we need to address ?
* What Qt functionality do we need in Slicer ?
* Which interaction are inherently 3D and which are best performed on slice views? How to reconcile these in the most logical and productive way.

== Schedule ==
* Wednesday - Dec 16th
** 1:00 Intro: What is the vision of the AIM project (Kilian)
** 1:15 Demo's
*** Measurement and Fiducial (Nicole)
*** ROI and LabelDiameterEstimation (Andriy, Alex)
*** MarkUp and Annotation (Kilian)
** 2:15 Current State of VTK 3D Widgets (Karthik) [[File:AIMVTKWidgets.ppt]] ppt
** 2:35 Current State of Qt in Slicer (Julien Finet and Jean-Christophe Fillion-Robin ?)
** 2:55 Break
** 3:15 Discussion Session:Integrate Modules Into One Coherent User Experience
*** Design overall architecture of the three module - possible [http://wiki.na-mic.org/Wiki/images/d/d5/AMI_MRMLMarkUpNode.ppt MRML ] structure
*** Create a feature list
*** Create a description of user-experience and target look & feel
** 5:00 Happy hour
* Thursday - Dec 17th
** 9:00 Programming
** 12:00 Final Wrap Up over Lunch
** 1:00 Fly home

== Attendance ==
Open to all self-declared Slicer developers:
#Kilian Pohl
#Steve Pieper
#Nicole Aucoin
#Andriy Fedorov
#Ron Kikinis (Wed only)
#Wendy Plesniak
#Alex Yarmarkovich (probably Wed)

== Kilian's ToDo ==

== Results ==
TBA

== Time Line ==
TBA

== References ==

* [http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelDiameterEstimation-Documentation-3.5 Slicer LabelDiameterEstimation extension documentation]
* [http://wiki.slicer.org/slicerWiki/index.php/Modules:ExractSubvolumeROI-Documentation-3.5 Slicer ExtractSubvolumeROI module documentation]

Dec-2009-SlicerAIMBrainstorming

2009-12-14T09:50:08Z

Karthik: /* Schedule */

== Current Status of Annotation and MarkUp Modules ==
* Summary of [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] that currently exists in annotation tools of large software vendors (created by Kilian after RSNA visit)
* Suggested design of GUI and MRML Structure
* [[ Projects:ARRA:SlicerAM | Progress report ]]

== Logistics ==
*Confirmed date: Wednesday and Thursday, '''December 16 (1-5pm) and 17 (9am-1pm), 2009'''
*Location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room
*Tcon Number: (218) 862-1115 Conference ID 348265#

== Goals ==
The purpose of this meeting is to coordinate the efforts of the [[Projects:ARRA:SlicerAM|Markup and Annotation project]] with the development of the fiducial, measurement model, ROI, and LabelDiameterEstimation. Important questions to consider at the meeting are
* What are similarities and differences between the modules ?
* How should we proceed with the development of the three modules ? Should they be totally separate, share a basic framework, or be combined to one ?
* What should be the overall design of the GUI for the three modules?
* What functionality do we need ? What are specific user scenarios we need to address ?
* What Qt functionality do we need in Slicer ?
* Which interaction are inherently 3D and which are best performed on slice views? How to reconcile these in the most logical and productive way.

== Schedule ==
* Wednesday - Dec 16th
** 1:00 Intro: What is the vision of the AIM project (Kilian)
** 1:15 Demo's
*** Measurement and Fiducial (Nicole)
*** ROI and LabelDiameterEstimation (Andriy, Alex)
*** MarkUp and Annotation (Kilian)
** 2:15 Current State of VTK 3D Widgets (Karthik) [[[File:AIMVTKWidgets.ppt]]ppt]
** 2:35 Current State of Qt in Slicer (Julien Finet and Jean-Christophe Fillion-Robin ?)
** 2:55 Break
** 3:15 Discussion Session:Integrate Modules Into One Coherent User Experience
*** Design overall architecture of the three module - possible [http://wiki.na-mic.org/Wiki/images/d/d5/AMI_MRMLMarkUpNode.ppt MRML ] structure
*** Create a feature list
*** Create a description of user-experience and target look & feel
** 5:00 Happy hour
* Thursday - Dec 17th
** 9:00 Programming
** 12:00 Final Wrap Up over Lunch
** 1:00 Fly home

== Attendance ==
Open to all self-declared Slicer developers:
#Kilian Pohl
#Steve Pieper
#Nicole Aucoin
#Andriy Fedorov
#Ron Kikinis (Wed only)
#Wendy Plesniak
#Alex Yarmarkovich (probably Wed)

== Kilian's ToDo ==

== Results ==
TBA

== Time Line ==
TBA

== References ==

* [http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelDiameterEstimation-Documentation-3.5 Slicer LabelDiameterEstimation extension documentation]
* [http://wiki.slicer.org/slicerWiki/index.php/Modules:ExractSubvolumeROI-Documentation-3.5 Slicer ExtractSubvolumeROI module documentation]

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2009-03-19T22:15:19Z

Karthik:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:widgets_storyboard_slicer3.png|thumb|320px|Concept screenshot of widgets in slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder
* BWH: Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found here [http://www.na-mic.org/Wiki/images/b/bb/VTKWidgets2.ppt]. Relevant widgets for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget
* Add interaction cues
** Some widgets (e.g., implicit plane widget) should modify the cursor, or change appearance, when the mouse is moved over interactive handles.

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the existing fiducial widget and replace it with vtkSeedWidget
** This involves generalizing vtkHandleWidget to support arbitrary polygonal shapes since Slicer3 has several geometrical representations for seeds (2D: dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow), (3D: Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done
* Livewire widget --- Exists

</div>

<br style="clear: both;" />

</div>

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2009-03-19T22:13:39Z

Karthik:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:widgets_storyboard_slicer3.png|thumb|320px|Concept screenshot of widgets in slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder
* BWH: Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found at this [http://www.na-mic.org/Wiki/images/b/bb/VTKWidgets2.ppt]. Relevant widgets for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget
* Add interaction cues
** Some widgets (e.g., implicit plane widget) should modify the cursor, or change appearance, when the mouse is moved over interactive handles.

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the existing fiducial widget and replace it with vtkSeedWidget
** This involves generalizing vtkHandleWidget to support arbitrary polygonal shapes since Slicer3 has several geometrical representations for seeds (2D: dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow), (3D: Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done
* Livewire widget --- Exists

</div>

<br style="clear: both;" />

</div>

File:VTKWidgets2.ppt

2009-03-19T22:12:28Z

Karthik:

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2009-03-19T22:10:46Z

Karthik:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:widgets_storyboard_slicer3.png|thumb|320px|Concept screenshot of widgets in slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder
* BWH: Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found at this [[Media:VTKWidgets2.ppt]][http://www.na-mic.org/Wiki/images/a/ab/VTKWidgets.ppt presentation]. Relevant widgets for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget
* Add interaction cues
** Some widgets (e.g., implicit plane widget) should modify the cursor, or change appearance, when the mouse is moved over interactive handles.

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the existing fiducial widget and replace it with vtkSeedWidget
** This involves generalizing vtkHandleWidget to support arbitrary polygonal shapes since Slicer3 has several geometrical representations for seeds (2D: dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow), (3D: Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done
* Livewire widget --- Exists

</div>

<br style="clear: both;" />

</div>

File:KarthikMRPhantomWithEndorectalCoilBalloon.jpg

2009-03-05T17:32:09Z

Karthik:

User:Karthik

2009-03-05T17:31:59Z

Karthik: /* Temporary hosting for NAMIC (RemoveMe) */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.zip]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

=== EM Segmenter ===
EM Segmenter simple example data for segmentation from a T1 MR. [[Media:EMSegmenterT1Example.zip]]

=== Temporary hosting for NAMIC (RemoveMe) ===
[[Image:KarthikMRPhantomWithEndorectalCoilBalloon.jpg]]

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2009-03-05T17:30:00Z

Karthik: /* EM Segmenter */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.zip]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

=== EM Segmenter ===
EM Segmenter simple example data for segmentation from a T1 MR. [[Media:EMSegmenterT1Example.zip]]

=== Temporary hosting for NAMIC (RemoveMe) ===
[[Image:KarthikMRPhantomWithEndorectalCoilBalloon.png]]

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

2009 Winter Project Week

2008-12-18T16:37:38Z

Karthik: /* Other NA-MIC Projects */

Back to [[Project Events]], [[AHM_2009]], [[Events]]

==Introduction to NA-MIC Project Week==

Please read an introduction about these events [[Project_Events#Introduction|here]].

== Dates.Venue.Registration ==

Please [[AHM_2009#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2009#Agenda|click here for the agenda for AHM 2009 and Project Week]].

==Projects==
Please note:
*Please use the [[2009_Winter_Project_Week_Template|'''2009 Project Week Template''']] to create a page for your project(s)
*[[2008_Summer_Project_Week#Projects|Last Event's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
*Next Project Week is at MIT -- June 22-26, 2009
The following is a list of all projects that will be pursued at this meeting.

===NA-MIC DBP Roadmap Projects===
Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

#[[DBP2:Harvard:Brain_Segmentation_Roadmap|Harvard Roadmap Project: Stochastic Tractography for VCFS]]
##[[2009_Winter_Project_Week:GT_TubularSurfaceSeg|Tubular Surface Segmentation for fiber bundle extraction]] (Vandana Mohan GATech, Allen Tannenbaum GATech, Marek Kubicki BWH, Stephen Aylward Kitware)
##[[2009_Winter_Project_Week_StochasticTractography |Stochastic Tractograhy Tool for Slicer]] (Marek Kubicki BWH, Julien de Siebenthal BWH, Steve Pieper Isomics)
##[[2009_Winter_Project_Week_Slicer3Functioning |Evaluation of basic Slicer 3.0 Functionality from a User Perspective]] (Doug Terry BWH, Marek Kubicki BWH, Sylvain Bouix BWH, Steve Pieper, Wendy Plesniak, Nicole Aucoin)
##[[2009_Winter_Project_Week:DTIGroupAnalysis |Group analysis of DTI fiber bundles]] (Casey Goodlett, Guido Gerig, Marek Kubicki, Sylvain Bouix)
#[[DBP2:UNC:Cortical_Thickness_Roadmap|UNC Roadmap Project: Cortical Thickness Measurement for Autism]]
##[[2009_Winter_Project_Week:LocalCorticalThicknessPipeline|Local Cortical Thickness Pipeline]] (Clement Vachet, Martin Styner, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz)
##[[2009_Winter_Project_Week:RegionalCorticalThicknessPipeline|Regional Cortical Thickness Pipeline]] (Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett)
#[[DBP2:MIND:Roadmap|MIND Roadmap Project: Brain Lesion Analysis in Lupus]]
##[[2009_Winter_Project_Week:HighLevelWizard|Slicer High Level Wizard Project]](Steve Pieper, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LesionAlgorithms|Review of Lesion Algorithms]](Ross Whitaker, Vincent Magnotta, Marcel Prastawa, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LongitudinalLesions|Determine Requirements of Longitudinal Lesion Analyses]](Jeremy Bockholt, Marcel Prastawa, Mark Scully, Andriy Fedorov)
#[[DBP2:JHU:Roadmap|JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]
##[[2009_Winter_Project_Week:SterotacticFrameModel|Generating a Model of a Stereotactic Frame for Neurosurgery]] (Rares Crisan, Queens, Gabor Fichtinger, Queens, Katie Hayes, BWH)
##[[prostateSegmentationAHM2009|Prostate segmentation module for Slicer3]] (Siddharth Vikal, Gabor Fichtinger, Queens University, Katie Hayes, Brigham and Women's Hospital, Yi Gao, Allen Tannenbaum, Georgia Tech)

===Other NA-MIC Projects===
#[[2009_Winter_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Winter_Project_Week_Hageman_UCLANSBrainLab | UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning]] Using Slicer and its link to BrainLab to investigate whether different tractography methods aid in preoperative planning of tumor resection.(Nathan Hageman UCLA)
#[[2009_Winter_Project_Week_Hageman_FEMSolverLib | Development of FEM / FVM solver library in ITK/VTK]] (and/or Python?) (Nathan Hageman UCLA, Vince, Luca, Steve)
#[[2009_Winter_Project_Week_Transform_Management | Transform Management]](Jim Miller)
#[[2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 | Interactive 3D Widgets - Introduce new interactors into Slicer; extensions to current widgets to support Slicer]] (Karthik, Will Schroeder, Nicole Aucoin)
#[[2009_Winter_Project_Week_vtkITK_Pipeline | Using ITK in VTK Pipelines]] (Jim, Steve)
#[[2009_Winter_Project_Week_SlicerLayouts | User Interface Flexible Layouts]] (Wendy, Jim, Steve, Sebastien, Ron)
#[[2009_Winter_Project_Week_Python | Python interface completion and packaging - Fortran and openssl problems]] (Luca, Steve, Demian)
#[[Two-tensor tractography in Slicer using Python and Teem]] (Madeleine Seeland, C-F Westin, Xiaodong Tao)
#[[2009_Winter_Project_Week_Rotation_Tangents | Diffusion Tensor Invariant gradients and rotation tangents in Python and Teem]] (Peter Savadjiev, C-F Westin, Luis Ibanez)
#[[2009_Winter_Project_Week_Automated_GUI_Testing | KWWidgets and Slicer automated GUI testing ]](Sebastien, Yumin, Interested User: Vince)
#[[2009_Winter_Project_Week_ColorModule | Slicer Colors Module update ]](Nicole)
#[[Volume Rendering]] (Alex, Curt, Nicholas)
#[[2009_Winter_Project_Week_XND | XNAT Desktop BatchMake integration & Slicer interface]] (Dan Marcus, Stephen Aylward, Wendy Plesniak, Curt Lisle)
#[[2009_Winter_Project_Week_Cortical_Correspondence | Cortical correspondence using DTI]] (Ipek, Martin, Xiaodong)
#[[2009_Winter_Project_Week_Command_Line_Program_Testing |Command Line Program Testing]] (Lorensen, Ron)
#[[2009_Winter_Project_Week_Slicer_VMTK |Vessel Segmentation in Slicer using VMTK]] ([[User:haehn|Daniel Haehn]], [[User:lantiga| Luca Antiga]])
#[[2009_Winter_Project_Week_fMRI_Clustering |Exploring Functional Connectivity in fMRI via Clustering]] (Archana Venkataraman, Marek Kubicki, Polina Golland)
#[[2009_Winter_Project_Week_Compiler_Warnings:Slicer3_Graffiti |Compiler Warnings:Slicer3's Graffiti]] (Lorensen, NA-MIC)
#[[2009_Winter_Project_Week_ChangeTracker |Measuring dynamics of tumor growth in Slicer3 with ChangeTracker]] (Andriy Fedorov)
#[[2009_Winter_Project_Week_GWE_Catalogs |GWE integration with catalog files]] (Marco)
#[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti)
#[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard)
#[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas)
#[[2009_Winter_Project_Week_UtahPlugins | Integration of Utah registration and segmentation methods as Slicer plugins]] (Marcel Prastawa)
#[[2009_Winter_Project_Week_OMTRegistration | DWI to MRI Registration Using Optimat Mass Transport]] (Sylvain Bouix, Ivan Kolesov GATech)

===External Collaborations===
* [[Iowa Meshing Tutorial]]
*Wake Forest - Virginia Tech
** [[2009_Winter_Project_Week_WFU1 | Move to All Slicer3 Workflow]]
** [[2009_Winter_Project_Week_WFU2 | Development of deformation based morphometry module]]
*Georgetown U: [[2009_Winter_Project_Week_NAVRFA | Prototype RF Lesion Ablation Workflow prototyped in Slicer]]
*UNC:
**[[2009_UNC_HAMMER_WML | MR-image registration and white matter lesion segmentation algorithms to be extended and added to namic kit]]
* [[Stanford SIMBIOS: Whole Body Segmentation for Simulation]]
* [[2009_Winter_Project_Week_MRSI | MRSI Module for Slicer (Bjoern Menze)]]
*[[NCI Evaluating NA-MIC Tools for Image Analysis]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 16th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 16: Engineering Infrastructure Projects
#*October 23: Funded External Collaboration Projects
#*November 6: DPB Projects
#*November 20: New Collaborations
#*December 4: Other Projects
#*December 18: Loose Ends
#By December 17, 2008: [[2009_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# FINAL TCON: December 18th 3pm ET to tie loose ends
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2008-12-18T16:33:11Z

Karthik:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:widgets_storyboard_slicer3.png|thumb|320px|Concept screenshot of widgets in slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder
* BWH: Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found at this [http://www.na-mic.org/Wiki/images/a/ab/VTKWidgets.ppt presentation]. Relevant widgets for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the existing fiducial widget and replace it with vtkSeedWidget
** This involves generalizing vtkHandleWidget to support arbitrary polygonal shapes since Slicer3 has several geometrical representations for seeds (2D: dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow), (3D: Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done
* Livewire widget --- Exists

</div>

<br style="clear: both;" />

</div>

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2008-12-18T16:32:38Z

Karthik:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:widgets_storyboard_slicer3.png|thumb|320px|Concept screenshot of widgets in slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder, Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found at this [http://www.na-mic.org/Wiki/images/a/ab/VTKWidgets.ppt presentation]. Relevant widgets for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the existing fiducial widget and replace it with vtkSeedWidget
** This involves generalizing vtkHandleWidget to support arbitrary polygonal shapes since Slicer3 has several geometrical representations for seeds (2D: dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow), (3D: Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done
* Livewire widget --- Exists

</div>

<br style="clear: both;" />

</div>

File:Widgets storyboard slicer3.png

2008-12-18T16:27:33Z

Karthik:

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2008-12-18T16:27:02Z

Karthik:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:widgets_storyboard_slicer3.png|thumb|320px|Concept screenshot of widgets in slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder, Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found at this [www.na-mic.org/Wiki/images/a/ab/VTKWidgets.ppt presentation]. Relevant ones for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the fiducial widgets and replace them with the vtkSeedWidget
** This involves generalize the vtkHandleWidget to support arbitrary polygonal shape since Slicer3 has several geometrical representations for seeds in 2D (dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow) and in 3D (Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done
* Livewire widget --- Exists

</div>

<br style="clear: both;" />

</div>

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2008-12-18T16:13:36Z

Karthik:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:squish_slicer3.png|thumb|320px|Image showing the end result of a Squish test with the clipbox of a volume in Slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder, Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found at this [www.na-mic.org/Wiki/images/a/ab/VTKWidgets.ppt presentation]. Relevant ones for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the fiducial widgets and replace them with the vtkSeedWidget
** This involves generalize the vtkHandleWidget to support arbitrary polygonal shape since Slicer3 has several geometrical representations for seeds in 2D (dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow) and in 3D (Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done
* Livewire widget --- Exists

</div>

<br style="clear: both;" />

</div>

===References===

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2008-12-18T15:26:17Z

Karthik:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:squish_slicer3.png|thumb|320px|Image showing the end result of a Squish test with the clipbox of a volume in Slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder, Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found at this [www.na-mic.org/Wiki/images/a/ab/VTKWidgets.ppt presentation]. Relevant ones for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the fiducial widgets and replace them with the vtkSeedWidget
** This involves generalize the vtkHandleWidget to support arbitrary polygonal shape since Slicer3 has several geometrical representations for seeds in 2D (dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow) and in 3D (Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done

</div>

<br style="clear: both;" />

</div>

===References===

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2008-12-18T15:21:25Z

Karthik: New page: {| |Project Week Main Page ]] |[[Image:squish_slicer3.png|thumb|320px|Image showing the end result of a Squish test...

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:squish_slicer3.png|thumb|320px|Image showing the end result of a Squish test with the clipbox of a volume in Slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder, Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found at this [www.na-mic.org/Wiki/images/a/ab/VTKWidgets.ppt presentation]. Relevant ones for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Generalize the handle widgets to support arbitrary polygonal shape since slicer3

</div>

<br style="clear: both;" />

</div>

===References===

File:EMSegmenterT1Example.zip

2008-11-27T00:03:51Z

Karthik:

User:Karthik

2008-11-26T23:58:47Z

Karthik: /* EM Segmenter */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.zip]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

=== EM Segmenter ===
EM Segmenter simple example data for segmentation from a T1 MR. [[Media:EMSegmenterT1Example.zip]]

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2008-11-26T23:58:27Z

Karthik:

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.zip]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

=== EM Segmenter ===
EM Segmenter simple example data for segmentation from a T1 MR. [[Media:Example.ogg]]

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2008-11-15T21:23:53Z

Karthik: /* Updating Fiducial list to vtkSeedWidget [Working on it] */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.zip]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

File:ImageActorConstrainedFiducial.zip

2008-11-15T21:23:10Z

Karthik:

User:Karthik

2008-11-15T21:14:25Z

Karthik:

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:ImageActorConstrainedFiducial.avi]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2008-11-15T21:13:57Z

Karthik:

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Image:Example.jpg]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

File:Example.ogg

2008-11-15T21:08:38Z

Karthik:

User:Karthik

2008-11-15T21:05:29Z

Karthik: /* Updating Fiducial list to vtkSeedWidget [Working on it] */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.
* Constraints on fiducials
** Constrained to an image actor as in [[Media:Example.ogg]]

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2008-11-07T21:49:47Z

Karthik: /* Angle measurement [Done] */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** vtkArcSource.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2008-11-07T21:35:00Z

Karthik: /* Widgets Slicer wish list */

== Widgets Slicer wish list ==

=== Angle measurement '''[Done]'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''[Done]''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

=== Picking issue with widgets [Done] ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75

===Updating Fiducial list to vtkSeedWidget '''[Working on it]'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]

User:Karthik

2008-11-07T21:12:01Z

Karthik:

== Widgets Slicer wish list ==

=== Angle measurement '''Done'''===
* A 3D representation to the angle widget has been added. The following were added to support this:
** vtkAngleRepresentation3D.cxx/h
** TestAngleWidget3D.cxx
** TestAngleWidget2D.cxx
* Bug fix: unnecessary renders were removed from the angle widget. This somehow went unnoticed in the 2D case, possibly because the data being rendered is fairly small.

=== Distance measurement widget '''Done''' ===
* Line Widget extended to support optional text annotations indicating the distance between its end-points. This should suffice to measure distances between 2 points in 3D.

===Updating Fiducial list to vtkSeedWidget '''Working on it'''===
Notes from talking with Nicole, Oct 7/08

Features needed:

* Ability to set properties per seed
* Ability to associate a label with a seed.
* Label visibility can be toggled on/off
* Ability to associate (optionally) a note with a seed (Ron's request)
* Glyps for seed shape
** 2D
*** All the ones in vtkGlyph2D
*** StarBurst2D,
** 3D
*** Sphere3D
*** Diamond3D
* Nicole to check if transform is applied to the fiducials in slicer registration. Really bad idea to do so with widgets.

=== Affine widget ===
* Mega widget (will take time)
* 6 degrees of freedom.

=== Live wire widget ===
* Live wire widget for the editor
* Exists in VTK HEAD Sep 08. Upgrade from VTK 5.2

=== Contour widget (just a wish, not urgent) ===
* Use case: Pick a series of models to place in a hierarchy
* Lasso around a bunch of objects in 3D

=== VTKEdge ===
* Steve and Will to talk about VTKEdge, licensing etc.
* Paintbrushes in VTKEdge
* GPU ray caster

=== Picking issue with widgets ===
* Bug picking implicit plane widget.
** Note to KK: Look at SlicerPlaneSWidget.tcl:75
TODO List:
* Distance Widget in 3D

[mailto:karthik.krishnan@kitware.com Karthik Krishnan]
Research Engineer
[http://www.kitware.com/profile/team/krishnan.html Home Page]