NAMIC Wiki - User contributions [en]

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-25T09:06:21Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
Image:Terminology_web_app.jpg|Component of the dcmqi web app for populating terminology
Image:Terminology_web_app-color.jpg|Component of the dcmqi web app for populating terminology, with color picker widget
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)
* Marco Nolden (DKFZ)
* Andras Lasso (Queen's)
* Christian Herz (BWH)

==Project Description==

This project is focussed on linking various types of information related to segmented structures. The new Segments editor is being extended to associate segments with standard terminolgy describing anatomical regions, expanding the color selection to index into the SNO-MED terminology hierarchy.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
|

* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview slides [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ SlicerRT] ([https://github.com/SlicerRt/SlicerRT/ github mirror]), with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmqi ([https://github.com/QIICR/dcmqi/tree/gh-pages github source])
** To view in slicer's webkit
view = qt.QWebView()
view.setUrl(qt.QUrl('http://qiicr.org/dcmqi/'))
view.show()
* From Andrey: disconnect segment ID from the color ID and from the terminology associated with it - it should be possible to have more than one distinctive segment that has the same color and the same terminology, but are differentiated by segment ID and segment label.
|

* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node. (Csaba)
*** When creating the new temp color node, also create a new terminology associated with it (Nicole)
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor (Csaba)
*** Bring up the CTK color picker by default on adding a new segment to set/edit the default color/terminology (Csaba)
*** Extend/fix the CTK color picker:
**** Show the custom color node by default not the Generic Anatomy one (Nicole - fixed in Colors module)
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?) (Nicole)
***** Not a bug, allows you to copy colors, but do set the first selection
**** Add display of the terminology associated with the color node displayed (Nicole)
**** Add terminology editing/look up to set a new terminology (Nicole - post project week)
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module, see [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Widgets/qMRMLColorModel.cxx#L340 qMRMLColorModel] (Csaba)
* Met with Andrey and he filled in use cases below
* Fixed color node selection in Colors module, providing UI to set it from other modules
* Next Steps:
** Continue working on CTK widget update/integration
|}

=== Use cases ===

* Category = Segmented Property Category
* Type = Segmented Property Type (+Modifier, optional)
* Anatomic region (+Modifier, optional)

==== Loading segmentation from DICOM ====
Assumptions:
* can expect that Category and Type will be initialized, if not - fall back to default codes (Tissue/Tissue codes)
* anatomic region may or may not be initialized (example: can specify anatomic location of the tumor, but may not be present)
* colors may or may not be specified
Consequences:
* need to be able to handle these various combinations
* if colors are not specified, would be nice to suggest some good default color choices (to optimize differentiation of the structures? lookup of default colors may not be easy for medium-large dictionaries)
* it is not clear that it is a good idea to restrict the choices of terminology (or colors) if a user wants to modify segmentation loaded from DICOM - so it might be helpful to choose from existing color maps / terminology dictionaries for a DICOM-loaded segmentation

==== Creating segmentation from scratch ====
* choose from predefined dictionaries (combinations of Type/Category/Anatomy customized for a specific use case)
* choose from predefined color tables, or perhaps color assignment strategies (e.g., high contrast, similar shades of color for the segments corresponding to the same kind of structure)

=== Workflow ===

To add a new segment:
* user clicks "add segment"
* terminology and color are populated to some default value
* user has an option to change the color and terminology separately TerminologyWidget (naming to be confirmed)
* user has the option to choose the dictionary in the TerminologyWidget
* the purpose of the dictionary is to define specific combinations of category/type/anatomy for the specific use case (GenericAnatomy LUT is one example, and we will also need a larger set of codes defined by the standard)

=== Implementation approach ===

Terminology browser widget:
* Slicer widget vs CTK widget: consensus seems to be that CTK widget makes sense
* Qt widget vs web app: considering that basic web app already exists, it may make sense to experiment reusing it; Marco notes that it may be futile to experiment with web app integration in Slicer using the current Qt 4
** Marco confirmed that qiicr.org/dcmqi renders correctly in Qt 5.6 (used in MITK); it does not render in Slicer Qt 4.x webkit
* We will continue with prototyping in the web app (add support for color picker and dictionary selection)
** web app color picker issue https://github.com/QIICR/dcmqi/issues/21

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-25T08:57:36Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
Image:Terminology_web_app.jpg|Component of the dcmqi web app for populating terminology
Image:Terminology_web_app-color.jpg|Component of the dcmqi web app for populating terminology, with color picker widget
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)
* Marco Nolden (DKFZ)
* Andras Lasso (Queen's)
* Christian Herz (BWH)

==Project Description==

This project is focussed on linking various types of information related to segmented structures. The new Segments editor is being extended to associate segments with standard terminolgy describing anatomical regions, expanding the color selection to index into the SNO-MED terminology hierarchy.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
|

* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview slides [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ SlicerRT] ([https://github.com/SlicerRt/SlicerRT/ github mirror]), with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmqi ([https://github.com/QIICR/dcmqi/tree/gh-pages github source])
** To view in slicer's webkit
view = qt.QWebView()
view.setUrl(qt.QUrl('http://qiicr.org/dcmqi/'))
view.show()
* From Andrey: disconnect segment ID from the color ID and from the terminology associated with it - it should be possible to have more than one distinctive segment that has the same color and the same terminology, but are differentiated by segment ID and segment label.
|

* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node. (Csaba)
*** When creating the new temp color node, also create a new terminology associated with it (Nicole)
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor (Csaba)
*** Bring up the CTK color picker by default on adding a new segment to set/edit the default color/terminology (Csaba)
*** Extend/fix the CTK color picker:
**** Show the custom color node by default not the Generic Anatomy one (Nicole - fixed in Colors module)
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?) (Nicole)
***** Not a bug, allows you to copy colors, but do set the first selection
**** Add display of the terminology associated with the color node displayed (Nicole)
**** Add terminology editing/look up to set a new terminology (Nicole - post project week)
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module, see [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Widgets/qMRMLColorModel.cxx#L340 qMRMLColorModel] (Csaba)
* Met with Andrey and he filled in use cases below
* Next Steps:
** Continue working on CTK widget update/integration
|}

=== Use cases ===

* Category = Segmented Property Category
* Type = Segmented Property Type (+Modifier, optional)
* Anatomic region (+Modifier, optional)

==== Loading segmentation from DICOM ====
Assumptions:
* can expect that Category and Type will be initialized, if not - fall back to default codes (Tissue/Tissue codes)
* anatomic region may or may not be initialized (example: can specify anatomic location of the tumor, but may not be present)
* colors may or may not be specified
Consequences:
* need to be able to handle these various combinations
* if colors are not specified, would be nice to suggest some good default color choices (to optimize differentiation of the structures? lookup of default colors may not be easy for medium-large dictionaries)
* it is not clear that it is a good idea to restrict the choices of terminology (or colors) if a user wants to modify segmentation loaded from DICOM - so it might be helpful to choose from existing color maps / terminology dictionaries for a DICOM-loaded segmentation

==== Creating segmentation from scratch ====
* choose from predefined dictionaries (combinations of Type/Category/Anatomy customized for a specific use case)
* choose from predefined color tables, or perhaps color assignment strategies (e.g., high contrast, similar shades of color for the segments corresponding to the same kind of structure)

=== Workflow ===

To add a new segment:
* user clicks "add segment"
* terminology and color are populated to some default value
* user has an option to change the color and terminology separately TerminologyWidget (naming to be confirmed)
* user has the option to choose the dictionary in the TerminologyWidget
* the purpose of the dictionary is to define specific combinations of category/type/anatomy for the specific use case (GenericAnatomy LUT is one example, and we will also need a larger set of codes defined by the standard)

=== Implementation approach ===

Terminology browser widget:
* Slicer widget vs CTK widget: consensus seems to be that CTK widget makes sense
* Qt widget vs web app: considering that basic web app already exists, it may make sense to experiment reusing it; Marco notes that it may be futile to experiment with web app integration in Slicer using the current Qt 4
** Marco confirmed that qiicr.org/dcmqi renders correctly in Qt 5.6 (used in MITK); it does not render in Slicer Qt 4.x webkit
* We will continue with prototyping in the web app (add support for color picker and dictionary selection)
** web app color picker issue https://github.com/QIICR/dcmqi/issues/21

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-25T08:07:30Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
Image:Terminology_web_app.jpg|Component of the dcmqi web app for populating terminology
Image:Terminology_web_app-color.jpg|Component of the dcmqi web app for populating terminology, with color picker widget
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)
* Marco Nolden (DKFZ)
* Andras Lasso (Queen's)
* Christian Herz (BWH)

==Project Description==

This project is focussed on linking various types of information related to segmented structures. The new Segments editor is being extended to associate segments with standard terminolgy describing anatomical regions, expanding the color selection to index into the SNO-MED terminology hierarchy.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
|

* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview slides [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ SlicerRT] ([https://github.com/SlicerRt/SlicerRT/ github mirror]), with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmqi ([https://github.com/QIICR/dcmqi/tree/gh-pages github source])
** To view in slicer's webkit
view = qt.QWebView()
view.setUrl(qt.QUrl('http://qiicr.org/dcmqi/'))
view.show()
* From Andrey: disconnect segment ID from the color ID and from the terminology associated with it - it should be possible to have more than one distinctive segment that has the same color and the same terminology, but are differentiated by segment ID and segment label.
|

* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node. (Csaba)
*** When creating the new temp color node, also create a new terminology associated with it (Nicole)
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor (Csaba)
*** Bring up the CTK color picker by default on adding a new segment to set/edit the default color/terminology (Csaba)
*** Extend/fix the CTK color picker:
**** Show the custom color node by default not the Generic Anatomy one (Nicole - fixed in Colors module)
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?) (Nicole)
***** Not a bug, allows you to copy colors, but do set the first selection
**** Add display of the terminology associated with the color node displayed (Nicole)
**** Add terminology editing/look up to set a new terminology (Nicole - post project week)
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module, see [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Widgets/qMRMLColorModel.cxx#L340 qMRMLColorModel] (Csaba)
* Met with Andrey and he filled in use cases below
|}

=== Use cases ===

* Category = Segmented Property Category
* Type = Segmented Property Type (+Modifier, optional)
* Anatomic region (+Modifier, optional)

==== Loading segmentation from DICOM ====
Assumptions:
* can expect that Category and Type will be initialized, if not - fall back to default codes (Tissue/Tissue codes)
* anatomic region may or may not be initialized (example: can specify anatomic location of the tumor, but may not be present)
* colors may or may not be specified
Consequences:
* need to be able to handle these various combinations
* if colors are not specified, would be nice to suggest some good default color choices (to optimize differentiation of the structures? lookup of default colors may not be easy for medium-large dictionaries)
* it is not clear that it is a good idea to restrict the choices of terminology (or colors) if a user wants to modify segmentation loaded from DICOM - so it might be helpful to choose from existing color maps / terminology dictionaries for a DICOM-loaded segmentation

==== Creating segmentation from scratch ====
* choose from predefined dictionaries (combinations of Type/Category/Anatomy customized for a specific use case)
* choose from predefined color tables, or perhaps color assignment strategies (e.g., high contrast, similar shades of color for the segments corresponding to the same kind of structure)

=== Workflow ===

To add a new segment:
* user clicks "add segment"
* terminology and color are populated to some default value
* user has an option to change the color and terminology separately TerminologyWidget (naming to be confirmed)
* user has the option to choose the dictionary in the TerminologyWidget
* the purpose of the dictionary is to define specific combinations of category/type/anatomy for the specific use case (GenericAnatomy LUT is one example, and we will also need a larger set of codes defined by the standard)

=== Implementation approach ===

Terminology browser widget:
* Slicer widget vs CTK widget: consensus seems to be that CTK widget makes sense
* Qt widget vs web app: considering that basic web app already exists, it may make sense to experiment reusing it; Marco notes that it may be futile to experiment with web app integration in Slicer using the current Qt 4
** Marco confirmed that qiicr.org/dcmqi renders correctly in Qt 5.6 (used in MITK); it does not render in Slicer Qt 4.x webkit
* We will continue with prototyping in the web app (add support for color picker and dictionary selection)
** web app color picker issue https://github.com/QIICR/dcmqi/issues/21

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-25T07:51:06Z

Naucoin:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
Image:Terminology_web_app.jpg|Component of the dcmqi web app for populating terminology
Image:Terminology_web_app-color.jpg|Component of the dcmqi web app for populating terminology, with color picker widget
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)
* Marco Nolden (DKFZ)
* Andras Lasso (Queen's)
* Christian Herz (BWH)

==Project Description==

This project is focussed on linking various types of information related to segmented structures. The new Segments editor is being extended to associate segments with standard terminolgy describing anatomical regions, expanding the color selection to index into the SNO-MED terminology hierarchy.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
|

* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ SlicerRT] ([https://github.com/SlicerRt/SlicerRT/ github mirror]), with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmqi ([https://github.com/QIICR/dcmqi/tree/gh-pages github source])
** To view in slicer's webkit
view = qt.QWebView()
view.setUrl(qt.QUrl('http://qiicr.org/dcmqi/'))
view.show()
* From Andrey: disconnect segment ID from the color ID and from the terminology associated with it - it should be possible to have more than one distinctive segment that has the same color and the same terminology, but are differentiated by segment ID and segment label.
|

* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node. (Csaba)
*** When creating the new temp color node, also create a new terminology associated with it (Nicole)
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor (Csaba)
*** Bring up the CTK color picker by default on adding a new segment to set/edit the default color/terminology (Csaba)
*** Extend/fix the CTK color picker:
**** Show the custom color node by default not the Generic Anatomy one (Nicole)
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?) (Nicole)
**** Add display of the terminology associated with the color node displayed (Nicole)
**** Add terminology editing/look up to set a new terminology (Nicole - post project week)
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module, see [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Widgets/qMRMLColorModel.cxx#L340 qMRMLColorModel] (Csaba)
|}

=== Use cases ===

* Category = Segmented Property Category
* Type = Segmented Property Type (+Modifier, optional)
* Anatomic region (+Modifier, optional)

==== Loading segmentation from DICOM ====
Assumptions:
* can expect that Category and Type will be initialized, if not - fall back to default codes (Tissue/Tissue codes)
* anatomic region may or may not be initialized (example: can specify anatomic location of the tumor, but may not be present)
* colors may or may not be specified
Consequences:
* need to be able to handle these various combinations
* if colors are not specified, would be nice to suggest some good default color choices (to optimize differentiation of the structures? lookup of default colors may not be easy for medium-large dictionaries)
* it is not clear that it is a good idea to restrict the choices of terminology (or colors) if a user wants to modify segmentation loaded from DICOM - so it might be helpful to choose from existing color maps / terminology dictionaries for a DICOM-loaded segmentation

==== Creating segmentation from scratch ====
* choose from predefined dictionaries (combinations of Type/Category/Anatomy customized for a specific use case)
* choose from predefined color tables, or perhaps color assignment strategies (e.g., high contrast, similar shades of color for the segments corresponding to the same kind of structure)

=== Workflow ===

To add a new segment:
* user clicks "add segment"
* terminology and color are populated to some default value
* user has an option to change the color and terminology separately TerminologyWidget (naming to be confirmed)
* user has the option to choose the dictionary in the TerminologyWidget
* the purpose of the dictionary is to define specific combinations of category/type/anatomy for the specific use case (GenericAnatomy LUT is one example, and we will also need a larger set of codes defined by the standard)

=== Implementation approach ===

Terminology browser widget:
* Slicer widget vs CTK widget: consensus seems to be that CTK widget makes sense
* Qt widget vs web app: considering that basic web app already exists, it may make sense to experiment reusing it; Marco notes that it may be futile to experiment with web app integration in Slicer using the current Qt 4
** Marco confirmed that qiicr.org/dcmqi renders correctly in Qt 5.6 (used in MITK); it does not render in Slicer Qt 4.x webkit
* We will continue with prototyping in the web app (add support for color picker and dictionary selection)
** web app color picker issue https://github.com/QIICR/dcmqi/issues/21

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-23T10:28:19Z

Naucoin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
|

* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ SlicerRT] ([https://github.com/SlicerRt/SlicerRT/ github mirror]), with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmqi ([https://github.com/QIICR/dcmqi/tree/gh-pages github source])
** To view in slicer's webkit
view = qt.QWebView()
view.setUrl(qt.QUrl('http://qiicr.org/dcmqi/'))
view.show()
* From Andrey: disconnect segment ID from the color ID and from the terminology associated with it - it should be possible to have more than one distinctive segment that has the same color and the same terminology, but are differentiated by segment ID and segment label.
|

* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node. (Csaba)
*** When creating the new temp color node, also create a new terminology associated with it (Nicole)
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor (Csaba)
*** Bring up the CTK color picker by default on adding a new segment to set/edit the default color/terminology (Csaba)
*** Extend/fix the CTK color picker:
**** Show the custom color node by default not the Generic Anatomy one (Nicole)
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?) (Nicole)
**** Add display of the terminology associated with the color node displayed (Nicole)
**** Add terminology editing/look up to set a new terminology (Nicole - post project week)
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module, see [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Widgets/qMRMLColorModel.cxx#L340 qMRMLColorModel] (Csaba)
|}

=== Use cases ===

* Category = Segmented Property Category
* Type = Segmented Property Type (+Modifier, optional)
* Anatomic region (+Modifier, optional)

==== Loading segmentation from DICOM ====
Assumptions:
* can expect that Category and Type will be initialized, if not - fall back to default codes (Tissue/Tissue codes)
* anatomic region may or may not be initialized (example: can specify anatomic location of the tumor, but may not be present)
* colors may or may not be specified
Consequences:
* need to be able to handle these various combinations
* if colors are not specified, would be nice to suggest some good default color choices (to optimize differentiation of the structures? lookup of default colors may not be easy for medium-large dictionaries)
* it is not clear that it is a good idea to restrict the choices of terminology (or colors) if a user wants to modify segmentation loaded from DICOM - so it might be helpful to choose from existing color maps / terminology dictionaries for a DICOM-loaded segmentation

==== Creating segmentation from scratch ====
* choose from predefined dictionaries (combinations of Type/Category/Anatomy customized for a specific use case)
* choose from predefined color tables, or perhaps color assignment strategies (e.g., high contrast, similar shades of color for the segments corresponding to the same kind of structure)

=== Workflow ===

To add a new segment:
* user clicks "add segment"
* terminology and color are populated to some default value
* user has an option to change the color and terminology separately TerminologyWidget (naming to be confirmed)
* user has the option to choose the dictionary in the TerminologyWidget
* the purpose of the dictionary is to define specific combinations of category/type/anatomy for the specific use case (GenericAnatomy LUT is one example, and we will also need a larger set of codes defined by the standard)

=== Implementation approach ===

Terminology browser widget:
* Slicer widget vs CTK widget: consensus seems to be that CTK widget makes sense
* Qt widget vs web app: considering that basic web app already exists, it may make sense to experiment reusing it; Marco notes that it may be futile to experiment with web app integration in Slicer using the current Qt 4

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-22T12:26:36Z

Naucoin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
|

* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ SlicerRT] ([https://github.com/SlicerRt/SlicerRT/ github mirror]), with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmq
* From Andrey: disconnect segment ID from the color ID and from the terminology associated with it - it should be possible to have more than one distinctive segment that has the same color and the same terminology, but are differentiated by segment ID and segment label.
|

* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node. (Csaba)
*** When creating the new temp color node, also create a new terminology associated with it (Nicole)
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor (Csaba)
*** Bring up the CTK color picker by default on adding a new segment to set/edit the default color/terminology (Csaba)
*** Extend/fix the CTK color picker:
**** Show the custom color node by default not the Generic Anatomy one (Nicole)
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?) (Nicole)
**** Add display of the terminology associated with the color node displayed (Nicole)
**** Add terminology editing/look up to set a new terminology (Nicole - post project week)
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module, see [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Widgets/qMRMLColorModel.cxx#L340 qMRMLColorModel] (Csaba)
|}

=== Use cases ===

* Category = Segmented Property Category
* Type = Segmented Property Type (+Modifier, optional)
* Anatomic region (+Modifier, optional)

==== Loading segmentation from DICOM ====
Assumptions:
* can expect that Category and Type will be initialized, if not - fall back to default codes (Tissue/Tissue codes)
* anatomic region may or may not be initialized (example: can specify anatomic location of the tumor, but may not be present)
* colors may or may not be specified
Consequences:
* need to be able to handle these various combinations
* if colors are not specified, would be nice to suggest some good default color choices (to optimize differentiation of the structures? lookup of default colors may not be easy for medium-large dictionaries)
* it is not clear that it is a good idea to restrict the choices of terminology (or colors) if a user wants to modify segmentation loaded from DICOM - so it might be helpful to choose from existing color maps / terminology dictionaries for a DICOM-loaded segmentation

==== Creating segmentation from scratch ====
* choose from predefined dictionaries (combinations of Type/Category/Anatomy customized for a specific use case)
* choose from predefined color tables, or perhaps color assignment strategies (e.g., high contrast, similar shades of color for the segments corresponding to the same kind of structure)

=== Workflow ===

To add a new segment:
* user clicks "add segment"
* terminology and color are populated to some default value
* user has an option to change the color and terminology separately TerminologyWidget (naming to be confirmed)
* user has the option to choose the dictionary in the TerminologyWidget
* the purpose of the dictionary is to define specific combinations of category/type/anatomy for the specific use case (GenericAnatomy LUT is one example, and we will also need a larger set of codes defined by the standard)

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-21T20:03:32Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx | Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ | SlicerRT], with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmq
* From Andrey: disconnect segment ID from the color ID and from the terminology associated with it - it should be possible to have more than one distinctive segment that has the same color and the same terminology, but are differentiated by segment ID and segment label.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node. (Csaba)
*** When creating the new temp color node, also create a new terminology associated with it (Nicole)
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor (Csaba)
*** Bring up the CTK color picker by default on adding a new segment to set/edit the default color/terminology (Csaba)
*** Extend/fix the CTK color picker:
**** Show the custom color node by default not the Generic Anatomy one (Nicole)
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?) (Nicole)
**** Add display of the terminology associated with the color node displayed (Nicole)
**** Add terminology editing/look up to set a new terminology (Nicole - post project week)
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module, see [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Widgets/qMRMLColorModel.cxx#L340 qMRMLColorModel] (Csaba)
</div>
</div>

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-21T11:52:17Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx | Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ | SlicerRT], with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmq
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node. (Csaba)
*** When creating the new temp color node, also create a new terminology associated with it (Nicole)
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor (Csaba)
*** Bring up the CTK color picker by default on adding a new segment to set/edit the default color/terminology (Csaba)
*** Extend/fix the CTK color picker:
**** Show the custom color node by default not the Generic Anatomy one (Nicole)
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?) (Nicole)
**** Add display of the terminology associated with the color node displayed (Nicole)
**** Add terminology editing/look up to set a new terminology (Nicole - post project week)
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module, see [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Widgets/qMRMLColorModel.cxx#L340 qMRMLColorModel] (Csaba)
</div>
</div>

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-21T11:44:16Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx | Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ | SlicerRT], with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmq
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node.
*** When creating the new temp color node, also create a new terminology associated with it
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor
*** Bring up the CTK color picker by default
*** Extend/fix the CTK color picker:
**** Bring up the custom color node by default when adding a new segment to set the color/terminology
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?)
**** Add display of the terminology associated with the color node displayed
**** Add terminology editing/look up to set a new terminology
** Consider loading a segmentation node from disk and rebuilding the custom terminology - will each segment need to have a the terminology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module
</div>
</div>

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-21T11:43:23Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx | Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ | SlicerRT], with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmq
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node.
*** When creating the new temp color node, also create a new terminology associated with it
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor
*** Bring up the CTK color picker by default
*** Extend/fix the CTK color picker:
**** Bring up the custom color node by default when adding a new segment to set the color/terminology
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?)
**** Add display of the terminology associated with the color node displayed
**** Add terminology editing/look up to set a new terminology
**** Consider loading a segmentation node from disk and rebuilding the new terminology - will each segment need to have a the terminoology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module
</div>
</div>

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-21T11:42:36Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx | Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ | SlicerRT], with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations Widgets qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmq
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Tue Jun 21: Csaba and Nicole met and discussed ways to incorporate the terminology information into the segment editor
** Each segmentation node has a custom temporary color table that's built up from color selected for each segment.
*** Add a node reference to the segmentation node pointing to the color node that is used to build the custom color table (generic anatomy colors has terminology associated with it). This will help on load as the segment has the color index and the custom color table will be rebuilt from the reference color node.
*** When creating the new temp color node, also create a new terminology associated with it
** Adding a new segment
*** A color RGB is set on the display node, that's used to rebuild the custom color table on load
*** Consolidate to the segment editor
*** Bring up the CTK color picker by default
*** Extend/fix the CTK color picker:
**** Bring up the custom color node by default
**** How to best show if adding a new color or editing an old one?
**** Fix the bug where you can pick a new color for a segment, but if you click on a different color in the color picker's table it still sets the color for the entry that was clicked in the editor GUI (disable selection highlight?)
**** Add display of the terminology associated with the color node displayed
**** Add terminology editing/look up to set a new terminology
**** Consider loading a segmentation node from disk and rebuilding the new terminology - will each segment need to have a the terminoology category, property, region and modifiers set?
** Add tool tips showing terminology, as in Colors module
</div>
</div>

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-20T13:48:47Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx | Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ | SlicerRT], with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations\Widgets\qMRMLSegmentsTableView)
* Compare to web app for populating SEG metadata: http://qiicr.org/dcmq
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-20T11:14:07Z

Naucoin:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:TerminologyInEditor.jpg|Slicer 4.5 Editor with terminology
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx | Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ | SlicerRT], with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations\Widgets\qMRMLSegmentsTableView)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

File:TerminologyInEditor.jpg

2016-06-20T11:12:38Z

Naucoin:

2016 Summer Project WEB and 3D DICOM viewer to the rest of us

2016-06-20T11:05:42Z

Naucoin:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Koji Kobayashi (Vocsis Corporation)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Compared with its huge potential, current ugage of it is quite limited. ANATOMIA, my company's service intends to provide the values to patient.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement advanced signal processing algorithms in internet server which generates intuitive 3D meshes.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Beta evaluation phase
</div>
</div>

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-06T21:26:45Z

Naucoin:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
* Review overview sildes [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx | Segmentations]
* Source code review: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/ | SlicerRT], with a focus on containers (vtkSegment, vtkSegmentation, vtkMRMLSegmentationNode), and widget GUI (Segmentations\Widgets\qMRMLSegmentsTableView)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2016 Summer Project Week/Segmentation Editor and Terminology

2016-06-06T20:34:08Z

Naucoin: Project description

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Csaba Pinter (Queens)
* Andrey Fedorov (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Build on the work done in the [[2016_Summer_Project_Week/Segmentations_Integration|Segmentations Integration]] project to incoporate terminology information from [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Extensions/Reporting Reporting module] as ported to the Editor module as documented in [http://www.na-mic.org/Bug/view.php?id=4047 issue 4047] and committed as [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24742 svn 24742].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The initial plan was for the Segment Editor to incoporate the display of terminology, ported from the Editor module. The next stage is to add support for editing the terminologies and adding new ones.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week

2016-05-17T19:42:43Z

Naucoin:

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

==Logistics==
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Monday''' at German Cancer Research Center - DKFZ
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

==Agenda==
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 <br> DKFZ
!style="width:3%" |Tuesday, June 21 <br> IPCAI
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|bgcolor="#ffffff"| DKFZ Discussions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|Breakout Session: Ultrasound Navigation
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffff"|
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffff"| 3:30pm: Breakout Session: Slicer Extensions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#ffffff"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|-
|}

== '''Background''' ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].

==Equipment==
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

=Projects=
* [[2016_Summer_Project_Week_Template | Template for project pages]]

#Medical Imaging WebApp Software (Steve Pieper, Marco Nolden, Hans Meine)
#[[2016_VRPN_Integration | VRPN Integration]]
#Needle Segmentation from MRI (Tina Kapur, Andre Mastmeyer, Guillaume Pernelle)
#Guided Ultrasound Calibration (Elvis Chen, Robarts Research) http://link.springer.com/article/10.1007/s11548-016-1390-7
#[[2016_MRI_Manipulator | Integrating/Using OpenIGTLink for the communications of Robotics devices.]] (Scheherazade Kraß, MIC of university of Bremen, Germany)
# Segmentation Editor and Terminology (Nicole Aucoin, Andrey Fedorov)

= '''Registrants''' =

'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html and then add your name to this list. DKFZ members who will only be attending Monday should only add their name to this list.

#Tina Kapur, BWH/HMS, Boston, USA
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal.
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy
# Steve Pieper, Isomics, Inc., USA
# Nicole Aucoin, Brigham and Women's Hospital
# Simon Drouin, Montreal Neurological Institute
# Thomas Kirchner, German Cancer Research Center
# Elvis Chen, Robarts Research Institute, Canada
# Christian Askeland, SINTEF, Norway
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA

2016 Summer Project Week

2016-05-17T19:25:59Z

Naucoin: adding new tcons

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

==Logistics==
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Monday''' at German Cancer Research Center - DKFZ
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

==Agenda==
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:15%" |Monday, June 20 <br> DKFZ
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|-
|}

== '''Background''' ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].

==Equipment==
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

=Projects=
* [[2016_Summer_Project_Week_Template | Template for project pages]]

#[[2016_VRPN_Integration | VRPN Integration]]
#Needle Segmentation from MRI (Tina Kapur, Andre Mastmeyer, Guillaume Pernelle)
#Guided Ultrasound Calibration (Elvis Chen, Robarts Research) http://link.springer.com/article/10.1007/s11548-016-1390-7
#[[2016_MRI_Manipulator | Integrating/Using OpenIGTLink for the communications of Robotics devices.]] (Scheherazade Kraß, MIC of university of Bremen, Germany)

= '''Registrants''' =

'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html and then add your name to this list. DKFZ members who will only be attending Monday should only add their name to this list.

#Tina Kapur, BWH/HMS, Boston, USA
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal.
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy
# Steve Pieper, Isomics, Inc., USA
# Nicole Aucoin, Brigham and Women's Hospital
# Simon Drouin, Montreal Neurological Institute
# Thomas Kirchner, German Cancer Research Center
# Elvis Chen, Robarts Research Institute, Canada
# Christian Askeland, SINTEF, Norway
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA

2016 Summer Project Week

2016-05-05T16:10:29Z

Naucoin: /* Registrants */

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS), in Heidelberg, Germany.

==Logistics==
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on June 21st for IPCAI.
*'''Location:''' Heidelberg, Germany. '''Monday''' at German Cancer Research Center - DKFZ, '''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS, '''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' TBD
*'''Hotel:''' TBD

==Agenda==
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:15%" |Monday, June 20 <br> DKFZ
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|-
|}

== '''Background''' ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].

=Projects=
* [[2016_Summer_Project_Week_Template | Template for project pages]]

==Equipment==
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

==Projects==
===Image-Guided Therapy===
===Feature Based Image Analysis===
===Chest Imaging Platform===
===QIICR===
===Infrastructure===
===Web===
===Astronomy===

== '''Registrants''' ==
* Dženan Zukić, Kitware, USA
* Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal.
* Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School
* Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany
* Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy
* Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy
* Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy
* Steve Pieper, Isomics, Inc., USA
* Nicole Aucoin, Brigham and Women's Hospital
Please add your name to the list. This is the registration mechanism for this project week.

2016 Winter Project Week/Projects/SlicerOpenCVExtension

2016-01-07T21:24:33Z

Naucoin: update progress

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Nicole Aucoin (BWH)
* Erich Bremmer (Stonybrook)
* Andrey Fedorov (BWH)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Add an extension to the Slicer extension repository that provides OpenCV as a library
|

* Create CMake files to check out and build OpenCV as an external project
* Create CMake files to check out and build the ITK OpenCV bridge as an external project
* Provide examples on how to use OpenCV from Slicer
|

* [https://github.com/naucoin/SlicerOpenCV SlicerOpenCV]
** CMake file created to build OpenCV
** Enabling the ITK OpenCV Bridge:
*** The Slicer version of ITK needed changes from this patch in order to be able to build with the module enabled: [https://github.com/InsightSoftwareConsortium/ITK/commit/412dd83a680cc024c12f971ec57f76881c7eab78 COMP: simplify ITKVideoBridgeOpenCV dependency]
*** Building the bridge outside of the source referred to ITK mailing list posts:
**** [http://itk-users.7.n7.nabble.com/Problems-building-ITK-Snap-outside-the-Insight-Applications-tree-td14733.html Building ITK SNAP outside of the application]
**** New post: [http://public.kitware.com/pipermail/community/2015-December/010521.html Building BridgeOpenCV outside of ITK]
*** Consulted with Jim on best practices for building ITK and linking to libs and include dirs
*** Worked with JC to craft CMake files to build the bridge
**** Pointed to relevant blog post: [http://www.kitware.com/blog/home/post/997 Build ITK Modules Outside the Main Repository]
*** Matt McCormick proposed a patch to ITK to enable building the bridge outside of ITK: [http://review.source.kitware.com/#/c/20633/3 Allow ITKVideoBridgeOpenCV to be built externally.]
*** Extension topic branch builds against the ITK trunk version of the bridge with Matt's patch, and loads into Slicer: [https://github.com/naucoin/SlicerOpenCV/tree/Enable-ITK-BridgeOpenCV Enable-ITK-BridgeOpenCV]
*** To do:
**** patch Slicer's branch of ITK
**** set up dependency with the digital pathology module so that it uses this version of OpenCV
|}

==Background and References==


* Project begun to support [http://wiki.na-mic.org/Wiki/index.php/2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation Digital Pathology Nuclear Segmentation]

2016 Winter Project Week/Projects/SlicerOpenCVExtension

2016-01-04T19:05:27Z

Naucoin:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Nicole Aucoin (BWH)
* Erich Bremmer (Stonybrook)
* Andrey Fedorov (BWH)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Add an extension to the Slicer extension repository that provides OpenCV as a library
|

* Create CMake files to check out and build OpenCV as an external project
* Create CMake files to check out and build the ITK OpenCV bridge as an external project
* Provide examples on how to use OpenCV from Slicer
|

* [https://github.com/naucoin/SlicerOpenCV SlicerOpenCV]
** CMake file created to build OpenCV
** Enabling the ITK OpenCV Bridge:
*** The Slicer version of ITK needed changes from this patch in order to be able to build with the module enabled: [https://github.com/InsightSoftwareConsortium/ITK/commit/412dd83a680cc024c12f971ec57f76881c7eab78 COMP: simplify ITKVideoBridgeOpenCV dependency]
*** Building the bridge outside of the source referred to ITK mailing list posts:
**** [http://itk-users.7.n7.nabble.com/Problems-building-ITK-Snap-outside-the-Insight-Applications-tree-td14733.html Building ITK SNAP outside of the application]
**** New post: [http://public.kitware.com/pipermail/community/2015-December/010521.html Building BridgeOpenCV outside of ITK]

|}

==Background and References==


* Project begun to support [http://wiki.na-mic.org/Wiki/index.php/2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation Digital Pathology Nuclear Segmentation]

2016 Winter Project Week/Projects/SlicerTerminologyEditor

2016-01-04T18:22:56Z

Naucoin:

2016 Winter Project Week

2016-01-04T18:08:24Z

Naucoin: /* Agenda */

__NOTOC__
[[image:PW-MIT2016.png|300px]]

'''Dates:''' January 4-8, 2016

'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
<br>

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Breast Surgery| MR, US, Mass Spect guided Breast Surgery]] (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) <br>
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) <br>
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy)<br>
'''11:30am-12pm''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Drug Delivery to Brain|Drug Delivery to Brain]] <br>
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''12pm:''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20160103%2F20160110
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20160103/20160110
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

='''Projects'''=
*Use this [[2016_Project_Week_Template | Updated Template for project pages]]

== IGT ==
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
* [[2016_Winter_Project_Week/Projects/PLUS | Improvement of PLUS communication with Slicer]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)

== Tractography ==
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

==Image Analysis==
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week/Projects/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Kelli Xu, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)
* [[2016_Winter_Project_Week/Projects/ChestImagingPlatformWorkflows|Nipype Workflows for the Chest Imaging Platform]] (James Ross, Raúl San José)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC (and Slicer?) Wiki]] (Mike Halle, JC)
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Nicole Aucoin, Csaba Pinter, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
* [[2016_Winter_Project_Week/Projects/PLUSOCR | Exploration of open-source OCR libraries for device meta-data capture without research interface ]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)

= '''Logistics''' =

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT, Kiva Conference room; 4th floor of Building 32.
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here]. Registration Fee: $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/namic16 registration site].

#Polina Golland, MIT
#Ron Kikinis, BWH
#Nicole Aucoin, BWH/SPL
#Peter Anderson
#Daniel Blezek, Isomics, Inc.
#Lucia Cevidanes, University of Michigan
#Adrian Dalca, MIT
#Simon Drouin, Montreal Neurological Institute
#Janek Groehl, German Cancer Research Center
#Tina Kapur, BWH/HMS
#Thomas Kirchner, German Cancer Research Center
#Hans Meine, University of Bremen/MEVIS
#Vivek Narayan, Dana Farber Cancer Institute
#Danielle Pace, MIT
#Laura Pascal, University of Michigan
#Steve Pieper, Isomics, Inc.
#Csaba Pinter, Queen's University
#Gregory Sharp, MGH
#James Miller, GE Research
#Kyle Sunderland, Queen's University
#Ethan Ulrich, University of Iowa
#Jean-Baptiste Vimort, University of Michigan
#Miaomiao Zhang, MIT
#Beatriz Paniagua, University of North Carolina at Chapel Hill
#Sonia Pujol, BWH
#Junichi Tokuda, BWH
#Katie Mastrogiacomo, BWH
#Niravkumar Patel, Worcester Polytechnic Institute
#Michael Onken, Open Connections (Germany)
#Erich Bremer, Stony Brook University
#Xiao Da, MGH
#Tobias Frank, Leibniz Universität Hannover
#Kirby Vosburgh, BWH
#P. Jason White, BWH
#Lauren O'Donnell, BWH
#Pegah Kahali, BWH
#Fan Zhang, BWH
#Adam Rankin, Robarts Research Institute
#Simon Leoard, Johns Hopkins University
#David Gering, HealthMyne
#Johan Andruejol, Kitware
#Jean-Christophe Fillion-Robin, Kitware
#Kelli Xu, MIT
#Christian Askeland, SINTEF
#Katharine Carter, BWH
#Nick Todd, BWH
#Ye Cheng, BWH
#Andriy Fedorov, BWH/HMS
#Sudhanshu Semwal, UCCS Professor
#Michael Halle, BWH
#Kallirroi Retzepi, MGH
#Jayender Jagadeesan, BWH
#Nathalie Agar, BWH
#Curtis Lisle, KnowledgeVis, LLC
#Andras Lasso, PerkLab, Queen's University
#Sarah Frisken, BWH
#Yi Gao, Stony Brook University
#Christian Herz, BWH
#Prashin Unadkat, SPL/BWH
#Jorge Onieva, BWH
#James Ross, BWH
#Raul SanJose, BWH
#Jayashree Kalpathy-Cramer, MGH/HMS
#Daniel Glazer, BWH
#Valentin Demeusy, SPL Intern
#Ameet Jain, Phillips Research
#Utsav Soni, BWH
#Matthew Toews, Ecole de Technologie Superieure
#Isaiah Norton, BWH
#Sean Doyle, MGH
#Stuart Pomerantz, MGH
#Randy Gollub, MGH
#Melissa Mallory, BWH
#Axel Krieger, Children's National Medical Center
#Nobuhiko Hata, BWH

2016 Winter Project Week/Projects/SlicerTerminologyEditor

2016-01-04T17:43:36Z

Naucoin: /* Background and References */

2016 Winter Project Week/Projects/SlicerTerminologyEditor

2016-01-04T13:21:49Z

Naucoin: /* Project Description */

2016 Winter Project Week/Projects/SlicerTerminologyEditor

2016-01-04T13:20:35Z

Naucoin: /* Project Description */

2016 Winter Project Week/Projects/SlicerOpenCVExtension

2015-12-29T18:35:50Z

Naucoin: /* Project Description */

2016 Winter Project Week/Projects/SlicerOpenCVExtension

2015-12-29T16:00:51Z

Naucoin: /* Project Description */

2016 Winter Project Week/Projects/SlicerOpenCVExtension

2015-12-23T16:37:49Z

Naucoin: /* Project Description */

2016 Winter Project Week/Projects/SlicerOpenCVExtension

2015-12-17T16:40:00Z

Naucoin: /* Project Description */

2016 Winter Project Week/Projects/SlicerOpenCVExtension

2015-12-17T16:34:28Z

Naucoin: /* Key Investigators */

2016 Winter Project Week

2015-12-10T20:52:41Z

Naucoin: /* Infrastructure */

__NOTOC__
[[image:PW-MIT2016.png|300px]]

'''Dates:''' January 4-8, 2016

'''Location:''' MIT, Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
<br>

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

==Agenda==

Tentative Agenda

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br>
|
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font>
<br>
|'''9:00-10:30am''' TBD <br>
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
'''2:45-4pm:''' [[Breakout Session: Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' <font color="#503020"> [[Breakout Session: What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[Breakout Session: Diffusion MRI]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

='''Projects'''=
* [[2016_Project_Week_Template | Template for project pages]]

* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
* [[2016_Winter_Project_Week:External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week:SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)

==Infrastructure==
* [[2016_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:SlicerTerminologyEditor | Terminology Editor]] (Csaba Pinter, Nicole Aucoin)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM SegObj with Segmentations]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week:Data Persisting | Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week:Workflows | Workflow module that enables the navigation and data sharing between different modules in a clinical workflow ]] (Raúl San José, Jorge Onieva)

= '''Logistics''' =

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT, Kiva Conference room; 4th floor of Building 32.
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here]. Registration Fee: $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit [https://www.regonline.com/namic16 this registration url].

2016 Winter Project Week

2015-12-10T20:52:23Z

Naucoin: /* Projects */

__NOTOC__
[[image:PW-MIT2016.png|300px]]

'''Dates:''' January 4-8, 2016

'''Location:''' MIT, Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
<br>

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

==Agenda==

Tentative Agenda

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br>
|
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font>
<br>
|'''9:00-10:30am''' TBD <br>
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
'''2:45-4pm:''' [[Breakout Session: Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' <font color="#503020"> [[Breakout Session: What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[Breakout Session: Diffusion MRI]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

='''Projects'''=
* [[2016_Project_Week_Template | Template for project pages]]

* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
* [[2016_Winter_Project_Week:External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week:SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)

==Infrastructure==
* [[2016_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:SlicerTerminologyEditor | TerminologyEditor]] (Csaba Pinter, Nicole Aucoin)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM SegObj with Segmentations]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week:Data Persisting | Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week:Workflows | Workflow module that enables the navigation and data sharing between different modules in a clinical workflow ]] (Raúl San José, Jorge Onieva)

= '''Logistics''' =

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT, Kiva Conference room; 4th floor of Building 32.
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here]. Registration Fee: $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit [https://www.regonline.com/namic16 this registration url].

2016 Winter Project Week

2015-10-21T15:05:48Z

Naucoin: /* Projects */

__NOTOC__

[[image:PW-MIT2016.png|300px|left]]
<br><br><br><br><br><br><br><br><br><br><br><br>
'''Dates:''' January 4-8, 2016

'''Location:''' MIT, Cambridge, MA.
<br>

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

==Agenda==

Tentative Agenda

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday
!style="width:18%" |Tuesday
!style="width:18%" |Wednesday
!style="width:18%" |Thursday
!style="width:18%" |Friday
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
|
'''11am-12noon'''TBD
<br>
|'''9:00-10:30am''' TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] (Stata Building 4th Floor R&D Common Dining Area)
<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
(Stata Building 4th Floor R&D Common Dining Area)

|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">TBD</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm'''TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">TBD
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

='''Projects'''=
* [[2014_Project_Week_Template | Template for project pages]]

(Project list to be populated in late 2015)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)

= '''Logistics''' =

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT
*'''REGISTRATION:''' Registration link will go live as the event gets closer: https://www.regonline.com/namic2016winterprojectweek.
**Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2016_Winter_Project_Week/RoomSharing|here]]

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2016winterprojectweek Please click here to register once the link goes live.])

2016 Winter Project Week

2015-10-21T15:01:49Z

Naucoin: /* Logistics */

__NOTOC__

[[image:PW-MIT2016.png|300px|left]]
<br><br><br><br><br><br><br><br><br><br><br><br>
'''Dates:''' January 4-8, 2016

'''Location:''' MIT, Cambridge, MA.
<br>

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

==Agenda==

Tentative Agenda

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday
!style="width:18%" |Tuesday
!style="width:18%" |Wednesday
!style="width:18%" |Thursday
!style="width:18%" |Friday
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
|
'''11am-12noon'''TBD
<br>
|'''9:00-10:30am''' TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] (Stata Building 4th Floor R&D Common Dining Area)
<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
(Stata Building 4th Floor R&D Common Dining Area)

|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">TBD</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm'''TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">TBD
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

(Project list to be populated in late 2015)

== '''Logistics''' ==

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT
*'''REGISTRATION:''' Registration link will go live as the event gets closer: https://www.regonline.com/namic2016winterprojectweek.
**Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2016_Winter_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2016winterprojectweek Please click here to register.])

2016 Winter Project Week

2015-10-21T15:01:30Z

Naucoin: /* Logistics */

__NOTOC__

[[image:PW-MIT2016.png|300px|left]]
<br><br><br><br><br><br><br><br><br><br><br><br>
'''Dates:''' January 4-8, 2016

'''Location:''' MIT, Cambridge, MA.
<br>

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

==Agenda==

Tentative Agenda

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday
!style="width:18%" |Tuesday
!style="width:18%" |Wednesday
!style="width:18%" |Thursday
!style="width:18%" |Friday
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
|
'''11am-12noon'''TBD
<br>
|'''9:00-10:30am''' TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] (Stata Building 4th Floor R&D Common Dining Area)
<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
(Stata Building 4th Floor R&D Common Dining Area)

|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">TBD</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm'''TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">TBD
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

(Project list to be populated in late 2015)

== '''Logistics''' ==

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT
*'''REGISTRATION:''' Registration link will go live as the even gets closer: https://www.regonline.com/namic2016winterprojectweek.
**Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2016_Winter_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2016winterprojectweek Please click here to register.])

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-24T15:51:19Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked on one fiducial in the CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
**[https://github.com/naucoin/SlicerExecutionModel/tree/2979-support-for-cli-point-coordinateSystem-files Slicer Execution Model topic branch]
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
* Some problems supporting the coordinateSystem flag, open to feedback on alternate ways to achieve it
** compile CLI module logic against Markups, use an attribute on the fiducial node
* [https://github.com/naucoin/Slicer/tree/2979-support-for-cli-point-coordinateSystem-files Slicer topic branch]
* TODO:
** update the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel wiki documentation] for Slicer 4
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-24T15:50:17Z

Naucoin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked on one fiducial in the CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
**[https://github.com/naucoin/SlicerExecutionModel/tree/2979-support-for-cli-point-coordinateSystem-files github topic branch]
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
* Some problems supporting the coordinateSystem flag, open to feedback on alternate ways to achieve it
** compile CLI module logic against Markups, use an attribute on the fiducial node
* [https://github.com/naucoin/Slicer/tree/2979-support-for-cli-point-coordinateSystem-files Slicer topic branch]
* TODO:
** update the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel wiki documentation] for Slicer 4
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-24T15:32:26Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked on one fiducial in the CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Hans Meine (University of Bremen / Fraunhofer MEVIS)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
**[https://github.com/naucoin/SlicerExecutionModel/tree/2979-support-for-cli-point-coordinateSystem-files github topic branch]
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
* Some problems supporting the coordinateSystem flag, open to feedback on alternate ways to achieve it
** compile CLI module logic against Markups, use an attribute on the fiducial node
* [https://github.com/naucoin/Slicer/tree/2979-support-for-cli-point-coordinateSystem-files Slicer topic branch]
* TODO:
** update the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel wiki documentation] for Slicer 4
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-24T14:58:03Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked on one fiducial in the CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Hans Meine (University of Bremen / Fraunhofer MEVIS)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
**[https://github.com/naucoin/SlicerExecutionModel/tree/2979-support-for-cli-point-coordinateSystem-files github topic branch]
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
* Some problems supporting the coordinateSystem flag, open to feedback on alternate ways to achieve it
** compile CLI module logic against Markups, use an attribute on the fiducial node
* [https://github.com/naucoin/Slicer/tree/2979-support-for-cli-point-coordinateSystem-files Slicer topic branch]
* TODO:
** finish up testing in SEM
** update the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel wiki documentation] for Slicer 4
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-24T10:32:58Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked on one fiducial in the CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Hans Meine (University of Bremen / Fraunhofer MEVIS)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
**[https://github.com/naucoin/SlicerExecutionModel/tree/2979-support-for-cli-point-coordinateSystem-files github topic branch]
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
* Some problems supporting the coordinateSystem flag, open to feedback on alternate ways to achieve it
** compile CLI module logic against Markups, use an attribute on the fiducial node
* [https://github.com/naucoin/Slicer/tree/2979-support-for-cli-point-coordinateSystem-files Slicer topic branch]
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-24T10:31:21Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked on one fiducial in the CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Hans Meine (University of Bremen / Fraunhofer MEVIS)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
**[https://github.com/naucoin/SlicerExecutionModel/commit/aa34a919c9e90b324292d09f7b14ef13da5a9cc5 github topic branch]
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
* Some problems supporting the coordinateSystem flag, open to feedback on alternate ways to achieve it
** compile CLI module logic against Markups, use an attribute on the fiducial node
* [https://github.com/naucoin/Slicer/tree/2979-support-for-cli-point-coordinateSystem-files Slicer topic branch]
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-23T15:59:40Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked on one fiducial in the CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Hans Meine (University of Bremen / Fraunhofer MEVIS)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
**[https://github.com/naucoin/SlicerExecutionModel/commit/aa34a919c9e90b324292d09f7b14ef13da5a9cc5 github topic branch]
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
* Some problems supporting the coordinateSystem flag
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-23T15:49:25Z

Naucoin: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked on one fiducial in the CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Hans Meine (University of Bremen / Fraunhofer MEVIS)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
* Some problems supporting the coordinateSystem flag
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-23T15:49:03Z

Naucoin:

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-23T14:56:25Z

Naucoin:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsBackFromCLI.jpg|Fiducial list reloaded into Slicer, having toggled vis, sel, locked
Image:FiducialsAsInputInCLIXML.jpg|Fiducial list set as input to a CLI
Image:FiducialsAsOutputInCLIXML.jpg|Fiducial list set as output from a CLI
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Hans Meine (University of Bremen / Fraunhofer MEVIS)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Flag added to the module description parser with new flag --pointfile
* Module CLI logic and GUI helper updated to use new flag
* Application logic updated to manage fiducial storage node
</div>
</div>

2015 Summer Project Week:Return Fiducials from CLIs

2015-06-23T14:32:28Z

Naucoin:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiducialsBackFromCLI.jpg
Image:FiducialsAsInputInCLIXML.jpg
Image:FiducialsAsOutputInCLIXML.jpg
</gallery>

==Key Investigators==
* Nicole Aucoin (BWH)
* Hans Meine (University of Bremen / Fraunhofer MEVIS)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix Slicer issue [http://www.na-mic.org/Bug/view.php?id=2979 2979]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Update the CLI module logic to support fiducial files as input and output
** [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/SlicerExecutionModel#Adding_a_new_parameter_type Adding new parameter type]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

File:FiducialsAsOutputInCLIXML.jpg

2015-06-23T14:31:52Z

Naucoin: Fiducials in CLI xml

Fiducials in CLI xml

File:FiducialsAsInputInCLIXML.jpg

2015-06-23T14:30:58Z

Naucoin: Fiducials as input file to a CLI

Fiducials as input file to a CLI