NAMIC Wiki - User contributions [en]

2017 Winter Project Week/Support for volumetric meshes

2017-01-16T15:36:37Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Previous works==
<gallery>
File:volumetricMeshSlicer3.png | FEMesh in Slicer 3
File:CleaverExtension.jpeg | Cleaver Extensio
</gallery>

==Results==
<gallery>
File:Models_VolumetricMesh3.png | Volumetric Mesh
File:Models_VolumetricMesh1.gif | Volumetric Mesh (gif)
File:Models_VolumetricMesh2.gif | Models module display widget (gif)
</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Pieper (Isomics, Inc.)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:20%" | Objective
! style="text-align: left; width:20%" | Approach and Plan
! style="text-align: left; width:20%" | Progress/Results
! style="text-align: left; width:20%" | Next steps/Future work
|- style="vertical-align:top;"
|

From top priority to possible future work:
* Being able to visualize, load and save volumetric meshes
* Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars).
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension. Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Can Read & Write Unstructured Grid mesh (vtk or vtu)
* Fix bug in vtk reader to retrieve all point data and cell data.
* vtkMRMLModelNode now holds a "mesh", either a polydata (surface mesh) or an unstructured grid (volumetric mesh)
* vtkMRMLDisplayNode had a major clean up to consolidate scalar range options (scalarRangeFlag and autoScalarRange). Other clean up made to retrieve the look-up table for specific nodes only holding color transfer functions (ex: vtkMRMLProceduralColorNode).
* DisplayableManager updated for 3D to allow cutting through volumetric mesh.
* SliceDisplableManager updated for 2D Slices to be able to use same display properties than 3D view.
* qMRMLModelDisplayNodeWidget updated to simplify scalar range mode selection, adapt number of decimals and single step for manual selection of the range based on the magnitude of the current values.
* Threshold displayed mesh by scalar values.
* Display information about the model type (surface or volumetric) for the user to be able to distinct it in the module widget.
* WIP branch on github: https://github.com/Slicer/Slicer/compare/master...agirault:volumetric-mesh-support
|

* Clean up and consolidate qSlicerModelsModuleWidget (display properties, representations, wireframe, clipping... just move options around to make it more usable)
* Add clipping option to smoothen the cut (using vtkClipDataSet vs vtkExtractGeometry)
* Add support to pass through CLI (SlicerCLILogic)
* Test with more cases, like fiber bundles etc... (changes could have a lot of impacts because there were changes to vtkMRMLDisplayNode and vtkMRMLModelNode. Make sure the updated API stays backward compatible).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-13T16:34:00Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Previous works==
<gallery>
File:volumetricMeshSlicer3.png | FEMesh in Slicer 3
File:CleaverExtension.jpeg | Cleaver Extensio
</gallery>

==Results==
<gallery>
File:Models_VolumetricMesh3.png | Volumetric Mesh
File:Models_VolumetricMesh1.gif | Volumetric Mesh (gif)
File:Models_VolumetricMesh2.gif | Models module display widget (gif)
</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Pieper (Isomics, Inc.)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:20%" | Objective
! style="text-align: left; width:20%" | Approach and Plan
! style="text-align: left; width:20%" | Progress/Results
! style="text-align: left; width:20%" | Next steps/Future work
|- style="vertical-align:top;"
|

From top priority to possible future work:
* Being able to visualize, load and save volumetric meshes
* Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars).
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension. Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Can Read & Write Unstructured Grid mesh (vtk or vtu)
* Fix bug in vtk reader to retrieve all point data and cell data.
* vtkMRMLModelNode now holds a "mesh", either a polydata (surface mesh) or an unstructured grid (volumetric mesh)
* vtkMRMLDisplayNode had a major clean up to consolidate scalar range options (scalarRangeFlag and autoScalarRange). Other clean up made to retrieve the look-up table for specific nodes only holding color transfer functions (ex: vtkMRMLProceduralColorNode).
* DisplayableManager updated for 3D to allow cutting through volumetric mesh.
* SliceDisplableManager updated for 2D Slices to be able to use same display properties than 3D view.
* qMRMLModelDisplayNodeWidget updated to simplify scalar range mode selection, adapt number of decimals and single step for manual selection of the range based on the magnitude of the current values.
* Progress made to threshold displayed mesh by scalar values.
* WIP branch on github: https://github.com/Slicer/Slicer/compare/master...agirault:volumetric-mesh-support
|

* Finalize threshold display option.
* Clean up and consolidate qSlicerModelsModuleWidget (display properties, representations, wireframe, clipping... just move options around to make it more usable)
* Add clipping option to smoothen the cut (using vtkClipDataSet vs vtkExtractGeometry)
* Add support to pass through CLI (SlicerCLILogic)
* Display information about the model type (surface or volumetric) for the user to be able to distinct it in the module widget.
* Test with more cases, like fiber bundles etc... (changes could have a lot of impacts because there were changes to vtkMRMLDisplayNode and vtkMRMLModelNode. Make sure the updated API stays backward compatible).
* Add creation, conversion and editing abilities (adapt former modules).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

File:Models VolumetricMesh1.gif

2017-01-13T16:27:50Z

Alexis.girault: Alexis.girault uploaded a new version of File:Models VolumetricMesh1.gif

2017 Winter Project Week/Improve Matlab integration

2017-01-13T16:23:35Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
File:MatlabCommanderInterface.png|Current MatlabCommander Interface

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)

==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;"
|

* Allowing the access to Matlab variables that are defined in a Matlab module once that module terminates, as if that code was run in the Matlab command line environment.
* Offer a more user-friendly interface to send matlab commands and display the results. Right now the way to do it is to go in MatlabCommander and to type the command in a LineEdit, after which the output result appears in another LineEdit. While it is functional, our end users have had difficulties handling it since the display isn't as nice as in a Matlab console.
* Offer a way to visualize the Matlab workspace variables just like in the Matlab environment: there is currently no way in MatlabBridge to see the variables of the current instance.
|

* Discuss with Andras to better understand the way MatlabBridge work, and showcase an example where we can not access the variables defined in a Matlab module once it has ended. This will lead to a work allowing to address the first objective.
* Look into using a custom ctkConsole (like the python console) in order to mimic the console from the main Matlab environment, OR try to get the commandwindow command from Matlab to directly open up.
* Retrieve workspace from the Matlab instance after each command sent (or matlab module run) and display the variables and their values in a table node, OR try to get the workspace command from Matlab to directly open up.
|

* Nothing implemented, just discussions made with Andras.
* To be able to work with the Matlab environment & MatlabBridge within Slicer, you need to :
** define variables as global in your code (matlab commander or matlab module)
** open Matlab & Slicer without running the matab commander server from Slicer
** run matlab commander server from Matlab
** run your matlab code from slicer
** stop matlab commander server on Matlab
** call global on variables defined in Slicer within Matlab to see them appear in your workspace and be able to use them in matlab's command window.
* A way to automatize the above would be to:
** run matlab environment from Slicer
** have a button in Slicer to Stop/Start the server in matlab environment
** when the server is stopped, run `whos global` to get a list of variables and `global variablename` to display them in the workspace automatically
* The given module was running some window interfaces with Matlab, which opens a new thread and therefore becomes out of scope from the slicer matlab server instance which would end without keeping an handle on variables defines later on. We would advise not to use Matlab GUI items and do Matlab modules within Slicer to be able to control every step of the way.
|}

==Background and References==

* MatlabBridge : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge
* ctkConsole : http://www.commontk.org/docs/html/classctkConsole.html
* Matlab commandwindow : https://www.mathworks.com/help/matlab/ref/commandwindow.html
* Matlab workspace : https://www.mathworks.com/help/matlab/ref/workspace.html

2017 Winter Project Week/Improve Matlab integration

2017-01-13T16:22:30Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
File:MatlabCommanderInterface.png|Current MatlabCommander Interface

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)

==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;"
|

* Allowing the access to Matlab variables that are defined in a Matlab module once that module terminates, as if that code was run in the Matlab command line environment.
* Offer a more user-friendly interface to send matlab commands and display the results. Right now the way to do it is to go in MatlabCommander and to type the command in a LineEdit, after which the output result appears in another LineEdit. While it is functional, our end users have had difficulties handling it since the display isn't as nice as in a Matlab console.
* Offer a way to visualize the Matlab workspace variables just like in the Matlab environment: there is currently no way in MatlabBridge to see the variables of the current instance.
|

* Discuss with Andras to better understand the way MatlabBridge work, and showcase an example where we can not access the variables defined in a Matlab module once it has ended. This will lead to a work allowing to address the first objective.
* Look into using a custom ctkConsole (like the python console) in order to mimic the console from the main Matlab environment, OR try to get the commandwindow command from Matlab to directly open up.
* Retrieve workspace from the Matlab instance after each command sent (or matlab module run) and display the variables and their values in a table node, OR try to get the workspace command from Matlab to directly open up.
|

* Nothing implemented, just discussions made with Andras.
* To be able to work with the Matlab environment & MatlabBridge within Slicer, you need to :
** define variables as global in your code (matlab commander or matlab module)
** open Matlab & Slicer without running the matab commander server from Slicer
** run matlab commander server from Matlab
** run your matlab code from slicer
** stop matlab commander server on Matlab
** call global on variables defined in Slicer within Matlab to see them appear in your workspace and be able to analyze it.
* A way to automatize the above would be to:
** run matab environement from Slicer
** have a button in Slicer to Stop/Start the server in matlab environment
** when the server is stopped, run `whos global` to get a list of variables and `global variablename` to display them in the workspace automatically
* The given module was running some window interfaces with Matlab, which opens a new thread and therefore becomes out of scope from the slicer matlab server instance which would end without keeping an handle on variables defines later on. We would advise not to use Matlab GUI items and do Matlab modules within Slicer to be able to control every step of the way.
|}

==Background and References==

* MatlabBridge : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge
* ctkConsole : http://www.commontk.org/docs/html/classctkConsole.html
* Matlab commandwindow : https://www.mathworks.com/help/matlab/ref/commandwindow.html
* Matlab workspace : https://www.mathworks.com/help/matlab/ref/workspace.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-13T16:08:37Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Previous works==
<gallery>
File:volumetricMeshSlicer3.png | FEMesh in Slicer 3
File:CleaverExtension.jpeg | Cleaver Extensio
</gallery>

==Results==
<gallery>
File:Models_VolumetricMesh3.png | Volumetric Mesh
File:Models_VolumetricMesh1.gif | Volumetric Mesh (gif)
File:Models_VolumetricMesh2.gif | Models module display widget (gif)
</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Pieper (Isomics, Inc.)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:20%" | Objective
! style="text-align: left; width:20%" | Approach and Plan
! style="text-align: left; width:20%" | Progress/Results
! style="text-align: left; width:20%" | Next steps/Future work
|- style="vertical-align:top;"
|

From top priority to possible future work:
* Being able to visualize, load and save volumetric meshes
* Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars).
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension. Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Can Read & Write Unstructured Grid mesh (vtk or vtu)
* Fix bug in vtk reader to retrieve all point data and cell data.
* vtkMRMLModelNode now holds a "mesh", either a polydata (surface mesh) or an unstructured grid (volumetric mesh)
* vtkMRMLDisplayNode had a major clean up to consolidate scalar range options (scalarRangeFlag and autoScalarRange). Other clean up made to retrieve the look-up table for specific nodes only holding color transfer functions (ex: vtkMRMLProceduralColorNode).
* DisplayableManager updated for 3D to allow cutting through volumetric mesh.
* SliceDisplableManager updated for 2D Slices to be able to use same display properties than 3D view.
* qMRMLModelDisplayNodeWidget updated to simplify scalar range mode selection, adapt number of decimals and single step for manual selection of the range based on the current values.
* Progress made to threshold displayed mesh by scalar values.
* WIP branch on github: https://github.com/Slicer/Slicer/compare/master...agirault:volumetric-mesh-support
|

* Finalize threshold display option.
* Clean up and consolidate qSlicerModelsModuleWidget (display properties, representations, wireframe, clipping... just move options around to make it more usable)
* Add clipping option to smoothen the cut (using vtkClipDataSet vs vtkExtractGeometry)
* Add support to pass through CLI (SlicerCLILogic)
* Display information about the model type (surface or volumetric) for the user to be able to distinct it in the module widget.
* Test with more cases, like fiber bundles etc... (changes could have a lot of impacts because there were changes to vtkMRMLDisplayNode and vtkMRMLModelNode. Make sure the updated API stays backward compatible).
* Add creation, conversion and editing abilities (adapt former modules).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-13T16:07:23Z

Alexis.girault:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Previous works==
<gallery>
File:volumetricMeshSlicer3.png | FEMesh in Slicer 3
File:CleaverExtension.jpeg | Cleaver Extensio
</gallery>

==Results==
<gallery>
File:Models_VolumetricMesh3.png | Volumetric Mesh
File:Models_VolumetricMesh1.gif | Volumetric Mesh (gif)
File:Models_VolumetricMesh2.gif | Models module display widget (gif)
</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Pieper (Isomics, Inc.)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:20%" | Objective
! style="text-align: left; width:20%" | Approach and Plan
! style="text-align: left; width:20%" | Progress/Results
! style="text-align: left; width:20%" | Next steps/Future work
|- style="vertical-align:top;"
|

From top priority to possible future work:
* Being able to visualize, load and save volumetric meshes
* Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars).
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension. Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Can Read & Write Unstructured Grid mesh (vtk or vtu)
* Fix bug in vtk reader to retrieve all point data and cell data.
* vtkMRMLModelNode now holds a "mesh", either a polydata (surface mesh) or an unstructured grid (volumetric mesh)
* vtkMRMLDisplayNode had a major clean up to consolidate scalar range options (scalarRangeFlag and autoScalarRange). Other clean up made to retrieve the look-up table for specific nodes only holding color transfer functions (ex: vtkMRMLProceduralColorNode).
* DisplayableManager updated for 3D to allow cutting through volumetric mesh.
* SliceDisplableManager updated for 2D Slices to be able to use same display properties than 3D view.
* qMRMLModelDisplayNodeWidget updated to simplify scalar range mode selection, adapt number of decimals and single step for manual selection of the range based on the current values.
* Progress made to threshold displayed mesh by scalar values.
* WIP branch on github: https://github.com/Slicer/Slicer/compare/master...agirault:volumetric-mesh-support
|

* Finalize threshold display option.
* Clean up and consolidate qSlicerModelsModuleWidget (display properties, representations, wireframe, clipping... just move options around to make it more usable)
* Add clipping option to smoothen the cut (using vtkClipDataSet vs vtkExtractGeometry)
* Add support to pass through CLI (SlicerCLILogic)
* Display information about the model type (surface or volumetric) for the user to be able to distinct it in the module widget.
* Test with more cases, like fiber bundles etc... (changes could have a lot of impacts because there were changes to vtkMRMLDisplayNode and vtkMRMLModelNode. Make sure the updated API stays backward compatible).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

File:Models VolumetricMesh3.png

2017-01-13T16:03:22Z

Alexis.girault:

File:Models VolumetricMesh2.gif

2017-01-13T15:59:02Z

Alexis.girault:

File:Models VolumetricMesh1.gif

2017-01-13T15:57:36Z

Alexis.girault:

2017 Winter Project Week/Support for volumetric meshes

2017-01-13T15:46:02Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
File:volumetricMeshSlicer3.png | FEMesh in Slicer 3
File:CleaverExtension.jpeg | Cleaver Extension

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Pieper (Isomics, Inc.)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:20%" | Objective
! style="text-align: left; width:20%" | Approach and Plan
! style="text-align: left; width:20%" | Progress/Results
! style="text-align: left; width:20%" | Next steps/Future work
|- style="vertical-align:top;"
|

From top priority to possible future work:
* Being able to visualize, load and save volumetric meshes
* Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars).
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension. Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Can Read & Write Unstructured Grid mesh (vtk or vtu)
* Fix bug in vtk reader to retrieve all point data and cell data.
* vtkMRMLModelNode now holds a "mesh", either a polydata (surface mesh) or an unstructured grid (volumetric mesh)
* vtkMRMLDisplayNode had a major clean up to consolidate scalar range options (scalarRangeFlag and autoScalarRange). Other clean up made to retrieve the look-up table for specific nodes only holding color transfer functions (ex: vtkMRMLProceduralColorNode).
* DisplayableManager updated for 3D to allow cutting through volumetric mesh.
* SliceDisplableManager updated for 2D Slices to be able to use same display properties than 3D view.
* qMRMLModelDisplayNodeWidget updated to simplify scalar range mode selection, adapt number of decimals and single step for manual selection of the range based on the current values.
* Progress made to threshold displayed mesh by scalar values.
|

* Finalize threshold display option.
* Clean up and consolidate qSlicerModelsModuleWidget (display properties, representations, wireframe, clipping... just move options around to make it more usable)
* Add clipping option to smoothen the cut (using vtkClipDataSet vs vtkExtractGeometry)
* Add support to pass through CLI (SlicerCLILogic)
* Display information about the model type (surface or volumetric) for the user to be able to distinct it in the module widget.
* Test with more cases, like fiber bundles etc... (changes could have a lot of impacts because there were changes to vtkMRMLDisplayNode and vtkMRMLModelNode. Make sure the updated API stays backward compatible).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-13T15:43:20Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
File:volumetricMeshSlicer3.png | FEMesh in Slicer 3
File:CleaverExtension.jpeg | Cleaver Extension

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Pieper (Isomics, Inc.)

==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;"
|

From top priority to possible future work:
* Being able to visualize, load and save volumetric meshes
* Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars).
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension. Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Can Read & Write Unstructured Grid mesh (vtk or vtu)
* Fix bug in vtk reader to retrieve all point data and cell data.
* vtkMRMLModelNode now holds a "mesh", either a polydata (surface mesh) or an unstructured grid (volumetric mesh)
* vtkMRMLDisplayNode had a major clean up to consolidate scalar range options (scalarRangeFlag and autoScalarRange). Other clean up made to retrieve the look-up table for specific nodes only holding color transfer functions (ex: vtkMRMLProceduralColorNode).
* DisplayableManager updated for 3D to allow cutting through volumetric mesh.
* SliceDisplableManager updated for 2D Slices to be able to use same display properties than 3D view.
* qMRMLModelDisplayNodeWidget updated to simplify scalar range mode selection, adapt number of decimals and single step for manual selection of the range based on the current values.
* Progress made to threshold displayed mesh by scalar values.
|

* Finalize threshold display option.
* Clean up and consolidate qSlicerModelsModuleWidget (display properties, representations, wireframe, clipping... just move options around to make it more usable)
* Add clipping option to smoothen the cut (using vtkClipDataSet vs vtkExtractGeometry)
* Add support to pass through CLI (SlicerCLILogic)
* Display information about the model type (surface or volumetric) for the user to be able to distinct it in the module widget.
* Test with more cases, like fiber bundles etc... (changes could have a lot of impacts because there were changes to vtkMRMLDisplayNode and vtkMRMLModelNode. Make sure the updated API stays backward compatible).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week/Dinner

2017-01-11T19:14:17Z

Alexis.girault: /* RSVPs */

==Dinner Specs==

*Date and Time: Thursday, January 12, 6pm
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from MIT)
*Food: Indian. Menu: Goat curry, chicken tikka masala, chana masala (vegan), saag paneer (veg), naan, rice
*Cost: $25 - CASH ONLY! To be given to Katie Mastrogiacomo (kmast@bwh) during the week. She will provide receipts.
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks.

==RSVPs==
# Adam Rankin
# Andras Lasso
# Curt Lisle
# Tina Kapur
# Andrey Fedorov
# Csaba Pinter
# Simon Drouin
# Alireza Mehrtash
# Henrik G. Jensen
# Beatriz Paniagua
# Beatriz Paniagua's +1
# Hans Meine
# Johan Andruejol
# Katie Mastrogiacomo
# Ron Kikinis
# Zora Kikinis
# Brian Helba
# Jennifer Nitsch
# Jean-Christophe Fillion-Robin
# Anneke Meyer
# Erik Ziegler
# Francois Rheault
# Rebekka Lauer
# Janne Beate Bakeng
# Louise Oram
# Teodora Szasz
# Danielle Pace
# David Garcia
# James Fishbaugh
# Sungmin Hong
# Mohsen Ghafoorian
# Miaomiao Zhang
# Alexis Girault
# Alexis Girault + 1

2017 Winter Project Week/Support for volumetric meshes

2017-01-09T19:50:10Z

Alexis.girault: typo

2017 Winter Project Week/Support for volumetric meshes

2017-01-09T19:44:36Z

Alexis.girault:

File:CleaverExtension.jpeg

2017-01-09T19:39:36Z

Alexis.girault:

File:VolumetricMeshSlicer3.png

2017-01-09T19:38:45Z

Alexis.girault:

2017 Winter Project Week/Improve Matlab integration

2017-01-09T19:13:27Z

Alexis.girault:

File:MatlabCommanderInterface.png

2017-01-09T19:03:07Z

Alexis.girault:

2017 Winter Project Week

2017-01-09T19:01:40Z

Alexis.girault: Improve Matlab integration contributors

__NOTOC__
[[image:PW-Winter2017.png|300px]]

=Welcome to the web page for the 24th Project Week!=

The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. 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:''' January 9-13, 2017.
*'''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)
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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_Project_Weeks|here]].

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

==Conference Calls for Preparation==

Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Deep Learning and GPUs ==
#[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)
#[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)
#[[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
#[[2017 Winter Project Week/Diffusely abnormal white matter segmentation with 3d U-net| Diffusely abnormal white matter segmentation with 3d U-net]] (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur, Charles Guttmann)
# [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
#[[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
#[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)
#[[2017 Winter Project Week/Convolutional neural nets for lung cancer survival prediction | Convolutional neural nets for lung cancer survival prediction]] (Ahmed Hosny, Chintan Parmar, Roman Zeleznik, Hugo Aerts)
#[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)

== Web Technologies ==
#[[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
#[[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
#[[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
#[[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
#[[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)
#[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)
#[[2017 Winter Project Week/AMI: A 3D Medical Imaging Javascript Library | AMI: A 3D Medical Imaging Javascript Library]] (Rudolph Pienaar, Jorge Luis Bernal Rusiel, Nicolas Rannou)
#[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)

== IGT: Navigation, Robotics, Surgical Planning ==
#[[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
#[[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
#[[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
#[[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
#[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)
#[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)

==dMRI==
#[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
#[[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Fredrik Westin)
#[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)
#[[2017 Winter Project Week/DiPy_in_Slicer | WMA & DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)
#[[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)

==Quantitative Imaging Informatics==
#[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
#[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)
#[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
#[[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

== Shape Analysis, Segmentation ==
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
#[[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
#[[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)
#[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
#[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen)
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)
#[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)

== Infrastructure ==
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)
#[[2017 Winter Project Week/ImprovementsToSegmentEditor | Improvements to Segment Editor]] (Csaba Pinter, Andras Lasso)
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Slicer Community Infrastructure (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault)
#[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)

==Training and Dissemination==
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)
#[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)

==Next project week==
#[[2017 Winter Project Week/Next project week| Next project week]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)

= '''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/2017projectweek registration site].

# Aman Shboul, Zaina :: Old Dominion University
# Aerts, Hugo :: DFCI-Harvard
# Alam, Mahbubul :: Old Dominion University
# Anderson, Peter :: Retired
# Andruejol, Johan :: Kitware, Inc.
# Bakeng, Janne Beate :: SINTEF
# Beers, Andrew :: Massachusetts General Hospital
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
# Bremer, Erich :: Stony Brook University
# Burke, Brice :: American University of Antigua College of Medicine
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# DiPrima, Tammy :: Stony Brook University
# Drouin, Simon :: Montreal Neurological Institute
# Fan, Zhipeng :: Brigham and Women's Hospital
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# Frisken, Sarah :: Brigham and Women's Hospital
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Ghafoorian, Mohsen :: Brigham and Women's Hospital
# Ghosh, Satrajit :: Massachusetts Institute of Technology
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Goncalves, Mathias :: Massachusetts Institute of Technology
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Halle, Michael :: Brigham and Women's Hospital
# Harris, Gordon :: Massachusetts General Hospital
# Helba, Brian :: Kitware, Inc.
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jarecka, Dorota :: Massachusetts Institute of Technology
# Jensen, Henrik G. :: University of Copenhagen
# Kaczmarzyk, Jakub :: Massachusetts Institute of Technology
# Kapur, Tina :: Brigham and Women's Hospital
# Kennedy, David :: UMass Medical School
# Kikinis, Ron :: Brigham and Women's Hospital
# Lasso, Andras :: PerkLab, Queen's University
# Lauer, Rebekka :: Humboldt University Berlin
# Lisle, Curtis :: KnowledgeVis, LLC
# Mastrogiacomo, Katie :: Brigham and Women's Hospital
# Mateus, D. :: TUM
# Mehrtash, Alireza :: Brigham and Women's Hospital
# Meine, Hans :: University of Bremen
# Meyer, Anneke :: University of Magdeburg
# Miller, James :: GE Research
# Mirabel, Clement :: University of Michigan
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Padhy, Smruti :: Massachusetts Institute of Technology
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Prieto, Juan :: NIRAL
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
# Rankin, Adam :: Robarts Research Institute
# Rheault, Francois :: Université de Sherbrooke
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
# Szczepankiewicz, Filip :: Lund University
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Szasz, Teodora :: University of Chicago
# Unadkat, Prashin :: Brigham and Women's Hospital
# Van Griethuysen , Joost :: Netherlands Cancer Institute
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Wang, Ziyang :: Brigham and Women's Hospital
# Wei, Dawei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# Xu, Wanxin :: Brigham and Women's Hospital
# Yang, Yixin :: Brigham and Women's Hospital
# Ye, Wu :: Brigham and Women's Hospital
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Zhang, Yuqian :: Brigham and Women's Hospital
# Zhou, Haoyin :: Brigham and Women's Hospital
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2017 Winter Project Week/Improve Matlab integration

2017-01-09T18:36:14Z

Alexis.girault: update

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)

==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;"
|

* Allowing the access to Matlab variables that are defined in a Matlab module once that module terminates, as if that code was run in the Matlab command line environment.
* Offer a more user-friendly interface to send matlab commands and display the results. Right now the way to do it is to go in MatlabCommander and to type the command in a LineEdit, after which the output result appears in another LineEdit. While it is functional, our end users have had difficulties handling it since the display isn't as nice as in a Matlab console.
* Offer a way to visualize the Matlab workspace variables just like in the Matlab environment: there is currently no way in MatlabBridge to see the variables of the current instance.
|

* Discuss with Andras to better understand the way MatlabBridge work, and showcase an example where we can not access the variables defined in a Matlab module once it has ended. This will lead to a work allowing to address the first objective.
* Look into using a custom ctkConsole (like the python console) in order to mimic the console from the main Matlab environment, OR try to get the commandwindow command from Matlab to directly open up.
* Retrieve workspace from the Matlab instance after each command sent (or matlab module run) and display the variables and their values in a table node, OR try to get the workspace command from Matlab to directly open up.
|

|}

==Background and References==

* MatlabBridge : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge
* ctkConsole : http://www.commontk.org/docs/html/classctkConsole.html
* Matlab commandwindow : https://www.mathworks.com/help/matlab/ref/commandwindow.html
* Matlab workspace : https://www.mathworks.com/help/matlab/ref/workspace.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-04T20:34:54Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Piper (Isomics, Inc.)

==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;"
|

From top priority to possible future work:
* Being able to visualize, load and save volumetric meshes
* Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars).
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension.
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week/Improve Matlab integration

2017-01-04T20:32:16Z

Alexis.girault: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Andras Lasso (PerkLab, Queen's University)

==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;"
|

* Allowing the access to Matlab variables that are defined in a Matlab module once that module terminates, as if that code was run in the Matlab command line environment.
* Offer a more user-friendly interface to send matlab commands and display the results. Right now the way to do it is to go in MatlabCommander and to type the command in a LineEdit, after which the output result appears in another LineEdit. While it is functional, our end users have had difficulties handling it since the display isn't as nice as in a Matlab console.
* Offer a way to visualize the Matlab workspace variables just like in the Matlab environment: there is currently no way in MatlabBridge to see the variables of the current instance.
|

* Discuss with Andras to better understand the way MatlabBridge work, and showcase an example where we can not access the variables defined in a Matlab module once it has ended. This will lead to a work allowing to address the first objective.
* Look into using a custom ctkConsole (like the python console) in order to mimic the console from the main Matlab environment, OR try to get the commandwindow command from Matlab to directly open up.
* Retrieve workspace from the Matlab instance after each command sent (or matlab module run) and display the variables and their values in a table node, OR try to get the workspace command from Matlab to directly open up.
|

|}

==Background and References==

* MatlabBridge : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge
* ctkConsole : http://www.commontk.org/docs/html/classctkConsole.html
* Matlab commandwindow : https://www.mathworks.com/help/matlab/ref/commandwindow.html
* Matlab workspace : https://www.mathworks.com/help/matlab/ref/workspace.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-04T20:08:55Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Piper (Isomics, Inc.)

==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;"
|

* Being able to visualize, load and save volumetric meshes
* Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars).
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension.
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-04T19:31:49Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Piper (Isomics, Inc.)

==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;"
|

* [TOP PRIORITY] Being able to visualize, load and save volumetric meshes
* [FUTURE WORK] Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension.
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

* Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis).
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-04T19:28:51Z

Alexis.girault: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Piper (Isomics, Inc.)

==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;"
|

* [TOP PRIORITY] Being able to visualize, load and save volumetric meshes
* [FUTURE WORK] Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension.
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes.
* Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).
|

*
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week/Support for volumetric meshes

2017-01-04T19:15:05Z

Alexis.girault: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Alexis Girault (Kitware, Inc.)
* Curtis Lisle (KnowledgeVis, LLC)
* Steve Piper (Isomics, Inc.)

==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;"
|

* Being able to visualize, load and save volumetric meshes
* Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them
|

* Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension.
* Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid.
|

*
|}

==Background and References==

* IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
* BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
* MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
* CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
* vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html

2017 Winter Project Week

2017-01-04T19:13:56Z

Alexis.girault: add two projects

__NOTOC__
[[image:PW-Winter2017.png|300px]]

=Welcome to the web page for the 24th Project Week!=

The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. 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:''' January 9-13, 2017.
*'''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/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 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_Project_Weeks|here]].

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

==Conference Calls for Preparation==

Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].

==Calendar==

'''''The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.''''' 

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
* [[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)

== Web Technologies ==
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)

== IGT: Navigation, Robotics, Surgical Planning ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
* [[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)

==dMRI==
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Frederik Westin)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)
* [[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)

== Infrastructure ==

* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)

==To be Categorized==

* [[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Piper)
* [[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)
* [[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)

= '''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/2017projectweek registration site].

# A, Zeina :: SHBOUL
# Aerts, Hugo :: DFCI-Harvard
# Alam, Mahbubul :: Old Dominion University
# Anderson, Peter :: Retired
# Andruejol, Johan :: Kitware, Inc.
# Bakeng, Janne Beate :: SINTEF
# Beers, Andrew :: Massachusetts General Hospital
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
# Bremer, Erich :: Stony Brook University
# Burke, Brice :: American University of Antigua College of Medicine
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Harris, Gordon :: Massachusetts General Hospital
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jensen, Henrik G. :: University of Copenhagen
# Kapur, Tina :: Brigham and Women's Hospital
# Kikinis, Ron :: Brigham and Women's Hospital
# Lasso, Andras :: PerkLab, Queen's University
# Lauer, Rebekka :: Humboldt University Berlin
# Lisle, Curtis :: KnowledgeVis, LLC
# Mastrogiacomo, Katie :: Brigham and Women's Hospital
# Mateus, D. :: TUM
# Mehrtash, Alireza :: Brigham and Women's Hospital
# Meine, Hans :: University of Bremen
# Meyer, Anneke :: University of Magdeburg
# Miller, James :: GE Research
# Mirabel, Clement :: University of Michigan
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
# Rankin, Adam :: Robarts Research Institute
# Rheault, Francois :: Université de Sherbrooke
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# Yang, Yixin :: Brigham and Women's Hospital
# Ye, Wu :: Brigham and Women's Hospital
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Zhang, Yuqian :: Brigham and Women's Hospital
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital