NAMIC Wiki - User contributions [en]

UKF Tractography in Slicer 4

2013-01-11T05:05:20Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)

* Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

* Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with the new changes

* Got CTest working for Slicer build

* Created and tested the .s4ext file

* Tested Superbuild, Slicer4 build, and local .s4ext build on a Mac and a Fedora Linux machine

* Made new git repo and updated the documentation

'''TODO'''
* Get CTest to work in Superbuild

* Finish running all the tests

* Create logo and take snapshots

* Upload .s4ext file

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T05:04:39Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)

* Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

* Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with the new changes

* Got CTest working for Slicer build

* Created and tested the .s4ext file

* Tested Superbuild, Slicer4 build, and local .s4ext build on a Mac and a Fedora Linux machine

* Made new git repo and updated the documentation

'''TODO'''
* Get CTest to work in Superbuild

* Finish running all the tests

* Finish documentation, create logo, and take snapshots

* Upload .s4ext file

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T05:03:33Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)

* Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

* Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with the new changes

* Got CTest working for Slicer build

* Created and tested the .s4ext file

* Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machines

* Made new git repo and updated the documentation

'''TODO'''
* Get CTest to work in Superbuild

* Finish running all the tests

* Finish documentation, create logo, and take snapshots

* Upload .s4ext file

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T05:02:48Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)

* Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

* Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with new changes

* Got CTest working for Slicer build

* Created and tested the .s4ext file

* Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machines

* Made new git repo and updated the documentation

'''TODO'''
* Get CTest to work in Superbuild

* Finish running all the tests

* Finish documentation, create logo, and take snapshots

* Upload .s4ext file

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T05:01:55Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
# Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)

# Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

# Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with new changes

# Got CTest working for Slicer build

# Created and tested the .s4ext file

# Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machines

# Made new git repo and updated the documentation

'''TODO'''
* Get CTest to work in Superbuild

* Finish running all the tests

* Finish documentation, create logo, and take snapshots

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T05:01:23Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
# Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)

# Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

# Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with new changes

# Got CTest working for Slicer build

# Created and tested the .s4ext file

# Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machines

# Made new git repo and updated the documentation

'''TODO'''
# Get CTest to work in Superbuild

# Finish running all the tests

# Finish documentation, create logo, and take snapshots

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T04:58:14Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
# Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)

# Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

# Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with new changes

# Got CTest working for Slicer build

# Created and tested the .s4ext file

# Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machines

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T04:57:22Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
# Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)

# Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

# Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with new changes

# Got CTest working for Slicer build

# Created the .s4ext file and tested it with a local build

# Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machines

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T04:56:40Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
# Refactored code as 3 modules bundled into an extension (as per the Slicer4 recommendation)

# Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

# Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with new changes

# Got CTest working for Slicer build

# Created the .s4ext file and tested it with a local build

# Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machines

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T04:55:48Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
# Refactored code as 3 modules bundled into an extension (as per the Slicer4 recommendation)

# Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

# Updated and fixed the Superbuild CMakelists.txt to be compatible with new changes

# Got CTest working for Slicer build

# Created the .s4ext file and tested it with a local build

# Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machine

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T04:51:54Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
# Refactored code as 3 modules bundled into an extension (as per the Slicer recommendation)

# Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt

# Updated and fixed the Superbuild CMakelists.txt to be compatible with new changes
# Got CTest working for Slicer build

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-11T04:51:38Z

Reckbo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
# Refactored code as 3 modules bundled into an extension (as per the Slicer recommendation)
# Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt
# Updated and fixed the Superbuild CMakelists.txt to be compatible with new changes
# Got CTest working for Slicer build

</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-04T21:20:49Z

Reckbo: /* References */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-04T21:12:52Z

Reckbo: /* References */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* '''High Priority''':
Have a working UKFtractography module in Slicer4 extension:
# Change and update the UKFTractography.xml file for receiving a .vtk file as output.
# Setup CTest and ensure its working.
# Verify that the Tractography module works on a test invivo data set
#* Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
# Design a logo for the extension module.
# Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
# Add the 2 utility functions to the extension module and verify if they work.

* '''Optional''':
# Use the VTK library to output the data (.vtp).

* '''Future Work''':
# Move from boost to ITK multithreading.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
</div>
</div>

==References==
Reference for 2-tensor tractography
# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
" A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.

UKF Tractography in Slicer 4

2013-01-04T21:12:22Z

Reckbo:

UKF Tractography in Slicer 4

2013-01-04T21:09:42Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:09:24Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:09:14Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:08:55Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:08:14Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:07:53Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:07:26Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:07:03Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:06:53Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:06:35Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:05:45Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:05:29Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:05:00Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:04:25Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:04:01Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:03:53Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-04T21:03:31Z

Reckbo: /* Project Description */

2013 Winter Project Week

2013-01-02T17:10:48Z

Reckbo: /* TBI */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2013]], [[Events]]

__NOTOC__
[[image:PW-SLC2013.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].
= Dates.Venue.Registration =

Please [[AHM_2013#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2013#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2013#Agenda|'''Click here for the agenda for AHM 2013 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

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

=Projects=
* [[2013_Project_Week_Template | Template for project pages]]

==TBI==
* [[4D DTI tractography in Slicer for TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Bo Wang, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented TBI connectivity analysis in Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Geometric metamorphosis for TBI]] (Danielle Pace, Stephen Aylward, Andrei Irimia, Micah Chambers)
* [[UKF Tractography in Slicer 4]] (Ryan Eckbo, Yogesh Rathi, Demian Wassermann, C.F Westin, Ron Kikinis)

==Atrial Fibrillation==
* [[2013_Project_Week:CARMA_Scar_Segmentation|Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)]]
* [[2013_Project_Week:CARMA_PV_Antrum_Cut|SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_LA_Seg_Gopal|SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_2D_Dilate|SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_PractialLASeg|SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_RT_MRI|PROJECT PLANNING: Real Time MRI in Slicer with OpenIGT (Alan Morris, Ashvin George, Josh Cates, Rob MacLeod)]]

==Huntington's Disease==
* [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson)
* [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch)
* [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch, Nicole Aucoin)

==Head and Neck Cancer==
* [[2013_Winter_Project_Week:MABS|Multi atlas-based segmentation]] (Sharp, Shusharina, Golland)
* [[2013_Winter_Project_Week:Hybrid_registration|Hybrid interactive-automatic registration]] (Shusharina, Sharp, Pieper)

==Prostate Interventions==
* [[2013_Project_Week:BRAINSFit_new_features|BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)]]
* [[2013_Project_Week:PkModeling_for_prostate_DCE_MRI|PkModeling for prostate DCE MRI (Jim, Andrey)]]

==Abdominal Interventions==
* Abdominal navigation module (Junichi Tokuda, Atsushi Yamada)

==Medical Robotics==
* [[Configurable fiducial-based device to image registration]] (Junichi Tokuda)
* Reviving ultrasound integration for visual servoing (Laurent Chauvin, Noby Hata)
* [[2013_Project_Week:AgileMedicalRobot | Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)]]
* Investigating role of open source in translational research (Miki Kumekawa)

==General Image Guided Therapy==
* United SlicerIGT extension, repository, website (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* Mobile image overlay augmented reality needle guidance (Adam Rankin, Tamas Ungi)

==Radiation Therapy==
* [[2013_Project_Week:DicomRtExport|SlicerRT: DICOM RT export]] (Kevin Wang, Greg Sharp, Csaba Pinter)
* [[2013_Project_Week:RtBeamGeometry|SlicerRT: Beam geometry widgets]] (Csaba Pinter, Greg Sharp)
* [[2013_Project_Week:MRIAblation|Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor]] (Laurent Chauvin)

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc?, Bill Lorensen,Bradley Lowekamp)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov?, Nicole Aucoin, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Nicole Aucoin Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper, Csaba Pinter)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and Sample Data Refactor]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?, Greg Sharp)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao)
*[[2013_Project_Week:Threaded SimpleITK Modules|Threaded SimpleITK Modules]] (Brad Lowekamp, Steve Pieper)

UKF Tractography in Slicer 4

2013-01-02T17:10:32Z

Reckbo: /* Key Investigators */

UKF Tractography in Slicer 4

2013-01-02T14:50:34Z

Reckbo:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* To convert Dr. Rathi's UKF tractography Slicer3 module to a Slicer4 extension

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
</div>
</div>

UKF Tractography in Slicer 4

2013-01-02T14:50:06Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-02T14:49:58Z

Reckbo: /* Project Description */

UKF Tractography in Slicer 4

2013-01-02T14:48:38Z

Reckbo: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:ScarSeg_EM.png‎| Scar tissue identification.
</gallery>

==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* We are developing methods for identifying scar tissue from CARMA data. Our previous method demonstrates an effective identification ability for DE-MRI data. In this method, the intensity distribution inside the LA myocardial wall is modeled as a mixture of Gaussians. To improve the performance of this method, we will integrate the intensity information from the LA chamber into the overall identification procedure.
* We will discuss possible improvements for scar identification.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Design an identification scheme using the LA intensity as a prior
* Test the method using CARMA data
* Deliver the implementation in CLI module.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

UKF Tractography in Slicer 4

2013-01-02T14:47:44Z

Reckbo: Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List Image:ScarSeg_EM.png‎| Scar tissue identification. </gallery> ==Key Investigators=…'

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:ScarSeg_EM.png‎| Scar tissue identification.
</gallery>

==Key Investigators==

* Ryan Eckbo

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>

* We are developing methods for identifying scar tissue from CARMA data. Our previous method demonstrates an effective identification ability for DE-MRI data. In this method, the intensity distribution inside the LA myocardial wall is modeled as a mixture of Gaussians. To improve the performance of this method, we will integrate the intensity information from the LA chamber into the overall identification procedure.
* We will discuss possible improvements for scar identification.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Design an identification scheme using the LA intensity as a prior
* Test the method using CARMA data
* Deliver the implementation in CLI module.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2013 Winter Project Week

2013-01-02T14:47:19Z

Reckbo: /* TBI */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2013]], [[Events]]

__NOTOC__
[[image:PW-SLC2013.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].
= Dates.Venue.Registration =

Please [[AHM_2013#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2013#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2013#Agenda|'''Click here for the agenda for AHM 2013 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

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

=Projects=
* [[2013_Project_Week_Template | Template for project pages]]

==TBI==
* [[4D DTI tractography in Slicer for TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Bo Wang, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented TBI connectivity analysis in Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Geometric metamorphosis for TBI]] (Danielle Pace, Stephen Aylward, Andrei Irimia, Micah Chambers)
* [[UKF Tractography in Slicer 4]] (Ryan Eckbo, Yogesh Rathi, C.F Westin, Ron Kikinis)

==Atrial Fibrillation==
* [[2013_Project_Week:CARMA_Scar_Segmentation|Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)]]
* [[2013_Project_Week:CARMA_PV_Antrum_Cut|SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_LA_Seg_Gopal|SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_2D_Dilate|SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_PractialLASeg|SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_RT_MRI|PROJECT PLANNING: Real Time MRI in Slicer with OpenIGT (Alan Morris, Ashvin George, Josh Cates, Rob MacLeod)]]

==Huntington's Disease==
* [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson)
* [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch)
* [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch, Nicole Aucoin)

==Head and Neck Cancer==
* [[2013_Winter_Project_Week:MABS|Multi atlas-based segmentation]] (Sharp, Shusharina, Golland)
* [[2013_Winter_Project_Week:Hybrid_registration|Hybrid interactive-automatic registration]] (Shusharina, Sharp, Pieper)

==Prostate Interventions==
* BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)
* PkModeling for prostate DCE MRI (Jim, Andrey)

==Abdominal Interventions==
* Abdominal navigation module (Junichi Tokuda, Atsushi Yamada)

==Medical Robotics==
* [[Configurable fiducial-based device to image registration]] (Junichi Tokuda)
* Reviving ultrasound integration for visual servoing (Laurent Chauvin, Noby Hata)
* [[2013_Project_Week:AgileMedicalRobot | Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)]]
* Investigating role of open source in translational research (Miki Kumekawa)

==General Image Guided Therapy==
* United SlicerIGT extension, repository, website (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* Mobile image overlay augmented reality needle guidance (Adam Rankin, Tamas Ungi)

==Radiation Therapy==
* [[2013_Project_Week:DicomRtExport|SlicerRT: DICOM RT export]] (Kevin Wang, Greg Sharp, Csaba Pinter)
* [[2013_Project_Week:RtBeamGeometry|SlicerRT: Beam geometry widgets]] (Csaba Pinter, Greg Sharp)
* [[2013_Project_Week:MRIAblation|Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor]] (Laurent Chauvin)

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc?, Bill Lorensen,Bradley Lowekamp)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov?, Nicole Aucoin, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Nicole Aucoin Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper, Csaba Pinter)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and Sample Data Refactor]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?, Greg Sharp)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao)
*[[2013_Project_Week:Threaded SimpleITK Modules|Threaded SimpleITK Modules]] (Brad Lowekamp, Steve Pieper)

2011 Summer Project Week DWI Atlas

2011-06-24T14:36:25Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).
We can then use this on a set of DWI's and average them to create a DWI atlas.

</div>

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

<h3>Approach, Plan</h3>
Finish and test the user interfaces:
1) Slicer GUI, and
2) Commandline interface

</div>

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

<h3>Progress</h3>

Completed and tested the GUI and command line interfaces on Mac and Linux.

TODO: Change the checkboxes to a radio toggle button.

</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a slicer Module (commandline)

2011 Summer Project Week DWI Atlas

2011-06-24T14:34:38Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).
We can then use this on a set of DWI's and average them to create a DWI atlas.

</div>

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

<h3>Approach, Plan</h3>
Finish and test the user interfaces:
1) Slicer GUI, and
2) Commandline interface

</div>

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

<h3>Progress</h3>

Completed and tested the GUI and command line interfaces.

TODO: Change the checkboxes to a radio toggle button.

</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a slicer Module (commandline)

2011 Summer Project Week DWI Atlas

2011-06-24T14:18:43Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).

</div>

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

<h3>Approach, Plan</h3>
Finish and test the user interfaces:
1) Slicer GUI, and
2) Commandline interface

</div>

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

<h3>Progress</h3>

Completed and tested the GUI and command line interfaces.

TODO: Change the checkboxes to a radio toggle button.

</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a slicer Module (commandline)

2011 Summer Project Week DWI Atlas

2011-06-24T14:18:22Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).

</div>

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

<h3>Approach, Plan</h3>
Finish and test the user interfaces:
1) GUI
2) Commandline interface

</div>

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

<h3>Progress</h3>

Completed and tested the GUI and command line interfaces.

TODO: Change the checkboxes to a radio toggle button.

</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a slicer Module (commandline)

2011 Summer Project Week DWI Atlas

2011-06-24T14:18:03Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).

</div>

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

<h3>Approach, Plan</h3>
Finish and test the user interfaces;
1) GUI
2) Commandline interface

</div>

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

<h3>Progress</h3>

Completed and tested the GUI and command line interfaces.

TODO: Change the checkboxes to a radio toggle button.

</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a slicer Module (commandline)

2011 Summer Project Week DWI Atlas

2011-06-24T14:17:05Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).

</div>

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

<h3>Approach, Plan</h3>
Finish the user interface, including the GUI, and test.

</div>

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

<h3>Progress</h3>

Completed and tested the GUI and command line interfaces.

TODO: Change the checkboxes to a radio toggle button.

</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a slicer Module (commandline)

2011 Summer Project Week DWI Atlas

2011-06-24T14:13:53Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).

</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>



</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a slicer Module (commandline)

2011 Summer Project Week DWI Atlas

2011-06-24T14:13:32Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).

</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>



</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a

#Slicer Module (commandline)

2011 Summer Project Week DWI Atlas

2011-06-24T14:13:07Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).

</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>



</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"

This work will be delivered to the NAMIC Kit as a

#Slicer Module
##Built-in:
##Extension -- commandline:

2011 Summer Project Week DWI Atlas

2011-06-24T14:10:57Z

Reckbo:

__NOTOC__
<gallery>
Image:Dwi_warper_screenshot.jpg|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DWI Warper'''

==Key Investigators==
* Brigham and Women's Hospital: Ryan Eckbo, Sylvain Bouix

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

To complete our DWI warper module. This warps a DWI and resamples the gradient directions (needed since the warp rotates them at each voxel).

</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>



</div>
</div>

<div style="width: 97%; float: left;">

</div>

==References==
Bouix, S., Rathi, Y., Sabuncu, M. "Building an Average Population HARDI Atlas"