NAMIC Wiki - User contributions [en]

2012 Summer Project Week:AIM for QIN

2012-06-26T15:56:02Z

Nurad: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Beichel-QINDataFlow.png|Diagram of various data types and connections that need to be organized
Image:Rubin-QINDataFlow.png|Diagram from Daniel Rubin
</gallery>

==Key Investigators==
* BWH: Andrey Fedorov, Nicole Aucoin, Paul Mercea, Fiona Fennessy
* Northwestern U.: Pat Mongkolwat
* Stanford: Daniel Rubin
* U. Iowa: Reinhard Beichel, Markus Van Tol
* MGH: Jayashree Kalpathy-Cramer
* NCI: Justin Kirby

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

<h3>Objective</h3>
Participants of the Quantitative Imaging Network (QIN) are in need of a standard-based or consensus-based format for consistent storage and organization of various types of data related to quantitative imaging of clinical patients undergoing cancer treatment. Typical dataset includes a subset of the following:
* several time-points with the multi-modal imaging data at each time-point
* segmentations of the lesions and/or reference and/or relevant anatomical structures
* measurements/calculations derived from the images and segmentations
* clinical and demographical information about the patient
* information related to treatment
* pathology correlation data

Ideally, we would like to be able to consistently organize these various types of information into a self-sufficient document/data structure to facilitate exchange of the information for subsequent analysis, presentation and archival. The possibilities currently considered include DICOM-based formats (DICOM Structured Reports), Annotation Image Markup (AIM) format, and Slicer MRML scene.

The goal of this project is to focus on the specific project of U. Iowa in longitudinal PET/CT imaging, and attempt to utilize the capabilities of AIM to organize the data provided by U. of Iowa collaborators. Specifically, the dataset we will use for experimentation includes:
* n PET/CT datasets acquired over the course of treatment
* binary segmentations of lesions, represented as 3d segmentations (lesions may disappear over the course of treatment)
* binary segmentations of the reference structures

BWH and MGH teams are also participants of the QIN, and will provide input related to how the use-cases at their sites are different from U. Iowa use case. BWH will also provide expertise in 3D Slicer in discussing its capabilities in visualizing and organizing the data for the Iowa QIN use case.

Big questions we would like to answer in the end:
* what are the capabilities of AIM with respect to addressing the needs of specific QIN use cases?
* how these capabilities are supported by the tools from the user perspective?

</div>

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

<h3>Approach, Plan</h3>

* We will have discussions and hands-on demonstrations of AIM capabilities to understand its applicability to QIN use cases.
* Tuesday 6/19 11am to 1pm Eastern time we will have a conference call that will include Daniel Rubin and Reinhard Beichel (joining remotely); project week participants interested to join will meet at room 32-262 at MIT (on the 2nd floor of the Stata Center)
* We will summarize our findings at the end of the project week

</div>

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

<h3>Progress</h3>

* We had a TCON that included participants from BWH, MGH, Northwestern, Stanford and NCI.
* discussed the specific mechanisms available in AIM for storing multi-timepoint data with multiple lesions at each time-point:
** separate AIM files should be used for each individual segmentation
** each annotation has to be associated with a single finding on an image or a set of images in the same series
** associations across the timepoints that correspond to a given patient can be recovered by means of querying the "AIM database" for a certain patient
** direct associations can be encoded using AnnotationOfAnnotations type; however, it is not supported by ClearCanvas (the only AIM workstation that is available to the QIN users). There is no plan to add this functionality in the foreseeable future
* discussed the plans for supporting cross-platform exchange of 3D segmentations
** support for DICOM segmentation objects is very limited and not available on the workstations readily available
** there is no plan for supporting DICOM seg objects in ClearCanvas
** BWH is in the process of implementing DICOM seg support in 3D Slicer, but testing is limited to cross-check with syngo.via
** an alternative has been suggested to use DICOM secondary capture to store segmentation label in NRRD format, which is widely supported by libraries and viewers
** BWH will work with Daniel Rubin to exchange NRRD date wrapped in secondary capture and point to the code that does this packaging

</div>
</div>

==Tuesday TCON==

Attended: Pat Mongkolwat, Daniel Rubin, Vlad Kleper, Nicole Aucoin, Andrey Fedorov, Reinhard Beichel, Marcus Van Tol, Jayashree Kalpathy-Cramer, Justin Kirby, Pallavi Tiwari

* Pat Mongkolwat:
** AIM stores informaton related to the image, so patient information will not be represented
** Separate nodes require separate AIM objects
** Elements stored:
*** Annotations
*** Measurements derived from annotations
*** Markup types (point, multipoint, polygon, circle) + segmentation object
** Annotations of annotations can be used to organize multiple timepoints and multiple modalities
* Support of Annotations of annotations
** in workstations is not currently available, but if this is justified by QIN use cases, Daniel and Pat can work on this
** Pat: this is not in going to be available in the foreseeable future
* Sharing of 3d segmentations
** support of DICOM SEG in ClearCanvas is not going to be available anytime soon
** since DICOM SEG is supported by very limited set of tools, we may consider using NRRD as a format referenced from AIM

'''Action items'''

* Daniel:
** will talk with Reinhard to learn more about the use case and learn if AIM is suitable
** Andrey will send SEG object example produced and a pointer to the code

* Reinhard:
** would like to know what infrastructure is available in NIH for sharing AIM, and also for storing patient information (age, tests, clinical info)

* Andrey:
** will send Slicer data bundle and a pointer to the code that creates/unpackages the scene and referenced data
** will look into wrapping just the NRRD file into a DICOM SC for the purposes of sharing segmentations

==Delivery Mechanism==

The summary of our findings will be available to the NA-MIC and QIN community on this wiki page.

==References==
* Quantitative Imaging Network (QIN) overview: https://wiki.nci.nih.gov/display/CIP/QIN
* BWH AIM/Slicer integration project: [[Projects:QIN:3D_Slicer_Annotation_Image_Markup]]
* QIN Motivating use cases: [[Projects:QIN:3D_Slicer_Annotation_Image_Markup:Use_cases]]

2012 Summer Project Week:CMake for AIM API

2012-06-21T22:06:23Z

Nurad: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Northwestern: Pat Mongklowat, Vlad Kleper
* BWH: Andrey Fedorov

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

<h3>Objective</h3>

Annotation Imaging and Markup is a format that can be used to organized various annotation information derived from the imaging data and save it in a consistent XML-based way. The library has originally been developed on Windows platform. It has not been compiled on other computing platform. Currently, this code has been modified to be independent from Windows specific elements. The library can be complied on Ubuntu. But, it must be on a particular path. Eventually, we would like to have the library for cross-platform by integrating it with CMake.

We are looking for Make and CMake expertise to help us with this porting task.

</div>

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

<h3>Approach, Plan</h3>
</div>
1. Working on the current make file to find out why the complied library must be on a specific path.
2. Looking for a person who knows CMake environment
<div style="width: 40%; float: left;">

<h3>Progress</h3>
1. Fixed the make file. It does not generating an AIM library for a particular path. (Thanks Greg at MGH.)
2. Started working with Andre on make file for Mac OS X.
</div>
</div>

==Delivery Mechanism==

AIM 3.0 API library distributed under NCI (BSD-like) license.
A make file for Linux.

==References==

2012 Summer Project Week:CMake for AIM API

2012-06-21T22:06:05Z

Nurad: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Northwestern: Pat Mongklowat, Vlad Kleper
* BWH: Andrey Fedorov

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

<h3>Objective</h3>

Annotation Imaging and Markup is a format that can be used to organized various annotation information derived from the imaging data and save it in a consistent XML-based way. The library has originally been developed on Windows platform. It has not been compiled on other computing platform. Currently, this code has been modified to be independent from Windows specific elements. The library can be complied on Ubuntu. But, it must be on a particular path. Eventually, we would like to have the library for cross-platform by integrating it with CMake.

We are looking for Make and CMake expertise to help us with this porting task.

</div>

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

<h3>Approach, Plan</h3>
</div>
1. Working on the current make file to find out why the complied library must be on a specific path.
2. Looking for a person who knows CMake environment
<div style="width: 40%; float: left;">

<h3>Progress</h3>
1. Fixed the make file. It does not generating an AIM library for a particular path. (Thanks Greg at MGH!)
2. Started working with Andre on make file for Mac OS X.
</div>
</div>

==Delivery Mechanism==

AIM 3.0 API library distributed under NCI (BSD-like) license.
A make file for Linux.

==References==

2012 Summer Project Week:CMake for AIM API

2012-06-21T21:04:51Z

Nurad: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Northwestern: Pat Mongklowat, Vlad Kleper
* BWH: Andrey Fedorov

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

<h3>Objective</h3>

Annotation Imaging and Markup is a format that can be used to organized various annotation information derived from the imaging data and save it in a consistent XML-based way. The library has originally been developed on Windows platform. It has not been compiled on other computing platform. Currently, this code has been modified to be independent from Windows specific elements. The library can be complied on Ubuntu. But, it must be on a particular path. Eventually, we would like to have the library for cross-platform by integrating it with CMake.

We are looking for Make and CMake expertise to help us with this porting task.

</div>

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

<h3>Approach, Plan</h3>
</div>
1. Working on the current make file to find out why the complied library must be on a specific path.
2. Looking for a person who knows CMake environment
<div style="width: 40%; float: left;">

<h3>Progress</h3>
1. Fixed the make file. It does not generating an AIM library for a particular path.
2. Started working with Andre on make file for Mac OS X.
</div>
</div>

==Delivery Mechanism==

AIM 3.0 API library distributed under NCI (BSD-like) license.
A make file for Linux.

==References==

2012 Summer Project Week:CMake for AIM API

2012-06-21T21:04:36Z

Nurad: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Northwestern: Pat Mongklowat, Vlad Kleper
* BWH: Andrey Fedorov

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

<h3>Objective</h3>

Annotation Imaging and Markup is a format that can be used to organized various annotation information derived from the imaging data and save it in a consistent XML-based way. The library has originally been developed on Windows platform. It has not been compiled on other computing platform. Currently, this code has been modified to be independent from Windows specific elements. The library can be complied on Ubuntu. But, it must be on a particular path. Eventually, we would like to have the library for cross-platform by integrating it with CMake.

We are looking for Make and CMake expertise to help us with this porting task.

</div>

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

<h3>Approach, Plan</h3>
</div>
1. Working on the current make file to find out why the complied library must be on a specific path.
2. Looking for a person who knows CMake environment
<div style="width: 40%; float: left;">

<h3>Progress</h3>
1. Fixed the make file. It does not generating an AIM library for a particular path.
2. Started working with Andre on make file for Mac OS X.
</div>
</div>

==Delivery Mechanism==

AIM 3.0 API library distributed under NCI (BSD-like) license.
Make file for Linux.

==References==

2012 Summer Project Week:CMake for AIM API

2012-06-21T21:03:45Z

Nurad: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Northwestern: Pat Mongklowat, Vlad Kleper
* BWH: Andrey Fedorov

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

<h3>Objective</h3>

Annotation Imaging and Markup is a format that can be used to organized various annotation information derived from the imaging data and save it in a consistent XML-based way. The library has originally been developed on Windows platform. It has not been compiled on other computing platform. Currently, this code has been modified to be independent from Windows specific elements. The library can be complied on Ubuntu. But, it must be on a particular path. Eventually, we would like to have the library for cross-platform by integrating it with CMake.

We are looking for Make and CMake expertise to help us with this porting task.

</div>

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

<h3>Approach, Plan</h3>
</div>
1. Working on the current make file to find out why the complied library must be on a specific path.
2. Looking for a person who knows CMake environment
<div style="width: 40%; float: left;">

<h3>Progress</h3>
1. Fixed the make file. It does not generating an AIM library for a particular path.
2. Started working with Andre on make file for Mac OS X.
</div>
</div>

==Delivery Mechanism==

Standalone cross-platform portable AIM 3.0 API library distributed under NCI (BSD-like) license.

==References==

2012 Summer Project Week:CMake for AIM API

2012-06-21T20:38:49Z

Nurad: /* Delivery Mechanism */

Collaboration/NWU/Radiology Workstation

2007-06-22T19:25:03Z

Nurad: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Nwuslicer3.jpg|thumb|320px|Our clinical workstation integrated with Slicer3's main viewer, under development at Northwestern]]
|}

__NOTOC__
===Key Investigators===
* Northwestern: David S. Channin, Pat Mongkolwat, Skip Talbot, Alex Kogan, Vladimir Kleper
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
The goal of our project is to be able to use Slicer3's advanced imaging algorithms and 3D functionality from inside a clinical workstation being developed at Northwestern University. We'd also like to reconfigure use of the main viewer for a new way to interact with the volume that might be more efficient for clinical use. Our main objectives to accomplish this goal include:
* Integrate the rendering and functionality of Slicer3 into a .Net foundation GUI for use in a clinical workstation
* Create a new representation of the 3D volume as a cube with an oblique cut plane rather than the default three orthogonal cut planes

</div>

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

<h1>Approach, Plan</h1>

To implement this integration process, we have taken the following steps:
* Convert Slicer3 into a managed class object
* Extract the renderers through existing accesor methods and add them to managed renderers using a VTK .Net wrapper
* Convert KWWidgets into .Net Controls
* Implement volume cube representation with existing Slicer3 code
</div>

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

<h1>Progress</h1>
In regards to the steps listed previously, we have made the following progress:
* Slicer3 compiled as a managed dynamically linked library that can be directly integrated into a .Net application
* The renderers and their interactors can be placed into .Net user controls for direct integration with a .Net GUI
* The basic foundation for converting KWWidgets has been devised, but much work remains. The process involves using a slight change to the KWObject class, and then deriving inherited controls on the .Net side
* The process needed to reassemble the 3D Main Viewer is under works, but this part of the project is in its infancy

</div>

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

</div>

===References===
* A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.
* Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007.

Collaboration/NWU/Radiology Workstation

2007-06-22T19:23:39Z

Nurad: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Nwuslicer3.jpg|thumb|320px|Our clinical workstation integrated with Slicer3's main viewer, under development at Northwestern]]
|}

__NOTOC__
===Key Investigators===
* Northwestern: David S. Channin, Pat Mongkolwat, Skip Talbot, Alex Kogan, Vladimir Kleper
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
The goal of our project is to be able to use Slicer3's advanced imaging algorithms and 3D functionality from inside a clinical workstation being developed at Northwestern University. We'd also like to reconfigure use of the main viewer for a new way to interact with the volume that might be more efficient for clinical use. Our main objectives to accomplish this goal include:
* Integrate the rendering and functionality of Slicer3 into a .Net foundation GUI for use in a clinical workstation
* Create a new representation of the 3D volume as a cube with an oblique cut plane rather than the default three orthogonal cut planes

</div>

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

<h1>Approach, Plan</h1>

To implement this integration process, we have taken the following steps:
* Convert Slicer3 into a managed class object
* Extract the renderers through existing accesor methods and add them to managed renderers using a VTK .Net wrapper
* Convert KWWidgets into .Net Controls
* Implement volume cube representation with existing Slicer3 code
</div>

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

<h1>Progress</h1>
In regards to the steps listed previously, we have made the following progress:
* Slicer3 compiled as a managed dynamically linked library that can be directly integrated into a .Net application
* The renderers and their interactors can be placed into .Net user controls for direct integration with a .Net GUI
* The basic foundation for converting KWWidgets has been devised, but much work remains. The process involves using a slight change to the KWObject class, and the deriving inherited controls on the .Net side
* The pieces needed to reassemble the 3D Main Viewer are under works, but this part of the project is in its infancy

</div>

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

</div>

===References===
* A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.
* Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007.

Collaboration/NWU/Radiology Workstation

2007-06-22T19:22:53Z

Nurad: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Nwuslicer3.jpg|thumb|320px|Our clinical workstation integrated with Slicer3's main viewer, under development at Northwestern]]
|}

__NOTOC__
===Key Investigators===
* Northwestern: David S. Channin, Pat Mongkolwat, Skip Talbot, Alex Kogan, Vladimir Kleper
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
The goal of our project is to be able to use Slicer3's advanced imaging algorithms and 3D functionality from inside a clinical workstation being developed at Northwestern University. We'd also like to reconfigure use of the main viewer for a new way to interact with the volume that might be more efficient for clinical use. Our main objectives to accomplish this goal include:
* Integrate the rendering and functionality of Slicer3 into a .Net foundation GUI for use in a clinical workstation
* Create a new representation of the 3D volume as a cube with an oblique cut plane rather than the default three orthogonal cut planes

</div>

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

<h1>Approach, Plan</h1>

To implement this integration process, we have taken the following steps:
* Convert Slicer3 into a managed class object
* Extract the renderers through existing accesor methods and add them to managed renderers using a VTK .Net wrapper
* Convert KWWidgets into .Net Controls
* Implement volume cube representation with existing Slicer3 code
</div>

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

<h1>Progress</h1>
In regards to the steps listed previously, we have made the following progress:
* Slicer3 compiled as a managed dynamically linked library that can be directly integrated into a .Net application
* The renderers and their interactors can be placed into .Net user controls for direct integrated with a .Net GUI
* The basic foundation for converting KWWidgets has been devised, but much work remains. The process involves using a slight change to the KWObject class, and the deriving inherited controls on the .Net side
* The pieces needed to reassemble the 3D Main Viewer are under works, but this part of the project is in its infancy

</div>

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

</div>

===References===
* A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.
* Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007.

Collaboration/NWU/Radiology Workstation

2007-06-22T19:15:40Z

Nurad:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Nwuslicer3.jpg|thumb|320px|Our clinical workstation integrated with Slicer3's main viewer, under development at Northwestern]]
|}

__NOTOC__
===Key Investigators===
* Northwestern: David S. Channin, Pat Mongkolwat, Skip Talbot, Alex Kogan, Vladimir Kleper
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
The goal of our project is to be able to use Slicer3's advanced imaging algorithms and 3D functionality from inside a clinical workstation being developed at Northwestern University. We'd also like to reconfigure use of the main viewer for a new way to interact with the volume that might be more efficient for clinical use. Our main objectives to accomplish this goal include:
* Integrate the rendering and functionality of Slicer3 into a .Net foundation GUI for use in a clinical workstation
* Create a new representation of the 3D volume as a cube with an oblique cut plane rather than the default three orthogonal cut planes

</div>

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

<h1>Approach, Plan</h1>

To implement this integration process, we have taken the following steps:
* Convert Slicer3 into a managed class object
* Extract the renderers through existing accesor methods and add them to managed renderers using a VTK .Net wrapper
* Convert KWWidgets into .Net Controls
* Implement volume cube representation with existing Slicer3 code
</div>

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

<h1>Progress</h1>

We integrated Slicer3 alpha with our 2D workstation by directly modifying the Slicer3 base code, passing window handles through Slicer3's GUI objects. Modifying the base code prevented maintainability of Slicer3 updates as changes had to be reimplimented. Currently, we can integrate the Slicer3 beta without modifying the base code by extracting the render windows through existing accessor methods and adding them to our workstation through a managed version of VTK.

</div>

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

</div>

===References===
* A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.
* Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007.

Collaboration/NWU/Radiology Workstation

2007-06-22T19:12:42Z

Nurad:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Nwuslicer3.jpg|thumb|320px|Our clinical workstation integrated with Slicer3's main viewer, under development at Northwestern]]
|}

__NOTOC__
===Key Investigators===
* Northwestern: David S. Channin, Pat Mongkolwat, Skip Talbot, Alex Kogan, Vladimir Kleper
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
The goal of our project is to be able to use Slicer3's advanced imaging algorithms and 3D functionality from inside a clinical workstation being developed at Northwestern University. We'd also like to reconfigure use of the main viewer for a new way to interact with the volume that might be more efficient for clinical use. Our main objectives to accomplish this goal include:
* Integrate the rendering and functionality of Slicer3 into a .Net foundation GUI for use in a clinical workstation
* Create a new representation of the 3D volume as a cube with an oblique cut plane rather than the default three orthogonal cut planes

</div>

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

<h1>Approach, Plan</h1>

Our plan is to finish integrating Slicer3 including support for custom modules, and to add a custom MRML scene to the main viewer featuring a 6 plane cubic representation of the volume with an additional oblique cut plane.
</div>

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

<h1>Progress</h1>

We integrated Slicer3 alpha with our 2D workstation by directly modifying the Slicer3 base code, passing window handles through Slicer3's GUI objects. Modifying the base code prevented maintainability of Slicer3 updates as changes had to be reimplimented. Currently, we can integrate the Slicer3 beta without modifying the base code by extracting the render windows through existing accessor methods and adding them to our workstation through a managed version of VTK.

</div>

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

</div>

===References===
* A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.
* Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007.

Collaboration/NWU/Radiology Workstation

2007-05-31T21:00:22Z

Nurad:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Nwuslicer3.jpg|thumb|320px|Our clinical workstation integrated with Slicer3's main viewer, under development at Northwestern]]
|}

__NOTOC__
===Key Investigators===
* Northwestern: David S. Channin, Pat Mongkolwat, Skip Talbot, Alex Kogan, Vladimir Kleper
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Our objective is to demonstrate integration of advanced visualization algorithms in a clinical workstation through the logic and functionality of Slicer3.

</div>

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

<h1>Approach, Plan</h1>

Our plan is to finish integrating Slicer3 including support for custom modules, and to add a custom MRML scene to the main viewer featuring a 6 plane cubic representation of the volume with an additional oblique cut plane.
</div>

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

<h1>Progress</h1>

We integrated Slicer3 alpha with our 2D workstation by directly modifying the Slicer3 base code, passing window handles through Slicer3's GUI objects. Modifying the base code prevented maintainability of Slicer3 updates as changes had to be reimplimented. Currently, we can integrate the Slicer3 beta without modifying the base code by extracting the render windows through existing accessor methods and adding them to our workstation through a managed version of VTK.

</div>

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

</div>

===References===
* A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.
* Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007.

File:Nwuslicer3.jpg

2007-05-31T19:55:13Z

Nurad: A screen shot of the clinical workstation under development at Northwestern, integrated with Slicer3

A screen shot of the clinical workstation under development at Northwestern, integrated with Slicer3

Collaboration/NWU/Radiology Workstation

2007-05-31T19:49:15Z

Nurad:

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please cut and paste the template from this page and use it here. This will be the replacement for the 4-block.
{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* Northwestern: David S. Channin, Pat Mongkolwat, Skip Talbot, Alex Kogan, Vladimir Kleper
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Our objective is to demonstrate integration of advanced visualization algorithms in a clinical workstation through the logic and functionality of Slicer3.

</div>

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

<h1>Approach, Plan</h1>

Our plan is to finish integrating Slicer3 including support for custom modules, and to add a custom MRML scene to the main viewer featuring a 6 plane cubic representation of the volume with an additional oblique cut plane.
</div>

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

<h1>Progress</h1>

We integrated Slicer3 alpha with our 2D workstation by directly modifying the Slicer3 base code, passing window handles through Slicer3's GUI objects. Modifying the base code prevented maintainability of Slicer3 updates as changes had to be reimplimented. Currently, we can integrate the Slicer3 beta without modifying the base code by extracting the render windows through existing accessor methods and adding them to our workstation through a managed version of VTK.

</div>

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

</div>

===References===
* A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.
* Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007.

Collaboration/NWU/Radiology Workstation

2007-05-31T19:46:00Z

Nurad: /* Additional Information */

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please cut and paste the template from this page and use it here. This will be the replacement for the 4-block.
{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* Northwestern: David S. Channin, Pat Mongkolwat, Skip Talbot, Alex Kogan, Vladimir Kleper
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
To demonstrate integration of advanced visualization algorithms in a clinical workstation through the logic and functionality of Slicer3.

</div>

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

<h1>Approach, Plan</h1>

To finish integrating Slicer3 including support for custome modules, and to add a custom MRML scene to the main viewer featuring a 6 plane cubic representation of the volume with an additional oblique cut plane.
</div>

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

<h1>Progress</h1>

We integrated Slicer3 alpha with our 2D workstation by directly modifying the Slicer3 base code, passing window handles through Slicer3's GUI objects. Modifying the base code prevented maintainability of Slicer3 updates as changes had to be reimplimented. Currently, we can integrate the Slicer3 beta without modifying the base code by extracting the render windows through existing accessor methods and adding them to our workstation through a managed version of VTK.

</div>

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

</div>

===References===
* A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.
* Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007.

2007 Programming/Project Week MIT

2007-05-23T17:18:09Z

Nurad: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast and lunch for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' There is no official hotel for the meeting. Here is some information about Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Draft Agenda===
Please note that this agenda is a draft and will be finalized by June 15th.

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce Projects using templated wiki pages (all Project Leads)
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9-945am: NA-MIC Software Process (Bill Hoffman - TBC)
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using the templated wiki pages
** noon lunch boxes and adjourn

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: Complete the templated wiki page for your project. THe final version of this template will be circulated by May 25th.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
*[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
*[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
*[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
*[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (John Melonakos, Brad Davis, Marek Kubicki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===
* [[Algorithm:UNC:DTI#Population_Analysis | DTI population analysis]] (Casey Goodlett)
* Slicer3 Whole brain Seeding platform: data representation and pipeline execution (Raul San Jose, Lauren O'Donnell, Alex Y.)
* Slicer3 Tractography editor (Lauren O'Donnell, Raul San Jose, Alex Y.)

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** [[2007_Project_Week_MIT_Display_Optimization | Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
** [[2007_Project_Week_MIT_MRML_Scenes_for_the_Execution_Model]], including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (Luca, Steve, Dan)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
** Drafting Human Interface and Slicer Style Guidelines (Wendy)
** Slicer Matlab Pipeline for scalars and tensors (Katharina, Sylvain, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT
** [[Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
** [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
** [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
* Registration
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
** [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe)
** [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
* [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek(GE))
* [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
* [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
* [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* AstroMed (Michael Halle, Douglas Alan)

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1, (Hotel at MIT request)
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
#Jim Miller, GE Core 2, Booked at the Hotel At MIT
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2, Booked at the Hotel At MIT
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
#Luis Ibanez, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator (Hotel at MIT request)
#Alex Kogan, Northwestern University, Collaborator (Hotel at MIT request)
#Vladimir Kleper, Northwestern University, Collaborator (Hotel at MIT request)
#Pat Mongkolwat, Northwestern University, Collaborator (Hotel at MIT request)
#Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
#Mark Scully, The MIND Institute, DBP2:MIND software engineer
#Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
#Greg Sharp, MGH, Collaborator
#Lauren O'Donnell, BWH
#Raul San Jose, BWH
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Kevin Teich, MGH
#Michael Halle, BWH/IIC
#James Ross, GE
#Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
#Douglas Alan, Harvard IIC
#Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
#Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
#Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)

Collaboration/NWU/Radiology Workstation

2007-05-21T20:07:29Z

Nurad:

'''Objective: Demonstrate integration of advanced (Slicer3) Visualization in a clinical workstation'''

'''Progress:

We integrated a Slicer3 alpha version with 2D workstation by directly modifying Slicer3 code using window handles. Modifying Slicer3 prevented maintainability of Slicer3 updates. Currently, we can integrate Slicer3 without modifying base code.'''

'''Next Steps:

To finish integrating Slicer3 with custom modules support. Adding custom MRML scene with a cube representation of the volume and oblique plane. '''

'''Key Investigators:
David S. Channin (NWU)
Pat Mongkolwat (NWU)
Skip Talbot (NWU)
Alex Kogan (NWU)
Vladimir Kleper (NWU)

Steve Piper (Isomics)'''

'''Publications:

A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.

Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007
'''

'''Additional Links:'''
* [[Media:2007_Project_Week_MIT_A_Translation_Workstation.ppt | 4 block ppt]]

File:2007 Project Week MIT A Translation Workstation.ppt

2007-05-21T20:02:37Z

Nurad: NWU 4-block MS Powerpoint

NWU 4-block MS Powerpoint

Collaboration/NWU/Radiology Workstation

2007-05-21T19:57:22Z

Nurad:

Collaboration/NWU/Radiology Workstation

2007-05-21T19:56:46Z

Nurad:

'''Objective: Demonstrate integration of advanced (Slicer3) Visualization in a clinical workstation'''
** A Translation Workstation workstation

'''Progress:

We integrated a Slicer3 alpha version with 2D workstation by directly modifying Slicer3 code using window handles. Modifying Slicer3 prevented maintainability of Slicer3 updates. Currently, we can integrate Slicer3 without modifying base code.'''

'''Next Steps:

To finish integrating Slicer3 with custom modules support. Adding custom MRML scene with a cube representation of the volume and oblique plane. '''

'''Key Investigators:
David S. Channin (NWU)
Pat Mongkolwat (NWU)
Skip Talbot (NWU)
Alex Kogan (NWU)
Vladimir Kleper (NWU)

Steve Piper (Isomics)'''

'''Publications:

A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.

Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007
'''

'''Additional Links:'''
*4 block ppt

Collaboration/NWU/Radiology Workstation

2007-05-21T19:53:59Z

Nurad:

'''Objective: Demonstrate integration of advanced (Slicer3) Visualization in a clinical workstation'''
** A Translation Workstation workstation

'''Progress:

We integrated a Slicer3 alpha version with 2D workstation by directly modify Slicer3 code using window handles. Modifying Slicer3 prevented maintainability of Slicer3 updates. Currently, we can integrate Slicer3 without modifying base code.'''

'''Next Steps:'''

'''Key Investigators:
David S. Channin (NWU)
Pat Mongkolwat (NWU)
Skip Talbot (NWU)
Alex Kogan (NWU)
Vladimir Kleper (NWU)

Steve Piper (Isomics)'''

'''Publications:

A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.

Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007
'''

'''Additional Links:'''
*4 block ppt

Collaboration/NWU/Radiology Workstation

2007-05-21T19:42:00Z

Nurad:

'''Objective: Demonstrate integration of advanced (Slicer3) Visualization in a clinical workstation'''
** A Translation Workstation workstation

'''Progress:'''

'''Next Steps:'''

'''Key Investigators:
David S. Channin (NWU)
Pat Mongkolwat (NWU)
Skip Talbot (NWU)
Alex Kogan (NWU)
Vladimir Kleper (NWU)

Steve Piper (Isomics)'''

'''Publications:

A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.

Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007
'''

'''Additional Links:'''
*4 block ppt

Collaboration/NWU/Radiology Workstation

2007-05-21T19:41:07Z

Nurad:

'''Objective: Demonstrate integration of advanced (Slicer3) Visualization in a clinical workstation'''
** A Translation Workstation workstation

'''Progress:'''

'''Next Steps:'''

'''Key Investigators:
David S. Channin (NWU)
Pat Mongkolwat (NWU)
Skip Talbot (NWU)
Alex Kogan (NWU)
Vladimir Kleper (NWU)

Steve Piper (Isomics)'''

'''Publications:
A Translation Station for Imaging: P. Mongkolwat, T. Lechner, T. Johnson, A. Kogan, S. Talbot, D. S. Channin; Radiological Society of North America, Chicago, IL. November 2006.

Advancing Advanced Visualization in the Clinical Environment: S. Talbot, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Providence, RI, To be presented, June 2007
'''

'''Additional Links:'''
*4 block ppt

Collaboration/NWU/Radiology Workstation

2007-05-21T19:37:37Z

Nurad:

Collaboration/NWU/Radiology Workstation

2007-05-21T19:35:27Z

Nurad:

Collaboration/NWU/Radiology Workstation

2007-05-21T19:34:15Z

Nurad:

'''Objective: Demonstrate integration of advanced (3DSLicer) Visualization in a clinical workstation'''
** A Translation Workstation workstation

'''Progress:'''

'''Next Steps:'''

'''Key Investigators:'''

'''Publications:'''

'''Additional Links:'''
*4 block ppt

Collaboration/NWU/Radiology Workstation

2007-05-21T19:30:51Z

Nurad:

'''Objective:'''
** A Translation Workstation workstation

'''Progress:'''

'''Next Steps:'''

'''Key Investigators:'''

'''Publications:'''

'''Additional Links:'''
*4 block ppt

2007 Programming/Project Week MIT

2007-05-10T23:18:12Z

Nurad: /* External Collaborations */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

June 25-29, 2007, MIT

==Please Note==

Programming/Project week is one of the major events in the NA-MIC calendar. This will be our third annual Summer Programmming/Project Week.

* Core 1 - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* Core 2 - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* Core 3 - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

== Results ==
Results of this event will be summarized here after it is completed.

== Projects ==

===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (Brad Davis, John Melonakis, Marek Kubiki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
** MRML Scenes for the Execution Model, including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (depends on Dan's availability)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT
** Tracker Integration (Noby, Haiying)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics)
* Registration
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
* vmtk (vmtk.sourceforge.net) integration within Slicer3 (Luca Antiga, MNI)
** Solve issues with consistency of transforms
** Exploiting the Python shell
* A Translation Station
** Integrating 3D Slicer version 3 into a radiological workstation (Skip, Alex, Vlad, Pat)

===Non-Medical Collaborations===

== Logistics ==

'''Dates:''' June 25-29, 2007
'''Registration Fee:''' Registration fee is TBD. It will be payable by check onsite.
'''Hotels:''' [[Boston_Hotels]]

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 14, 2007: Complete the top half of [[media:NA-MIC_Latest_4-Block_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# [[Engineering:TCON_2007#2005-06-14|June 14, 2007: TCON#3 Review of 4-Blocks (Structural, DTI, Collaboration, Other)]]
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Review of 4-Blocks (NA-MIC Kit)]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
#Jim Miller, GE Core 2
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2 (Tentative)
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Sebastien Barre, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator
#Noby Hata, BWH Collaborator (June 25 only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Rhiannon Carlson, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator

2007 Programming/Project Week MIT

2007-05-10T20:59:52Z

Nurad: /* External Collaborations */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

June 25-29, 2007, MIT

==Please Note==

Programming/Project week is one of the major events in the NA-MIC calendar. This will be our third annual Summer Programmming/Project Week.

* Core 1 - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* Core 2 - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* Core 3 - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

== Results ==
Results of this event will be summarized here after it is completed.

== Projects ==

===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (Brad Davis, John Melonakis, Marek Kubiki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
** MRML Scenes for the Execution Model, including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (depends on Dan's availability)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT
** Tracker Integration (Noby, Haiying)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics)
* Registration
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
* vmtk (vmtk.sourceforge.net) integration within Slicer3 (Luca Antiga, MNI)
** Solve issues with consistency of transforms
** Exploiting the Python shell
* A Translation Station
** Integrating 3D Slicer version 3 into a radiological workstation

===Non-Medical Collaborations===

== Logistics ==

'''Dates:''' June 25-29, 2007
'''Registration Fee:''' Registration fee is TBD. It will be payable by check onsite.
'''Hotels:''' [[Boston_Hotels]]

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 14, 2007: Complete the top half of [[media:NA-MIC_Latest_4-Block_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# [[Engineering:TCON_2007#2005-06-14|June 14, 2007: TCON#3 Review of 4-Blocks (Structural, DTI, Collaboration, Other)]]
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Review of 4-Blocks (NA-MIC Kit)]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
#Jim Miller, GE Core 2
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2 (Tentative)
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Sebastien Barre, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator
#Noby Hata, BWH Collaborator (June 25 only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Rhiannon Carlson, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator

2007 Programming/Project Week MIT

2007-05-10T20:56:06Z

Nurad: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

June 25-29, 2007, MIT

==Please Note==

Programming/Project week is one of the major events in the NA-MIC calendar. This will be our third annual Summer Programmming/Project Week.

* Core 1 - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* Core 2 - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* Core 3 - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

== Results ==
Results of this event will be summarized here after it is completed.

== Projects ==

===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (Brad Davis, John Melonakis, Marek Kubiki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
** MRML Scenes for the Execution Model, including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (depends on Dan's availability)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT
** Tracker Integration (Noby, Haiying)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics)
* Registration
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
* vmtk (vmtk.sourceforge.net) integration within Slicer3 (Luca Antiga, MNI)
** Solve issues with consistency of transforms
** Exploiting the Python shell

===Non-Medical Collaborations===

== Logistics ==

'''Dates:''' June 25-29, 2007
'''Registration Fee:''' Registration fee is TBD. It will be payable by check onsite.
'''Hotels:''' [[Boston_Hotels]]

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 14, 2007: Complete the top half of [[media:NA-MIC_Latest_4-Block_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# [[Engineering:TCON_2007#2005-06-14|June 14, 2007: TCON#3 Review of 4-Blocks (Structural, DTI, Collaboration, Other)]]
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Review of 4-Blocks (NA-MIC Kit)]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
#Jim Miller, GE Core 2
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2 (Tentative)
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Sebastien Barre, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator
#Noby Hata, BWH Collaborator (June 25 only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Rhiannon Carlson, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator

2007 Project Half Week

2007-03-16T18:52:03Z

Nurad: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==

This event was successfully concluded on January 12, 2007. A summary powerpoint for this event is available [[Media:2007 Project Half Week Summary.ppt| here]].

Some statistics:

For the AHM:
* 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
** 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
** 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), UIowa(6), Virginia Tech (1).
* 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex) [[Media:2007WS3DSlicer.ppt_ ‎| 4 block PPT Jan 2007]]
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] [[Execution_Model_Reference_Systems|discussion on reference systems]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Vis-Updated-012606.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh namic1.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
##Mapped Meshing Using ITK - [[Media:2007_AHM_Programming_Half_Week_MappedMesh.ppt|ITK FEM Registration Mapped Meshing Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

2007 Project Half Week

2007-03-16T18:48:14Z

Nurad: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==

This event was successfully concluded on January 12, 2007. A summary powerpoint for this event is available [[Media:2007 Project Half Week Summary.ppt| here]].

Some statistics:

For the AHM:
* 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
** 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
** 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), UIowa(6), Virginia Tech (1).
* 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex) [[Media:2007WS3DSlicer.ppt ‎| 4 block PPT Jan 2007]]
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] [[Execution_Model_Reference_Systems|discussion on reference systems]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Vis-Updated-012606.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh namic1.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
##Mapped Meshing Using ITK - [[Media:2007_AHM_Programming_Half_Week_MappedMesh.ppt|ITK FEM Registration Mapped Meshing Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

2007 Project Half Week

2007-03-16T18:47:13Z

Nurad: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==

This event was successfully concluded on January 12, 2007. A summary powerpoint for this event is available [[Media:2007 Project Half Week Summary.ppt| here]].

Some statistics:

For the AHM:
* 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
** 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
** 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), UIowa(6), Virginia Tech (1).
* 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex) [[Image:2007WS3DSlicer.ppt ‎| 4 block PPT Jan 2007]]
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] [[Execution_Model_Reference_Systems|discussion on reference systems]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Vis-Updated-012606.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh namic1.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
##Mapped Meshing Using ITK - [[Media:2007_AHM_Programming_Half_Week_MappedMesh.ppt|ITK FEM Registration Mapped Meshing Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

2007 Project Half Week

2007-03-16T18:44:59Z

Nurad: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==

This event was successfully concluded on January 12, 2007. A summary powerpoint for this event is available [[Media:2007 Project Half Week Summary.ppt| here]].

Some statistics:

For the AHM:
* 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
** 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
** 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), UIowa(6), Virginia Tech (1).
* 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex) [[Media:2007WS3DSlicer.ppt ‎| 4 block PPT Jan 2007]]
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] [[Execution_Model_Reference_Systems|discussion on reference systems]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Vis-Updated-012606.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh namic1.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
##Mapped Meshing Using ITK - [[Media:2007_AHM_Programming_Half_Week_MappedMesh.ppt|ITK FEM Registration Mapped Meshing Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

File:2007WS3DSlicer.ppt

2007-03-16T18:42:54Z

Nurad:

2007 Project Half Week

2007-03-16T18:37:46Z

Nurad: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==

This event was successfully concluded on January 12, 2007. A summary powerpoint for this event is available [[Media:2007 Project Half Week Summary.ppt| here]].

Some statistics:

For the AHM:
* 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
** 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
** 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), UIowa(6), Virginia Tech (1).
* 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex) [[Media:2007_Project_Half_Week_TranslationWS_with_3DSlicer.ppt_ ‎| 4 block PPT Jan 2007]]
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] [[Execution_Model_Reference_Systems|discussion on reference systems]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Vis-Updated-012606.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh namic1.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
##Mapped Meshing Using ITK - [[Media:2007_AHM_Programming_Half_Week_MappedMesh.ppt|ITK FEM Registration Mapped Meshing Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

2007 Project Half Week

2007-03-16T18:37:15Z

Nurad: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==

This event was successfully concluded on January 12, 2007. A summary powerpoint for this event is available [[Media:2007 Project Half Week Summary.ppt| here]].

Some statistics:

For the AHM:
* 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
** 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
** 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), UIowa(6), Virginia Tech (1).
* 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex) [[Media:2007_Project_Half_Week_TranslationWS_with_3DSlicer.ppt ‎| 4 block PPT Jan 2007]]
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] [[Execution_Model_Reference_Systems|discussion on reference systems]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Vis-Updated-012606.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh namic1.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
##Mapped Meshing Using ITK - [[Media:2007_AHM_Programming_Half_Week_MappedMesh.ppt|ITK FEM Registration Mapped Meshing Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

2007 Project Half Week

2007-03-16T18:31:31Z

Nurad: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==

This event was successfully concluded on January 12, 2007. A summary powerpoint for this event is available [[Media:2007 Project Half Week Summary.ppt| here]].

Some statistics:

For the AHM:
* 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
** 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
** 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), UIowa(6), Virginia Tech (1).
* 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex)[[Media:2007_Project_Half_Week_TranslationWS_with_3DSlicer.ppt‎|4 block PPT Jan 2007]]
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] [[Execution_Model_Reference_Systems|discussion on reference systems]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Vis-Updated-012606.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh namic1.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
##Mapped Meshing Using ITK - [[Media:2007_AHM_Programming_Half_Week_MappedMesh.ppt|ITK FEM Registration Mapped Meshing Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

File:2007 Project Half Week TranslationWS with 3DSlicer.ppt

2007-03-16T18:29:17Z

Nurad: Northwestern Radiology workstation

Northwestern Radiology workstation

File:NU Slicer3v2.jpg

2006-12-27T18:49:09Z

Nurad:

Slicer:Feedback

2006-12-27T18:46:20Z

Nurad: /* Peer reviewed exhibits: */

[http://www.slicer.org 3D Slicer] is a free open source software package distributed under a BSD style [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl license]. The majority of funding for the development of 3D slicer comes from a number of grants and contracts from the National Institutes of Health (see [http://www.slicer.org slicer acknowledgements] for more information).

We are currently preparing an application to extend funding for one of the major grants that contribute to this effort.

We are looking to include information about the impact that slicer has had. Specifically, we are looking for peer reviewed journal papers and funded grants which rely on 3D Slicer. Please email us or add to the bottom of this page.

= Peer reviewed journal papers: =

# AJNR Am J Neuroradiol. 2006 May;27(5):1032-6.

* A method for clustering white matter fiber tracts.
* O'Donnell LJ, Kubicki M, Shenton ME, Dreusicke MH, Grimson WE, Westin CF.
* MIT Computer Science and AI Lab, Cambridge, MA 02139, USA.
* BACKGROUND/PURPOSE: Despite its potential for visualizing white matter fiber tracts in vivo, diffusion tensor tractography has found only limited applications in clinical research in which specific anatomic connections between distant regions need to be evaluated. We introduce a robust method for fiber clustering that guides the separation of anatomically distinct fiber tracts and enables further estimation of anatomic connectivity between distant brain regions. METHODS: Line scanning diffusion tensor images (LSDTI) were acquired on a 1.5T magnet. Regions of interest for several anatomically distinct fiber tracts were manually drawn; then, white matter tractography was performed by using the Runge-Kutta method to interpolate paths (fiber traces) following the major directions of diffusion, in which traces were seeded only within the defined regions of interest. Next, a fully automatic procedure was applied to fiber traces, grouping them according to a pairwise similarity function that takes into account the shapes of the fibers and their spatial locations. RESULTS: We demonstrated the ability of the clustering algorithm to separate several fiber tracts which are otherwise difficult to define (left and right fornix, uncinate fasciculus and inferior occipitofrontal fasciculus, and corpus callosum fibers). CONCLUSION: This method successfully delineates fiber tracts that can be further analyzed for clinical research purposes. Hypotheses regarding specific fiber connections and their abnormalities in various neuropsychiatric disorders can now be tested.
* Grant Support:
** 1-R01-NS051826-01/NS/NINDS
** K02 MH 01110/MH/NIMH
** P41 RR13218/RR/NCRR
** R03 MH 068464-02/MH/NIMH
** U54 EB005149/EB/NIBIB

# your paper here

= Peer reviewed exhibits: =

# RSNA 2006.

* A Translation Station for Imaging
* P Mongkolwat, PhD; T Lechner, MS; A Kogan; S Talbot; B Johnson, OD; D S Channin, MD
* Imaging Informatics Section, Northwestern University, Chicago, IL 60611, USA
* Abstract: while providing clinical feedback to the basic sciences. In imaging informatics, this means enabling collaborations between radiologists and computer scientists. Commercial workstations do not allow for experimentation nor do they evolve fast enough. Research imaging packages, while innovative, do not provide for clinical activities or regulatory compliance. We added IHE workflow functionality, hanging protocols and other clinical functions to the SLICER research platform. We leveraged the functionality and methodology of the Insight and Visualization Toolkits, and the DCM4CHE tools. A research mode allows for the evaluation of experimental algorithms against a PACS while protecting patient confidentiality. This combined functionality allows researchers to develop algorithms against clinical cases while at the same allowing clinicians to explore and validate these developments.
[[Image:NU_Slicer3v2.jpg]]

File:NU Slicer3.jpg

2006-12-27T18:44:39Z

Nurad:

Slicer:Feedback

2006-12-27T18:41:49Z

Nurad: /* Peer reviewed exhibits: */

Slicer:Feedback

2006-12-27T18:39:58Z

Nurad: /* Peer reviewed exhibits: */

Slicer:Feedback

2006-12-27T18:38:53Z

Nurad: /* Peer reviewed exhibits: */

Slicer:Feedback

2006-12-27T18:38:35Z

Nurad: /* Peer reviewed journal papers: */

File:Example.jpg

2006-12-27T18:31:44Z

Nurad: