NAMIC Wiki - User contributions [en]

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:17:24Z

Dcpeters: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]

</gallery>
[[File:LVscarfusion.jpg|400px|thumb|left|Fusion of LGE scar data with EP data]]

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is a sparse point cloud.
</div>

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

<h3>Progress</h3>
We are able to display the scar and a representation of the scar in 3D Slicer.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:16:34Z

Dcpeters: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]

</gallery>
[[File:LVscarfusion.jpg|400px|thumb|left|Fusion of LGE scar data with EP data]]

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is a sparse point cloud.
</div>

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

<h3>Progress</h3>
We are able to disply the scar and a representation of the scar in 3D Slicer.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:15:12Z

Dcpeters: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]

</gallery>
[[File:LVscarfusion.jpg|400px|thumb|left|Fusion of LGE scar data with EP data]]

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is a sparse point cloud.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:14:20Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]

</gallery>
[[File:LVscarfusion.jpg|400px|thumb|left|Fusion of LGE scar data with EP data]]

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is sparse.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:14:06Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
[[File:LVscarfusion.jpg|400px|thumb|left|Fusion of LGE scar data with EP data]]

</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is sparse.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:13:49Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[File:LVscarfusion.jpg|400px|thumb|left|Fusion of LGE scar data with EP data]]

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is sparse.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:13:37Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[File:LVscarfusion.jpg|200px|thumb|left|Fusion of LGE scar data with EP data]]

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is sparse.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:11:57Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
[[Image:LVscarfusion.jpg]]|LV scar fusion with EP
</gallery>

[[File:LVscarfusion.jpg]]
http://commons.wikimedia.org/wiki/File:LVscarfusion.jpg

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is sparse.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

File:LVscarfusion.jpg

2010-06-21T16:03:53Z

Dcpeters: Shows an LGE slice showing scar in the myocardium, a voltage map, and a representation of the scar.

Shows an LGE slice showing scar in the myocardium, a voltage map, and a representation of the scar.

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T16:03:03Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
[[Image:LVscarfusion.jpg]]|LV scar fusion with EP
</gallery>

http://commons.wikimedia.org/wiki/File:LVscarfusion.jpg

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is sparse.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T15:59:14Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
[[File:LVscarfusion.jpg]]|LV scar fusion with EP
</gallery>

http://commons.wikimedia.org/wiki/File:LVscarfusion.jpg

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is sparse.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-21T15:48:15Z

Dcpeters: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
[[Image:LVscarfusion.jpg]]|LV scar fusion with EP
</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
Our goal is to process 3D late gadolinium enhancement (LGE) MR images of the left ventricular myocardium, and to segment scar, and display it in 3D. The scar can be represented as scar transmurality, or using other metrics. We wish to represent the MR scar images in 3D to compare with voltage maps of the myocardium obtained using invasive voltage mapping, by fusing the voltage maps with the scar images. This will lead to interpretation of the relationship between EP findings and scar. This technique can be applied to other areas of study, such as atrial fibrillation.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation. We will use 3D Slicer, and matlab. A main concern is how to represent/fuse the voltage data, since the voltage data set is sparse.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-15T22:26:30Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
[[Image:LVscarfusion.jpg]]|LV scar fusion with EP
</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
We wish to represent the MR scar images in 3D to compare with voltage maps. This will lead to interpretation of the relationship between EP findings and scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-11T18:30:43Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:LVscarfusion.jpg|LV scar fusion with EP
</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
We wish to represent the MR scar images in 3D to compare with voltage maps. This will lead to interpretation of the relationship between EP findings and scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-11T18:30:27Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:LVscarfusion.jpg|400px|LV scar fusion with EP
</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
We wish to represent the MR scar images in 3D to compare with voltage maps. This will lead to interpretation of the relationship between EP findings and scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-11T18:29:37Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
[[Image:LVscarfusion.jpg|400px|LV scar fusion with EP]]
</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
We wish to represent the MR scar images in 3D to compare with voltage maps. This will lead to interpretation of the relationship between EP findings and scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-11T18:23:02Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:LVscarfusion.jpg|Magnetic resonance late gadolinium enhancement images compared with voltage maps of the heart using electrophysiology, and a representation of the MR scar pattern.
</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
We wish to represent the MR scar images in 3D to compare with voltage maps. This will lead to interpretation of the relationship between EP findings and scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-11T18:18:07Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:LVscarFusion.jpg|Magnetic resonance late gadolinium enhancement images compared with voltage maps of the heart using electrophysiology, and a representation of the MR scar pattern.
</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
We wish to represent the MR scar images in 3D to compare with voltage maps. This will lead to interpretation of the relationship between EP findings and scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week Left ventricular scar segmentation

2010-06-11T18:16:01Z

Dcpeters: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:LVscarFusion.jpg|Magnetic resonance late gadolinium enhancement images compared with voltage maps of the heart using electrophysiology, and a representation of the MR scar pattern.
</gallery>

==Key Investigators==
* Beth Israel Deaconess Medical Center: Dana C. Peters, Felix Liu

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

<h3>Objective</h3>
We wish to represent the MR scar images in 3D to compare with voltage maps. This will lead to interpretation of the relationship between EP findings and scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach includes segmentation of the scar, representation, registration with voltage maps, and quantitative evaluation.
</div>

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

<h3>Progress</h3>
None so far.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Wolf T, Gepstein L, Dror U, Hayam G, Shofti R, Zaretzky A, Uretzky G, Oron U, Ben-Haim SA. Detailed endocardial mapping accurately predicts the transmural extent of myocardial infarction. J Am Coll Cardiol 2001; 37:1590-1597.
*Desjardins B, Crawford T, Good E, Oral H, Chugh A, Pelosi F, Morady F, Bogun F. Infarct architecture and characteristics on delayed enhanced magnetic resonance imaging and electroanatomic mapping in patients with postinfarction ventricular arrhythmia. Heart Rhythm 2009; 6:644-651.
*Bogun FM, Desjardins B, Good E, Gupta S, Crawford T, Oral H, Ebinger M, Pelosi F, Chugh A, Jongnarangsin K, Morady F. Delayed-enhanced magnetic resonance imaging in nonischemic cardiomyopathy: utility for identifying the ventricular arrhythmia substrate. J Am Coll Cardiol 2009; 53:1138-1145

</div>

2010 Summer Project Week

2010-06-03T19:08:05Z

Dcpeters: /* Segmentation */

__NOTOC__

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

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other 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.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanesz)
**3-4pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, ?)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo)

=== IGT ===
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* Arnaud Gelas, Sean Megason, Badri Roysam: Wrapping FARSIGHT nuclear segmentation algorithm as a GoFigure plugin.
* Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju: ITK Spherical Harmonics filter for shape analysis of cell nuclei

=== Shape Analysis ===
* Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)
=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)

=== Python ===
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, will, Schroeder, Nicole, Ron)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

#Aucoin, Nicole, BWH
#Audette, Michel, Kitware
#Aylward, Stephen, Kitware, Inc
#Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories
#Bouix, Sylvain, BWH
#Budin, Francois, UNC
#Burdette, Everette, Acoustic MedSystems, Inc.
#Chen, Min, Johns Hopkins University
#Datar, Manasi, SCI Institute
#Eckbo, Ryan, BWH
#Fedorov, Andriy, Surgical Planning Lab
#Fillion-Robin, Jean-Christophe, Kitware Inc.
#Finet, Julien, Kitware Inc
#Fishbaugh, James, SCI Institute
#Gao, Yi, Gerogia Tech
#GELAS, Arnaud, Harvard Medical School
#gouaillard, alexandre, CoSMo Software
#Gouttard, Sylvain, SCI Institute
#Haehn, Daniel, University of Pennsylvania
#Hageman, Nathan
#Hahn, Dieter, University Erlangen
#Hamel, Corentin, UNC Chapel Hill
#Hata, Nobuhiko, Brigham and Women's Hospital
#Hayes, Kathryn, Brigham and Women's Hospital
#Holton, Leslie, Medtronic Navigation
#Ibanez, Luis, KITWARE Inc.
#Johnson, Hans, University of Iowa
#Kapur, Tina, Brigham and Women's Hospital
#Kikinis, Ron, Brigham and Women's Hospital
#Kim, Minjeong, UNC-Chapel Hill
#Kolesov, Ivan, Georgia Institute of Technology
#Larson, Garrett, UNC-CH
#Li, Rui, MGH
#Lisle, Curtis, KnowledgeVis, LLC
#Liu, Haiying, Brigham and Women's Hospital
#Liu, Yanling, SAIC-Frederick, Inc.
#Magnotta, Vincent, The University of Iowa
#malaterre, mathieu, CoSMo Software
#Mastrogiacomo, Katie, Brigham and Women's Hospital
#Matsui, Joy, University
#Megason, Sean, Harvard Medical School
#Meier, Dominik, BWH, Boston MA
#menze, bjoern, CSAIL MIT
#Mosaliganti, Kishore, Harvard Medical School
#Niethammer, Marc, UNC Chapel Hill
#Norton, Isaiah, BWH Neurosurgery
#Paniagua, Beatriz, University of North Caolina at Chapel Hill
#Papademetris, Xenophon, Yale University
#Partyka, David, Kitware Inc
#Pathak, Sudhir, Univeristy Of Pittsburgh
#Peroni, Marta, Politecnico di Milano
#Perrot-Audet, Antonin, Harvard Medical School
#Pieper, Steve, Isomics, Inc.
#Plesniak, Wendy, BWH
#Pohl, Kilian, IBM
#Pujol, Sonia, Brigham and Women's Hospital
#Rannou, Nicolas, Harvard Medical School
#Riklin Raviv, Tammy, MIT, CSAIL
#Ruiz, Marco, UCSD
#Schroeder, William, Kitware
#Scully, Mark, The Mind Research Network
#Sharp, Greg, MGH
#Shi, Yundi, UNC Chapel Hill
#Shusharina, Nadya, MGH
#Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)
#Souhait, Lydie, Harvard Medical School
#Spinczyk, Dominik, Silesian University of Technology
#Srinivasan, Padmapriya
#Tao, Xiaodong, GE Research
#Ungi, Tamas, Queen's University
#Vachet, Clement, UNC Chapel Hill
#Veni, Gopalkrishna, SCI Institute
#Wassermann, Demian, SPL/LMI/PNL
#Wells, Sandy, BWH
#Wu, Guorong, University of North Carolina at Chapel Hill

2009 Summer Project Week fusion of MRI with voltage mapping

2009-06-26T13:55:53Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Lascar.jpg| left atrial scar by EP mapping and MRI
Image:scar_cartovoltage.jpg| left atrial scar by EP mapping and MRI--fused!!
</gallery>

==Key Investigators==
* Dana C. Peters PhD, and Jason Taclas, MS, Beth Israel Deaconess Medical Center

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

<h3>Objective</h3>
Scar in the left atrium can be visualized using the cardiac MR late gadolinium enhancement technique. It can also be detected as low electrical voltages by invasive electrophysiology (EP) mapping systems, e.g CARTO maps. We wish to correlate the EP maps with cardiac MR images, by registering the two representations of scar, and displaying the voltage as a 3D color map. Figure 1 compares a CARTO map of the left atrium to an image of the left atrium, demonstrating the relationship between low voltage by EP, and enhancement by Cardiac MR.

</div>

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

<h3>Approach, Plan</h3>

Display surfaces using VTK/ITK tool already developed, with color coding to indicate voltage, with registered scar data. Extract registered voltage data to display on MR images.<foo>.

</div>

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

<h3>Progress</h3>
We were able to combine the voltage data from EP fused with MR. However our approach needs work. We would like to show the voltages on the MR slices, not the rendering. We would like to show the voltages maybe displayed as points not a shell--the shells are never perfect!

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

==References==
*Taclas J, Wylie J, Nezafat R, Josephson M, Manning WJ, Peters DC. Correlation of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. In:Journal of Cardiovascular MR. Los Angeles, CA, 2008.
* Peters DC, Wylie JV, Hauser TH, et al. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.

File:Scar cartovoltage.jpg

2009-06-26T13:52:05Z

Dcpeters: Scar by mri compared to voltage by EP

Scar by mri compared to voltage by EP

2009 Summer Project Week fusion of MRI with voltage mapping

2009-06-22T15:34:23Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Lascar.jpg| left atrial scar by EP mapping and MRI
</gallery>

==Key Investigators==
* Dana C. Peters PhD, and Jason Taclas, MS, Beth Israel Deaconess Medical Center

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

<h3>Objective</h3>
Scar in the left atrium can be visualized using the cardiac MR late gadolinium enhancement technique. It can also be detected as low electrical voltages by invasive electrophysiology (EP) mapping systems, e.g CARTO maps. We wish to correlate the EP maps with cardiac MR images, by registering the two representations of scar, and displaying the voltage as a 3D color map. Figure 1 compares a CARTO map of the left atrium to an image of the left atrium, demonstrating the relationship between low voltage by EP, and enhancement by Cardiac MR.

</div>

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

<h3>Approach, Plan</h3>

Display surfaces using VTK/ITK tool already developed, with color coding to indicate voltage, with registered scar data. Extract registered voltage data to display on MR images.<foo>.

</div>

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

<h3>Progress</h3>

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

==References==
*Taclas J, Wylie J, Nezafat R, Josephson M, Manning WJ, Peters DC. Correlation of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. In:Journal of Cardiovascular MR. Los Angeles, CA, 2008.
* Peters DC, Wylie JV, Hauser TH, et al. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.

File:Lascar.jpg

2009-06-22T15:32:48Z

Dcpeters: Left atrial scar by EP mapping and MRI

Left atrial scar by EP mapping and MRI

2009 Summer Project Week fusion of MRI with voltage mapping

2009-06-22T14:02:37Z

Dcpeters:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:lascar.jpg
</gallery>

==Key Investigators==
* Dana C. Peters PhD, and Jason Taclas, MS, Beth Israel Deaconess Medical Center

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

<h3>Objective</h3>
Scar in the left atrium can be visualized using the cardiac MR late gadolinium enhancement technique. It can also be detected as low electrical voltages by invasive electrophysiology (EP) mapping systems, e.g CARTO maps. We wish to correlate the EP maps with cardiac MR images, by registering the two representations of scar, and displaying the voltage as a 3D color map. Figure 1 compares a CARTO map of the left atrium to an image of the left atrium, demonstrating the relationship between low voltage by EP, and enhancement by Cardiac MR.

</div>

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

<h3>Approach, Plan</h3>

Display surfaces using VTK/ITK tool already developed, with color coding to indicate voltage, with registered scar data. Extract registered voltage data to display on MR images.<foo>.

</div>

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

<h3>Progress</h3>

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

==References==
*Taclas J, Wylie J, Nezafat R, Josephson M, Manning WJ, Peters DC. Correlation of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. In:Journal of Cardiovascular MR. Los Angeles, CA, 2008.
* Peters DC, Wylie JV, Hauser TH, et al. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.

2009 Summer Project Week fusion of MRI with voltage mapping

2009-06-22T13:59:44Z

Dcpeters:

2009 Summer Project Week fusion of MRI with voltage mapping

2009-06-22T13:58:56Z

Dcpeters: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|

</gallery>

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:lascar.jpg
</gallery>

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]

</gallery>
==Key Investigators==
* Dana C. Peters PhD, and Jason Taclas, MS, Beth Israel Deaconess Medical Center

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

<h3>Objective</h3>
Scar in the left atrium can be visualized using the cardiac MR late gadolinium enhancement technique. It can also be detected as low electrical voltages by invasive electrophysiology (EP) mapping systems, e.g CARTO maps. We wish to correlate the EP maps with cardiac MR images, by registering the two representations of scar, and displaying the voltage as a 3D color map. Figure 1 compares a CARTO map of the left atrium to an image of the left atrium, demonstrating the relationship between low voltage by EP, and enhancement by Cardiac MR.

</div>

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

<h3>Approach, Plan</h3>

Display surfaces using VTK/ITK tool already developed, with color coding to indicate voltage, with registered scar data. Extract registered voltage data to display on MR images.<foo>.

</div>

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

<h3>Progress</h3>

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

==References==
*Taclas J, Wylie J, Nezafat R, Josephson M, Manning WJ, Peters DC. Correlation of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. In:Journal of Cardiovascular MR. Los Angeles, CA, 2008.
* Peters DC, Wylie JV, Hauser TH, et al. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.

[[File:[[File:Example.jpg]]]]</div>

2009 Summer Project Week fusion of MRI with voltage mapping

2009-06-22T13:57:30Z

Dcpeters: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|

</gallery>

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:lascar.jpg
</gallery>

==Key Investigators==
* Dana C. Peters PhD, and Jason Taclas, MS, Beth Israel Deaconess Medical Center

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

<h3>Objective</h3>
Scar in the left atrium can be visualized using the cardiac MR late gadolinium enhancement technique. It can also be detected as low electrical voltages by invasive electrophysiology (EP) mapping systems, e.g CARTO maps. We wish to correlate the EP maps with cardiac MR images, by registering the two representations of scar, and displaying the voltage as a 3D color map. Figure 1 compares a CARTO map of the left atrium to an image of the left atrium, demonstrating the relationship between low voltage by EP, and enhancement by Cardiac MR.

</div>

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

<h3>Approach, Plan</h3>

Display surfaces using VTK/ITK tool already developed, with color coding to indicate voltage, with registered scar data. Extract registered voltage data to display on MR images.<foo>.

</div>

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

<h3>Progress</h3>

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

==References==
*Taclas J, Wylie J, Nezafat R, Josephson M, Manning WJ, Peters DC. Correlation of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. In:Journal of Cardiovascular MR. Los Angeles, CA, 2008.
* Peters DC, Wylie JV, Hauser TH, et al. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.

[[File:[[File:Example.jpg]]]]</div>

2009 Summer Project Week fusion of MRI with voltage mapping

2009-06-22T13:53:37Z

Dcpeters: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Projects List Image:genuFAp.jpg| </gallery> ==Key Investigators== * Dana C. Peters PhD, and Jason...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|

</gallery>

==Key Investigators==
* Dana C. Peters PhD, and Jason Taclas, MS, Beth Israel Deaconess Medical Center

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

<h3>Objective</h3>
Scar in the left atrium can be visualized using the cardiac MR late gadolinium enhancement technique. It can also be detected as low electrical voltages by invasive electrophysiology (EP) mapping systems, e.g CARTO maps. We wish to correlate the EP maps with cardiac MR images, by registering the two representations of scar, and displaying the voltage as a 3D color map. Figure 1 compares a CARTO map of the left atrium to an image of the left atrium, demonstrating the relationship between low voltage by EP, and enhancement by Cardiac MR.

</div>

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

<h3>Approach, Plan</h3>

: Display surfaces using VTK/ITK tool already developed, with color coding to indicate voltage, with registered scar data. Extract registered voltage data to display on MR images.<foo>.

Our plan for the project week is to first try out <bar>,...

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

==References==
*Taclas J, Wylie J, Nezafat R, Josephson M, Manning WJ, Peters DC. Correlation of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. In:Journal of Cardiovascular MR. Los Angeles, CA, 2008.
* Peters DC, Wylie JV, Hauser TH, et al. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.

[[File:[[File:Example.jpg]]]]</div>

2009 Summer Project Week

2009-06-22T13:44:24Z

Dcpeters: /* Projects */

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alexandre Gouaillard)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==
#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation |Lupus Lesion Segmentation]] (Jeremy Bockholt MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Ion-Florin Talos BWH)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration| Slicer 3 registration ]] (Andrew Rausch BWH PNL)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT| Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins Acousticmed)
#acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT | GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser | GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[2009_Summer_Project_Week_fusion_of_MRI_with_voltage_mapping|Fusion of MRI with EP voltage mapping]] (Dana Peters BIDMC)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other 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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
{|
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{|class="wikitable"
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|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week

2009-06-05T16:12:02Z

Dcpeters: /* Attendee List */

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)]]
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
#integration of stereo video into Slicer (Mehdi)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (1st day only)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)
#Dana Peters, Beth Israel Deaconess

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other 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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

NA-MIC/Projects/Collaboration/Carto scar BIDMC

2008-06-30T21:40:29Z

Dcpeters: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Key Investigators===
* Beth Israel Deaconess: Dana C. Peters
* Beth Israel Deaconess: Jason Taclas
* Kitware: Luis Ibanez, NAMIC: Steve Pieper, GE: Jim Miller (providing advice)

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

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

<h1>Objective</h1>
We are developing methods for registering peri-procedural electrophysiological data showing sites of RF energy application (called Carto data) in the left atrium, with post-procedural MRI data, which shows regions of scarred left atrium (see figure above), using an interative closest point algorithm (Z. Malchano et al). The goal is to measure the distance between scar by MRI and ablation sites (Carto data) by EP.

</div>

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

<h1>Approach, Plan</h1>

Our approach for comparing the locations of scar to sites of RF ablation is summarized in the ISMRM 2008 reference below. The main challenge to this approach is to measure the distance between each scarred pixel, and each RF ablation site, and then the distance from each RF ablation site, to the nearest scarred pixel. <foo>.

Our plan for the project week is to first try to measure the closest distances between MRI scar and Carto data <bar>,and then to measure distances between Carto data and closest scar. We also wish to colorize the Carto surface, based on voltage data. We also wish to streamline the MR angiography segmentation method.
</div>

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

<h1>Progress</h1>

Software for the registration between electrophysiology Carto data and the MR angiogram has been implemented, using the ITK/VTK platform (see ISMRM 2008 abstract, Taclas et al, and figure above). This week we wrote code to quantitatively determine the distances between each ablation location, and the closest region of scar, and to determine the distances between each pixel of scar, and the nearest ablation point. Therefore we accomplished our goal!

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

NA-MIC/Projects/Collaboration/Carto scar BIDMC

2008-06-30T21:37:53Z

Dcpeters: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Key Investigators===
* Beth Israel Deaconess: Dana C. Peters
* Beth Israel Deaconess: Jason Taclas
* ITK: Luis Ibanez, NAMIC: Steve Peiper and Jim Billig

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

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

<h1>Objective</h1>
We are developing methods for registering peri-procedural electrophysiological data showing sites of RF energy application (called Carto data) in the left atrium, with post-procedural MRI data, which shows regions of scarred left atrium (see figure above), using an interative closest point algorithm (Z. Malchano et al). The goal is to measure the distance between scar by MRI and ablation sites (Carto data) by EP.

</div>

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

<h1>Approach, Plan</h1>

Our approach for comparing the locations of scar to sites of RF ablation is summarized in the ISMRM 2008 reference below. The main challenge to this approach is to measure the distance between each scarred pixel, and each RF ablation site, and then the distance from each RF ablation site, to the nearest scarred pixel. <foo>.

Our plan for the project week is to first try to measure the closest distances between MRI scar and Carto data <bar>,and then to measure distances between Carto data and closest scar. We also wish to colorize the Carto surface, based on voltage data. We also wish to streamline the MR angiography segmentation method.
</div>

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

<h1>Progress</h1>

Software for the registration between electrophysiology Carto data and the MR angiogram has been implemented, using the ITK/VTK platform (see ISMRM 2008 abstract, Taclas et al, and figure above). This week we wrote code to quantitatively determine the distances between each ablation location, and the closest region of scar, and to determine the distances between each pixel of scar, and the nearest ablation point. Therefore we accomplished our goal!

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

NA-MIC/Projects/Collaboration/Carto scar BIDMC

2008-06-30T21:36:50Z

Dcpeters: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Key Investigators===
* Beth Israel Deaconess: Dana C. Peters
* Beth Israel Deaconess: Jason Taclas

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

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

<h1>Objective</h1>
We are developing methods for registering peri-procedural electrophysiological data showing sites of RF energy application (called Carto data) in the left atrium, with post-procedural MRI data, which shows regions of scarred left atrium (see figure above), using an interative closest point algorithm (Z. Malchano et al). The goal is to measure the distance between scar by MRI and ablation sites (Carto data) by EP.

</div>

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

<h1>Approach, Plan</h1>

Our approach for comparing the locations of scar to sites of RF ablation is summarized in the ISMRM 2008 reference below. The main challenge to this approach is to measure the distance between each scarred pixel, and each RF ablation site, and then the distance from each RF ablation site, to the nearest scarred pixel. <foo>.

Our plan for the project week is to first try to measure the closest distances between MRI scar and Carto data <bar>,and then to measure distances between Carto data and closest scar. We also wish to colorize the Carto surface, based on voltage data. We also wish to streamline the MR angiography segmentation method.
</div>

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

<h1>Progress</h1>

Software for the registration between electrophysiology Carto data and the MR angiogram has been implemented, using the ITK/VTK platform (see ISMRM 2008 abstract, Taclas et al, and figure above). This week we wrote code to quantitatively determine the distances between each ablation location, and the closest region of scar, and to determine the distances between each pixel of scar, and the nearest ablation point. Therefore we accomplished our goal!

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

NA-MIC/Projects/Collaboration/Carto scar BIDMC

2008-06-24T18:59:38Z

Dcpeters: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Key Investigators===
* Beth Israel Deaconess: Dana C. Peters
* Beth Israel Deaconess: Jason Taclas

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

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

<h1>Objective</h1>
We are developing methods for registering peri-procedural electrophysiological data showing sites of RF energy application (called Carto data) in the left atrium, with post-procedural MRI data, which shows regions of scarred left atrium (see figure above), using an interative closest point algorithm (Z. Malchano et al). The goal is to measure the distance between scar by MRI and ablation sites (Carto data) by EP.

</div>

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

<h1>Approach, Plan</h1>

Our approach for comparing the locations of scar to sites of RF ablation is summarized in the ISMRM 2008 reference below. The main challenge to this approach is to measure the distance between each scarred pixel, and each RF ablation site, and then the distance from each RF ablation site, to the nearest scarred pixel. <foo>.

Our plan for the project week is to first try to measure the closest distances between MRI scar and Carto data <bar>,and then to measure distances between Carto data and closest scar. We also wish to colorize the Carto surface, based on voltage data. We also wish to streamline the MR angiography segmentation method.
</div>

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

<h1>Progress</h1>

Software for the registration between electrophysiology Carto data and the MR angiogram has been implemented, using the ITK/VTK platform (see ISMRM 2008 abstract, Taclas et al, and figure above). Today we were able to measure scar /carto distances, except the measurements were not correct!

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

NA-MIC/Projects/Collaboration/Carto scar BIDMC

2008-06-11T19:42:35Z

Dcpeters:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Key Investigators===
* Beth Israel Deaconess: Dana C. Peters
* Beth Israel Deaconess: Jason Taclas

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

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

<h1>Objective</h1>
We are developing methods for registering peri-procedural electrophysiological data showing sites of RF energy application (called Carto data) in the left atrium, with post-procedural MRI data, which shows regions of scarred left atrium (see figure above), using an interative closest point algorithm (Z. Malchano et al). The goal is to measure the distance between scar by MRI and ablation sites (Carto data) by EP.

</div>

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

<h1>Approach, Plan</h1>

Our approach for comparing the locations of scar to sites of RF ablation is summarized in the ISMRM 2008 reference below. The main challenge to this approach is to measure the distance between each scarred pixel, and each RF ablation site, and then the distance from each RF ablation site, to the nearest scarred pixel. <foo>.

Our plan for the project week is to first try to measure the closest distances between MRI scar and Carto data <bar>,and then to measure distances between Carto data and closest scar. We also wish to colorize the Carto surface, based on voltage data. We also wish to streamline the MR angiography segmentation method.
</div>

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

<h1>Progress</h1>

Software for the registration between electrophysiology Carto data and the MR angiogram has been implemented, using the ITK/VTK platform (see ISMRM 2008 abstract, Taclas et al, and figure above).

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

2008 Summer Project Week

2008-06-11T19:38:34Z

Dcpeters: /* External Collaborations */

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

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

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

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

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

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.]This rate is good only through June 1.

Here is some information about several other 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==

NA-MIC Project Week is a 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-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
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|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 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|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|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 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.

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Ron Kikinis)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stephen Aylward)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# 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]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[2008_Summer_Project_Week:RegionalCorticalThicknessTool|Work Flow Tool for regional cortical thickness pipeline]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:NITRCRegistration|NITRC registration of cortical thickness modules]] (Clement Vachet UNC)
##DTI tools for a) DWI preparation and b) DTI atlas building (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[2008_Summer_Project_Week:TransRectal_Prostate_Biopsy_Module|Trans-Rectal Prostate Biopsy module]] (David Gobbi, Gabor Fichtinger, Queens/JHU)
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration]] (Yi Gao GATech, Gabor Fichtinger JHU)
##[[2008_Summer_Project_Week:PerkStation|Hardware/software overlay for percutaneous intervention (PERK Station)]] (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC]] (Dana Peters Group)

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 3
# David Gobbi, Queen's, Core 3
# Purang Abolmaesumi, Queen's, Core 3, June 23-25
# Siddharth Vikal, Queen's, Core 3
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 3
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University (Monday - Wednesday)
# Tim Olsen, Washington University (Monday - Wednesday)
# Kevin Archie, Washington University (Monday - Wednesday)
# Misha Milchenko, Washington University (Monday - Wednesday)
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT
# Peter Kazanzides, JHU, Collaborator (June 24)
# Scott Hoge, BWH, (Wed, Jun 25)
#*WE HAVE REACHED CAPACITY. REGISTRATION IS CLOSED. [[User:Tkapur|Tkapur]] 19:42, 6 June 2008 (UTC)

==Pictures==

2008 Summer Project Week

2008-06-11T19:38:09Z

Dcpeters: /* External Collaborations */

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

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

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

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

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

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.]This rate is good only through June 1.

Here is some information about several other 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==

NA-MIC Project Week is a 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-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
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|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 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|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|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 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.

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Ron Kikinis)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stephen Aylward)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# 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]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[2008_Summer_Project_Week:RegionalCorticalThicknessTool|Work Flow Tool for regional cortical thickness pipeline]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:NITRCRegistration|NITRC registration of cortical thickness modules]] (Clement Vachet UNC)
##DTI tools for a) DWI preparation and b) DTI atlas building (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[2008_Summer_Project_Week:TransRectal_Prostate_Biopsy_Module|Trans-Rectal Prostate Biopsy module]] (David Gobbi, Gabor Fichtinger, Queens/JHU)
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration]] (Yi Gao GATech, Gabor Fichtinger JHU)
##[[2008_Summer_Project_Week:PerkStation|Hardware/software overlay for percutaneous intervention (PERK Station)]] (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC (Dana Peters Group)

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 3
# David Gobbi, Queen's, Core 3
# Purang Abolmaesumi, Queen's, Core 3, June 23-25
# Siddharth Vikal, Queen's, Core 3
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 3
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University (Monday - Wednesday)
# Tim Olsen, Washington University (Monday - Wednesday)
# Kevin Archie, Washington University (Monday - Wednesday)
# Misha Milchenko, Washington University (Monday - Wednesday)
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT
# Peter Kazanzides, JHU, Collaborator (June 24)
# Scott Hoge, BWH, (Wed, Jun 25)
#*WE HAVE REACHED CAPACITY. REGISTRATION IS CLOSED. [[User:Tkapur|Tkapur]] 19:42, 6 June 2008 (UTC)

==Pictures==

NA-MIC/Projects/Theme/Carto scar

2008-06-11T19:37:04Z

Dcpeters: Removing all content from page

NA-MIC/Projects/Collaboration/Carto scar BIDMC

2008-06-11T19:36:47Z

Dcpeters: New page: {| |Project Week Main Page ]] |[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium u...

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

===Key Investigators===
* Beth Israel Deaconess: Dana C. Peters
* Beth Israel Deaconess: Jason Taclas

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

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

<h1>Objective</h1>
We are developing methods for registering peri-procedural electrophysiological data showing sites of RF energy application (called Carto data) in the left atrium, with post-procedural MRI data, which shows regions of scarred left atrium (see figure above), using an interative closest point algorithm (Z. Malchano et al). The goal is to measure the distance between scar by MRI and ablation sites (Carto data) by EP.

</div>

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

<h1>Approach, Plan</h1>

Our approach for comparing the locations of scar to sites of RF ablation is summarized in the ISMRM 2008 reference below. The main challenge to this approach is to measure the distance between each scarred pixel, and each RF ablation site, and then the distance from each RF ablation site, to the nearest scarred pixel. <foo>.

Our plan for the project week is to first try to measure the closest distances between MRI scar and Carto data <bar>,and then to measure distances between Carto data and closest scar. We also wish to colorize the Carto surface, based on voltage data. We also wish to streamline the MR angiography segmentation method.
</div>

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

<h1>Progress</h1>

Software for the registration between electrophysiology Carto data and the MR angiogram has been implemented, using the ITK/VTK platform (see ISMRM 2008 abstract, Taclas et al, and figure above).

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

NA-MIC/Projects/Theme/Carto scar

2008-06-11T19:30:13Z

Dcpeters:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

===Key Investigators===
* Beth Israel Deaconess: Dana C. Peters
* Beth Israel Deaconess: Jason Taclas

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

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

<h1>Objective</h1>
We are developing methods for registering peri-procedural electrophysiological data showing sites of RF energy application (called Carto data) in the left atrium, with post-procedural MRI data, which shows regions of scarred left atrium (see figure above), using an interative closest point algorithm (Z. Malchano et al). The goal is to measure the distance between scar by MRI and ablation sites (Carto data) by EP.

</div>

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

<h1>Approach, Plan</h1>

Our approach for comparing the locations of scar to sites of RF ablation is summarized in the ISMRM 2008 reference below. The main challenge to this approach is to measure the distance between each scarred pixel, and each RF ablation site, and then the distance from each RF ablation site, to the nearest scarred pixel. <foo>.

Our plan for the project week is to first try to measure the closest distances between MRI scar and Carto data <bar>,and then to measure distances between Carto data and closest scar. We also wish to colorize the Carto surface, based on voltage data. We also wish to streamline the MR angiography segmentation method.
</div>

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

<h1>Progress</h1>

Software for the registration between electrophysiology Carto data and the MR angiogram has been implemented, using the ITK/VTK platform (see ISMRM 2008 abstract, Taclas et al, and figure above).

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

File:Scar carto namic.jpg

2008-06-11T19:28:54Z

Dcpeters:

File:Scarmri namic.jpg

2008-06-11T19:28:11Z

Dcpeters:

NA-MIC/Projects/Theme/Carto scar

2008-06-11T19:26:47Z

Dcpeters:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

===Key Investigators===
* Beth Israel Deaconess: Dana C. Peters
* Beth Israel Deaconess: Jason Taclas

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

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

<h1>Objective</h1>
We are developing methods for registering peri-procedural electrophysiological data showing sites of RF energy application (called Carto data) in the left atrium, with post-procedural MRI data, which shows regions of scarred left atrium, using an interative closest point algorithm (Z. Malchano et al). The goal is to measure the distance between scar by MRI and ablation sites (Carto data) by EP.

</div>

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

<h1>Approach, Plan</h1>

Our approach for comparing the locations of scar to sites of RF ablation is summarized in the ISMRM 2008 reference below. The main challenge to this approach is to measure the distance between each scarred pixel, and each RF ablation site, and then the distance from each RF ablation site, to the nearest scarred pixel. <foo>.

Our plan for the project week is to first try to measure the closest distances between MRI scar and Carto data <bar>,and then to measure distances between Carto data and closest scar. We also wish to colorize the Carto surface, based on voltage data. We also wish to streamline the MR angiography segmentation method.
</div>

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

<h1>Progress</h1>

Software for the registration between electrophysiology Carto data and the MR angiogram has been implemented, using the ITK/VTK platform (see ISMRM 2008 abstract, Taclas et al).

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

NA-MIC/Projects/Theme/Carto scar

2008-06-11T18:19:40Z

Dcpeters:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
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===Instructions for Use of this Template===
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===Key Investigators===
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

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

<h1>Objective</h1>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h1>Approach, Plan</h1>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...
</div>

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

<h1>Progress</h1>

Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>

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

</div>

===References===
* Fletcher, P.T., Tao, R., Jeong, W.-K., Whitaker, R.T., "A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI," to appear Information Processing in Medical Imaging (IPMI) 2007.
* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., and Gerig, G., "Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis," Medical Image Analysis 10 (2006), 786--798.
* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore J.H., and Gerig, G., Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Lecture Notes in Computer Science LNCS, James S. Duncan and Guido Gerig, editors, Springer Verlag, Vol. 3749, Oct. 2005, pp. 131 -- 138
* C. Goodlett, I. Corouge, M. Jomier, and G. Gerig, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

NA-MIC/Projects/Theme/Carto scar

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</td><td><div class="thumb tright"><div class="thumbinner" style="width:322px;"><a href="/Wiki/index.php/Image:GenuFAp.jpg" class="image" title="Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain."><img alt="Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain." src="/Wiki/images/thumb/7/7f/GenuFAp.jpg/320px-GenuFAp.jpg" width="320" height="255" border="0" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/Wiki/index.php/Image:GenuFAp.jpg" class="internal" title="Enlarge"><img src="/Wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div>Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.</div></div></div>

</td><td><div class="thumb tright"><div class="thumbinner" style="width:322px;"><a href="/Wiki/index.php/Image:GenuFA.jpg" class="image" title="Regression of FA data; solid line represents the mean and dotted lines the standard deviation."><img alt="Regression of FA data; solid line represents the mean and dotted lines the standard deviation." src="/Wiki/images/thumb/0/0f/GenuFA.jpg/320px-GenuFA.jpg" width="320" height="256" border="0" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/Wiki/index.php/Image:GenuFA.jpg" class="internal" title="Enlarge"><img src="/Wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div>Regression of FA data; solid line represents the mean and dotted lines the standard deviation.</div></div></div>
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<a name="Instructions_for_Use_of_this_Template"></a><h3> <span class="mw-headline">Instructions for Use of this Template</span></h3>
<ol><li>Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
</li><li>Copy the entire text of this page into the page created above
</li><li>Link the created page into the list of projects for the project event
</li><li>Delete this section from the created page
</li><li>Send an email to tkapur at bwh.harvard.edu if you are stuck
</li></ol>
<a name="Key_Investigators"></a><h3> <span class="mw-headline">Key Investigators</span></h3>

<ul><li> UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
</li><li> Utah: Tom Fletcher, Ross Whitaker
</li></ul>
<p><br />
</p>
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<a name="Objective"></a><h1> <span class="mw-headline">Objective</span></h1>
<p>We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
</p><p><br />
</p>
</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<a name="Approach.2C_Plan"></a><h1> <span class="mw-headline">Approach, Plan</span></h1>
<p>Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.
</p><p>Our plan for the project week is to first try out <bar>,...
</p>
</div>
<div style="width: 40%; float: left;">
<a name="Progress"></a><h1> <span class="mw-headline">Progress</span></h1>
<p>Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the <a href="/Wiki/index.php/NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure" class="mw-redirect" title="NA-MIC/Projects/Diffusion Image Analysis/DTI Software and Algorithm Infrastructure">DTI Software Infrastructure</a> project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</p>
</div>
<p><br style="clear: both;" />
</p>
</div>
<p><br />
</p>
<a name="References"></a><h3> <span class="mw-headline">References</span></h3>
<ul><li> Fletcher, P.T., Tao, R., Jeong, W.-K., Whitaker, R.T., "A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI," to appear Information Processing in Medical Imaging (IPMI) 2007.
</li><li> Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., and Gerig, G., "Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis," Medical Image Analysis 10 (2006), 786--798.
</li><li> Corouge, I., Fletcher, P.T., Joshi, S., Gilmore J.H., and Gerig, G., Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Lecture Notes in Computer Science LNCS, James S. Duncan and Guido Gerig, editors, Springer Verlag, Vol. 3749, Oct. 2005, pp. 131 -- 138
</li><li> C. Goodlett, I. Corouge, M. Jomier, and G. Gerig, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: <a href="http://hdl.handle.net/1926/39" class="external free" title="http://hdl.handle.net/1926/39" rel="nofollow">http://hdl.handle.net/1926/39</a> .

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NA-MIC/Projects/Theme/Carto scar

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2008 Summer Project Week

2008-05-01T18:10:21Z

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