NAMIC Wiki - User contributions [en]

2012 Summer Project Week:iGyne

2012-08-30T14:20:24Z

Xiaojun:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne-version 0521-registration.png|Screenshot of Registration
Image:iGyne.png|Screenshot of Needle Visualization
Image:iGyne-version 0521.png|Screenshot of Tumor and Needle Visualization
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
The ojective in this project week is to perform registration using both the template and obturator information so that more precise and robust registration result can be achieved.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>
This research module enables on-time processing of the intra-operative MRI data via a DICOM connection to the scanner followed by a multi-stage registration of CAD models of the template and the obturator to the patient images. This allows the virtual placement of interstitial needles during the intervention to assist the physician positioning decision.

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-08-30T14:19:37Z

Xiaojun: /* Key Investigators */

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne-version 0521-registration.png|Screenshot of Registration
Image:iGyne.png|Screenshot of Needle Visualization
Image:iGyne-version 0521.png|Screenshot of Tumor and Needle Visualization
Image:iGyne-registration using both the template and obturator information.png|Screenshot of registration using both the template and obturator information
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
The ojective in this project week is to perform registration using both the template and obturator information so that more precise and robust registration result can be achieved.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>
This research module enables on-time processing of the intra-operative MRI data via a DICOM connection to the scanner followed by a multi-stage registration of CAD models of the template and the obturator to the patient images. This allows the virtual placement of interstitial needles during the intervention to assist the physician positioning decision.

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-06-22T14:14:08Z

Xiaojun: /* Key Investigators */

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne-version 0521-registration.png|Screenshot of Registration
Image:iGyne.png|Screenshot of Needle Visualization
Image:iGyne-version 0521.png|Screenshot of Tumor and Needle Visualization
Image:iGyne-registration using both the template and obturator information.png|Screenshot of registration using both the template and obturator information
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
The ojective in this project week is to perform registration using both the template and obturator information so that more precise and robust registration result can be achieved.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>
An ICP-based algorithm is used to register the CAD model of the obturator to the MRI image volume, just similar to the method of the template registration.It works, however it seems that the result is still not satisfactory,and we are working on this issue.

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-06-22T14:13:52Z

Xiaojun: /* Key Investigators */

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne-version 0521-registration.png|Screenshot of Registration
Image:iGyne.png|Screenshot of Needle Visualization
Image:iGyne-version 0521.png|Screenshot of Tumor and Needle Visualization
Image:iGyne-registration using both the template and obturator information.png|Screenshot of registration using both the template and obturator information
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
The ojective in this project week is to perform registration using both the template and obturator information so that more precise and robust registration result can be achieved.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>
An ICP-based algorithm is used to register the CAD model of the obturator to the MRI image volume, just similar to the method of the template registration.It works, However it seems that the result is still not satisfactory,and we are working on this issue.

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-06-22T13:56:43Z

Xiaojun: /* Key Investigators */

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne-version 0521-registration.png|Screenshot of Registration
Image:iGyne.png|Screenshot of Needle Visualization
Image:iGyne-version 0521.png|Screenshot of Tumor and Needle Visualization
Image:iGyne-registration using both the template and obturator information.png|Screenshot of registration using both the template and obturator information
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
The ojective in this project week is to perform registration using both the template and obturator information so that more precise and robust registration result can be achieved.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>
An ICP-based algorithm is used to register the CAD model of the obturator to the MRI image volume, just similar to the method of the template registration. However, some problems still exist,and we are working on this issue.

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-06-22T03:14:56Z

Xiaojun:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne-version 0521-registration.png|Screenshot of Registration
Image:iGyne.png|Screenshot of Needle Visualization
Image:iGyne-version 0521.png|Screenshot of Tumor and Needle Visualization
Image:iGyne-registration using both the template and obturator information.png|Screenshot of registration using both the template and obturator information
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
The ojective in this project week is to perform registration using both the template and obturator information so that more precise and robust registration result can be achieved.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-06-22T03:14:17Z

Xiaojun:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne-version 0521-registration.png|Screenshot of Registration
Image:iGyne.png|Screenshot of Needle Visualization
Image:iGyne-version 0521.png|Screenshot of Tumor and Needle Visualization
Image:iGyne-registration using both the template and obturator information|Screenshot of registration using both the template and obturator information
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
The ojective in this project week is to perform registration using both the template and obturator information so that more precise and robust registration result can be achieved.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>

</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 YES
#Other (Please specify)

==References==

</div>

File:IGyne-registration using both the template and obturator information.png

2012-06-22T03:12:50Z

Xiaojun:

2012 Summer Project Week:iGyne

2012-06-18T03:45:01Z

Xiaojun:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne-version 0521-registration.png|Screenshot of Registration
Image:iGyne.png|Screenshot of Needle Visualization
Image:iGyne-version 0521.png|Screenshot of Tumor and Needle Visualization
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
The ojective in this project week is to perform registration using both the template and obturator information so that more precise and robust registration result can be achieved.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-05-31T18:55:29Z

Xiaojun:

2012 Summer Project Week:iGyne

2012-05-31T18:52:45Z

Xiaojun:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:iGyne.png|iGyne
Image:iGyne-version 0521.png|iGyne
Image:iGyne-version 0521-registration.png|iGyne
</gallery>

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* Radiation Oncology: Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>

</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 YES
#Other (Please specify)

==References==

</div>

File:IGyne-version 0521-registration.png

2012-05-31T18:49:42Z

Xiaojun: iGyne:Screenshot of Registration

iGyne:Screenshot of Registration

File:IGyne-version 0521.png

2012-05-31T18:48:40Z

Xiaojun: iGyne:ScreenShot of Tumor and Needle Visualization

iGyne:ScreenShot of Tumor and Needle Visualization

2012 Summer Project Week:iGyne

2012-05-03T20:53:36Z

Xiaojun: /* Key Investigators */

__NOTOC__
<gallery>

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

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* LROC: Akila Viswanathan, Kanokpis Townamchai, Antonio Damato

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-05-03T20:52:47Z

Xiaojun:

__NOTOC__
<gallery>

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

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* LROC: Antonio Damato, Kanokpis Townamchai, Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:iGyne

2012-05-03T20:49:39Z

Xiaojun: /* Key Investigators */

__NOTOC__
<gallery>

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

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* LROC: Antonio Damato, Kanokpis Townamchai, Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>

</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 YES
#Other (Please specify)

==References==

</div>

File:IGyne.png

2012-05-03T20:46:26Z

Xiaojun:

2012 Summer Project Week:iGyne

2012-05-03T20:39:46Z

Xiaojun: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List Image:Nifty_reg_logo.png|iGyne </gallery> ==Key Investigators== * SPL: Xiaojun Che…'

__NOTOC__
<gallery>

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

==Key Investigators==
* SPL: Xiaojun Chen,Jan Egger,Tina Kapur,Steve Pieper
* LROC: Antonio Damato, Kanokpis Townamchai, Akila Viswanathan

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

<h3>Objective</h3>
The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.

</div>

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

<h3>Approach, Plan</h3>

[https://github.com/xjchen/igyne.git iGyne],an open-source loadable module based on Slicer4, is developed for MR-guided gynecologic brachytherapy.

</div>

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

<h3>Progress</h3>

</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 YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:NiftyReg

2012-05-03T20:29:55Z

Xiaojun: Undo revision 75053 by Xiaojun (Talk)

__NOTOC__
<gallery>

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

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objective is to make NiftyReg available in Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

</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 YES
##Extension -- loadable
#Other (Please specify)

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

2012 Summer Project Week:NiftyReg

2012-05-03T20:26:09Z

Xiaojun: /* Key Investigators */

__NOTOC__
<gallery>

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

==Key Investigators==
* SPL: Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper
* LROC: Akila Viswanathan, Kanokpis Townamchai, Antonio Damato

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

<h3>Objective</h3>

The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
</div>

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

<h3>Approach, Plan</h3>

A software prototype supporting Gynecologic Radiation Treatment has already been pre-developed. The pre-developed software prototype has been brought to AMIGO cases and the workflow of the prototype has been discussed with the treating physician.

</div>

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

<h3>Progress</h3>

Currently, a module for Slicer is under development. The module already allows the visualization of a gynecological template for brachytherapy in a preoperative patient dataset. Furthermore, interstitial needles can already be visualized for treatment planning.

</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 YES
##Extension -- loadable
#Other (Please specify)

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

2012 Summer Project Week

2012-05-03T20:21:22Z

Xiaojun: /* Device Integration with Slicer and General Image Guided Therapy */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
#

==='''Radiation Therapy'''===

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
#
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)

==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#
==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th 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 40-50 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], [http://www.cimit.org CIMIT], and OCAIRO. 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 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== 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 26, 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 Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[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 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## 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.)
## Where possible, 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. (Matt)
# 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.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Summer Project Week

2012-05-03T20:16:22Z

Xiaojun:

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
#

==='''Radiation Therapy'''===

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
#
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:NiftyReg|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)

==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#
==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th 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 40-50 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], [http://www.cimit.org CIMIT], and OCAIRO. 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 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== 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 26, 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 Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[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 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## 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.)
## Where possible, 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. (Matt)
# 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.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Summer Project Week

2012-05-03T20:12:46Z

Xiaojun: /* Device Integration with Slicer and General Image Guided Therapy */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
#

==='''Radiation Therapy'''===

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
#
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:IGT|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)

==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#
==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th 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 40-50 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], [http://www.cimit.org CIMIT], and OCAIRO. 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 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== 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 26, 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 Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[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 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## 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.)
## Where possible, 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. (Matt)
# 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.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Summer Project Week

2012-05-03T20:10:31Z

Xiaojun: /* Device Integration with Slicer and General Image Guided Therapy */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
#

==='''Radiation Therapy'''===

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
#
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:NiftyReg|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)

==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#
==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th 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 40-50 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], [http://www.cimit.org CIMIT], and OCAIRO. 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 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== 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 26, 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 Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[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 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## 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.)
## Where possible, 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. (Matt)
# 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.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Summer Project Week

2012-05-03T19:58:37Z

Xiaojun: /* Device Integration with Slicer and General Image Guided Therapy */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
#

==='''Radiation Therapy'''===

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
#
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)

==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#
==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th 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 40-50 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], [http://www.cimit.org CIMIT], and OCAIRO. 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 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== 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 26, 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 Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[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 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## 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.)
## Where possible, 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. (Matt)
# 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.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Winter Project Week:iGyne

2012-01-13T05:21:13Z

Xiaojun:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the pre-developed iGyne Prototype
Image:IGyne-ScreenShot-Slicer4.png|Screenshot of the actual iGyne Module under Slicer4
Image:IGyne-ScreenShot of Needle Visualization.png|ScreenShot of Needle Visualization under the iGyne Module
</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur
* LROC: Antonio Damato, Kanokpis Townamchai, Akila Viswanathan

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

<h3>Objective</h3>

The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
</div>

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

<h3>Approach, Plan</h3>

A software prototype supporting Gynecologic Radiation Treatment has already been pre-developed. The pre-developed software prototype has been brought to AMIGO cases and the workflow of the prototype has been discussed with the treating physician.

</div>

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

<h3>Progress</h3>

Currently, a module for Slicer is under development. The module already allows the visualization of a gynecological template for brachytherapy in a preoperative patient dataset. Furthermore, interstitial needles can already be visualized for treatment planning.

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

2012 Winter Project Week:iGyne

2012-01-13T05:17:47Z

Xiaojun:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:IGyneNeedles.png|Screenshot of the pre-developed iGyne Prototype
Image:IGyne-ScreenShot-Slicer4.png|Screenshot of the actual iGyne Module under Slicer4
Image:IGyne-ScreenShot of Needle Visualization.png|ScreenShot of Needle Visualization
</gallery>

Project Title: '''iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO'''

==Key Investigators==
* SPL: Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Tina Kapur
* LROC: Antonio Damato, Kanokpis Townamchai, Akila Viswanathan

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

<h3>Objective</h3>

The aim of this project is to support Gynecologic Radiation Treatment in AMIGO. Gynecologic malignancies, which include cervical, endometrial, and vaginal/vulvar cancers, are the 4th leading cause of death in women in the US, with 83,750 new cases in the US in 2010 and 26,930 deaths per year. Treatment consists of external beam radiation followed by brachytherapy.
</div>

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

<h3>Approach, Plan</h3>

A software prototype supporting Gynecologic Radiation Treatment has already been pre-developed. The pre-developed software prototype has been brought to AMIGO cases and the workflow of the prototype has been discussed with the treating physician.

</div>

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

<h3>Progress</h3>

Currently, a module for Slicer is under development. The module already allows the visualization of a gynecological template for brachytherapy in a preoperative patient dataset. Furthermore, interstitial needles can already be visualized for treatment planning.

</div>
</div>

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

==Delivery Mechanism==

Towards a 3DSlicer module...

</div>

File:IGyne-ScreenShot of Needle Visualization.png

2012-01-13T05:13:42Z

Xiaojun: iGyne-ScreenShot of Needle Visualization

iGyne-ScreenShot of Needle Visualization