NAMIC Wiki - User contributions [en]

2013 Summer Project Week:Radnostics

2013-06-21T03:11:39Z

AnthonyBlumfield: /* Key Investigators */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:RadnosticsSlicerResults.png|Radnostics Osteoporosis Detection Beta2 integrated into 3D Slicer
Image:RadnosticsAuxData.png|Vertebral Data
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: [mailto:Anthony.Blumfield@Radnostics.com Anthony Blumfield]
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>
Complete

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

2013 Summer Project Week:Radnostics

2013-06-21T02:39:19Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:RadnosticsSlicerResults.png|Radnostics Osteoporosis Detection Beta2 integrated into 3D Slicer
Image:RadnosticsAuxData.png|Vertebral Data
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>
Complete

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

2013 Summer Project Week:Radnostics

2013-06-20T21:27:25Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:RadnosticsSlicerResults.png|Radnostics(R) Osteoporosis Detection Beta2 integrated into 3D Slicer
Image:RadnosticsAuxData.png|Vertebral Data
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>
Complete

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

2013 Summer Project Week:Radnostics

2013-06-20T21:26:05Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:RadnosticsSC1.png|Secondary Capture
Image:RadnosticsAuxData.png|Vertebral Data
Image:RadnosticsSlicerResults.png|Radnostics(R) Osteoporosis Detection Beta2 integrated into 3D Slicer
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>
Complete

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

File:RadnosticsSlicerResults.png

2013-06-20T21:24:38Z

AnthonyBlumfield: Radnostics Osteoporosis Detection Beta2 integrated into 3D Slicer

Radnostics Osteoporosis Detection Beta2 integrated into 3D Slicer

2013 Summer Project Week:Radnostics

2013-06-20T21:00:14Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:RadnosticsSC1.png|Secondary Capture
Image:RadnosticsAuxData.png|Vertebral Data
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>
Complete

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

File:RadnosticsAuxData.png

2013-06-20T20:58:06Z

AnthonyBlumfield:

2013 Summer Project Week:Radnostics

2013-06-20T20:54:03Z

AnthonyBlumfield: /* Key Investigators */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:RadnosticsSC1.png|Secondary Capture
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>
Complete

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

2013 Summer Project Week:Radnostics

2013-06-11T21:48:34Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:RadnosticsSC1.png|Secondary Capture
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

File:RadnosticsSC1.png

2013-06-11T21:45:21Z

AnthonyBlumfield: Radnostics osteoporosis detection secondary capture

Radnostics osteoporosis detection secondary capture

Project Week/Template

2013-06-11T21:39:19Z

AnthonyBlumfield: Undo revision 81496 by AnthonyBlumfield (Talk)

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_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:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention 2013_Summer_Project_Week:<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==
* 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%;">

<h3>Objective</h3>
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%;">

<h3>Approach, Plan</h3>

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;">

<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>

==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==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, 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 .

2013 Summer Project Week:Radnostics

2013-06-11T21:38:25Z

AnthonyBlumfield: Created page with '__NOTOC__ = Spine Segmentation & Osteoporosis Detection In CT Imaging Studies = <gallery> Image:PW-MIT2013.png|Projects List Image:spine.png…'

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:Radnostics64-3.png|Osteoporosis Detection
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

Project Week/Template

2013-06-11T21:35:41Z

AnthonyBlumfield: Summer 2013 Radnostics page created

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:Radnostics64-3.png|Osteoporosis Detection
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* Jacobi Medical Center: Jay Leb, MD
* BWH: Ron Kikinis, MD

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

<h3>Objective</h3>
Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
*Tens of millions of CT scans are performed annually for various medical conditions
*We measure osteoporosis biomarkers and detect patients at risk
*100% automated & integrated into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Create a 3D Slicer v4 command line module for Radnostics Beta2.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
*http://www.radnostics.com

2013 Summer Project Week

2013-06-11T21:14:17Z

AnthonyBlumfield: /* Brain Segmentation */

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT 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'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[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)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|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''' ==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.

===Huntington's Disease===
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Kent)
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[Enhance and update SPL atlas]] (Dave, Hans)

===Traumatic Brain Injury===
* Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Guido Gerig, Jack van Horn)
* Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Investigation of the peri-lesional penumbra in traumatic brain injury using diffusion tensor imaging to isolate longitudinal changes in white matter integrity (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Reconstruction and visualization of the corticospinal tract in traumatic brain injury in the presence of severe hematoma and CSF-perfused edematous tissue using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)

===Atrial Fibrillation===
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov, anyone else?)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)

===Device Integration with Slicer===
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpnIGTLink]] (Sebastian Tauscher, Nobuhiko Hata)

===IGT===
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas, Junichi, Laurent)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Steven Aylward, Tamas Ungi)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent, Junichi)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent, Junichi)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ron Kikinis)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)

=== '''Informatics'''===
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
* Provenance
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Csaba Pinter, Andras Lasso, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[Plastimatch in NiPype]] (Paolo, Dave, Hans)
** look for commonalities/reuse of CompareVolumes
* iPython in Slicer (Hans, Jc, Dave)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Daniel Haehn, Steve Pieper, Rudolph Pienaar, Lilla Zollei, Nathaniel Reynolds)

==='''Brain & Spine Segmentation'''===
* [[2013_Summer_Project_Week:Multi_Atlas_Based_Multi_Image_Segmentation | Multi-Atlas-Based Multi-Image Segmentation for Brain MR Images]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)

== '''Background''' ==

We are pleased to announce the 17th 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 25th 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 17-21, 2013.
*'''Location:''' MIT.
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''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 projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. 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 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, 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 13: 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.

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699 Please click here to register.])

#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2013 Summer Project Week/RoomSharing

2013-05-28T12:05:49Z

AnthonyBlumfield:

This page aims to keep track of people who would like to split the lodging cost by renting an apartment using platform like https://www.airbnb.com

* On May 27th, interested people are expected to have updated this table.
* On May 28th, I will schedule a Google Hangout with interested people to discuss our option and start booking place.

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:70%" |Participant name(s)
!style="width:30%" |Date
|-
| Jean-Christophe Fillion-Robin (Kitware Inc.)
| Sunday 16/06 to Wed 20/06
|-
| Francois Budin (UNC - NIRAL)
| Monday 17/06 to Friday 21/06
|-
| Vinicius Boen (UNC/Michigan)
| Monday 17/06 to Friday 21/06
|-
| Bo Wang (Utah)
| Sunday 16/06 to Friday 21/06
|}

People with rooms that are interested in sharing.
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:30%" |Participant name(s)
!style="width:40%" |Location
!style="width:20%" |Date
|-
| Micah Chambers (UCLA)
| The Kendall (350 Main Street Cambridge, MA 02142)
| Sunday 16/06 to Friday 21/06
|}

== Google hangout ==

* <big>'''Google hangout is planned for May 28th at 10am EST time - Please confirm your attendance by editing the doodle: http://www.doodle.com/vet88pfk8b35fhtt'''</big>

== Options ==
* Micah apartement - How many people ? [Jc: I could sleep on the floor with my mat]
* [http://www.ihg.com/holidayinnexpress/hotels/us/en/reservation/roomrate Holiday Inn Express BOSTON - CAMBRIDGE]: ~$230 / 2 people / night => 460$/pers for 4 nights
* Apt on Irving St: https://www.airbnb.com/rooms/478653: $1516 / 4 nights / 4 (or 3)people => 379$ (or $506) per pers for 4 nights
* Apt on Cambridge St: https://www.airbnb.com/rooms/217942 : $1061 / 4 nights / 4 (or 3) people) => $266 (or $354) per pers for 4 nights
* [http://www.ihg.com/holidayinn/hotels/us/en/brookline/bklma/hoteldetail Holiday Inn Boston-Brookline]: $224 standard room /2 people / night => 560$/pers for 5 nights

== Questions ==
* Would it be sufficient to simply get the airbnb receipt ?
* Is it okay to use airbnb so that it can be charged to a grant ? [Jc: Checking with our Finance department]

2013 Summer Project Week/RoomSharing

2013-05-24T20:46:29Z

AnthonyBlumfield:

2012 Summer Project Week:Radnostics

2012-06-26T17:28:36Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:Radnostics64-3.png|Osteoporosis Detection
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
<b>Radnostics Osteoporosis Detection</b>

A solution for early diagnosis of osteoporosis
*Tens of millions of CT scans are performed annually for various medical conditions
*Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
*No need for a dedicated procedure
*No additional radiation
*No need for phantoms
*100% automated
*Integration into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</div>

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

<h3>Progress</h3>
*Radnostics Beta 1 command line module migrated to 3D Slicer v4
**Blocking bugs resolved or worked around
**Feature request 2223: Access to DICOM header info from CLI executable assigned to Jim

</div>

</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://www.radnostics.com

</div>

File:Radnostics64-3.png

2012-06-26T17:25:15Z

AnthonyBlumfield: uploaded a new version of "File:Radnostics64-3.png"

Source of CT study: The Cancer Imaging Archive (http://cancerimagingarchive.net/) sponsored by the Cancer Imaging Program, DCTD/NCI/NIH

2012 Summer Project Week:Radnostics

2012-06-26T03:04:11Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
<b>Radnostics Osteoporosis Detection</b>

A solution for early diagnosis of osteoporosis
*Tens of millions of CT scans are performed annually for various medical conditions
*Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
*No need for a dedicated procedure
*No additional radiation
*No need for phantoms
*100% automated
*Integration into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</div>

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

<h3>Progress</h3>
*Radnostics Beta 1 command line module migrated to 3D Slicer v4
**Blocking bugs resolved or worked around
**Feature request 2223: Access to DICOM header info from CLI executable assigned to Jim

</div>

</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://www.radnostics.com

</div>

2012 Summer Project Week:Radnostics

2012-06-24T13:26:15Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
Image:Radnostics64-3.png|Osteoporosis Detection in CT
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
<b>Radnostics Osteoporosis Detection</b>

A solution for early diagnosis of osteoporosis
*Tens of millions of CT scans are performed annually for various medical conditions
*Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
*No need for a dedicated procedure
*No additional radiation
*No need for phantoms
*100% automated
*Integration into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</div>

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

<h3>Progress</h3>
*Radnostics Beta 1 command line module migrated to 3D Slicer v4
**Blocking bugs resolved or worked around
**Feature request 2223: Access to DICOM header info from CLI executable assigned to Jim

<gallery>
Image:Radnostics64-3.png|Osteoporosis Detection in CT
</gallery>

</div>

</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://www.radnostics.com

</div>

2012 Summer Project Week:Threat Modeling

2012-06-22T14:13:27Z

AnthonyBlumfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Threat.jpg|Unsecured code can be a launching pad to take control of the host computer.
</gallery>

==Key Investigators==
* Kitware: Jean-Christophe Fillion-Robin (JC), Julien Finet (J2)
* Radnostics: Anthony Blumfield
* Isomics: Steve Pieper

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

<h3>Objective</h3>
Identify “low hanging fruit” architecture enhancements that will limit the ability of using 3D slicer as a launching pad to take control of the host computer.

Why now? Earlier architectural changes are cheaper and reduce the application compatibility burden.

</div>

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

<h3>Approach, Plan</h3>
During project week we will create a high level threat model for 3D Slicer v4 and identify possible mitigations

Focus on elevation of privilege threats; punt other threat types to a later stage

Meeting Tuesday noon-3PM, Room 32-D407 (walk through D408)

</div>

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

<h3>Progress</h3>
Four major areas identified:
*Code from many sources
*Complex file formats (e.g. DICOM)
*Network interfaces
*Build

Strategy:
*Start with low hanging fruit
*Invest in measures that enhance security & quality simultaneously

Mitigations:
*CLIs:
**Default to executable CLIs running in low privileged child processes. Use in proc libs only when necessary.
**Reduce execution of CLIs to those actually used by supporting an xml file rather than --xml
**Investigate sandboxes for python. (i.e [https://github.com/haypo/pysandbox/ pysandbox])
*Complex file formats
**Investigate loading and validating files in low privileged child process
*Network interfaces
**Investigate limiting functionality and sandboxing
**What is the situation with OpenIGTLink?
*Secure build: compiler/linker options
**These are basically "freebees".
*Best practices

</div>
</div>

==Delivery Mechanism==

#Document

==References==
*Swiderski F, Snyder W. Threat Modeling. ISBN-0735619913
*Howard M, LeBlanc D. Writing Secure Code, Second Edition. ISBN-0735617228

File:Radnostics64-3.png

2012-06-22T13:29:41Z

AnthonyBlumfield: uploaded a new version of "File:Radnostics64-3.png"

Source of CT study: The Cancer Imaging Archive (http://cancerimagingarchive.net/) sponsored by the Cancer Imaging Program, DCTD/NCI/NIH

2012 Summer Project Week:Radnostics

2012-06-22T03:53:02Z

AnthonyBlumfield: /* Key Investigators */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
<b>Radnostics Osteoporosis Detection</b>

A solution for early diagnosis of osteoporosis
*Tens of millions of CT scans are performed annually for various medical conditions
*Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
*No need for a dedicated procedure
*No additional radiation
*No need for phantoms
*100% automated
*Integration into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</div>

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

<h3>Progress</h3>
*Radnostics Beta 1 command line module migrated to 3D Slicer v4
**Blocking bugs resolved or worked around
**Feature request 2223: Access to DICOM header info from CLI executable assigned to Jim

<gallery>
Image:Radnostics64-3.png|Osteoporosis Detection in CT
</gallery>

</div>

</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://www.radnostics.com

</div>

2012 Summer Project Week:Radnostics

2012-06-22T03:46:58Z

AnthonyBlumfield: /* Spine Segmentation & Osteoporosis Detection In CT Imaging Studies */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
<b>Radnostics Osteoporosis Detection</b>

A solution for early diagnosis of osteoporosis
*Tens of millions of CT scans are performed annually for various medical conditions
*Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
*No need for a dedicated procedure
*No additional radiation
*No need for phantoms
*100% automated
*Integration into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</div>

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

<h3>Progress</h3>
*Radnostics Beta 1 command line module migrated to 3D Slicer v4
**Blocking bugs resolved or worked around
**Feature request 2223: Access to DICOM header info from CLI executable assigned to Jim

</div>
</div>

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

<gallery>
Image:Radnostics64-3.png|Osteoporosis Detection in CT
</gallery>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://www.radnostics.com

</div>

2012 Summer Project Week:Radnostics

2012-06-22T03:39:39Z

AnthonyBlumfield: /* Key Investigators */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
<b>Radnostics Osteoporosis Detection</b>

A solution for early diagnosis of osteoporosis
*Tens of millions of CT scans are performed annually for various medical conditions
*Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
*No need for a dedicated procedure
*No additional radiation
*No need for phantoms
*100% automated
*Integration into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</div>

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

<h3>Progress</h3>
*Radnostics Beta 1 command line module migrated to 3D Slicer v4
**Blocking bugs resolved or worked around
**Feature request 2223: Access to DICOM header info from CLI executable assigned to Jim

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://www.radnostics.com

</div>

File:Radnostics64-3.png

2012-06-22T03:37:21Z

AnthonyBlumfield: Source of CT study: The Cancer Imaging Archive (http://cancerimagingarchive.net/) sponsored by the Cancer Imaging Program, DCTD/NCI/NIH

Source of CT study: The Cancer Imaging Archive (http://cancerimagingarchive.net/) sponsored by the Cancer Imaging Program, DCTD/NCI/NIH

2012 Summer Project Week

2012-06-22T03:23:04Z

AnthonyBlumfield: /* Infrastructure */

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:''' [[2012 Project Week Breakout Session: Slicer4|What's new in Slicer4 (Charts - Jim, DICOM - Steve, Multivolume - Andrey)]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' [[2012 Project Week Breakout Session:Slicer4 Python Q&A|Slicer4 Python Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Slicer in Networked Environment|Slicer in Networked Environment]] (Junichi)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[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)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2012 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2012 Summer Project Week Breakout Session:Slicer DICOM|Breakout Session: DICOM, Networking, RT, Segmentations]] (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:QtTesting|QtTesting]] (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
<br>----------------------------------------<br>
'''3:00-4:00pm''' [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer (Andras)]]<br>
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier 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==

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'''===

# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Danielle Pace, Stephen Aylward, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:Intraoperative_Tract_Detection | Intraoperative White Matter Tract Detection Module]] (Lauren O'Donnell, Isaiah Norton)
# [[2012_Summer_Project_Week:Ultrasound_Aberration_Correction | An Ultrasound-based Method for Aberration Correction in TCFUS]] (Jason White, Greg Clement)
# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck| Atlas-based segmentation for head and neck]] (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
#[[2012_Summer_Project_Week:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, James Shackleford, Steve Pieper)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch loadable module]] (James Shackleford, Greg Sharp)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
#[[2012_Summer_Project_Week:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:PET_Image_Analysis | SUV Threshold Computation]] (Nadya Shusharina, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams, Hans Johnson)
# [[2012_Summer_Project_Week:4D shape analysis|4D Shape Analysis: Software Tools]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Greg Gardner, Alan Morris, Danny Perry, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Greg Gardner, Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Greg Gardner, Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:SlicerWeb|Web Interface to Slicer 4]] (Steve Pieper)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda, Laurent Chauvin)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder and other IGT modules]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:iGyne|iGyne for Gynecological Cancer Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
#[[2012_Summer_Project_Week:Interactive_Needle_Segmentation|Interactive Needle Segmentation for Gynecological Cancer Brachytherapy]] (Nabgha Farhat, Neha Agrawal, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Needle Tip Tracking |Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Pietro Nardelli, Padraig Cantillon-Murphy, Raul San Jose Estepar)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer, Andrey Fedorov)
#[[2012_Summer_Project_Week:ABC_Slicer4|Porting ABC extension to Slicer 4]] (Marcel Prastawa, Bo Wang, Guido Gerig)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#[[2012_Summer_Project_Week:SegmentationWithLabelFusion|Segmentation with Label Fusion]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)

==='''General Registration'''===
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
#[[2012_Summer_Project_Week:ElastixIntegration|Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, Petter Risholm, Dominik Meier, William Wells)

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:CMake_for_AIM_API|CMake-fying AIM API]] (Pat Mongklowat, Vlad Kleper, Andrey Fedorov)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim, Brendan Moloney)
# [[2012_Summer_Project_Week:PythonCLIandWidget|Python CLI modules (Demian, JC, Julien, Steve)]].
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:GPUEditor|GPU Editor Effects]] (Steve, Jim)
# [[2012_Summer_Project_Week:XTK|XTK/WebGL Exporter]] (Daniel, Nicolas - Boston Children's Hospital)
# [[2012_Summer_Project_Week:EventOptimization|Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)]]
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony, Steve)
# [[2012_Summer_Project_Week:CUDA Volume Rendering Extension|CUDA Volume Rendering as Extension]] (J2, Elvis)

==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:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== 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.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blevins, Scott, BWH, stblevins@gmail.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chambers, Micah, UCLA, micahcc@ucla.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gao, Yi, BWH, gaoyi@bwh.harvard.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Golland, Polina, MIT CSAIL, polina@csail.mit.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Gupta, Aditya, NIRAL UNC, aditya_gupta@med.unc.edu
#Irimia, Andrei, UCLA, andrei.irimia@loni.ucla.edu
#Jagadeesan, Jayender, SPL, jayender@bwh.harvard.edu
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kalpathy-Cramer, Jayashree, MGH, kalpathy@nmr.mgh.harvard.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, (cancelled registration) Erasmus MC, s.klein@erasmusmc.nl
#Kleper, Vladimir, Northwestern Univ, vkleper@northwestern.edu
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Mastrogiacomo, Katie, SPL, BWH, kmast@bwh.harvard.edu
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Mercea, Paul, SPL, pmercea@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Mizutani, Tatsushi, Nagoya Univ, tatsushi0207@me.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Montillo, Albert, GE Research, montillo@ge.com
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Norton, Isaiah, BWH, inorton@partners.org
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#O'Donnell, Lauren, BWH, odonnell@bwh.harvard.edu
#Oyama, Rie, BWH, royama@bwh.harvard.edu
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Penzkofer, Tobias, SPL, pt@bwh.harvard.edu
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Rannou, Nicolas, Childrens Hospital, nicolas.rannou@childrens.harvard.edu
#Razzaque, Sharif, InnerOptic Technology, sharif@inneroptic.com
#Risholm, Petter, Harvard, pettri@bwh.harvard.edu
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Schroeder, William, Kitware, will.schroeder@kitware.com
#Shackleford, James, MGH, jshackleford@partners.org
#Sharp, Greg, MGH, gcsharp@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
#Sridharan, Ramesh, MIT CSAIL, rameshvs@MIT.EDU
#State, Andrei, InnerOptic Technology, andrei@inneroptic.com
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Tokuda, Junichi, BWH, tokuda@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wang, Kevin, Princess Margaret Hospital, kevin.wang@rmp.uhn.on.ca
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Wells, William, HMS BWH, sw@bwh.harvard.edu
#Whitaker, Ross, SCI, whitaker@cs.utah.edu
#White, Phillip, BWH HMS, white@bwh.harvard.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Summer Project Week:Threat Modeling

2012-06-22T03:22:19Z

AnthonyBlumfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Threat.jpg|Unsecured code can be a launching pad to take control of the host computer.
</gallery>

==Key Investigators==
* Kitware: Jean-Christophe Fillion-Robin (JC), Julien Finet (J2)
* Radnostics: Anthony Blumfield
* Isomics: Steve Pieper

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

<h3>Objective</h3>
Identify “low hanging fruit” architecture enhancements that will limit the ability of using 3D slicer as a launching pad to take control of the host computer.

Why now? Earlier architectural changes are cheaper and reduce the application compatibility burden.

</div>

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

<h3>Approach, Plan</h3>
During project week we will create a high level threat model for 3D Slicer v4 and identify possible mitigations

Focus on elevation of privilege threats; punt other threat types to a later stage

Meeting Tuesday noon-3PM, Room 32-D407 (walk through D408)

</div>

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

<h3>Progress</h3>
Four major areas identified:
*Code from many sources
*Complex file formats (e.g. DICOM)
*Network interfaces
*Build

Strategy:
*Start with low hanging fruit
*Invest in measures that enhance security & quality simultaneously

Mitigations:
*CLIs:
**Default to executable CLIs running in low privileged child processes. Use in proc libs only when necessary.
**Reduce execution of CLIs to those actually used by supporting an xml file rather than --xml
**Investigate sandboxes for python
*Complex file formats
**Investigate loading and validating files in low privileged child process
*Network interfaces
**Investigate limiting functionality and sandboxing
*Secure build: compiler/linker options
**These are basically "freebees".

</div>
</div>

==Delivery Mechanism==

#Document

==References==
*Swiderski F, Snyder W. Threat Modeling. ISBN-0735619913
*Howard M, LeBlanc D. Writing Secure Code, Second Edition. ISBN-0735617228

2012 Summer Project Week:Threat Modeling

2012-06-22T03:20:11Z

AnthonyBlumfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Threat.jpg|Unsecured code can be a launching pad to take control of the host computer.
</gallery>

==Key Investigators==
* Kitware: Jean-Christophe Fillion-Robin (JC), Julien Finet (J2)
* Radnostics: Anthony Blumfield

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

<h3>Objective</h3>
Identify “low hanging fruit” architecture enhancements that will limit the ability of using 3D slicer as a launching pad to take control of the host computer.

Why now? Earlier architectural changes are cheaper and reduce the application compatibility burden.

</div>

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

<h3>Approach, Plan</h3>
During project week we will create a high level threat model for 3D Slicer v4 and identify possible mitigations

Focus on elevation of privilege threats; punt other threat types to a later stage

Meeting Tuesday noon-3PM, Room 32-D407 (walk through D408)

</div>

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

<h3>Progress</h3>
Four major areas identified:
*Code from many sources
*Complex file formats (e.g. DICOM)
*Network interfaces
*Build

Strategy:
*Start with low hanging fruit
*Invest in measures that enhance security & quality simultaneously

Mitigations:
*CLIs:
**Default to executable CLIs running in low privileged child processes. Use in proc libs only when necessary.
**Reduce execution of CLIs to those actually used by supporting an xml file rather than --xml
**Investigate sandboxes for python
*Complex file formats
**Investigate loading and validating files in low privileged child process
*Network interfaces
**Investigate limiting functionality and sandboxing
*Secure build: compiler/linker options
**These are basically "freebees".

</div>
</div>

==Delivery Mechanism==

#Document

==References==
*Swiderski F, Snyder W. Threat Modeling. ISBN-0735619913
*Howard M, LeBlanc D. Writing Secure Code, Second Edition. ISBN-0735617228

2012 Summer Project Week:Threat Modeling

2012-06-19T14:11:35Z

AnthonyBlumfield: /* Key Investigators */

2012 Summer Project Week:Threat Modeling

2012-06-19T13:13:37Z

AnthonyBlumfield: /* Key Investigators */

2012 Summer Project Week:Threat Modeling

2012-06-17T22:03:17Z

AnthonyBlumfield: /* Key Investigators */

2012 Summer Project Week:Threat Modeling

2012-06-17T21:08:09Z

AnthonyBlumfield:

2012 Summer Project Week

2012-06-07T03:13:32Z

AnthonyBlumfield: /* Infrastructure */

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:''' What's new in Slicer4 (Group. Multivolumes, Charts.) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python <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-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[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)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' Slicer4 Extensions (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font>Qt Testing (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> Ultrasound (Tamas)
[[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)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# An Intraoperative Transcranial Ultrasound Brain Shift Monitor (Jason White, Alex Golby, Isaiah Norton)

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

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT|Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D shape analysis]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
# [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[DBP3:Utah:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[DBP3:Utah:SlicerModuleInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# OpenIGT for realtime MRI-guided RF ablation (Rob MacLeod, Junichi Tokuda)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''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)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Steve Pieper)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Padraig Cantillon-Murphy, Raul San Jose Estepar, Pietro Nardelli)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer)

==='''General Registration'''===
# Interactive registration (Kunlin Cao GRC, Guillaume Pernelle BWH, Simrin Nagpal Queens)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, William Wells)

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

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

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien). See [http://www.na-mic.org/Bug/view.php?id=2039 #2039]
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# 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,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:Reporting|Reporting]] (Andrey)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)

==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:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html |hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== 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.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Datar, Manasi, Utah SCI, brenda@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Miller, Jim, GE Research, millerjv@ge.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Summer Project Week:Threat Modeling

2012-06-06T15:30:00Z

AnthonyBlumfield:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Threat.jpg|Unsecured code can be a launching pad to take control of the host computer.
</gallery>

==Key Investigators==
* Kitware: Julien Finet (JC)
* Radnostics: Anthony Blumfield

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

<h3>Objective</h3>
Identify “low hanging fruit” architecture enhancements that will limit the ability of using 3D slicer as a launching pad to take control of the host computer.

Why now? Earlier architectural changes are cheaper and reduce the application compatibility burden.

</div>

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

<h3>Approach, Plan</h3>
During project week we will create a high level threat model for 3D Slicer v4 and identify possible mitigations
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

#Document

==References==
*Swiderski F, Snyder W. Threat Modeling. ISBN-0735619913
*Howard M, LeBlanc D. Writing Secure Code, Second Edition. ISBN-0735617228

File:Threat.jpg

2012-06-06T15:26:10Z

AnthonyBlumfield: image of computer security threat

image of computer security threat

2012 Summer Project Week:Threat Modeling

2012-06-06T15:24:07Z

AnthonyBlumfield: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_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.
</gallery>

==Key Investigators==
* Kitware: Julien Finet (JC)
* Radnostics: Anthony Blumfield

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

<h3>Objective</h3>
Identify “low hanging fruit” architecture enhancements that will limit the ability of using 3D slicer as a launching pad to take control of the host computer.

Why now? Earlier architectural changes are cheaper and reduce the application compatibility burden.

</div>

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

<h3>Approach, Plan</h3>
During project week we will create a high level threat model for 3D Slicer v4 and identify possible mitigations
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

#Document

==References==
*Swiderski F, Snyder W. Threat Modeling. ISBN-0735619913
*Howard M, LeBlanc D. Writing Secure Code, Second Edition. ISBN-0735617228

2012 Summer Project Week

2012-06-06T14:41:03Z

AnthonyBlumfield: /* Infrastructure */

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:''' What's new in Slicer4 (Group. Multivolumes, Charts.) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python <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-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[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)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' Slicer4 Extensions (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font>Qt Testing (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> Ultrasound (Tamas)
[[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)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# An Intraoperative Transcranial Ultrasound Brain Shift Monitor (Jason White, Alex Golby, Isaiah Norton)

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

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT|Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D shape analysis]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
# [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[DBP3:Utah:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[DBP3:Utah:SlicerModuleInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# OpenIGT for realtime MRI-guided RF ablation (Rob MacLeod, Junichi Tokuda)

==='''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)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Steve Pieper)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Padraig Cantillon-Murphy, Raul San Jose Estepar, Pietro Nardelli)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer)

==='''General Registration'''===
# Interactive registration (Kunlin Cao GRC, Guillaume Pernelle BWH, Simrin Nagpal Queens)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, William Wells)

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

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

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien). See [http://www.na-mic.org/Bug/view.php?id=2039 #2039]
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# 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,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:Reporting|Reporting]] (Andrey)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, Anthony)

==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:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html |hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== 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.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Datar, Manasi, Utah SCI, brenda@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Miller, Jim, GE Research, millerjv@ge.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Summer Project Week:Radnostics

2012-05-13T17:36:47Z

AnthonyBlumfield:

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
</gallery>

<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
<b>Radnostics Osteoporosis Detection</b>

A solution for early diagnosis of osteoporosis
*Tens of millions of CT scans are performed annually for various medical conditions
*Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
*No need for a dedicated procedure
*No additional radiation
*No need for phantoms
*100% automated
*Integration into the clinical workflow

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</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

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://www.radnostics.com

</div>

2012 Winter Project Week:Radnostics

2012-05-13T14:41:30Z

AnthonyBlumfield: /* References */

__NOTOC__
= Spine Segmentation & Osteoporosis Screening In CT Imaging Studies =

<gallery>
[[image:PW-SLC2012.png|300px]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation

</gallery>

Osteoporosis is a condition of decreased bone mass that leads to fractures and negatively impacts millions of people, causing immobility, pain, and mortality, and costing billions of dollars annually. Although an effective technique (DXA) for early diagnosis exists and the condition is treatable, screening compliance is low. Preliminary diagnosis of osteoporosis is achievable by inspecting vertebral bodies in CT scans performed for other clinical reasons based on morphology, structure, and density. However, this is time consuming and the condition is frequently under diagnosed.

To address this problem, we are building a fully automated tool for spine segmentation and detection of osteoporosis findings.



[[File:RadnosticsWorkFlow.png|350px]]

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD

To join or collaborate with this project, please contact Anthony dot Blumfield At Radnostics dot Com.

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

<h3>Objective</h3>

Osteoporosis is common, devastating, and treatable.

We are building a fully automated tool to detect findings of osteoporosis by inspecting the morphology, structure, and density of vertebral bodies in CT studies performed for other clinical reasons.

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 integration into 3D Slicer 3.6

Stage 1: private

Stage 2: public

</div>

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

<h3>Progress</h3>

Beta integration complete as 3D Slicer command line module

To participate mailto:Beta@Radnostics.com

Thanks to Nicole Aucoin & Steve Peiper

</div>
</div>

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

==References==

http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

http://www.radnostics.com

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#Beta binary distribution
#Slicer commandline module

2012 Summer Project Week:Radnostics

2012-05-13T14:34:50Z

AnthonyBlumfield: /* References */

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
</gallery>
<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

<b>Radnostics Osteoporosis Detection in CT</b>

A solution for early diagnosis of osteoporosis
* Tens of millions of CT scans are performed annually for various medical conditions
* Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
* No need for a dedicated procedure
* No additional radiation
* No need for phantoms
* 100% automated
* Integration into the clinical workflow

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
We are building a fully automated tool to detect findings of osteoporosis by inspecting the morphology, structure, and density of vertebral bodies in CT studies performed for other clinical reasons and making it available as a 3D Slicer command line module

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</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

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://www.radnostics.com

</div>

2012 Summer Project Week:Radnostics

2012-05-13T14:25:26Z

AnthonyBlumfield:

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
</gallery>
<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: close to $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

<b>Radnostics Osteoporosis Detection in CT</b>

A solution for early diagnosis of osteoporosis
* Tens of millions of CT scans are performed annually for various medical conditions
* Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
* No need for a dedicated procedure
* No additional radiation
* No need for phantoms
* 100% automated
* Integration into the clinical workflow

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
We are building a fully automated tool to detect findings of osteoporosis by inspecting the morphology, structure, and density of vertebral bodies in CT studies performed for other clinical reasons and making it available as a 3D Slicer command line module

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</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

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://radnostics.com/default.aspx

</div>

2012 Summer Project Week

2012-05-13T14:21:44Z

AnthonyBlumfield: /* Neurosurgery, Brain and Spine, Traumatic Brain Injury */

2012 Summer Project Week:Radnostics

2012-05-13T14:20:53Z

AnthonyBlumfield: Create Radnositcs Summer 2012 project week wiki

__NOTOC__
= Spine Segmentation & Osteoporosis Detection In CT Imaging Studies =

<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation
</gallery>
<b>Osteoporosis</b>

A condition of bone mineral loss affecting the aging population
* Impacts 200 million people WW
* Leads to 9 million fractures each year
* Inflicts pain, morbidity, and mortality
* Direct annual costs: $20 billion in the US, €30+ billion in Europe
* Fractures and complications are preventable with lifestyle changes, diet, and medication
* However, <b>Osteoporosis is largely underdiagnosed</b>

<b>Radnostics Osteoporosis Detection in CT</b>

A solution for early diagnosis of osteoporosis
* Tens of millions of CT scans are performed annually for various medical conditions
* Radnostics measures osteoporosis biomarkers in CT scans and detects patients at risk
* No need for a dedicated procedure
* No additional radiation
* No need for phantoms
* 100% automated
* Integration into the clinical workflow

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD
* BWH: Ron Kikinis, MD
* Montefiore Medical Center: Ruth Freeman, MD
* Albert Einstein College of Medicine: Hilary Umans, MD

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

<h3>Objective</h3>
We are building a fully automated tool to detect findings of osteoporosis by inspecting the morphology, structure, and density of vertebral bodies in CT studies performed for other clinical reasons and making it available as a 3D Slicer command line module

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 command line module migration to 3D Slicer v4

</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

#Slicer Module
##Extension -- commandline

==References==
*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

*http://radnostics.com/default.aspx

</div>

2012 Summer Project Week

2012-05-13T13:37:19Z

AnthonyBlumfield: add Radnostics to project list

2012 Winter Project Week:Radnostics

2012-01-13T01:06:50Z

AnthonyBlumfield: progress update

__NOTOC__
= Spine Segmentation & Osteoporosis Screening In CT Imaging Studies =

<gallery>
[[image:PW-SLC2012.png|300px]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation

</gallery>

Osteoporosis is a condition of decreased bone mass that leads to fractures and negatively impacts millions of people, causing immobility, pain, and mortality, and costing billions of dollars annually. Although an effective technique (DXA) for early diagnosis exists and the condition is treatable, screening compliance is low. Preliminary diagnosis of osteoporosis is achievable by inspecting vertebral bodies in CT scans performed for other clinical reasons based on morphology, structure, and density. However, this is time consuming and the condition is frequently under diagnosed.

To address this problem, we are building a fully automated tool for spine segmentation and detection of osteoporosis findings.



[[File:RadnosticsWorkFlow.png|350px]]

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD

To join or collaborate with this project, please contact Anthony dot Blumfield At Radnostics dot Com.

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

<h3>Objective</h3>

Osteoporosis is common, devastating, and treatable.

We are building a fully automated tool to detect findings of osteoporosis by inspecting the morphology, structure, and density of vertebral bodies in CT studies performed for other clinical reasons.

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 integration into 3D Slicer 3.6

Stage 1: private

Stage 2: public

</div>

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

<h3>Progress</h3>

Beta integration complete as 3D Slicer command line module

To participate mailto:Beta@Radnostics.com

Thanks to Nicole Aucoin & Steve Peiper

</div>
</div>

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

==References==

http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

http://radnostics.com/default.aspx

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#Beta binary distribution
#Slicer commandline module

2012 Winter Project Week:Radnostics

2012-01-09T12:58:16Z

AnthonyBlumfield: Add workflow image

__NOTOC__
= Spine Segmentation & Osteoporosis Screening In CT Imaging Studies =

<gallery>
[[image:PW-SLC2012.png|300px]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation

</gallery>

Osteoporosis is a condition of decreased bone mass that leads to fractures and negatively impacts millions of people, causing immobility, pain, and mortality, and costing billions of dollars annually. Although an effective technique (DXA) for early diagnosis exists and the condition is treatable, screening compliance is low. Preliminary diagnosis of osteoporosis is achievable by inspecting vertebral bodies in CT scans performed for other clinical reasons based on morphology, structure, and density. However, this is time consuming and the condition is frequently under diagnosed.

To address this problem, we are building a fully automated tool for spine segmentation and detection of osteoporosis findings.



[[File:RadnosticsWorkFlow.png|350px]]

==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD

To join or collaborate with this project, please contact Anthony dot Blumfield At Radnostics dot Com.

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

<h3>Objective</h3>

Osteoporosis is common, devastating, and treatable.

We are building a fully automated tool to detect findings of osteoporosis by inspecting the morphology, structure, and density of vertebral bodies in CT studies performed for other clinical reasons.

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 integration into 3D Slicer 3.6

Stage 1: private

Stage 2: public

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==References==

http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

http://radnostics.com/default.aspx

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#Beta binary distribution
#Slicer commandline module

File:RadnosticsWorkFlow.png

2012-01-09T12:39:20Z

AnthonyBlumfield:

2012 Winter Project Week:Radnostics

2012-01-08T03:06:31Z

AnthonyBlumfield: updated plan

__NOTOC__
= Spine Segmentation & Osteoporosis Screening In CT Imaging Studies =

<gallery>
[[image:PW-SLC2012.png|300px]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation

</gallery>

Osteoporosis is a condition of decreased bone mass that leads to fractures and negatively impacts millions of people, causing immobility, pain, and mortality, and costing billions of dollars annually. Although an effective technique (DXA) for early diagnosis exists and the condition is treatable, screening compliance is low. Preliminary diagnosis of osteoporosis is achievable by inspecting vertebral bodies in CT scans performed for other clinical reasons based on morphology, structure, and density. However, this is time consuming and the condition is frequently under diagnosed.

To address this problem, we are building a fully automated tool for spine segmentation and detection of osteoporosis findings.



==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD

To join or collaborate with this project, please contact Anthony dot Blumfield At Radnostics dot Com.

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

<h3>Objective</h3>

Osteoporosis is common, devastating, and treatable.

We are building a fully automated tool to detect findings of osteoporosis by inspecting the morphology, structure, and density of vertebral bodies in CT studies performed for other clinical reasons.

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 integration into 3D Slicer 3.6

Stage 1: private

Stage 2: public

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==References==

http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

http://radnostics.com/default.aspx

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#Beta binary distribution
#Slicer commandline module

2012 Winter Project Week:Radnostics

2011-12-04T17:15:42Z

AnthonyBlumfield: reposition title

__NOTOC__
= Spine Segmentation & Osteoporosis Screening In CT Imaging Studies =

<gallery>
[[image:PW-SLC2012.png|300px]]
Image:spine.png|CT Spine
Image:SegmentedSpine.png|Automated Segmentation

</gallery>

Osteoporosis is a condition of decreased bone mass that leads to fractures and negatively impacts millions of people, causing immobility, pain, and mortality, and costing billions of dollars annually. Although an effective technique (DXA) for early diagnosis exists and the condition is treatable, screening compliance is low. Preliminary diagnosis of osteoporosis is achievable by inspecting vertebral bodies in CT scans performed for other clinical reasons based on morphology, structure, and density. However, this is time consuming and the condition is frequently under diagnosed.

To address this problem, we are building a fully automated tool for spine segmentation and detection of osteoporosis findings.



==Key Investigators==
* Radnostics: Anthony Blumfield
* Albert Einstein College of Medicine: Einat Blumfield, MD

To join or collaborate with this project, please contact Anthony dot Blumfield At Radnostics dot Com.

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

<h3>Objective</h3>

Osteoporosis is common, devastating, and treatable.

We are building a fully automated tool to detect findings of osteoporosis by inspecting the morphology, structure, and density of vertebral bodies in CT studies performed for other clinical reasons.

</div>

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

<h3>Approach, Plan</h3>

Radnostics Beta 1 integration into 3D Slicer 3.6

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==References==

http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

http://radnostics.com/default.aspx

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#Beta binary distribution
#Slicer commandline module