NAMIC Wiki - User contributions [en]

User:Pmercea

2012-10-01T22:08:40Z

Pmercea: /* Literature */

= Wikipage of Paul Mercea =
<br />
== About Myself ==

I am a Medical Informatics masters student from the University of Heidelberg, Germany. Before coming to the SPL I worked for two years part time at the German Cancer Research Center (DKFZ) in Heidelberg at the Medical and Biological Informatics department. At the moment I am working on my master's thesis at SPL on the project described below.

== Contact Information ==

If you would like to contact me feel free to write me an e-mail.
E-mail: pmercea (at sign) bwh.harvard.edu

== Project - Longitudinal Analysis of PET/CT Image Series ==

In my project I will develop a loadable Slicer 4 Module which will provide an user friendly workflow management for the analysis of multi timepoint PET/CT image data.

=== TODO list before Slicer 4.2 feature freeze ===

# Evaluating if plotting SUV values can be done with jqPlot or by using vtkCharts.
# Enhancing volume cropping for voxel space.
# Exploring utlility of multiple volume rendering views for qualitative analysis.
# Figure out if customized layout can be done without core modification (on the fly)

=== Documentation of the Progress ===

* Download the draft for the internal structure [[Media:LongPETCT-Structure-v01.pdf | here]] (last updated: 07/12/2012).
* Download the flowchart for the workflow [[Media:LongPETCT-Flowchart-v02.pdf | here]] (last updated: 07/10/2012).
* Download the current mockups for the workflow [[Media:Mercea_Long_PETCT_Workflow_120617.zip | here]].

=== Download links ===

* Opensource tool used for GUI prototyping: [http://pencil.evolus.vn/en-US/Home.aspx Pencil]

=== Source code links ===
* Source code for workflow demo application: [https://github.com/paulcm/repos.git demo repository]
* Source code of Longitudinal PET/CT Analysis Module for Slicer 4 [https://github.com/paulcm/LongPETCT.git module repository]

=== Literature ===
* J. Zhang et al. (2003) Using usability heuristics to evaluate patient safety of medical devices [http://www.google.de/url?sa=t&rct=j&q=zhang%20et%20al%20usability&source=web&cd=1&ved=0CCoQFjAA&url=http%3A%2F%2Fuserportal.iha.dk%2F~sw%2Fkurser%2Fbrga_04%2FLitteratur%2FUsing%2520usability%2520heuristics%2520to%2520evaluate%2520patient%2520safety%2520of%2520medical%2520devices%2520.pdf&ei=EhNqUMeJEuLv0gGutYCwCA&usg=AFQjCNGf3heX-DIeO9Kxuc7aFEkBV4cpoA&cad=rja]

User:Pmercea

2012-10-01T22:07:21Z

Pmercea: /* Literature */

= Wikipage of Paul Mercea =
<br />
== About Myself ==

I am a Medical Informatics masters student from the University of Heidelberg, Germany. Before coming to the SPL I worked for two years part time at the German Cancer Research Center (DKFZ) in Heidelberg at the Medical and Biological Informatics department. At the moment I am working on my master's thesis at SPL on the project described below.

== Contact Information ==

If you would like to contact me feel free to write me an e-mail.
E-mail: pmercea (at sign) bwh.harvard.edu

== Project - Longitudinal Analysis of PET/CT Image Series ==

In my project I will develop a loadable Slicer 4 Module which will provide an user friendly workflow management for the analysis of multi timepoint PET/CT image data.

=== TODO list before Slicer 4.2 feature freeze ===

# Evaluating if plotting SUV values can be done with jqPlot or by using vtkCharts.
# Enhancing volume cropping for voxel space.
# Exploring utlility of multiple volume rendering views for qualitative analysis.
# Figure out if customized layout can be done without core modification (on the fly)

=== Documentation of the Progress ===

* Download the draft for the internal structure [[Media:LongPETCT-Structure-v01.pdf | here]] (last updated: 07/12/2012).
* Download the flowchart for the workflow [[Media:LongPETCT-Flowchart-v02.pdf | here]] (last updated: 07/10/2012).
* Download the current mockups for the workflow [[Media:Mercea_Long_PETCT_Workflow_120617.zip | here]].

=== Download links ===

* Opensource tool used for GUI prototyping: [http://pencil.evolus.vn/en-US/Home.aspx Pencil]

=== Source code links ===
* Source code for workflow demo application: [https://github.com/paulcm/repos.git demo repository]
* Source code of Longitudinal PET/CT Analysis Module for Slicer 4 [https://github.com/paulcm/LongPETCT.git module repository]

=== Literature ===
* J. Zhang et al. (2003) '''Using usability heuristics to evaluate patient safety of medical devices''' [http://www.google.de/url?sa=t&rct=j&q=zhang%20et%20al%20usability&source=web&cd=1&ved=0CCoQFjAA&url=http%3A%2F%2Fuserportal.iha.dk%2F~sw%2Fkurser%2Fbrga_04%2FLitteratur%2FUsing%2520usability%2520heuristics%2520to%2520evaluate%2520patient%2520safety%2520of%2520medical%2520devices%2520.pdf&ei=EhNqUMeJEuLv0gGutYCwCA&usg=AFQjCNGf3heX-DIeO9Kxuc7aFEkBV4cpoA&cad=rja | target='_blank']

User:Pmercea

2012-10-01T22:05:11Z

Pmercea: /* Project - Longitudinal Analysis of PET/CT Image Series */

User:Pmercea

2012-08-21T18:58:17Z

Pmercea: /* TODO list before Slicer 4.2 feature freeze */

User:Pmercea

2012-08-21T18:57:15Z

Pmercea:

= Wikipage of Paul Mercea =
<br />
== About Myself ==

I am a Medical Informatics masters student from the University of Heidelberg, Germany. Before coming to the SPL I worked for two years part time at the German Cancer Research Center (DKFZ) in Heidelberg at the Medical and Biological Informatics department. At the moment I am working on my master's thesis at SPL on the project described below.

== Contact Information ==

If you would like to contact me feel free to write me an e-mail.
E-mail: pmercea (at sign) bwh.harvard.edu

== Project - Longitudinal Analysis of PET/CT Image Series ==

In my project I will develop a loadable Slicer 4 Module which will provide an user friendly workflow management for the analysis of multi timepoint PET/CT image data.

=== TODO list before Slicer 4.2 feature freeze ===

1. Evaluating if plotting SUV values can be done with jqPlot or by using vtkCharts.
2. Enhancing volume cropping for voxel space.
3. Exploring utlility of multiple volume rendering views for qualitative analysis.
4. Figure out if customized layout can be done without core modification (on the fly)

=== Documentation of the Progress ===

* Download the draft for the internal structure [[Media:LongPETCT-Structure-v01.pdf | here]] (last updated: 07/12/2012).
* Download the flowchart for the workflow [[Media:LongPETCT-Flowchart-v02.pdf | here]] (last updated: 07/10/2012).
* Download the current mockups for the workflow [[Media:Mercea_Long_PETCT_Workflow_120617.zip | here]].

=== Download links ===

* Opensource tool used for GUI prototyping: [http://pencil.evolus.vn/en-US/Home.aspx Pencil]

=== Source code links ===
* Source code for workflow demo application: [https://github.com/paulcm/repos.git demo repository]

User:Pmercea

2012-07-12T17:44:46Z

Pmercea: /* Documentation of the Progress */

File:LongPETCT-Structure-v01.pdf

2012-07-12T17:42:52Z

Pmercea:

File:LongPETCT-Flowchart-v02.pdf

2012-07-10T20:48:54Z

Pmercea: uploaded a new version of "File:LongPETCT-Flowchart-v02.pdf"

File:LongPETCT-Flowchart-v02.pdf

2012-07-10T19:07:18Z

Pmercea: uploaded a new version of "File:LongPETCT-Flowchart-v02.pdf"

User:Pmercea

2012-07-10T18:54:34Z

Pmercea:

File:LongPETCT-Flowchart-v02.pdf

2012-07-10T18:53:03Z

Pmercea:

User:Pmercea

2012-07-09T17:21:03Z

Pmercea:

User:Pmercea

2012-07-02T18:10:23Z

Pmercea: /* Documentation of the Progress */

File:LongPETCT-Flowchart-v01.pdf

2012-07-02T18:08:50Z

Pmercea:

2012 Summer Project Week:LongitudinalPETCTModule

2012-06-22T14:37:28Z

Pmercea:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Long_PETCT_ImageSeriesSelection.png|1. Image Series Selection
Image:Long_PETCT_Registration-Automatic.png|1a. PET/CT Registration (automatic)
Image:Long_PETCT_Registration-Manual.png|1a. PET/CT Registratoin (manual)
Image:Long_PETCT_ROIs.png|2a. Regions of Interest
Image:Long_PETCT_Segmentation.png|2b. Segmentation
Image:Long_PETCT_Qualitative.png|3a. Qualitative Analysis
Image:Long_PETCT_Quantitative.png|3b. Quantitative Analysis
Image:Long_PETCT_ReportDialog.png|Report Dialog
Image:Long_PETCT_ToolBox1.png|ToolBox approach example 1
Image:Long_PETCT_ToolBox2.png|ToolBox approach example 2
Image:Long_PETCT_Progress.jpg|Progress: Workflow Demo Application and OHLC plot for SUV

</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. possibility of automatic CT-CT or PET-CT image registration, support of non PET/CT image series, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Discussed the initial mockups and compared steps of the workflow with other PET/CT analysis related project.
Started to work on a "clickable" demo application based on some improvement decision taken at project week. We also made a request for a OHLC-plot extension to the available plot types in Slicer.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

=== Download links ===

* Opensource tool used for GUI prototyping: [http://pencil.evolus.vn/en-US/Home.aspx Pencil]

File:Long PETCT Progress.jpg

2012-06-22T14:34:48Z

Pmercea:

File:Long PETCT Progress.png

2012-06-22T14:12:11Z

Pmercea: uploaded a new version of "File:Long PETCT Progress.png"

2012 Summer Project Week:LongitudinalPETCTModule

2012-06-22T14:04:06Z

Pmercea: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Long_PETCT_ImageSeriesSelection.png|1. Image Series Selection
Image:Long_PETCT_Registration-Automatic.png|1a. PET/CT Registration (automatic)
Image:Long_PETCT_Registration-Manual.png|1a. PET/CT Registratoin (manual)
Image:Long_PETCT_ROIs.png|2a. Regions of Interest
Image:Long_PETCT_Segmentation.png|2b. Segmentation
Image:Long_PETCT_Qualitative.png|3a. Qualitative Analysis
Image:Long_PETCT_Quantitative.png|3b. Quantitative Analysis
Image:Long_PETCT_ReportDialog.png|Report Dialog
Image:Long_PETCT_ToolBox1.png|ToolBox approach example 1
Image:Long_PETCT_ToolBox2.png|ToolBox approach example 2
Image:Long_PETCT_Progress.png|Progress: Workflow Demo Application

</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. possibility of automatic CT-CT or PET-CT image registration, support of non PET/CT image series, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Discussed the initial mockups and compared steps of the workflow with other PET/CT analysis related project.
Started to work on a "clickable" demo application based on some improvement decision taken at project week.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

=== Download links ===

* Opensource tool used for GUI prototyping: [http://pencil.evolus.vn/en-US/Home.aspx Pencil]

2012 Summer Project Week:LongitudinalPETCTModule

2012-06-22T14:03:27Z

Pmercea:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Long_PETCT_ImageSeriesSelection.png|1. Image Series Selection
Image:Long_PETCT_Registration-Automatic.png|1a. PET/CT Registration (automatic)
Image:Long_PETCT_Registration-Manual.png|1a. PET/CT Registratoin (manual)
Image:Long_PETCT_ROIs.png|2a. Regions of Interest
Image:Long_PETCT_Segmentation.png|2b. Segmentation
Image:Long_PETCT_Qualitative.png|3a. Qualitative Analysis
Image:Long_PETCT_Quantitative.png|3b. Quantitative Analysis
Image:Long_PETCT_ReportDialog.png|Report Dialog
Image:Long_PETCT_ToolBox1.png|ToolBox approach example 1
Image:Long_PETCT_ToolBox2.png|ToolBox approach example 2
Image:Long_PETCT_Progress.png|Progress: Workflow Demo Application

</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. possibility of automatic CT-CT or PET-CT image registration, support of non PET/CT image series, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Discussed the initial mockups with several people and compared steps of the workflow with other PET/CT analysis related project.
Started to work on a "clickable" demo application based on some improvement decision taken at project week.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

=== Download links ===

* Opensource tool used for GUI prototyping: [http://pencil.evolus.vn/en-US/Home.aspx Pencil]

2012 Summer Project Week:LongitudinalPETCTModule

2012-06-22T14:02:16Z

Pmercea:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Long_PETCT_ImageSeriesSelection.png|1. Image Series Selection
Image:Long_PETCT_Registration-Automatic.png|1a. PET/CT Registration (automatic)
Image:Long_PETCT_Registration-Manual.png|1a. PET/CT Registratoin (manual)
Image:Long_PETCT_ROIs.png|2a. Regions of Interest
Image:Long_PETCT_Segmentation.png|2b. Segmentation
Image:Long_PETCT_Qualitative.png|3a. Qualitative Analysis
Image:Long_PETCT_Quantitative.png|3b. Quantitative Analysis
Image:Long_PETCT_ReportDialog.png|Report Dialog
Image:Long_PETCT_ToolBox1.png|ToolBox approach example 1
Image:Long_PETCT_ToolBox2.png|ToolBox approach example 2
Image:Long_PETCT_Progress.png|Workflow Demo Application

</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. possibility of automatic CT-CT or PET-CT image registration, support of non PET/CT image series, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Discussed the initial mockups with several people and compared steps of the workflow with other PET/CT analysis related project.
Started to work on a "clickable" demo application based on some improvement decision taken at project week.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

=== Download links ===

* Opensource tool used for GUI prototyping: [http://pencil.evolus.vn/en-US/Home.aspx Pencil]

File:Long PETCT Progress.png

2012-06-22T13:58:20Z

Pmercea:

2012 Summer Project Week

2012-06-22T13:40:58Z

Pmercea:

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: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:Evaluation Module|QA Evaluation Module]] (Dave Welch, Hans Johnson, Steve Pieper, JC Fillion-Robin)
# [[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, Simrin Nagpal, 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]] (Saman Nouranian, Samira Sojoudi, 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)

==='''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|Editor Effects]] (Steve, Jim, Brad, Ivan, Yi)
# [[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

2012-06-22T03:26:15Z

Pmercea:

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: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:LongitudinalPETCTModule

2012-06-21T16:05:09Z

Pmercea:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Long_PETCT_ImageSeriesSelection.png|1. Image Series Selection
Image:Long_PETCT_Registration-Automatic.png|1a. PET/CT Registration (automatic)
Image:Long_PETCT_Registration-Manual.png|1a. PET/CT Registratoin (manual)
Image:Long_PETCT_ROIs.png|2a. Regions of Interest
Image:Long_PETCT_Segmentation.png|2b. Segmentation
Image:Long_PETCT_Qualitative.png|3a. Qualitative Analysis
Image:Long_PETCT_Quantitative.png|3b. Quantitative Analysis
Image:Long_PETCT_ReportDialog.png|Report Dialog
Image:Long_PETCT_ToolBox1.png|ToolBox approach example 1
Image:Long_PETCT_ToolBox2.png|ToolBox approach example 2

</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. possibility of automatic CT-CT or PET-CT image registration, support of non PET/CT image series, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Since this project just started we are working on the requirement analysis and are planning to present the mockups at the project week for discussion.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

=== Download links ===

* Opensource tool used for GUI prototyping: [http://pencil.evolus.vn/en-US/Home.aspx Pencil]

User:Pmercea

2012-06-20T05:26:05Z

Pmercea:

2012 Summer Project Week:LongitudinalPETCTModule

2012-06-18T03:22:22Z

Pmercea:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Long_PETCT_ImageSeriesSelection.png|1. Image Series Selection
Image:Long_PETCT_Registration-Automatic.png|1a. PET/CT Registration (automatic)
Image:Long_PETCT_Registration-Manual.png|1a. PET/CT Registratoin (manual)
Image:Long_PETCT_ROIs.png|2a. Regions of Interest
Image:Long_PETCT_Segmentation.png|2b. Segmentation
Image:Long_PETCT_Qualitative.png|3a. Qualitative Analysis
Image:Long_PETCT_Quantitative.png|3b. Quantitative Analysis
Image:Long_PETCT_ReportDialog.png|Report Dialog
Image:Long_PETCT_ToolBox1.png|ToolBox approach example 1
Image:Long_PETCT_ToolBox2.png|ToolBox approach example 2

</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. possibility of automatic CT-CT or PET-CT image registration, support of non PET/CT image series, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Since this project just started we are working on the requirement analysis and are planning to present the mockups at the project week for discussion.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

==References==

2012 Summer Project Week:LongitudinalPETCTModule

2012-06-17T21:05:13Z

Pmercea:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Long_PETCT_ImageSeriesSelection.png|1. Image Series Selection
Image:Long_PETCT_Registration-Automatic.png|1a. PET/CT Registration (automatic)
Image:Long_PETCT_Registration-Manual.png|1a. PET/CT Registratoin (manual)
Image:Long_PETCT_ROIs.png|2a. Regions of Interest
Image:Long_PETCT_Segmentation.png|2b. Segmentation
Image:Long_PETCT_Qualitative.png|3a. Qualitative Analysis
Image:Long_PETCT_Quantitative.png|3b. Quantitative Analysis
Image:Long_PETCT_ReportDialog.png|Report Dialog
Image:Long_PETCT_ToolBox1.png|ToolBox approach example 1
Image:Long_PETCT_ToolBox2.png|ToolBox approach example 2

</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. number of follow up image series, possibility of non PET/CT image support, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Since this project just started we are working on the requirement analysis and are planning to present the mockups at the project week for discussion.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

==References==

File:Long PETCT ToolBox2.png

2012-06-17T21:03:41Z

Pmercea:

File:Long PETCT ToolBox1.png

2012-06-17T21:03:29Z

Pmercea:

2012 Summer Project Week:LongitudinalPETCTModule

2012-06-17T20:36:30Z

Pmercea:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Long_PETCT_ImageSeriesSelection.png|1. Image Series Selection
Image:Long_PETCT_Registration-Automatic.png|1a. PET/CT Registration (automatic)
Image:Long_PETCT_Registration-Manual.png|1a. PET/CT Registratoin (manual)
Image:Long_PETCT_ROIs.png|2a. Regions of Interest
Image:Long_PETCT_Segmentation.png|2b. Segmentation
Image:Long_PETCT_Qualitative.png|3a. Qualitative Analysis
Image:Long_PETCT_Quantitative.png|3b. Quantitative Analysis
Image:Long_PETCT_ReportDialog.png|Report Dialog
</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. number of follow up image series, possibility of non PET/CT image support, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Since this project just started we are working on the requirement analysis and are planning to present the mockups at the project week for discussion.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

==References==

File:Long PETCT ReportDialog.png

2012-06-17T20:32:42Z

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File:Long PETCT Quantitative.png

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File:Long PETCT Qualitative.png

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File:Long PETCT Segmentation.png

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File:Long PETCT ROIs.png

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File:Long PETCT Registration-Manual.png

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File:Long PETCT Registration-Automatic.png

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File:Long PETCT ImageSeriesSelection.png

2012-06-17T20:28:32Z

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User:Pmercea

2012-06-17T20:20:45Z

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File:Mercea Long PETCT Workflow 120617.zip

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User:Pmercea

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2012-06-13T16:14:16Z

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= Wikipage of Paul Mercea =

== About Myself ==

I am a Medical Informatics masters student from the University of Heidelberg, Germany. Before coming to the SPL I worked for two years part time at the German Cancer Research Center (DKFZ) in Heidelberg at the Medical and Biological Informatics department. At the moment I am working on my master's thesis at SPL on the project described below.

== Contact Information ==

If you would like to contact me feel free to write me an e-mail.

E-mail: pmercea (at sign) bwh.harvard.edu

== Project - Longitudinal Analysis of PET/CT Image Series ==

In my project I will develop a loadable Slicer 4 Module which will provide an user friendly workflow management for the analysis of multi timepoint PET/CT image data.

=== Documentation of the Progress ===

* Download the current mockups for the workflow [[Media:Mercea_Long_PETCT_Workflow.zip | here]].

User:Pmercea

2012-06-13T16:13:34Z

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User:Pmercea

2012-06-13T16:13:00Z

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User:Pmercea

2012-06-13T16:12:32Z

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User:Pmercea

2012-06-13T16:12:18Z

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File:Mercea Long PETCT Workflow.zip

2012-06-13T16:09:30Z

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User:Pmercea

2012-06-13T16:07:04Z

Pmercea: Created page with '= Wikipage of Paul Mercea = == About Myself == I am a Medical Informatics masters student from the University of Heidelberg, Germany. Before coming to the SPL I worked for two …'

2012 Summer Project Week:LongitudinalPETCTModule

2012-06-04T21:12:52Z

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__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Longpetct.png|PET/CT image showing segmented hot node.
Image:Longpetctmockup.png|Mockups for longitudinal PET/CT analysis module.
</gallery>

==Key Investigators==
* University of Heidelberg: Paul Mercea
* SPL: Paul Mercea, Andriy Fedorov, Ron Kikinis
* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol

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

<h3>Objective</h3>
We are developing a loadable Slicer module which can be used for analysis of longitudinal PET/CT follow up examination image series. The focus is especially on maximizing the usability of the graphic user interface in order to make the whole process of selection and registeration of (multiple) image series, definition of regions of interests and evaluation of the results as accessible as possible.

</div>

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

<h3>Approach, Plan</h3>
1. Defining the constraints for this module (e.g. number of follow up image series, possibility of non PET/CT image support, etc.)

2. Creating and evaluating mockups for the graphic user interface.

3. Implementation of the module based on the results of the previous steps.

</div>

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

<h3>Progress</h3>
Since this project just started we are working on the requirement analysis and are planning to present the mockups at the project week for discussion.

</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)

#Slicer Module
##Built-in
##Extension -- loadable

==References==

File:Longpetctmockup.png

2012-06-04T21:10:35Z

Pmercea: