NAMIC Wiki - User contributions [en]

2014 Summer Project Week

2014-06-09T16:25:39Z

Matt.mccormick: /* Infrastructure */ I will not be able to make Project Week

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|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'''
|
|'''10-11:30pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11am: <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session:Registration Algorithms|Registration Algorithms]]'''(Sandy Wells)
[[MIT_Project_Week_Rooms#Star|Star]]
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[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''' [[2014 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:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Tina Kapur)
<br>----------------------------------------<br>
|
|-
|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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

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

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==

==Atrial Fibrillation==

==Huntington's Disease==

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg, Ivan)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg, Ivan)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg, Paolo)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp)

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Junichi Tokuda)
* Gestural Point of Care Interface for IGT (Saskia, Franklin, Tobias)
* MR-Ultrasound Registration for Prostate Interventions (Chenxi Zhang, Andriy Fedorov, Andras)
* Surface approximation from contour points (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)
* Image To Mesh Conversion for Brain MRI (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)

==Radiation Therapy==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg, ?)

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Andras, Steve, Jim, ...)
* Segmentation object support (Andrey, Csaba, Steve, ...)

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
*Chronicle (Steve Pieper)
*Volume Registration (Steve Pieper)
*Markups (Nicole Aucoin)
*Pluggable Label Statistics (Andrey , Ethan, Steve, Brad?, Jim? Dirk?)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras?, ?)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc, ?)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba, ?)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

==Feature Extraction==
*Breast Tumor Segmentation and Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)

==Other==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp, Danielle Pace?)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. 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 [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Yangming Li, University of Washington, ymli81@uw.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Jim Miller, GE Research, millerjv@ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Adam Rankin, Queen's University, rankin@queensu.ca
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#David Welch, University of Iowa, david-welch@uiowa.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Winter Project Week:ParameterSerialization

2014-01-10T16:25:55Z

Matt.mccormick: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Matt McCormick, Kitware
* Steve Pieper, Isomics
* Jim Miller, GE

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Many analysis algorithms have advanced parameters that must be tuned to work with given datasets.
* Exposing all the advanced parameters in the GUI confuses a user who is only interested in applying the algorithm.
* Exploring an algorithm parameter space is more thorough, efficient, and revealing when done programmically instead of manually in a GUI.
* Provenance with saved parameter files is important for reproducibility.
* The object is to allows CLI modules serialize and deserialize CLI parameters in a JSON file.
** The CLI XML parameters can then be used for "important" or "common" parameters can be tweaked by a user.
** Advanced parameters that deviate from the default can be stored in the file for manual or programmatic adjustment.
** JSON is format that is concise, has good human readability and editability, and widely supported by programming languages.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a unit test.
* Add [http://jsoncpp.sourceforge.net/ JsonCpp] and [https://github.com/TubeTK/TubeTK-ParameterSerializer ParameterSerializer] to the Slicer superbuild.
* Enable the SlicerExecutionModel_USE_SERIALIZER in [https://github.com/Slicer/SlicerExecutionModel SlicerExecutionModel].
* Consider writing a [http://json-schema.org/ JSON Schema] for CLIs that can be used with [https://github.com/garycourt/JSV a validator].
* Consider implications for CLI Web Services with REST APIs

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [https://github.com/thewtex/Slicer/tree/cli-serializer Slicer branch]
* [https://github.com/Slicer/SlicerExecutionModel/pull/22 SlicerExecutionModel FindJsonCpp fix]
</div>
</div>

== Resources ==

* [https://github.com/pieper/sem-html5 an SEM to HTML experiment]

2014 Winter Project Week:ParameterSerialization

2014-01-10T16:06:39Z

Matt.mccormick: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Matt McCormick, Kitware
* Steve Pieper, Isomics
* Jim Miller, GE

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Many analysis algorithms have advanced parameters that must be tuned to work with given datasets.
* Exposing all the advanced parameters in the GUI confuses a user who is only interested in applying the algorithm.
* Exploring an algorithm parameter space is more thorough, efficient, and revealing when done programmically instead of manually in a GUI.
* Provenance with saved parameter files is important for reproducibility.
* The object is to allows CLI modules serialize and deserialize CLI parameters in a JSON file.
** The CLI XML parameters can then be used for "important" or "common" parameters can be tweaked by a user.
** Advanced parameters that deviate from the default can be stored in the file for manual or programmatic adjustment.
** JSON is format that is concise, has good human readability and editability, and widely supported by programming languages.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a unit test.
* Add [http://jsoncpp.sourceforge.net/ JsonCpp] and [https://github.com/TubeTK/TubeTK-ParameterSerializer ParameterSerializer] to the Slicer superbuild.
* Enable the SlicerExecutionModel_USE_SERIALIZER in [https://github.com/Slicer/SlicerExecutionModel SlicerExecutionModel].
* Consider writing a [http://json-schema.org/ JSON Schema] for CLIs that can be used with [https://github.com/garycourt/JSV a validator].
* Consider implications for CLI Web Services with REST APIs

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [https://github.com/thewtex/Slicer/tree/cli-serializer Slicer branch]
</div>
</div>

== Resources ==

* [https://github.com/pieper/sem-html5 an SEM to HTML experiment]

2014 Winter Project Week:ParameterSerialization

2014-01-02T23:10:47Z

Matt.mccormick: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Matt McCormick, Kitware

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Many analysis algorithms have advanced parameters that must be tuned to work with given datasets.
* Exposing all the advanced parameters in the GUI confuses a user who is only interested in applying the algorithm.
* Exploring an algorithm parameter space is more thorough, efficient, and revealing when done programmically instead of manually in a GUI.
* Provenance with saved parameter files is important for reproducibility.
* The object is to allows CLI modules serialize and deserialize CLI parameters in a JSON file.
** The CLI XML parameters can then be used for "important" or "common" parameters can be tweaked by a user.
** Advanced parameters that deviate from the default can be stored in the file for manual or programmatic adjustment.
** JSON is format that is concise, has good human readability and editability, and widely supported by programming languages.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a unit test.
* Add [http://jsoncpp.sourceforge.net/ JsonCpp] and [https://github.com/TubeTK/TubeTK-ParameterSerializer ParameterSerializer] to the Slicer superbuild.
* Enable the SlicerExecutionModel_USE_SERIALIZER in [https://github.com/Slicer/SlicerExecutionModel SlicerExecutionModel].
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Winter Project Week:ParameterSerialization

2014-01-02T23:02:47Z

Matt.mccormick:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Matt McCormick, Kitware

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Many analysis algorithms have advanced parameters that must be tuned to work with given datasets.
* Exposing all the advanced parameters in the GUI confuses a user who is only interested in applying the algorithm.
* Exploring an algorithm parameter space is more thorough, efficient, and revealing when done programmically instead of manually in a GUI.
* Provenance with saved parameter files is important for reproducibility.
* The object is to allows CLI modules serialize and deserialize CLI parameters in a JSON file.
** The CLI XML parameters can then be used for "important" or "common" parameters can be tweaked by a user.
** Advanced parameters that deviate from the default can be stored in the file for manual or programmatic adjustment.
** JSON is format that is concise, has good human readability and editability, and widely supported by programming languages.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a unit test.
* Add JsonCpp and ParameterSerializer to the Slicer superbuild.
* Enable the SlicerExecutionModel_USE_SERIALIZER in SlicerExecutionModel.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Winter Project Week:ParameterSerialization

2014-01-02T22:42:01Z

Matt.mccormick:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Matt McCormick, Kitware

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Many analysis algorithms have advanced parameters that must be tuned to work with given datasets.
* Exposing all the advanced parameters in the GUI confuses a user who is only interested in applying the algorithm.
* Exploring an algorithm parameter space is more thorough, efficient, and revealing when done programmically instead of manually in a GUI.
* Provenance with saved parameter files is important for reproducibility.
* The object is to allows CLI modules serialize and deserialize CLI parameters in a JSON file.
** The CLI XML parameters can then be used for "important" or "common" parameters can be tweaked by a user.
** Advanced parameters that deviate from the default can be stored in the file for manual or programmatic adjustment.
** JSON is format that is concise, has good human readability and editability, and widely supported by programming languages.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2013-01-04T18:19:22Z

Matt.mccormick: Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List Image:ScarSeg_EM.png‎| PGP Keysigning. </gallery> ==Key Investigators== * Matt Mc…'

2013 Project Week:ITKv4Default

2013-01-04T17:59:34Z

Matt.mccormick: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Kitware: Matt McCormick
* Kitware: Luis Ibanez

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Switch Slicer to use ITKv4 by default.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Get Slicer-ITKv4 dashboard build working.
* Test packaging on all platforms.
* Address the Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727]
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

2013 Project Week:ITKv4Default

2013-01-04T15:39:45Z

Matt.mccormick:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Kitware: Matt McCormick
* Kitware: Luis Ibanez

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Switch Slicer to use ITKv4 by default.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Get Slicer-ITKv4 dashboard build working.
* Test packaging on all algorithms.
* Address the Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727]
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

2013 Project Week:ITKv4Default

2013-01-04T15:38:37Z

Matt.mccormick:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Kitware: Matt McCormick
* Kitware: Luis Ibanez

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Switch Slicer to use ITKv4 by default.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Get Slicer-ITKv4 dashboard build working.
* Test packaging on all algorithms.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

2013 Project Week:ITKv4Default

2013-01-04T15:35:29Z

Matt.mccormick: Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List  </gallery> ==Key Investigators== …'

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Matt McCormick, Kitware
* Luis Ibanez, Kitware

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Switch Slicer to use ITKv4 by default.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Get Slicer-ITKv4 dashboard build working.
* Test packaging on all algorithms.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

2013 Winter Project Week

2012-12-07T19:53:39Z

Matt.mccormick: /* NA-MIC Kit Internals */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2013]], [[Events]]

__NOTOC__
[[image:PW-SLC2013.png|300px]]

= Dates.Venue.Registration =

Please [[AHM_2013#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2013#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2013#Agenda|'''Click here for the agenda for AHM 2013 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

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

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

=Projects=

==TBI==

==Atrial Fibrillation==
* Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)

==Huntington's Disease==
* [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson)
* [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch)
* [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch)

==Head and Neck Cancer==

==Prostate Interventions==
* BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)
* PkModeling for prostate DCE MRI (Jim, Andrey)

==Neurosurgery==

==General Image Guided Therapy==
* United SlicerIGT extension, repository, website (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* Mobile image overlay augmented reality needle guidance (Adam Rankin, Tamas Ungi)

==Radiation Therapy==
* SlicerRT: Radiotherapy extension (Csaba Pinter, Kevin Wang)

==General Image Segmentation==

==General Image Registration==

==NA-MIC Kit Internals==
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc?, Bill Lorensen)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov?, Nicole Aucoin?, Steve Pieper)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and [http://slicer-devel.65872.n3.nabble.com/ANN-Oldies-But-Goodies-Volume-Data-tt4026821.html Sample Data Refactor]]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Nicole Aucoin?, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Jim Miller, Steve Pieper, Kunlin Cao)