NAMIC Wiki - User contributions [en]

2013 Summer Project Week: Computer Assisted Surgery

2013-06-03T16:01:33Z

Fritschk:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MGH/BWH/UMIT: Karl Fritscher
* GATECH: Peter Karasev
* BWH: Ron Kikinis

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

<h3>Objective</h3>
The repositioning of fracture fragments during a surgical intervention often requires a trial and error approach, which leads to a significant prolongation of the surgery and causes additional trauma to the fragments and the surrounding soft tissue. Wound healing failure, infections, or joint stiffness can be the consequence. Therefore, there is a clear trend towards the development of less invasive techniques to reconstruct complex fractures. In order to support this trend, software tools for calculating and visualizing the optimal way of repositioning fracture fragments based on the usage of segmented CT images as input data have been developed. In several studies, they have successfully demonstrated their potential to decrease operation times and increase reduction accuracy. However, existing software tools are often restricted to particular types of fractures and require a large amount of user interaction.
Hence, the main objective of the project is to overcome these limitations by developing an algorithmic pipeline that is calculating and visualizing the optimal way of repositioning fracture fragments with a minimal amount of user interaction and without restrictions to particular types of fractures.
</div>

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

Novel concepts like the usage of prior knowledge about the shape of the healthy (=non-fractured) bone during the reconstruction process will be applied. Moreover, information coming from CT volumes will be combined with information on geometric surface properties in order to identify corresponding (fragment) surface points.

</div>

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

<h3>Progress/Goals</h3>

A slicer command line module + loadable module has been created. Until the project week they will be available as an extension. Different implmentation details like usage of CUDA code and improved manual interactions shall be discussed in the project week.

</div>
</div>

==Delivery Mechanism==

The code for automated fracture reconstruction will be provided as Slicer extension.

2013 Summer Project Week: Computer Assisted Surgery

2013-06-03T16:00:27Z

Fritschk:

2013 Summer Project Week: Computer Assisted Surgery

2013-06-03T16:00:17Z

Fritschk:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image: NAMIC_HeadNeck_segmentation.png|Parotid gland + brainstem
</gallery>

==Key Investigators==
* MGH/BWH/UMIT: Karl Fritscher
* GATECH: Peter Karasev
* BWH: Ron Kikinis

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

<h3>Objective</h3>
The repositioning of fracture fragments during a surgical intervention often requires a trial and error approach, which leads to a significant prolongation of the surgery and causes additional trauma to the fragments and the surrounding soft tissue. Wound healing failure, infections, or joint stiffness can be the consequence. Therefore, there is a clear trend towards the development of less invasive techniques to reconstruct complex fractures. In order to support this trend, software tools for calculating and visualizing the optimal way of repositioning fracture fragments based on the usage of segmented CT images as input data have been developed. In several studies, they have successfully demonstrated their potential to decrease operation times and increase reduction accuracy. However, existing software tools are often restricted to particular types of fractures and require a large amount of user interaction.
Hence, the main objective of the project is to overcome these limitations by developing an algorithmic pipeline that is calculating and visualizing the optimal way of repositioning fracture fragments with a minimal amount of user interaction and without restrictions to particular types of fractures.
</div>

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

Novel concepts like the usage of prior knowledge about the shape of the healthy (=non-fractured) bone during the reconstruction process will be applied. Moreover, information coming from CT volumes will be combined with information on geometric surface properties in order to identify corresponding (fragment) surface points.

</div>

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

<h3>Progress/Goals</h3>

A slicer command line module + loadable module has been created. Until the project week they will be available as an extension. Different implmentation details like usage of CUDA code and improved manual interactions shall be discussed in the project week.

</div>
</div>

==Delivery Mechanism==

The code for automated fracture reconstruction will be provided as Slicer extension.

2013 Summer Project Week: Computer Assisted Surgery

2013-06-03T15:57:56Z

Fritschk: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List Image: NAMIC_HeadNeck_segmentation.png|Parotid gland + brainstem </gallery> ==Key I…'

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image: NAMIC_HeadNeck_segmentation.png|Parotid gland + brainstem
</gallery>

==Key Investigators==
* MGH/BWH/UMIT: Karl Fritscher
* GATECH: Peter Karasev
* BWH: Ron Kikinis

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

<h3>Objective</h3>
The repositioning of fracture fragments during a surgical intervention often requires a trial and error approach, which leads to a significant prolongation of the surgery and causes additional trauma to the fragments and the surrounding soft tissue. Wound healing failure, infections, or joint stiffness can be the consequence. Therefore, there is a clear trend towards the development of less invasive techniques to reconstruct complex fractures. In order to support this trend, software tools for calculating and visualizing the optimal way of repositioning fracture fragments based on the usage of segmented CT images as input data have been developed. In several studies, they have successfully demonstrated their potential to decrease operation times and increase reduction accuracy. However, existing software tools are often restricted to particular types of fractures and require a large amount of user interaction.
Hence, the main objective of the project is to overcome these limitations by developing an algorithmic pipeline that is calculating and visualizing the optimal way of repositioning fracture fragments with a minimal amount of user interaction and without restrictions to particular types of fractures.
</div>

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

Novel concepts like the usage of prior knowledge about the shape of the healthy (=non-fractured) bone during the reconstruction process will be applied. Moreover, information coming from CT volumes will be combined with information on geometric surface properties in order to identify corresponding (fragment) surface points.

</div>

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

<h3>Progress</h3>

A slicer command line module + loadable module has been created. Until the project week they will be available as an extension.

</div>
</div>

2013 Summer Project Week

2013-06-03T15:44:49Z

Fritschk: /* IGT */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

===Radiation Therapy===
* Landmark Registration (Steve, Nadya, Greg, Paolo, Erol)
* [[Slicer RT: DICOM-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, anyone else?)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp)

===Device Integration with Slicer===
* Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

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

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

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
* Brain atlas optimisations demo (Marianna)
* Provenance
* [[Patient hierarchy]] (Csaba Pinter)
* Sample data (Steve Pieper, Jim Miller)
** content addressable data, in external data processing in Slicer, cmake file for external data, when write test can decorate the data file name with macro keywords saying it's external
* Plastimatch in NiPype (Paolo, Dave, Hans)
** look for commonalities/reuse of CompareVolumes
* iPython in Slicer (Hans, Jc, Dave)
* Optimizing start time of slicer (Jc)
* [[Common resampling and conversion utility functions in Slicer]] (Steve Pieper, Hans, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

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

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

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:40:10Z

Fritschk:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image: NAMIC_HeadNeck_segmentation.png|Parotid gland + brainstem
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

</div>

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

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>
</div>

==References==
* [1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
* [2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

File:NAMIC HeadNeck segmentation.png

2013-06-03T15:37:24Z

Fritschk:

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:29:56Z

Fritschk: /* References */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

</div>

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

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>
</div>

==References==
* [1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
* [2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:24:55Z

Fritschk: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

</div>

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

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>
</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:24:38Z

Fritschk:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

</div>

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

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>
</div>
</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:24:15Z

Fritschk: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

</div>

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

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>
</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:23:22Z

Fritschk: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

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

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:20:15Z

Fritschk: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

<h3>Plan</h3>

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

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

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:19:58Z

Fritschk: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

<h3>Plan</h3>

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:19:24Z

Fritschk: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

<h3>Plan</h3>

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

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

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:18:56Z

Fritschk: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

<h3>Plan</h3>

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:18:31Z

Fritschk: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

<h3>Plan</h3>

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

</div>

<h3>Progress</h3>

3 different segmentation approaches based on the usage of multiple atlases [1], statistical appearance models [2] and a method based on using image patches in combination with Gaussian processes for segmentation have been tested for their suitability to segment the parotid gland using a dataset of 18 CT images. Different approaches to combine the atlas and model based approaches [1,2] in different ways are currently under development.

</div>
</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

Analysis of different atlas-based segmentation techniques for parotid glands

2013-06-03T15:09:21Z

Fritschk:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MIT: Christian Wachinger
* MGH: Karl Fritscher, Greg Sharp

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

<h3>Objective</h3>
Our goal is to investigate various segmentation approaches for identifying parotid glands on head and neck CT images. The focus will be on atlas-based methods, which exploit the information from a number of previously labeled images. Several different strategies exist on how to employ this prior information to achieve the segmentation.

</div>

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

<h3>Plan</h3>

We will try to work out the differences in terms of parameterization and regularization of various atlas-based methods. We will further try to characterize properties of such methods for the segmentation of parotid glands, which show high structural variability. Finally, we would like to investigate, which combination of methods may be promising.

</div>

==References==
[1] Peroni M, Methods and Algorithms for Image Guided Adaptive Radio- and Hadron Therapy. PhD Thesis, Politecnico di Milano, 2011
[2] Fritscher KD, Gruenerbl A, Schubert R, 3D image segmentation using combined shape-intensity prior models. Journal of Computer Assisted Radiology and Surgery, 2007;1:341–350

2013 Summer Project Week

2013-05-29T13:58:14Z

Fritschk: /* Radiation Therapy */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

===Radiation Therapy===
* Landmark Registration (Steve, Nadya, Greg, Paolo, Erol)
* [[Slicer RT: DICOM-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* Proton dose calculation (Greg Sharp, Kevin Wang, Maxime Desplanques)
* Deformable registration validation toolkit (Greg Sharp, anyone else?)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp)

===Device Integration with Slicer===
* Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

===IGT===
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas, Junichi, Laurent)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Steven Aylward, Tamas Ungi)
* Application of Statistical Shape Modeling to Robot Assisted Spine Surgery (Marine Clogenson)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* Is Neurosurgical Rigid Registration really rigid? (Athena)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent, Junichi)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent, Junichi)

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

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
* Brain atlas optimisations demo (Marianna)
* Provenance
* Patient hierarchies (Csaba Pinter)
* Sample data (Steve Pieper, Jim Miller)
** content addressable data, in external data processing in Slicer, cmake file for external data, when write test can decorate the data file name with macro keywords saying it's external
* Plastimatch in NiPype (Paolo, Dave, Hans)
** look for commonalities/reuse of CompareVolumes
* iPython in Slicer (Hans, Jc, Dave)
* Optimizing start time of slicer (Jc)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

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

#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Nadya Shusharina, MGH, nshusharina@partners.org
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#David Welch, Univ Iowa, david-welch@uiowa.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it

2013 Summer Project Week

2013-05-29T00:55:58Z

Fritschk: /* Radiation Therapy */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

===Radiation Therapy===
* Landmark Registration (Steve, Nadya, Greg, Paolo, Erol)
* [[Slicer RT: DICOM-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* Proton dose calculation (Greg Sharp, Kevin Wang, Maxime Desplanques)
* Deformable registration validation toolkit (Greg Sharp, anyone else?)
* [[Analysis_of_different_atlas-based_segmentation_techniques_for_parotid_glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp)

===Device Integration with Slicer===
* Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

===IGT===
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas, Junichi, Laurent)
* Ultrasound Calibration (Matthew Toews, William Wells, Steven Aylward, Tamas Ungi)
* Application of Statistical Shape Modeling to Robot Assisted Spine Surgery (Marine Clogenson)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* Is Neurosurgical Rigid Registration really rigid? (Athena)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent, Junichi)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent, Junichi)

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

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
* Brain atlas optimisations demo (Marianna)
* Provenance
* Patient hierarchies (Csaba Pinter)
* Sample data (Steve Pieper, Jim Miller)
** content addressable data, in external data processing in Slicer, cmake file for external data, when write test can decorate the data file name with macro keywords saying it's external
* Plastimatch in NiPype (Paolo, Dave, Hans)
** look for commonalities/reuse of CompareVolumes
* iPython in Slicer (Hans, Jc, Dave)
* Optimizing start time of slicer (Jc)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

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

#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Nadya Shusharina, MGH, nshusharina@partners.org
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#David Welch, Univ Iowa, david-welch@uiowa.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it

2013 Summer Project Week

2013-05-29T00:55:32Z

Fritschk: /* Radiation Therapy */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

===Radiation Therapy===
* Landmark Registration (Steve, Nadya, Greg, Paolo, Erol)
* [[Slicer RT: DICOM-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* Proton dose calculation (Greg Sharp, Kevin Wang, Maxime Desplanques)
* Deformable registration validation toolkit (Greg Sharp, anyone else?)
* [[Analysis_of_different_atlas-based_segmentation_techniques_for_parotid_glands]] Analysis of different atlas-based segmentation techniques for parotid glands (Christian Wachinger, Karl Fritscher, Greg Sharp)

===Device Integration with Slicer===
* Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

===IGT===
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas, Junichi, Laurent)
* Ultrasound Calibration (Matthew Toews, William Wells, Steven Aylward, Tamas Ungi)
* Application of Statistical Shape Modeling to Robot Assisted Spine Surgery (Marine Clogenson)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* Is Neurosurgical Rigid Registration really rigid? (Athena)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent, Junichi)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent, Junichi)

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

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
* Brain atlas optimisations demo (Marianna)
* Provenance
* Patient hierarchies (Csaba Pinter)
* Sample data (Steve Pieper, Jim Miller)
** content addressable data, in external data processing in Slicer, cmake file for external data, when write test can decorate the data file name with macro keywords saying it's external
* Plastimatch in NiPype (Paolo, Dave, Hans)
** look for commonalities/reuse of CompareVolumes
* iPython in Slicer (Hans, Jc, Dave)
* Optimizing start time of slicer (Jc)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

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

#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Nadya Shusharina, MGH, nshusharina@partners.org
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#David Welch, Univ Iowa, david-welch@uiowa.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it

Analysis of different atlas-based segmentation techniques for parotid glands

2013-05-29T00:53:57Z

Fritschk:

Analysis of different atlas-based segmentation techniques for parotid glands

2013-05-29T00:52:43Z

Fritschk:

Analysis of different atlas-based segmentation techniques for parotid glands

2013-05-29T00:52:19Z

Fritschk: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List </gallery> ==Key Investigators== * MIT: Christian Wachinger * MGH: Karl Fritscher, …'

2013 Summer Project Week

2013-05-29T00:48:39Z

Fritschk: /* Radiation Therapy */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

===Radiation Therapy===
* Landmark Registration (Steve, Nadya, Greg, Paolo, Erol)
* [[Slicer RT: DICOM-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* Proton dose calculation (Greg Sharp, Kevin Wang, Maxime Desplanques)
* Deformable registration validation toolkit (Greg Sharp, anyone else?)
* Analysis of different atlas-based segmentation techniques for parotid glands (Christian Wachinger, Karl Fritscher, Greg Sharp)

===Device Integration with Slicer===
* Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

===IGT===
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas, Junichi, Laurent)
* Ultrasound Calibration (Matthew Toews, William Wells, Steven Aylward, Tamas Ungi)
* Application of Statistical Shape Modeling to Robot Assisted Spine Surgery (Marine Clogenson)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* Is Neurosurgical Rigid Registration really rigid? (Athena)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent, Junichi)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent, Junichi)

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

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
* Brain atlas optimisations demo (Marianna)
* Provenance
* Patient hierarchies (Csaba Pinter)
* Sample data (Steve Pieper, Jim Miller)
** content addressable data, in external data processing in Slicer, cmake file for external data, when write test can decorate the data file name with macro keywords saying it's external
* Plastimatch in NiPype (Paolo, Dave, Hans)
** look for commonalities/reuse of CompareVolumes
* iPython in Slicer (Hans, Jc, Dave)
* Optimizing start time of slicer (Jc)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

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

#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Nadya Shusharina, MGH, nshusharina@partners.org
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#David Welch, Univ Iowa, david-welch@uiowa.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it

2010 Summer Project Week

2010-06-17T19:11:59Z

Fritschk: /* Analysis */

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

[[Image:PW-MIT2010.png|500px|right]]

__TOC__
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 21
!width="250px"|Tuesday, June 22
!width="250px"|Wednesday, June 23
!width="250px"|Thursday, June 24
!width="250px"|Friday, June 25
|-
|
|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:''' NA-MIC Kit Update (Jim Miller)<br>----------------------------------------<br>'''9:45am:''' 3D Slicer Update (Steve Pieper)<br>----------------------------------------<br>'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)<br>----------------------------------------<br>'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
|bgcolor="#ffffdd"|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes<br>Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br>----------------------------------------<br>'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>----------------------------------------<br>'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)<br>----------------------------------------<br>'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br>----------------------------------------<br>'''4-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br>----------------------------------------<br>'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)<br>----------------------------------------<br>'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br>----------------------------------------<br>'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)<br>----------------------------------------<br>'''2-3pm:''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br>----------------------------------------<br>'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)
|
|-
|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
|
|}

Please note:
*We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
*Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
*Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

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

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Lauren Chauvin, Junichi Tokuda, Noby Hata)
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas)
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

=== Workflows and Integration ===
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

==Background==

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

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

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

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

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

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

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

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

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== Preparation ==

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

==Attendee List==

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

# Yousef Al-Kofahi , CompuCyte Corporation
# Peter Anderson , retired
# Nicole Aucoin , BWH
# Michel Audette , Kitware
# Stephen Aylward , Kitware, Inc
# Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories
# Sylvain Bouix , BWH
# Michael Bowers , Johns Hopkins University
# Francois Budin , UNC
# Everette Burdette , Acoustic MedSystems, Inc.
# Laurent CHAUVIN , Brigham and Women's Hospital
# Min Chen , Johns Hopkins University
# Jason Crane , UCSF
# Manasi Datar , SCI Institute
# Liya Ding , The Ohio State University
# Ryan Eckbo , BWH
# Ilker Ersoy , University of Missouri Columbia
# Andriy Fedorov , Surgical Planning Lab
# Jean-Christophe Fillion-Robin , Kitware Inc.
# Julien Finet , Kitware Inc
# James Fishbaugh , SCI Institute
# Karl Fritscher , UMIT
# Yi Gao , Gerogia Tech
# Arnaud GELAS , Harvard Medical School
# Randy Gollub , MGH
# Chris Gorgolewski , SPL
# alexandre gouaillard , CoSMo Software
# Sylvain Gouttard , SCI Institute
# Kedar Grama , Rensselaer Polytechnic Institute
# Daniel Haehn , University of Pennsylvania
# Adel Hafiane , ENSI-Bourges
# Nathan Hageman ,
# Dieter Hahn , University Erlangen
# Michael Halle , BWH/SPL
# Corentin Hamel , UNC Chapel Hill
# Nobuhiko Hata , Brigham and Women's Hospital
# Kathryn Hayes , Brigham and Women's Hospital
# Nicholas Herlambang , AZE, Ltd.
# Leslie Holton , Medtronic Navigation
# Luis Ibanez , KITWARE Inc.
# Jayender Jagadeesan , SPL
# Hans Johnson , University of Iowa
# Tina Kapur , Brigham and Women's Hospital
# Ron Kikinis , Brigham and Women's Hospital
# Minjeong Kim , UNC-Chapel Hill
# Ivan Kolesov , Georgia Institute of Technology
# Garrett Larson , UNC-CH
# Joohwi Lee , UNC Chapel Hill
# Rui Li , MGH
# Stefan Lienhard , LMI
# Curtis Lisle , KnowledgeVis, LLC
# Haiying Liu , Brigham and Women's Hospital
# Felix Liu , Beth Israel Deaconess Medical Center
# Yanling Liu , SAIC-Frederick, Inc.
# Bradley Lowekamp , Lockheed Martin
# raghu machiraju , The Ohio State University
# Vincent Magnotta , The University of Iowa
# mathieu malaterre , CoSMo Software
# Daniel Marcus , Washington University
# William Marks , Focused Ultrasound Lab, BWH, HMS
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University
# Sean Megason , Harvard Medical School
# Dominik Meier , BWH, Boston MA
# bjoern menze , CSAIL MIT
# Mikhail Milchenko , WUSTL
# James Miller , GE Research
# Kishore Mosaliganti , Harvard Medical School
# Marc Niethammer , UNC Chapel Hill
# Isaiah Norton , BWH Neurosurgery
# Beck Olson , UCSF
# John Onofrey , Yale University
# Raghav Padmanabhan , RPI
# Kannappan Palaniappan , university of Missouri
# Beatriz Paniagua , University of North Caolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Eun-Joo Park , Brigham & Women's Hospital
# David Partyka , Kitware Inc
# Pratik Patel ,
# Sudhir Pathak , Univeristy Of Pittsburgh
# Thierry PECOT , Ohio State University
# Marta Peroni , Politecnico di Milano
# Antonin Perrot-Audet , Harvard Medical School
# Steve Pieper , Isomics, Inc.
# Wendy Plesniak , BWH
# Kilian Pohl , IBM
# Sonia Pujol , Brigham and Women's Hospital
# Nicolas Rannou , Harvard Medical School
# Tammy Riklin Raviv , MIT, CSAIL
# Marco Ruiz , UCSD
# Johannes Schick , SPL
# William Schroeder , Kitware
# Mark Scully , The Mind Research Network
# Greg Sharp , MGH
# Yundi Shi , UNC Chapel Hill
# Nadya Shusharina , MGH
# Shantanu Singh , The Ohio State University
# Gareth Smith , Wolfson Medical Imaging Centre (WMIC)
# Lydie Souhait , Harvard Medical School
# Dominik Spinczyk , Silesian University of Technology
# Padmapriya Srinivasan ,
# Xiaodong Tao , GE Research
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School
# Junichi Tokuda , Brigham and Women's Hospital
# Tamas Ungi , Queen's University
# Clement Vachet , UNC Chapel Hill
# Veda Vadyar , Brigham and Women's Hospital
# Gopalkrishna Veni , SCI Institute
# Stuart Wallace , Massachusetts General Hospital
# Demian Wassermann , SPL/LMI/PNL
# Adam Weinrich , Nokia
# Sandy Wells , BWH
# Phillip White , BWH/HMS
# Guorong Wu , University of North Carolina at Chapel Hill
# Yin Wu , Mass General Hospital
# Atsushi Yamada , Nagoya Institute of Technology
# Alexander Yarmarkovich , ISOMICS
# Alexander Zaitsev , Brigham and Womens Hospital

2010 Summer Project Week

2010-06-16T18:50:13Z

Fritschk: /* Analysis */

__NOTOC__

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

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

==Background==

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

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

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

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

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

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

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

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

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="200px"|Monday, June 21
!width="200px"|Tuesday, June 22
!width="200px"|Wednesday, June 23
!width="200px"|Thursday, June 24
!width="200px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|8:30
|rowspan="5"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|9:00-9:45
|NA-MIC Kit Update (Jim Miller) - include: Module nomenclature (Extensions: cmdline vs loadable, Built-in)<br>_____________________<br> QT - include: Superbuild demo by Dave P.
|rowspan="4"|'''Breakout Session:''' [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
|rowspan="4"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
|rowspan="4"|[[#Projects|Project Progress Updates]]
|-
|9:45-10:30
|bgcolor="#c1c2ec"|3D Slicer Update (Steve Pieper)
|-
|10:30-11:00
|OpenIGTLink Update (Junichi Tokuda)
|-
|11:00-12:00
|bgcolor="#c1c2ec"|Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
|-
|12:00-1:00
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes
|-
|12:45-1:00
|
|
|bgcolor="#ccffcc"|[[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
|
|
|-
|1:00-1:30
|rowspan="5"|<font color="#0000cc">Ron Kikinis: Welcome<br> </font> (5 minutes)<br>_____________________<br> Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
|rowspan="4"|'''Breakout Session:''' QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
|rowspan="4"|'''Breakout Session:''' [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
|rowspan="2"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
|bgcolor="#f0e68b"|Adjourn by 1:30pm
|-
|1:30-2:00
|rowspan="9"|
|-
|2:00-2:30
|bgcolor="#ccffcc"|Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
|-
|2:30-3:00
|rowspan="6"|
|-
|3:00-3:30
|rowspan="2" style="background: #ccffcc;"|[[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
|rowspan="5"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br>_____________________<br>'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widget]] (Nicole, Kilian, JC)
|-
|3:30-4:00
|rowspan="4" style="background: #ccffcc;"|Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
|-
|4:00-4:30
|rowspan="3"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session: Data Management|Data Management]] (Dan Marcus, Stephen Aylward)
|-
|4:30-5:00
|-
|5:00-5:30
|-
|5:30
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|}

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

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

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

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

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

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

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

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#Prostate Intervention(Junichi, Sam Song, Tamas Ungi)
# Liver Ablation (Haiying Liu)
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnota, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

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

==Attendee List==

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

# Anderson Peter , GE Navigation (Retired)
# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Bowers Michael , Johns Hopkins University
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Ding Liya , The Ohio State University
# Eckbo Ryan , BWH
# Ersoy Ilker , University of Missouri Columbia
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Fritscher Karl , UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# Gorgolewski Chris , SPL
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Grama Kedar , Rensselaer Polytechnic Institute
# Haehn Daniel , University of Pennsylvania
# Hafiane Adel , ENSI-Bourges
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Halle Michael , BWH/SPL
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Jagadeesan Jayender , SPL
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Lee Joohwi , UNC Chapel Hill
# Li Rui , MGH
# Lienhard Stefan , LMI
# Lisle Curtis , KnowledgeVis, LLC
# Liu Felix , Beth Israel Deaconess Medical Center
# Liu Yanling , SAIC-Frederick, Inc.
# Liu Haiying , Brigham and Women's Hospital
# Lowekamp Bradley , Lockheed Martin
# machiraju raghu , The Ohio State University
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Marks William , Focused Ultrasound Lab, BWH, HMS
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Olson Beck , UCSF
# Onofrey John , Yale University
# Padmanabhan Raghav , RPI
# Palaniappan Kannappan , university of Missouri
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Patel Pratik , Brainlab Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# PECOT Thierry , Ohio State University
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Singh Shantanu , The Ohio State University
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , BWH
# Tao Xiaodong , GE Research
# Tokuda Junichi , Brigham and Women's Hospital
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Weinrich Adam , Nokia
# Wells Sandy , BWH
# White Phillip , BWH/HMS
# Wu Guorong , University of North Carolina at Chapel Hill
# Yamada Atsushi , Nagoya Institute of Technology
# Yarmarkovich Alexander , ISOMICS
# Zaitsev Alexander , Brigham and Womens Hospital

2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:49:14Z

Fritschk: moved 2010 Summer Project Week FractureClassification Brainstorming to 2010 Summer Project Week Fracture Classification Brainstorming

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry (Image provided by Peter Karasev)

</gallery>

==Key Investigators==
* UMIT: Karl Fritscher
* BWH: Ron Kikinis
* Georgia Tech: Peter Karasev
* University of Iowa: Vince Magnotta
* Isomics: Curt Lisle

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

<h3>Objective</h3>

Fracture classification is of essential importance

* as a treatment guide
* to assist with prognosis
* to speak a common language with others in order to compare results

Unfortunately the interobserver variability concerning the classification of different fractures is rather high [1]. Consequently (semi)-automatic methods to classify fractures according to established fracture classification systems, could be a helpful aid for an objective and consistent classification of fractures.

</div>

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

<h3>Approach, Plan</h3>

During the project week a first brainstorming session about potential appraoches for (automatic) fracture classification based on geometric surface properties [2] will be discussed.

</div>

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

<h3>Progress</h3>
This project is still in its planning phase!

</div>
</div>

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

==References==
[1] NO Thomsen, S Overgaard, LH Olsen, H Hansen, and ST Nielsen, Observer variation in the radiographic classification of ankle fractures, Journal of Bone and Joint Surgery - British Volume, Vol 73-B, Issue 4, 676-678

[2] P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.

</div>

2010 Summer Project Week FractureClassification Brainstorming

2010-06-16T18:49:14Z

Fritschk: moved 2010 Summer Project Week FractureClassification Brainstorming to 2010 Summer Project Week Fracture Classification Brainstorming

#REDIRECT [[2010 Summer Project Week Fracture Classification Brainstorming]]

Talk:2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:49:14Z

Fritschk: moved Talk:2010 Summer Project Week FractureClassification Brainstorming to Talk:2010 Summer Project Week Fracture Classification Brainstorming

'''Welcome to ''NAMIC''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Kikinis|Ron]] 12:25, 14 June 2010 (UTC)

Talk:2010 Summer Project Week FractureClassification Brainstorming

2010-06-16T18:49:14Z

Fritschk: moved Talk:2010 Summer Project Week FractureClassification Brainstorming to Talk:2010 Summer Project Week Fracture Classification Brainstorming

#REDIRECT [[Talk:2010 Summer Project Week Fracture Classification Brainstorming]]

2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:48:44Z

Fritschk:

2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:47:26Z

Fritschk:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry (Image provided by Peter Karasev)

</gallery>

==Key Investigators==
* UMIT: Karl Fritscher
* SPL: Ron Kikinis
* Georgia Tech: Peter Karasev
* University of Iowa: Vince Magnotta
* Isomics: Curt Lisle

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

<h3>Objective</h3>

Fracture classification is of essential importance

* as a treatment guide
* to assist with prognosis
* to speak a common language with others in order to compare results

Unfortunately the interobserver variability concerning the classification of different fractures is rather high [1]. Consequently (semi)-automatic methods to classify fractures according to established fracture classification systems, could be a helpful aid for an objective and consistent classification of fractures.

</div>

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

<h3>Approach, Plan</h3>

During the project week a first brainstorming session about potential appraoches for (automatic) fracture classification based on geometric surface properties [2] will be discussed.

</div>

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

<h3>Progress</h3>
This project is still in its planning phase!

</div>
</div>

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

==References==
[1] NO Thomsen, S Overgaard, LH Olsen, H Hansen, and ST Nielsen, Observer variation in the radiographic classification of ankle fractures, Journal of Bone and Joint Surgery - British Volume, Vol 73-B, Issue 4, 676-678

[2] P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.

</div>

2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:46:58Z

Fritschk:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry (Image provided by Peter Karasev)

</gallery>

==Key Investigators==
* UMIT: Karl Fritscher
* Georgia Tech: Peter Karasev
* SPL: Ron Kikinis
* University of Iowa: Vince Magnotta
* Isomics: Curt Lisle

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

<h3>Objective</h3>

Fracture classification is of essential importance

* as a treatment guide
* to assist with prognosis
* to speak a common language with others in order to compare results

Unfortunately the interobserver variability concerning the classification of different fractures is rather high [1]. Consequently (semi)-automatic methods to classify fractures according to established fracture classification systems, could be a helpful aid for an objective and consistent classification of fractures.

</div>

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

<h3>Approach, Plan</h3>

During the project week a first brainstorming session about potential appraoches for (automatic) fracture classification based on geometric surface properties [2] will be discussed.

</div>

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

<h3>Progress</h3>
This project is still in its planning phase!

</div>
</div>

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

==References==
[1] NO Thomsen, S Overgaard, LH Olsen, H Hansen, and ST Nielsen, Observer variation in the radiographic classification of ankle fractures, Journal of Bone and Joint Surgery - British Volume, Vol 73-B, Issue 4, 676-678

[2] P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.

</div>

2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:45:34Z

Fritschk:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry (Image provided by Peter Karasev)

</gallery>

==Key Investigators==
* UMIT: Karl Fritscher
* Georgia Tech: Peter Karasev
* SPL: Ron Kikinis
* Vince Magnotta
* Curt Lisle

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

<h3>Objective</h3>

Fracture classification is of essential importance

* as a treatment guide
* to assist with prognosis
* to speak a common language with others in order to compare results

Unfortunately the interobserver variability concerning the classification of different fractures is rather high [1]. Consequently (semi)-automatic methods to classify fractures according to established fracture classification systems, could be a helpful aid for an objective and consistent classification of fractures.

</div>

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

<h3>Approach, Plan</h3>

During the project week a first brainstorming session about potential appraoches for (automatic) fracture classification based on geometric surface properties [2] will be discussed.

</div>

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

<h3>Progress</h3>
This project is still in its planning phase!

</div>
</div>

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

==References==
[1] NO Thomsen, S Overgaard, LH Olsen, H Hansen, and ST Nielsen, Observer variation in the radiographic classification of ankle fractures, Journal of Bone and Joint Surgery - British Volume, Vol 73-B, Issue 4, 676-678

[2] P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.

</div>

2010 Summer Project Week

2010-06-16T18:44:16Z

Fritschk: /* Analysis */

__NOTOC__

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

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

==Background==

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

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

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

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

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

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

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

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

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="200px"|Monday, June 21
!width="200px"|Tuesday, June 22
!width="200px"|Wednesday, June 23
!width="200px"|Thursday, June 24
!width="200px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|8:30
|rowspan="5"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|9:00-9:45
|NA-MIC Kit Update (Jim Miller) - include: Module nomenclature (Extensions: cmdline vs loadable, Built-in)<br>_____________________<br> QT - include: Superbuild demo by Dave P.
|rowspan="4"|'''Breakout Session:''' [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
|rowspan="4"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
|rowspan="4"|[[#Projects|Project Progress Updates]]
|-
|9:45-10:30
|bgcolor="#c1c2ec"|3D Slicer Update (Steve Pieper)
|-
|10:30-11:00
|OpenIGTLink Update (Junichi Tokuda)
|-
|11:00-12:00
|bgcolor="#c1c2ec"|Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
|-
|12:00-1:00
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes
|-
|12:45-1:00
|
|
|bgcolor="#ccffcc"|[[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
|
|
|-
|1:00-1:30
|rowspan="5"|<font color="#0000cc">Ron Kikinis: Welcome<br> </font> (5 minutes)<br>_____________________<br> Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
|rowspan="4"|'''Breakout Session:''' QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
|rowspan="4"|'''Breakout Session:''' [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
|rowspan="2"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
|bgcolor="#f0e68b"|Adjourn by 1:30pm
|-
|1:30-2:00
|rowspan="9"|
|-
|2:00-2:30
|bgcolor="#ccffcc"|Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
|-
|2:30-3:00
|rowspan="6"|
|-
|3:00-3:30
|rowspan="2" style="background: #ccffcc;"|[[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
|rowspan="5"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br>_____________________<br>'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widget]] (Nicole, Kilian, JC)
|-
|3:30-4:00
|rowspan="4" style="background: #ccffcc;"|Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
|-
|4:00-4:30
|rowspan="3"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session: Data Management|Data Management]] (Dan Marcus, Stephen Aylward)
|-
|4:30-5:00
|-
|5:00-5:30
|-
|5:30
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|}

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

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

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

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

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

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

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

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#Prostate Intervention(Junichi, Sam Song, Tamas Ungi)
# Liver Ablation (Haiying Liu)
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]]Superbuild (David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

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

==Attendee List==

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

# Anderson Peter , GE Navigation (Retired)
# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Bowers Michael , Johns Hopkins University
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Ding Liya , The Ohio State University
# Eckbo Ryan , BWH
# Ersoy Ilker , University of Missouri Columbia
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Fritscher Karl , UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# Gorgolewski Chris , SPL
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Grama Kedar , Rensselaer Polytechnic Institute
# Haehn Daniel , University of Pennsylvania
# Hafiane Adel , ENSI-Bourges
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Halle Michael , BWH/SPL
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Jagadeesan Jayender , SPL
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Lee Joohwi , UNC Chapel Hill
# Li Rui , MGH
# Lienhard Stefan , LMI
# Lisle Curtis , KnowledgeVis, LLC
# Liu Felix , Beth Israel Deaconess Medical Center
# Liu Yanling , SAIC-Frederick, Inc.
# Liu Haiying , Brigham and Women's Hospital
# Lowekamp Bradley , Lockheed Martin
# machiraju raghu , The Ohio State University
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Marks William , Focused Ultrasound Lab, BWH, HMS
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Olson Beck , UCSF
# Onofrey John , Yale University
# Padmanabhan Raghav , RPI
# Palaniappan Kannappan , university of Missouri
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Patel Pratik , Brainlab Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# PECOT Thierry , Ohio State University
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Singh Shantanu , The Ohio State University
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , BWH
# Tao Xiaodong , GE Research
# Tokuda Junichi , Brigham and Women's Hospital
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Weinrich Adam , Nokia
# Wells Sandy , BWH
# White Phillip , BWH/HMS
# Wu Guorong , University of North Carolina at Chapel Hill
# Yamada Atsushi , Nagoya Institute of Technology
# Yarmarkovich Alexander , ISOMICS
# Zaitsev Alexander , Brigham and Womens Hospital

Talk:2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:43:09Z

Fritschk: moved Talk:FractureClassification-Brainstorming to Talk:2010 Summer Project Week FractureClassification Brainstorming

Talk:FractureClassification-Brainstorming

2010-06-16T18:43:09Z

Fritschk: moved Talk:FractureClassification-Brainstorming to Talk:2010 Summer Project Week FractureClassification Brainstorming

#REDIRECT [[Talk:2010 Summer Project Week FractureClassification Brainstorming]]

2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:43:08Z

Fritschk: moved FractureClassification-Brainstorming to 2010 Summer Project Week FractureClassification Brainstorming

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry (Image provided by Peter Karasev)

</gallery>

==Key Investigators==
* UMIT: Karl Fritscher
* Georgia Tech: Peter Karasev
* SPL: Ron Kikinis

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

<h3>Objective</h3>

Fracture classification is of essential importance

* as a treatment guide
* to assist with prognosis
* to speak a common language with others in order to compare results

Unfortunately the interobserver variability concerning the classification of different fractures is rather high [1]. Consequently (semi)-automatic methods to classify fractures according to established fracture classification systems, could be a helpful aid for an objective and consistent classification of fractures.

</div>

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

<h3>Approach, Plan</h3>

During the project week a first brainstorming session about potential appraoches for (automatic) fracture classification based on geometric surface properties [2] will be discussed.

</div>

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

<h3>Progress</h3>
This project is still in its planning phase!

</div>
</div>

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

==References==
[1] NO Thomsen, S Overgaard, LH Olsen, H Hansen, and ST Nielsen, Observer variation in the radiographic classification of ankle fractures, Journal of Bone and Joint Surgery - British Volume, Vol 73-B, Issue 4, 676-678

[2] P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.

</div>

FractureClassification-Brainstorming

2010-06-16T18:43:08Z

Fritschk: moved FractureClassification-Brainstorming to 2010 Summer Project Week FractureClassification Brainstorming

#REDIRECT [[2010 Summer Project Week FractureClassification Brainstorming]]

2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:41:06Z

Fritschk: moved User:Fritschk to FractureClassification-Brainstorming

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry (Image provided by Peter Karasev)

</gallery>

==Key Investigators==
* UMIT: Karl Fritscher
* Georgia Tech: Peter Karasev
* SPL: Ron Kikinis

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

<h3>Objective</h3>

Fracture classification is of essential importance

* as a treatment guide
* to assist with prognosis
* to speak a common language with others in order to compare results

Unfortunately the interobserver variability concerning the classification of different fractures is rather high [1]. Consequently (semi)-automatic methods to classify fractures according to established fracture classification systems, could be a helpful aid for an objective and consistent classification of fractures.

</div>

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

<h3>Approach, Plan</h3>

During the project week a first brainstorming session about potential appraoches for (automatic) fracture classification based on geometric surface properties [2] will be discussed.

</div>

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

<h3>Progress</h3>
This project is still in its planning phase!

</div>
</div>

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

==References==
[1] NO Thomsen, S Overgaard, LH Olsen, H Hansen, and ST Nielsen, Observer variation in the radiographic classification of ankle fractures, Journal of Bone and Joint Surgery - British Volume, Vol 73-B, Issue 4, 676-678

[2] P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.

</div>

User:Fritschk

2010-06-16T18:41:06Z

Fritschk: moved User:Fritschk to FractureClassification-Brainstorming

#REDIRECT [[FractureClassification-Brainstorming]]

Talk:2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:41:06Z

Fritschk: moved User talk:Fritschk to Talk:FractureClassification-Brainstorming

User talk:Fritschk

2010-06-16T18:41:06Z

Fritschk: moved User talk:Fritschk to Talk:FractureClassification-Brainstorming

#REDIRECT [[Talk:FractureClassification-Brainstorming]]

2010 Summer Project Week Fracture Classification Brainstorming

2010-06-16T18:40:38Z

Fritschk: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry (Image provided by…'

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry (Image provided by Peter Karasev)

</gallery>

==Key Investigators==
* UMIT: Karl Fritscher
* Georgia Tech: Peter Karasev
* SPL: Ron Kikinis

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

<h3>Objective</h3>

Fracture classification is of essential importance

* as a treatment guide
* to assist with prognosis
* to speak a common language with others in order to compare results

Unfortunately the interobserver variability concerning the classification of different fractures is rather high [1]. Consequently (semi)-automatic methods to classify fractures according to established fracture classification systems, could be a helpful aid for an objective and consistent classification of fractures.

</div>

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

<h3>Approach, Plan</h3>

During the project week a first brainstorming session about potential appraoches for (automatic) fracture classification based on geometric surface properties [2] will be discussed.

</div>

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

<h3>Progress</h3>
This project is still in its planning phase!

</div>
</div>

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

==References==
[1] NO Thomsen, S Overgaard, LH Olsen, H Hansen, and ST Nielsen, Observer variation in the radiographic classification of ankle fractures, Journal of Bone and Joint Surgery - British Volume, Vol 73-B, Issue 4, 676-678

[2] P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.

</div>