NAMIC Wiki - User contributions [en]

2013 Summer Project Week

2013-06-21T13:52:51Z

Nathanielareynolds: /* Additional Collaborations */

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

<gallery widths="800px" heights="300px" perrow="1" caption="Lunch in the Amphitheater at Stata, June 20 2013">
Image:Lunch at Project week IMG 0367.JPG|Shade was a popular commodity
</gallery>

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]] (Steve Pieper) <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 Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|
'''9:30-10:30am''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|[http://www.na-mic.org/Wiki/index.php/File:NamicToAmphi.png Lunch in Outdoor Amphitheather!]
|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|32-262]]
|
|<br>----------------------------------------<br>'''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.

==Some Stats==
73 Projects, 104 Attendees. First time attendees 25.

===Huntington's Disease===
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Josh, Hans, Ross)


7 projects

===Traumatic Brain Injury===
* [[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)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)


5 projects

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)


8 projects

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Creating DICOM series from ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Karl Fritscher, Christian Wachinger, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, Alireza Mehrtash)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab - without building Slicer or Matlab MEX files]] (Andras Lasso, Jc)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim)


8 projects

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Ultrasound_Needle_Detection| Ultrasound Needle Detection]] (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:ProstateBRP| MRI-guided robotic prostate interventinos]] (Junichi Tokuda, Greg Fischer, Nirav Patel, Nobuhiko Hata, Clare Tempnay)


12 projects

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)


3 projects

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:VicomTech| VicomTech visit: Imaging solutions and Slicer use]] (Ivan Macia)
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: 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:CMFReg | Cranio-Maxillofacial Registration]] (Francois Budin, Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Nathaniel Reynolds, Lilla Zollei, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar)
* [[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:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Kayhan Batmanghelich, Polina Golland)
* [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)
* [[2013_Summer_Project_Week:Documentation for Slicer 4.2 Data Loading and 3D Visualization|Documentation for Slicer 4.2 Data Loading and 3D Visualization]] (Parth Amin WIT, Matt Flynn WIT, Dr. Pujol HMS)
* [[2013_Summer_Project_Week:WM Geometry Tools|Integration in Slicer of white matter geometry tools]] (Peter Savadjiev, Carl-Fredrik Westin)


16 projects

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[ITK -VTK wrapper]] (Paolo Zaffino, Greg Sharp, Steve Pieper)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Dave Welch, Brad Lowekamp, Hans Johnson, Steve)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter (time) Hierarchy]] (Adam Rankin)
* [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Jim,Brad Lowekamp, Jc)
* [[2013_Summer_Project_Week:Python_Embedding| Python Embedding Library]] (Rui, Jim, Jc, Steve)

14 projects

== '''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_Project_Week_Rooms| Stata Center / RLE 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.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#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
#Kayhan Batmanghelich, MIT, kayhan@csail.mit.edu
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Taylor Braun-Jones, GE Healthcare, taylor.braun-jones@ge.com
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Alexandra Golby, BWH, agolby@partners.org
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Dan Groszmann, GE Healthcare, daniel.groszmann@ge.com
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Sylvain Jaume, WIT, jaumes@wit.edu
#Daniel Jimenez, daniel.jimenez@gmail.com
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#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
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#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
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#William Plishker, IGI Technologies, will@igitechnologies.com
#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
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Tobias Schroeder, GE Healthcare, tobias.schroeder@ge.com
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-21T13:51:20Z

Nathanielareynolds: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Nathaniel Reynolds, Randy Gollub, Lilla Zollei (MGH)
* Rudolph Pienaar, Ellen Grant, Daniel Haehn, Nicolas Rannou (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
Right now, the multiple volumes of the training data get loaded one-by-one on demand. We want to load either everything at the beginning (maybe from a 4D dataset or separate 3D ones) or leverage webworkers to load the rest odf the data in the background while the user interacts with the page.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
We leveraged Web Workers and the new developments of the [https://github.com/xtk/XIO XIO] to download multiple MRI datasets in parallel and not interfere with operation of the main thread. An example can be found here: http://sandbox.goxtk.com/xio/ Our next move is to incorporate these developments into our [http://fnndsc.github.com/babybrain Pedi-Brain Atlas Learning Prototype].

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-21T13:41:08Z

Nathanielareynolds: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Rudolph Pienaar, Ellen Grant, Daniel Haehn, Nicolas Rannou (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
Right now, the multiple volumes of the training data get loaded one-by-one on demand. We want to load either everything at the beginning (maybe from a 4D dataset or separate 3D ones) or leverage webworkers to load the rest odf the data in the background while the user interacts with the page.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
We leveraged Web Workers and the new developments of the [https://github.com/xtk/XIO XIO] to download multiple MRI datasets in parallel and not interfere with operation of the main thread. An example can be found here: http://sandbox.goxtk.com/xio/ Our next move is to incorporate these developments into our [http://fnndsc.github.com/babybrain Pedi-Brain Atlas Learning Prototype].

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-21T13:40:09Z

Nathanielareynolds: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Rudolph Pienaar, Ellen Grant, Daniel Haehn, Nicolas Rannou (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
Right now, the multiple volumes of the training data get loaded one-by-one on demand. We want to load either everything at the beginning (maybe from a 4D dataset or separate 3D ones) or leverage webworkers to load the rest odf the data in the background while the user interacts with the page.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* A prototype was created: http://fnndsc.github.com/babybrain
* We leveraged Web Workers and the new developments of the [https://github.com/xtk/XIO XIO] to download multiple MRI datasets in parallel and not interfere with operation of the main thread. An example can be found here: http://sandbox.goxtk.com/xio/ Our next move is to incorporate these developments into our Pedi-Brain Atlas Learning Prototype.

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-21T13:39:10Z

Nathanielareynolds: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Rudolph Pienaar, Ellen Grant, Daniel Haehn, Nicolas Rannou (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
Right now, the multiple volumes of the training data get loaded one-by-one on demand. We want to load either everything at the beginning (maybe from a 4D dataset or separate 3D ones) or leverage webworkers to load the rest odf the data in the background while the user interacts with the page.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* A prototype was created: http://fnndsc.github.com/babybrain
* We leveraged Web Workers and the new developments of the XIO to download multiple MRI datasets in parallel and not interfere with operation of the main thread. An example can be found here: http://sandbox.goxtk.com/xio/ Our next move is to incorporate these developments into our Pedi-Brain Atlas Learning Prototype.

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-17T16:03:13Z

Nathanielareynolds:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Rudolph Pienaar, Ellen Grant, Daniel Haehn, Nicolas Rannou (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
Right now, the multiple volumes of the training data get loaded one-by-one on demand. We want to load either everything at the beginning (maybe from a 4D dataset or separate 3D ones) or leverage webworkers to load the rest odf the data in the background while the user interacts with the page.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* A prototype was created: http://fnndsc.github.com/babybrain

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-11T19:21:21Z

Nathanielareynolds:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* ...
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* ...

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

File:PediBrainAtlas.jpg

2013-06-11T19:20:35Z

Nathanielareynolds: screen shot of PediBrainAtlas Learning Tool

screen shot of PediBrainAtlas Learning Tool

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-11T19:00:56Z

Nathanielareynolds:

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-11T18:58:25Z

Nathanielareynolds:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:Mi2b2_1.png|Screenshot of the prototype
Image:Mi2b2_2.png|Screenshot of the prototype
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* Enable switching between different testing scenarios (fetal brains, liver etc.)
* Start with the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications Liver tutorial dataset and slides] from the NA-MIC training core which includes a limited number of questions and answers
* Load a visual scene linked to a question catalog from a defined file format (XML?)
* The visualization and the questions are linked so answers can be provided in a fully interactive fashion (picking of a 3D mesh.. etc.)
* Track user-specified answers and provide statistics after testing mode
* Use 3D Slicer to generate content for training and testing
* Prototype will be built on top of existing visualization infrastructure ([http://goXTK.com XTK] and [http://fetalmri.org web-based fetal atlas tool])
* We envision a system somewhat like existing online quiz systems ([http://www.surveymonkey.com], [http://www.classmarker.com/], [http://dontshake.org/lms/lms_information/lms_quiz.php], [http://www.proprofs.com/quiz-school/]) but with interactive 3D content drawn from the clinical use cases.
* May use a helper library like [https://github.com/jewlofthelotus/SlickQuiz SlickQuiz] [http://www.jewlofthelotus.com/2011/12/23/slickquiz-jquery-plugin-now-on-github/comment-page-1/]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* User interface mockups are being prepared
* Development repository: https://github.com/FNNDSC/mi2b2_aim3
* Problems/ToDo:
** <strike>Update WebGLExport module to new XTK version</strike>
** <strike>Fix XTK with Liver CT volume (right now scalar range messes things up) or convert (normalize) the volume</strike>
* First working prototype is online!
** http://fnndsc.github.com/mi2b2_aim3/

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* Hand-coded (html, javascript) mockups using to create content from existing content
** Liver tutorial from Sonia
** Fetal brain atlas
* Identify best practices and experiment with different Question and Answer modes
* Identify best practices and experiment with user interaction
* Getting feedback on mi2b2 team and refining the mockups

=== Phase II: Limited Beta ===
During second half of 2013:
* Identify first set of training content suitable for wider trial
* Set up a site to host training materials
** Set up back end system to record test results?
** Review [http://en.wikipedia.org/wiki/Redcap_(Research_Electronic_Data_Capture) RedCap] as a back end ([http://www.project-redcap.org/ home page], [https://redcap.vanderbilt.edu/surveys/index.php?hash=40008b9a5380fcacce3976bf7c08af5b example survey)]
** Consider tie-in to RSNA Audience Response Tool
* Open site to radiology trainees and gather feedback
* Integrate infant brain atlas data as it becomes available

=== Phase III: Authoring Tools ===
During 2014:
* Develop system for clinician-educators to easily create content
** Define images, models, annotations, atlases to display
** Define didactic material
** Export content to hosting site
* Leverage tools like Scene Views and WebGL Export from Slicer

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-11T18:55:25Z

Nathanielareynolds:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:Mi2b2_1.png|Screenshot of the prototype
Image:Mi2b2_2.png|Screenshot of the prototype
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [[https://github.com/xtk/X#readme|XTK]] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* Enable switching between different testing scenarios (fetal brains, liver etc.)
* Start with the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications Liver tutorial dataset and slides] from the NA-MIC training core which includes a limited number of questions and answers
* Load a visual scene linked to a question catalog from a defined file format (XML?)
* The visualization and the questions are linked so answers can be provided in a fully interactive fashion (picking of a 3D mesh.. etc.)
* Track user-specified answers and provide statistics after testing mode
* Use 3D Slicer to generate content for training and testing
* Prototype will be built on top of existing visualization infrastructure ([http://goXTK.com XTK] and [http://fetalmri.org web-based fetal atlas tool])
* We envision a system somewhat like existing online quiz systems ([http://www.surveymonkey.com], [http://www.classmarker.com/], [http://dontshake.org/lms/lms_information/lms_quiz.php], [http://www.proprofs.com/quiz-school/]) but with interactive 3D content drawn from the clinical use cases.
* May use a helper library like [https://github.com/jewlofthelotus/SlickQuiz SlickQuiz] [http://www.jewlofthelotus.com/2011/12/23/slickquiz-jquery-plugin-now-on-github/comment-page-1/]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* User interface mockups are being prepared
* Development repository: https://github.com/FNNDSC/mi2b2_aim3
* Problems/ToDo:
** <strike>Update WebGLExport module to new XTK version</strike>
** <strike>Fix XTK with Liver CT volume (right now scalar range messes things up) or convert (normalize) the volume</strike>
* First working prototype is online!
** http://fnndsc.github.com/mi2b2_aim3/

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* Hand-coded (html, javascript) mockups using to create content from existing content
** Liver tutorial from Sonia
** Fetal brain atlas
* Identify best practices and experiment with different Question and Answer modes
* Identify best practices and experiment with user interaction
* Getting feedback on mi2b2 team and refining the mockups

=== Phase II: Limited Beta ===
During second half of 2013:
* Identify first set of training content suitable for wider trial
* Set up a site to host training materials
** Set up back end system to record test results?
** Review [http://en.wikipedia.org/wiki/Redcap_(Research_Electronic_Data_Capture) RedCap] as a back end ([http://www.project-redcap.org/ home page], [https://redcap.vanderbilt.edu/surveys/index.php?hash=40008b9a5380fcacce3976bf7c08af5b example survey)]
** Consider tie-in to RSNA Audience Response Tool
* Open site to radiology trainees and gather feedback
* Integrate infant brain atlas data as it becomes available

=== Phase III: Authoring Tools ===
During 2014:
* Develop system for clinician-educators to easily create content
** Define images, models, annotations, atlases to display
** Define didactic material
** Export content to hosting site
* Leverage tools like Scene Views and WebGL Export from Slicer

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-11T18:42:56Z

Nathanielareynolds: Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List Image:Mi2b2_1.png|Screenshot of the prototype Image:Mi2b2_2.png|Screenshot of the pro…'

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:Mi2b2_1.png|Screenshot of the prototype
Image:Mi2b2_2.png|Screenshot of the prototype
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. The goal of this project is to create a prototype application for this purpose which can be easily extended to other testing scenarios.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* Enable switching between different testing scenarios (fetal brains, liver etc.)
* Start with the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications Liver tutorial dataset and slides] from the NA-MIC training core which includes a limited number of questions and answers
* Load a visual scene linked to a question catalog from a defined file format (XML?)
* The visualization and the questions are linked so answers can be provided in a fully interactive fashion (picking of a 3D mesh.. etc.)
* Track user-specified answers and provide statistics after testing mode
* Use 3D Slicer to generate content for training and testing
* Prototype will be built on top of existing visualization infrastructure ([http://goXTK.com XTK] and [http://fetalmri.org web-based fetal atlas tool])
* We envision a system somewhat like existing online quiz systems ([http://www.surveymonkey.com], [http://www.classmarker.com/], [http://dontshake.org/lms/lms_information/lms_quiz.php], [http://www.proprofs.com/quiz-school/]) but with interactive 3D content drawn from the clinical use cases.
* May use a helper library like [https://github.com/jewlofthelotus/SlickQuiz SlickQuiz] [http://www.jewlofthelotus.com/2011/12/23/slickquiz-jquery-plugin-now-on-github/comment-page-1/]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* User interface mockups are being prepared
* Development repository: https://github.com/FNNDSC/mi2b2_aim3
* Problems/ToDo:
** <strike>Update WebGLExport module to new XTK version</strike>
** <strike>Fix XTK with Liver CT volume (right now scalar range messes things up) or convert (normalize) the volume</strike>
* First working prototype is online!
** http://fnndsc.github.com/mi2b2_aim3/

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* Hand-coded (html, javascript) mockups using to create content from existing content
** Liver tutorial from Sonia
** Fetal brain atlas
* Identify best practices and experiment with different Question and Answer modes
* Identify best practices and experiment with user interaction
* Getting feedback on mi2b2 team and refining the mockups

=== Phase II: Limited Beta ===
During second half of 2013:
* Identify first set of training content suitable for wider trial
* Set up a site to host training materials
** Set up back end system to record test results?
** Review [http://en.wikipedia.org/wiki/Redcap_(Research_Electronic_Data_Capture) RedCap] as a back end ([http://www.project-redcap.org/ home page], [https://redcap.vanderbilt.edu/surveys/index.php?hash=40008b9a5380fcacce3976bf7c08af5b example survey)]
** Consider tie-in to RSNA Audience Response Tool
* Open site to radiology trainees and gather feedback
* Integrate infant brain atlas data as it becomes available

=== Phase III: Authoring Tools ===
During 2014:
* Develop system for clinician-educators to easily create content
** Define images, models, annotations, atlases to display
** Define didactic material
** Export content to hosting site
* Leverage tools like Scene Views and WebGL Export from Slicer

2013 Summer Project Week

2013-06-11T18:41:13Z

Nathanielareynolds: /* Infrastructure */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

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

== '''Projects''' ==

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

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

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

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

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

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

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

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

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

==='''Brain Segmentation'''===
* [[2013_Summer_Project_Week:Multi_Atlas_Based_Multi_Image_Segmentation | Multi-Atlas-Based Multi-Image Segmentation for Brain MR Images]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

== '''Background''' ==

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

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

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

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

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

== '''Registrants''' ==

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

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

2013 Summer Project Week

2013-06-11T18:40:04Z

Nathanielareynolds: /* Infrastructure */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

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

== '''Projects''' ==

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

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

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

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

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

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

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

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

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

==='''Brain Segmentation'''===
* [[2013_Summer_Project_Week:Multi_Atlas_Based_Multi_Image_Segmentation | Multi-Atlas-Based Multi-Image Segmentation for Brain MR Images]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

== '''Background''' ==

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

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

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

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

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

== '''Registrants''' ==

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

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