NAMIC Wiki - User contributions [en]

2013 Summer Project Week:XNAT 3D Viewer

2013-06-14T14:08:27Z

DanMarcus: /* Key Investigators */

==Key Investigators==
*Washington University : Amanda Hartung, Dan Marcus (in absentia)
*Brigham and Women's Hospital/Harvard Medical School: Steve Pieper, Daniel Haehn

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

<h3>Objective</h3>

Develop a web-based viewer for XNAT that can display 3D information from:
<ul>
<li>Slicer scenes</li>
<li>Freesurfer meshes</li>
</ul>
with functionality similar to that of Connectome Workbench.

</div>

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

<h3>Approach, Plan</h3>
<ul>
<li>Using XTK, be able to load and view a variety of file formats.</li>
<li>Integrate into existing 2D XNAT image viewer.</li>
</ul>

2013 Summer Project Week:XNAT 3D Viewer

2013-06-14T13:59:42Z

DanMarcus: /* Key Investigators */

==Key Investigators==
*Washington University : Amanda Hartung, Dan Marcus (in absentia)
*Brigham and Women's Hospital/Harvard Medical School: Steve Pieper, Daniel Haehn

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

<h3>Objective</h3>

Develop a web-based viewer for XNAT that can display 3D information from:
<ul>
<li>Slicer scenes</li>
<li>Freesurfer meshes</li>
</ul>

with functionality similar to that of Connectome Workbench.

</div>

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

<h3>Approach, Plan</h3>

2013 Summer Project Week:XNAT 3D Viewer

2013-06-13T18:37:23Z

DanMarcus: Created page with '==Key Investigators== *Washington University : Amanda Hartung, Dan Marcus (in absentia) *Brigham and Women's Hospital/Harvard Medical School: Steve Pieper, Daniel Haehn <div sty…'

2013 Summer Project Week

2013-06-13T18:36:04Z

DanMarcus: /* Informatics */

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]]
|<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.

===Huntington's Disease===
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Kent Williams)
* [[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)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Hans, Ross)

===Traumatic Brain Injury===
* [[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)
* [[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)
* [[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)

===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, Isaiah Norton, 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)
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering]] (Lauren O'Donnell)

=== '''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)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)

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

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

===""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)

== '''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.])

#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
#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
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.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
#Adrian Dalca, MIT, adalca@MIT.EDU
#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
#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
#Michael Halle, BWH-SPL, mhalle@bwh.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
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#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
#Xu Li, BWH, lixu0103@gmail.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
#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
#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
#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
#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
#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

2012 Summer Project Week

2012-05-03T19:28:50Z

DanMarcus: /* Infrastructure */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[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)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
#

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

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
#
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
#iGyne for Gyne Brachytherapy (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)

==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

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

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

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Summer Project Week

2012-05-03T19:18:42Z

DanMarcus: /* Infrastructure */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[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)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
#

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

#
#

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
#
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
#
#
==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

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

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

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Progress Report Science Wiki Version Engineering

2012-04-20T20:44:37Z

DanMarcus: /* 5.2.3. Data Management Platform */

= 5.2. Engineering =
<em>Key Investigators </em>
* Will Schroeder, Kitware
* Stephen R. Aylward, Kitware
* Steve Pieper, Isomics
* Jim Miller, GE Research

The Engineering component of the Computer Science Core (Core 1b) has been focusing on the
infrastructure needed for the Algorithms component to implement their methods, and has been
working closely with them so that the functionality we provide can serve to inspire new methods
as well. Herein we provide more details regarding our accomplishments in those directions

== 5.2.1. End-user Platform: 3D Slicer ==
<em>Steve Pieper</em>
=== Release of 3D Slicer version 4.0 and 4.1 ===
As shown in Figure 1, 3D Slicer version 4.0 (commonly called Slicer4) is having an immediate world-wide impact. Version 4.0, released at the Radiology Society of North America (RSNA) meeting in late November 2011, is the result of a major effort by the NA-MIC engineering cores, in collaboration with the wider Slicer community, to re-implement and streamline the software in response to feedback from NA-MIC DBPs and algorithm developers. A new 3D Slicer version 4.1 release, being finalized at the time of this writing, adds back many of the advanced features of Slicer3, notably the Extension system by which new functionality can be downloaded and installed independent of the main executable. As described more fully below, these sweeping changes required touching not only most of the code in Slicer, but also feeding important feature and bug fix changes back into the rest of the NA-MIC Kit and upstream libraries. As a result of these efforts, 3D Slicer in now an improved reference implementation of a modern medical image computing package and a strong foundation for research.

[[image:2012_Engineering_EndUserPlatform_Fig1.png]]

<em>Figure 1: 3D Slicer version 4.0 end-user downloads during the first 3 months of 2012, a rate of 45,360 per year (over 100 downloads per day). Interactive geolocated download statistics are available at http://download.slicer.org/stats.</em>

===Major Developments and New Functionality in Slicer4===
* ''Modern Cross-Platform Design Patterns:'' As a by-product of the port of the user interface from KWWidgets to Qt, a comprehensive suite of non-GUI OS abstractions and utility functions from Qt became available to support core application functions such as preference settings, multi-processing, application resource data. This was a direct benefit from the GUI port supported by an ARRA supplement to the Neuroimage Analysis Center, a NA-MIC collaborating P41 grant. Slicer4 supports native windows 64 bit environments and can be bundled into a standard Mac OS X application bundle.
* ''Efficiency and Robustness:'' Careful review of core data management and processing pipeline steps allowed us to remove much redundant processing. The result is that Slicer is easier for developers to understand and debug, and end users experience faster startup and more responsive behavior.
* ''DICOM Networking:'' Slicer4 includes a DICOM listener and DICOM Query/Retrieve capabilities for integration with standard clinical image management environments and workflows. For example, intraprocedural imaging obtained during image guided procedures can now be auto-routed to Slicer for analysis and navigation.
* ''Additional Features:'' Slicer4 includes: an improved flexible view layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster hardware accelerated volume rendering; improved markups and annotations; improved atlas and model hierarchy support; a streamlined and revised diffusion MRI implementation.

=== Plans ===
With the introduction of the Slicer4 Extension system we plan to stabilize the core slicer distribution and move to less frequent releases with more of the algorithm innovation becoming available through as Extensions. This will allow further stabilization and streamlining of the core while speeding up the delivery of new technologies to end users for testing.

== 5.2.2. Computational Platform ==
<em>Jim Miller</em>

Efforts in the Computational Platform have focused on developing a general and flexible computing architecture and analysis platform to meet the needs of NA-MIC scientists and engineers as well as the larger medical imaging community.
=== Major Developments ===
* ''Interactive methods:'' The Editor module has supported interactive segmentation techniques that were deeply integrated with the Editor codebase. We have broadened the Slicer Extension mechanisms to support Editor Extensions, allowing interactive segmentation techniques to be developed separately from the Slice codebase. We have also refined the interaction patterns for interactive segmentation within the Editor and are starting to develop interactive registration techniques.
* ''Multivolume analysis:'' The infrastructure for Diffusion Weighted MRI (DWI) IO and visualization has been generalized to be used for other time varying acquisitions like Dynamic Contrast Enhanced MRI (DCE) and Gated Cardiac CT. Massively univariate processing of DCE to produce parametric maps is being developed as a Slicer Extension.
* ''Distributed computing:'' Slicer Execution Model modules (also known as Command Line Modules) are now available as Nipype tools, enabling local and distributed scripted execution of processing pipelines.
* ''Exploratory image analysis:'' Infrastructure for the interactive exploration of images and the relationships of features calculated over regions of images was developed, including: feature libraries for Gabor, Haralick, entropy, polynomial, and histograms; and charting capabilities to display line, bar, and scatter plots within Slicer.
* ''Compatibility with ITK version 4:'' Compatibility with ITK version 4 was developed and continuously maintained over the past year as ITKv4 matured. Slicer will officially switch to ITKv4 in the coming months.
=== Plans ===
At the time of this writing, 3D Slicer 4.1 is being finalized. After the release of Slicer 4.1, the Slicer development codebase will migrate to using ITK version 4. This migration will enable new image registration methods, introduce SimpleITK APIs, and introduce GPU support for image analysis algorithms. Other plans for the Computational Platform include further developments for interactive analysis methods, infrastructure for private cloud computing, and interfaces for statistical analysis.

== 5.2.3. Data Management Platform ==
<em>Dan Marcus</em>

Efforts in the Data Management Platform have focused on developing an ergonomic user interface and internal networking logical to efficiently exchange data between Slicer and XNAT.
=== Major Developments ===
* ''User Interface:'' The XNAT development team is working with a web usability firm (Integrity St. Louis) to design and implement a web interface that can be deployed in Slicer 4's Qt framework for exploring data hosted in a remote XNAT data repository. Prototypes have been implemented and are currently being reviewed by stakeholders with the goal of a functioning interface by June, 2012.
* ''Networking logic:'' An alpha implementation of the infrastructure for actually exchanging data between XNAT and Slicer has been developed and revealed that significant additional work is required to handle parsing of MRML files within Slicer in the context of remotely hosted data. This work is now underway and will require several months to complete.
* ''Use cases:'' Several use cases have been identified, including projects within the Quantitative Imaging Network (QIN), to drive the development of the Slicer/XNAT integration.

=== Plans ===
The bulk of the effort in the coming year will continue to focus on the user interface and networking logic for remote data management. As the initial development completes, we will turn to developing more efficient mechanisms for caching data locally and synchronizing local caches with remote repositories.

== 5.2.4. Community Software Process ==
<em>Stephen R. Aylward</em>

The goal of the Community Software Process effort is to provide tools and processes that make it easy for algorithms developers to contribute methods to the NA-MIC Kit, while maintaining the NA-MIC Kit's high-quality software standards.

=== Major Developments ===

This year, we have seen massive expansion and significant stabilization of the NA-MIC Kit. While these two accomplishments may seem at odds, they actually represent the planned progression of our community software processes. The specific aims and approaches we pursued to achieve these accomplishments are as follows:

* <em>Provide a modern, stable platform:</em> Slicer 4.0 has been released. This is a major milestone in the NA-MIC community. Slicer 4.0 represents a re-write of the majority of the slicer core to achieve stability, remove redundancy, refactor inefficiencies, and provide new pathways for growth. The most noticeable change is the conversion of the user interface to Qt - which provided speed, stability, and support from the well established Qt community.

* <em>Provide a simple interface for algorithm developers to extend Slicer:</em>
** Python has been adopted as the preferred scripting language, and it has been tightly integrated into Slicer 4.0. Python is a powerful scripting language with strong scientific computing support via add-on libraries such as SciPy, NumPy, and NiPy. We have tightly integrated it with Slicer so that python scripts can modify and extend the Slicer GUI, manipulate Slicer's data representations (i.e., the MRML Scene), and call other extensions in Slicer to specify novel workflows.
** Slicer Extension Manager is now the "Slicer Catalog." It is a new web-based system that builds upon the "App Store" concept that is familiar to Android and Apple users. Users can easily install, uninstall, rate, and comment on extensions. Developers can easily add new extensions, upload revisions, add screenshots, and respond to feedback from users.

* <em>Provide access to the best algorithms:</em> ITKv4 has been released by the Insight Software Consortium, and we have begun integrating this new version of ITK and its associated wrapping for Python (i.e., SimpleITK) into Slicer 4.0.

* <em>Provide easy access to clinical data:</em> Upgraded the version of the DICOM library (DCMTK) used by Slicer and provided improved DICOM RT support. We also have begun supporting Ultrasound (e.g., video) and 4D (e.g., gated CT) data in Slicer.

* <em>Provide easy-to-create and easy-to-access documentation:</em> We have integrated the extension writing and the documentation generation processes. The documentation created when an extension is written is now automatically ported to a web host for easier access from within and from outside of Slicer.

=== Plans ===

The planned efforts of the Community Software Processes are continuations of ongoing work:

* <em>Provide a modern, stable platform:</em> Slicer quality will continue to be improved via refactoring and via expanded emphasis on testing. Refactoring of the core is nearly complete and new efforts will be directed by the Algorithms team - to support their evolving needs and to inspire future research directions. Testing will evolve from code unit testing to GUI testing. Kitware's ParaView team has developed a semi-automated GUI testing system. It can record and then play-back user interactions. It can also verify that the user interface and Slicer output matches a pre-defined state. In this way, algorithm developers can more easily implement regression tests to ensure the continued operation of their modules.

* <em>Provide a simple interface for algorithm developers to extend Slicer:</em>
** Python: We will continue to promote Python as the preferred language for scripting in Slicer. It will be used for algorithm prototyping, parameter exploration, and workflow development and delivery. In particular, we expect future development to facilitate scripts that feature interactive algorithms running within Slicers 2D and 3D visualizations.
** Slicer Catalog: Future work will focus on extending the foundation introduced in Slicer 4.1. New developments will address hosting "extension packages" (e.g., the microscopy package or the DTI package of extensions) as well as hosting data, tutorials, videos, and other adjunct material.

* <em>Provide access to the best algorithms:</em> We will complete integration of ITKv4 and its associated SimpleITK (for python) into Slicer 4. Special attention will be given to ensuring that the upgrade will not disrupt the operation of existing modules.

* <em>Provide easy access to clinical data:</em> The OFFIS and CTK developers anticipate further updated to DCMTK and other clinical data systems used by Slicer. We will continue, in particular, to broaden and stabilize Slicer's support of DICOM, DICOM RT, Ultrasound, video, and 4D data.

= 5.3. NA-MIC Kit =
The NA-MIC Kit is designed to accelerate the pace of research and transition to clinical evaluation providing (a) a flexible yet stable execution and visualization engine with strong support for clinical data (Slicer), (b) tools for extending that platform and sharing those extensions with others, and (c)
community-developed analysis modules can be rapidly deployed to clinical researchers and the
broader community via Slicer.
[[image:2012_Engineering_NAMICKit.png|700px|center]]
== 5.3.1. Expansion ==
<em>Stephen R. Aylward</em>

=== Progress ===
* Package Manager
* Updates to ITK, VTK, Qt, CMake, DCMTK, ...
* CTK
* GUI Testing

=== Plans ===
== 5.3.2. Release ==
<em>Stephen R. Aylward</em>
=== Release Schedule ===
=== Recent Change Logs ===

2012 Project Week:DICOM

2012-01-05T00:23:33Z

DanMarcus:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:Slicer4-DICOM-2011-12-05.png|Slicer4 DICOM current state
</gallery>

==Key Investigators==
* BWH: Andrey Fedorov
* Isomics: Steve Pieper
* Queen's: Andras Lasso
* WUSTL: Misha Milchenko

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

<h3>Objective</h3>
Discuss and test DICOM current state and use cases in slicer4
</div>

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

<h3>Approach, Plan</h3>
* Test DICOM networking with sample servers.
* Review layout of the widget.
* Consider how DWI and DICOMRT should integrate with DICOM module
* Review the Slicer Data Bundle (lollipop)
* DICOM RT
* DICOM SR
* Consider how 4D data should integrate ?
* In general, modules should be able to access all DICOM fields of a loaded image
* Introduce DICOM import plugin modules? (modules that are notified when the user selects a DICOM file for loading and can extract various objects: images, models, etc.)
* Consider how DICOM module mechanisms could be used by the CLI modules for accessing/parsing DICOM studies?
</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a core functionality of 3D Slicer v.4

==References==
* Networking and Qt
** http://www.commontk.org
* Utilities
* http://dicom.offis.de
* http://code.google.com/p/pydicom/
* RT
** http://support.dcmtk.org/wiki/dcmrt/start
** http://plastimatch.org/
* Surfaces and segmentations:
** http://qibawiki.rsna.org/index.php?title=Segmentation_and_Markup_Formats
** ftp://medical.nema.org/medical/dicom/final/sup132_ft.pdf
** ftp://medical.nema.org/medical/dicom/final/sup111_ft.pdf
</div>

Survey stealthlink openigtlink

2011-06-23T16:18:24Z

DanMarcus: /* Key Investigators */

==Key Investigators==
* Brigham and Women's Hospital: Nobuhiko Hata, Ron Kikinis
* Washington University: Dan Marcus
* Swedish Hospital: Sara Jost

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

<h3>Objective</h3>
# The purpose of this page is to compile a list of institutions indicating interest to use Stealthlink from Medtronics through OpenIGTLink.

</div>

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

<h3>Approach, Plan</h3>
#'''Solicit input from participants from this list.
#'''Past contacts who indicated the interest'''
*Eduard Neuman, Czech Republic, Brno, eneuman AT MARK volny.cz
*Daisuke Inoue, MD, Department of Neurosurgery, Kyusyu University, Japan, dinoue AT MARK ns.med.kyushu-u.ac.jp

</div>

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

<h3>Progress</h3>

*I went back my email box and tried to pick past contactes who indicated interest to use Stealth Station with Slicer, but not successful.
*I continue to record the contacts in case OpenIGTLink interface becomes available for StealthStation in the future.
*I found that Medtronic and Tina created the following page for us (http://www.na-mic.org/Wiki/index.php/Stealthlink_Protocol) with detail on StealthLink 2. Very helpful.

2011 Winter Project Week:XNATSceneSupport

2011-01-06T20:45:14Z

DanMarcus: Created page with '==Key Investigators== * Wash U: Dan Marcus, Misha Milchenko <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Objective</h3> Engineer XN…'

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Engineer XNAT support for Slicer scene files.

</div>

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

<h3>Approach, Plan</h3>
XNAT expects files to be located within the XNAT data hierarchy. Slicer scenes often include files from multiple levels of the hierarchy. So where should the scene files be posted into XNAT? What sort of searches for scene files need to be supported?</div>

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

<h3>Progress</h3>
High level discussions.
</div>
</div>

2011 Winter Project Week

2011-01-06T20:41:13Z

DanMarcus: /* Informatics */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2011]], [[Events]]

__NOTOC__
[[image:PW-SLC2011.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2011#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2011#Agenda|click here for the agenda for AHM 2011 and Project Week]].

==Background==

From January 10-14, 2011, the twelfth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

=== Segmentation ===
* [[2011_Winter_Project_Week:Extension of ABC to detect pathology categories|Extension of ABC (Atlas-Based Classification) to detect pathology categories, with tests on TBI images]] (Bo Wang, Jack Van Horn, Marcel Prastawa, Guido Gerig).
* [[2011_Winter_Project_Week:Atrial_Fibrillation|Segmentation of the left atrial wall for atrial fibrillation ablation therapy]] (Behnood Gholami, Yi Gao, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
* [[2011_Winter_Project_Week:TubeTK_VascularImageSegmentationAndAnalysis|TubeTK for vascular image segmentation and analysis]] (Stephen Aylward, Danielle Pace, Steve Pieper)
* [[2011_Winter_Project_Week:StenosisDetector|A stenosis detector in Slicer4 using VMTK ]](Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)
* [[2011_Winter_Project_Week:MeshCurvolver|Surface Region Segmentation for Surgical Planning and Mapping ]] (Peter Karasev, Karol Chudy, Allen Tannenbaum)
* [[2011_Winter_Project_Week:SPECTRE_Integration|Integration of SPECTRE into Slicer]] (Nicole Aucoin, Min Chen)
* [[2011_Winter_Project_Week:NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ehud Schmidt, Polina Golland)

=== Registration ===
*[[2011_Winter_Project_Week:RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier,Ron Kikinis)
*[[2011_Winter_Project_Week:RegistrationAnisotropy|Voxel Anisotropy and Bias Field Effects on Slicer Image Registration]] (Dominik Meier, Andriy Fedorov, William Wells) (tentative)
* [[2011_Winter_Project_Week:DTIRegistrationWizard|DTI registration & resampling wizard]] (Dominik Meier, Hans Johnson, Francois Budin, Mark Scully)
* [[2011_Winter_Project_Week:Efficient co-registration of multiple MR modalities using the ABC|Efficient co-registration of multiple MR modalities using the ABC (atlas-based classification) framework, joint visualization of multiple co-registered modalities]] (Bo Wang, Jack Van Horn, Marcel Prastawa, Guido Gerig).
* [[2011_Winter_Project_Week:DTI_MRI_Registration|DTI MRI Registration- Evaluation of registration schemes]] (Anuja Sharma, Guido Gerig)
* [[2011_Winter_Project_Week:Atlas_Registration_in_Slicer3|Atlas Registration in Slicer3]] (Daniel Haehn, Dominik Meier, Kilian Pohl, Ryan Eckbo)
* [[2011_Winter_Project_Week:RegistrationInPresenceOfAnatomicVariation|Registration in the presence of anatomic variation (sliding organ registration)]] (Danielle Pace, Marc Niethammer, Petter Risholm, Tina Kapur, Sandy Wells, Stephen Aylward)
* [[2011_Winter_Project_Week:UncertaintyVisualization|Visualizing registration uncertainty in Slicer3]] (Peter Risholm, William Wells)
* [[2011_Winter_Project_Week:LandmarkRegularization|Landmark-based registration with analytic regularization]] (Nadya Shusharina, Gregory Sharp)
* [[2011_Winter_Project_Week:DTIPipeline|DTI registration/processing pipeline in Slicer3]] (Francois Budin, Clement Vachet)

=== IGT ===
*[[2011_Winter_Project_Week:OpenIGTLink| OpenIGTLink 2.0]] (Junichi Tokuda, Nobuhiko Hata)
*[[2011_Winter_Project_Week:Osteomark|Osteormark, navigation tool for Osteotomy]] (Laurent Chauvin, Nobuhiko Hata)
*[[2011_Winter_Project_Week:Intra-ProceduralProstateMotion|Detection and compensation for prostate motion during MR-guided prostate biopsy]] (A.Fedorov, Andras Lasso)
*[[2011_Winter_Project_Week:ThinClientQtInterfaceForIGT|Thin Client QT Interface for IGT]] (Nicholas Herlambang, Steve Pieper, Julien Finet, JC)
*[[2011_Winter_Project_Week:TransformRecorderAndProcedureAnnotation|Transform recorder and (surgical) procedure annotation module]] (Tamas Ungi, Junichi Tokuda)
*[[2011_Winter_Project_Week:SurgicalToolsTracking|Surgical Tools Tracking]] (Martin Rajchl, Feng Li)
*[[2011_Winter_Project_Week:Slicer IGT Looking Forward| Slicer IGT Looking forward]] (Nobuhiko Hata, Junichi Tokuda, Andriy Fedorov, Sandy Wells, Danielle Pace)

=== Radiotherapy ===
* [[2011_Winter_Project_Week:SegEye|Segmentation of the eye structures for Adaptive Radiotherapy]] (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:DicomRtExport|DICOM-RT export]] (Greg Sharp, Steve Pieper)

=== Analysis ===
* [[2011_Winter_Project_Week:GAMBITCorticalThicknessAnalysis |GAMBIT - Cortical thickness analysis]] - Clement Vachet, Martin Styner
* [[2011_Winter_Project_Week:ParticleShapeAnalysis|Particle shape analysis incorporating surface normals ]] - Beatriz Paniagua, Martin Styner
* [[2011_Winter_Project_Week:NAMICShapeAnalysis |NAMIC shape analysis pipeline in Slicer 3]] - Lucile Bompard, Martin Styner, Clement Vachet, Chris Gloschat
* [[2011_Winter_Project_Week:ParticleShapeEngineering|Particle Systems for Shape Analysis]] - Josh Cates, Manasi Datar, Ross Whitaker
* [[2011_Winter_Project_Week:MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] - Bjoern Menze, Jason Crane, Beck Olson, Polina Golland

=== Informatics ===
* [[2011_Winter_Project_Week:UIowaTHPDTIData|Share all UIowa Traveling Human Phantom DTI data with NAMIC]] - Mark Scully, Hans Johnson, Zack M.
* [[2011_Winter_Project_Week:FetchMIAPI|Recode FetchMI API to work with XNAT 1.5 API]] - Dan Marcus, Misha Milchenko
* [[2011_Winter_Project_Week:XNATSceneSupport|Engineer XNAT infrastructure for handling slicer scene files]] - Dan Marcus, Misha Milchenko

=== Diffusion ===
* [[2011_Winter_Project_Week:DicomToNrrdTestSuite |Test suite for DicomToNrrdConverter]] - Mark Scully, Zach Mullen, Xiaodong Tao, Hans Johnson
* [[2011_Winter_Project_Week:DicomToNrrdRefactoring |Requirements gathering for refactoring DicomToNrrdConverter]] - Mark Scully, Xiaodong Tao, Hans Johnson
* [[2011_Winter_Project_Week:DTIPrepDocumentation |Documentation and 1st Draft Tutorial for DTIPrep]] - Clement Vachet, Mark Scully, Hans Johnson
* [[2011_Winter_Project_Week:VoxelwizeFiberDistributionFromTractography |Voxelwise fiber distribution from tractography]] - Yinpeng Li, Martin Styner
* [[2011_Winter_Project_Week:TwoTensorTracts |Two-tensor full brain tractography pipeline]] - Lauren O'Donnell, Yogesh Rathi, C-F Westin
* [[2011_Winter_Project_Week:FreeWaterElimination |Free-water elimination]] - Ofer Pasternak, Demian Wassermann, C-F Westin
* Finsler tractography in ITK - Antonio Tristan-Vega, C-F Westin
* [[Statistical analysis of WM tracts generated by Tractography and Volumetric framework]] - Gopal Veni, Ross Whitaker

=== NA-MIC Kit Internals ===

* [[2011_Winter_Project_Week:Command_line_module_logic_redesign|Command line module logic redesign]] (passing paramenters, tie into workflows) - Jim, Steve
* 64bit Windows Builds - Dave P
* Dashboards: Factory machine, subprojects, and CDash@Home - Dave P, Zack M, Steve, and Stephen
* MIDAS for data hosting - Zach M and Hans
* [[2011_Winter_Project_Week:VTK_Widgets|vtkWidgets]] JC and Will, Nicole Aucoin
* [[2011_Winter_Project_Week:Annotation_module_in_Slicer4_Display_widget_intersections|Annotation module in Slicer4: Display widget intersections]] (Daniel Haehn, Nicole Aucoin, Steve Pieper)
* [[2011_Winter_Project_Week: Python and Slicer4| Python and Slicer4]]: Workflows, Scripting, and Porting - JC, Jim, Steve, and Danielle
* [[2011_Winter_Project_Week: Slice View Performance| Improve Performance of Slice Rendering in slicer3 and slicer4]] (Steve, Will, Jc, J2, Jim, Luca)
* [[2011_NAMIC_Project_week:_Real-Time_Volume_Rendering_for_Virtual_Colonoscopy| Real-Time Volume Rendering for Virtual Colonoscopy]] (Steve, Alex)
* [[2011_Winter_Project_Week:_Slicer4-ITK4_Continuous_Integration| Slicer4 - ITK4 Integration]] (Bill, Luis)

=== Execution Model ===
* [[2011_Winter_Project_Week::ExtractSEM|Extract SlicerExecutionModel (SEM) into separate entity]]. SEM is the only component needed to build modules compatible with Slicer3D, so it should be easy incorporate into external applications without all of Slicer3D. Jim, Hans
* [[2011_Winter_Project_Week:ExtendSEMXml|Extend SEM xml]] to include sections for explicit grant acknowledgements, pointers to documentation, and pointers to examples. - Hans, Andriy
* [[2011_Winter_Project_Week:SEMXMLSchema|Create a formal schema for the SEM xml so that eternal tools (i.e. nipype) can validate the xml.]] - Hans Johnson, Jim Miller, Tim Olsen
* [[2011_Winter_Project_Week:XMLToMediaWiki|Improve documentation extractor script that converts XML to MediaWiki format so that it can directly push this information into the Slicer3D MediaWiki.]] - (Wiki Systems Admin), Hans Johnson, Steve Pieper, Stephen Aylward
* [[2011_Winter_Project_Week:ExternalToolsMergingStrategies | Improve merging strategies between software that is part of externals tools and part of Slicer.]] - Mark Scully, Hans Johnson

=== Workflows and Integration ===
# [[Winter_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 28th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 28: Engineering Infrastructure Projects
#*November 4: Engineering Infrastructure Projects
#*November 11: DPB Projects: Iowa, Outcomes from Alg Core Retreat
#*November 18: DPB Projects: MGH
#*November 25: DBP Projects, Funded External Collaborations
#*December 2: Funded External Collaborations
#*December 9: Other External Collaborations
#*December 16:Finalize Engineering Projects
#*January 6: Loose Ends
#By December 16, 2010: [[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 December 16, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##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. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2010-02-09T16:20:07Z

DanMarcus:

Engineering:WUSTL

2010-02-09T16:18:49Z

DanMarcus: /* Overview of Washington University Projects (PI: Dan Marcus) */

Back to [[Engineering:Main|NA-MIC Engineering]]
__NOTOC__
= Overview of Washington University Projects (PI: Dan Marcus) =

The Neuroinformatics Research Group at Washington University is responsible for
developing desktop and enterprise level data management software for research imaging
studies. We work in close collaboration with Core 1 engineering investigators to implement
seamless integration between our tools and the other components in the NA-MIC kit.

[[image:xnat-enterprise.jpg|thumb|left|300px|XNAT Enterprise]]
[[image:xnat-desktop.jpg|thumb|left|300px|XNAT Desktop]]

= Wash U Projects =

== [http://www.xnat.org XNAT Enterprise] ==

XNAT is an open source imaging informatics platform designed to facilitate management and exploration of biomedical imaging and related data. XNAT includes a secure database backend and a rich web-based user interface. A REST API provides programmatic access to the image file repository and metadata. A more detailed description of XNAT can be found [http://www.xnat.org/xnat_neuroinformatics.pdf here].

The XNAT project is a joint venture that includes people and support from Washington University, Harvard University, Howard Hughes Medical Institute, the Biomedical Informatics Research Network (BIRN), NA-MIC, and a community of open source developers. [http://www.xnat.org More...]

XNAT 1.4 is scheduled for release on March 1, 2010. Release candidate 3 of this version is currently available for testing. 1.4 includes the full REST API, an improved user interface, and full DICOM integration.

<hr>

== [http://nrg.wustl.edu/xnd/xnd_tutorial.html XNAT Desktop] ==

XNAT Desktop (XND) is a desktop application for organizing, sharing, and distributing imaging and related files. It is operating system-independent, easily installed, and has no external dependencies. XND can be used to tag and upload data to XNAT Enterprise systems and to streamline workflows that utilize Slicer and other components of the NA-MIC Kit. XND includes a built-in web server that allows it to act as a file server using the same REST [http://nrg.wikispaces.com/XNAT+Web+Services+API web services API] that is being implemented for XNAT Enterprise [http://www.xnat.org/xnd/ More...]

XND v0.91 is currently available. This version includes an work-in-progress user interface implementation that provides a look-and-feel and operations that more closely align with common medical imaging workstations.

<hr>

== [http://central.xnat.org XNAT Central] ==

XNAT Central is a free, publicly accessible instance of the XNAT Enterprise system. It supports MRI, PET, CT, and a range of other imaging modalities. Researchers are invited to use XNAT Central to share their imaging studies with select colleagues or as open access projects under one of several licenses (public domain, creative commons, etc). [http://central.xnat.org More...]

XNAT Central currently hosts a number of NA-MIC data sets, as described [http://www.na-mic.org/Wiki/index.php/Downloads here].

<hr>

File:Xnat-enterprise.jpg

2010-02-09T16:08:38Z

DanMarcus: uploaded a new version of "File:Xnat-enterprise.jpg"

File:Xnat-enterprise.jpg

2010-02-09T16:05:31Z

DanMarcus: uploaded a new version of "File:Xnat-enterprise.jpg"

2010-02-09T15:31:00Z

DanMarcus: /* XNAT Desktop */

Back to [[Engineering:Main|NA-MIC Engineering]]
__NOTOC__
= Overview of Washington University Projects (PI: Dan Marcus) =

The Neuroinformatics Research Group at Washington University is responsible for
developing desktop and enterprise level data management software for research imaging
studies. We work in close collaboration with Core 1 engineering investigators to implement
seamless integration between our tools and the other components in the NA-MIC kit.

= Wash U Projects =

==Tutorial==
*October 2008: develop a tutorial for the following scenario:
**I have a directory tree full with data on my local machine. They are part of a project. I would like to:
#. Install xnat on my machine
## where to install
## where to put the data
#. configure xnat for a new project
## what to consider when thinking about the schema
## where does information go like gender or age of the patient
## where does information go about the study as a whole
# import my data into xnat
# start slicer and use it to get data from xnat
## how do I tell slicer where to find my xnat instance?
# do things in slicer and upload the results into xnat
## how to upload a mrml file and all its associated files?
# on a different day: take the results back into Slicer
## how to download a mrml file and all its associated files?

== [http://www.xnat.org XNAT Enterprise] ==

XNAT is an open source software platform designed to facilitate management and exploration of biomedical imaging and related data. XNAT includes a secure database backend and a rich web-based user interface. A REST API provides programmatic access to the image file repository and metadata. A more detailed description of XNAT can be found [http://www.xnat.org/xnat_neuroinformatics.pdf here].

The XNAT project is a joint venture that includes people and support from Washington University, Harvard University, Howard Hughes Medical Institute, the Biomedical Informatics Research Network (BIRN), NA-MIC, and a community of open source developers. [http://www.xnat.org More...]

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== [http://nrg.wustl.edu/xnd/xnd_tutorial.html XNAT Desktop] ==

XNAT Desktop (XND) is a desktop application for organizing, sharing, and distributing imaging and related files. It is operating system-independent, easily installed, and has no external dependencies. XND can be used to tag and upload data to XNAT Enterprise systems and to streamline workflows that utilize Slicer and other components of the NA-MIC Kit. XND includes a built-in web server that allows it to act as a file server using the same REST [http://nrg.wikispaces.com/XNAT+Web+Services+API web services API] that is being implemented for XNAT Enterprise [http://www.xnat.org/xnd/ More...]

XND v0.91 is currently available. This version includes an work-in-progress user interface implementation that provides a look-and-feel and operations that more closely align with common medical imaging workstations.

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== [http://central.xnat.org XNAT Central] ==

XNAT Central is a free, publicly accessible instance of the XNAT Enterprise system. It supports MRI, PET, CT, and a range of other imaging modalities. Researchers are invited to use XNAT Central to share their imaging studies with select colleagues or as open access projects under one of several licenses (public domain, creative commons, etc). XNAT Central is currently in Beta testing. [http://central.xnat.org More...]

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== [http://www.xcede.org XCEDE] ==

XCEDE is an XML format and web service API for representing biomedical imaging protocols, raw data, derived data, and related non-imaging measures. Wash U is an active participant in the XCEDE working group and is working to generate a reference implementation of the emerging standard. [http://www.xcede.org More...]
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