https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=Dkauf 2026-04-23T06:40:27Z User contributions MediaWiki 1.33.0 https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=51565 2010-04-21T13:01:35Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[Project Events]], [[Events]]<br /> <br /> [[Image:PW-MIT2010.png|300px]]<br /> <br /> <br /> ==Background==<br /> <br /> We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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. <br /> <br /> Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br /> <br /> The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br /> <br /> This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br /> <br /> A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br /> <br /> == TENTATIVE Agenda==<br /> <br /> '''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.<br /> '''<br /> === Monday, June 21, 2010 === <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br /> ** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)<br /> <br /> === Tuesday, June 22, 2010 ===<br /> ** 8:30am breakfast<br /> ** 8:30am-9:30am TALK<br /> **9:15-10am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.<br /> ** 10-10:30am 3D Slicer Update (Steve Pieper) <br /> **10:30am OpenIGTLink Update (Junichi Tokuda)<br /> ** noon lunch<br /> ** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2)<br /> ** 5:30pm adjourn for day<br /> <br /> === Wednesday, June 23, 2010 ===<br /> ** 8:30am breakfast<br /> ** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> **1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)<br /> **1-2pm: GWE (Marco Ruiz)<br /> **1-5pm: Breakout Session: Prostate Interventions (Junichi Tokuda)<br /> **3pm: Breakout Session: VTK Widgets (Nicole, Kilian, JC)<br /> ** 5:30pm adjourn for day<br /> <br /> === Thursday, June 24, 2010 ===<br /> ** 8:30am breakfast<br /> ** 10-11am [[Events:TutorialContestJune2010|Tutorial Contest Presentations]]<br /> ** 11am: Breakout Session: Data Management (Dan Marcus, Stephen Aylward)<br /> ** noon lunch<br /> ** 1:00pm: Breakout Session TBD<br /> ** 5:30pm adjourn for day<br /> <br /> === Friday, June 25, 2010 === <br /> ** 8:30am breakfast<br /> ** 10am-noon: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br /> *** Noon: Lunch boxes and adjourn by 1:30pm.<br /> ***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br /> ***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br /> ***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]<br /> <br /> ==Projects==<br /> <br /> <br /> <br /> === Segmentation ===<br /> <br /> === Registration ===<br /> <br /> === IGT ===<br /> <br /> === Radiotherapy ===<br /> <br /> <br /> === Analysis ===<br /> *[[Microscopy Image Analysis]] (Arnaud Gelas)<br /> === Informatics ===<br /> <br /> === Diffusion ===<br /> <br /> === Python ===<br /> <br /> === Slicer Internals ===<br /> *Module Inventory (Steve, Jim)<br /> <br /> === Execution Model ===<br /> <br /> ===Other NA-MIC Kit Internals===<br /> *VTKWidgets (JC, Nicole)<br /> *Superbuild (Dave Partika)<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> # The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!<br /> # By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br /> # By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> # People doing Slicer related projects should come to project week with slicer built on your laptop.<br /> ## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br /> ## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br /> <br /> == Logistics ==<br /> *'''Dates:''' June 21-25, 2010<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> *'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). <br /> *'''Registration Method''' WE WILL USE AN ONLINE (CREDIT CARD) REGISTRATION THIS SUMMER. STAY TUNED.<br /> *'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&amp;app=resvlink&amp;fromDate=6/20/10&amp;toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process. <br /> <br /> ''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''<br /> ''' $189/night/room (plus tax).'''<br /> ''' This rate is good only through June 1.'''<br /> <br /> Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availibility, please call Marriott Central Reservations at 1-800-228-9290. <br /> <br /> *Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> *For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>

Dkauf https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week&diff=51415 2010-04-13T15:20:16Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[Project Events]], [[Events]]<br /> <br /> [[Image:PW-MIT2010.png|300px]]<br /> <br /> <br /> ==Background==<br /> <br /> We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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. <br /> <br /> Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br /> <br /> The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br /> <br /> This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br /> <br /> A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br /> <br /> == TENTATIVE Agenda==<br /> <br /> '''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.<br /> '''<br /> === Monday, June 21, 2010 === <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br /> ** 3:30-5:30pm Start project work<br /> === Tuesday, June 22, 2010 ===<br /> ** 8:30am breakfast<br /> ** 8:30am-9:30am TALK<br /> **9:30-10am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Superbuild<br /> ** 10-10:30am 3D Slicer Update (Steve Pieper) <br /> **10:30am OpenIGTLink Update (Junichi Tokuda)<br /> ** noon lunch<br /> ** 1:00-3:00pm: Breakout Session: QT/Slicer (Steve, JC, J2)<br /> ** 3:00pm-4.00pm: Breakout Session: Superbuild (Dave Partyka) -- should this be a project instead?<br /> ** 4:00pm: Breakout Session: Module Inventory (Jim, Steve) -- should this be a project instead?<br /> ** 4:00pm: Breakout Session: OpenIGTLink 2.0 Users Group (Junichi Tokuda) <br /> ** 5:30pm adjourn for day<br /> <br /> === Wednesday, June 23, 2010 ===<br /> ** 8:30am breakfast<br /> ** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> **1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)<br /> **2:30pm: Breakout Session: VTK Widget (Nicole, Kilian)<br /> ** 5:30pm adjourn for day<br /> <br /> === Thursday, June 24, 2010 ===<br /> ** 8:30am breakfast<br /> ** 10-11am [[Events:TutorialContestJune2010|Tutorial Contest Presentations]]<br /> ** 11am: Breakout Session TBD<br /> ** noon lunch<br /> ** 1:00pm: Breakout Session TBD<br /> ** 5:30pm adjourn for day<br /> <br /> === Friday, June 25, 2010 === <br /> ** 8:30am breakfast<br /> ** 10am-noon: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br /> *** Noon: Lunch boxes and adjourn by 1:30pm.<br /> ***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br /> ***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br /> ***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]<br /> <br /> ==Projects==<br /> <br /> [[Microscopy Image Analysis]]<br /> <br /> === Segmentation ===<br /> <br /> === Registration ===<br /> <br /> === IGT ===<br /> <br /> === Radiotherapy ===<br /> <br /> <br /> === Analysis ===<br /> <br /> <br /> === Informatics ===<br /> <br /> === Diffusion ===<br /> <br /> === Python ===<br /> <br /> === Slicer Internals ===<br /> <br /> <br /> === Execution Model ===<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> # Join the kickoff TCON on April 15, 3pm ET.<br /> # By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br /> # By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> # People doing Slicer related projects should come to project week with slicer built on your laptop.<br /> ## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br /> ## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br /> <br /> == Logistics ==<br /> *'''Dates:''' June 21-25, 2010<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> *'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). <br /> *'''Registration Method''' WE WILL USE AN ONLINE (CREDIT CARD) REGISTRATION THIS SUMMER. STAY TUNED.<br /> *'''Hotel:''' We have a group rate of $189/night/room (plus tax) at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&amp;app=resvlink&amp;fromDate=6/20/10&amp;toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process. <br /> <br /> Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availibility, please call Marriott Central Reservations at 1-800-228-9290. <br /> <br /> All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate. <br /> This rate is good only through June 1.<br /> <br /> *Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> *For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>

Dkauf https://www.na-mic.org/w/index.php?title=Boston_Hotels&diff=51411 2010-04-13T13:01:45Z

<p>Dkauf: </p> <hr /> <div>Here are some hotels in Boston that are conveniently located to various NA-MIC events. Most of the information here is mostly verified by NA-MIC folk who have stayed at these hotels, but please double check with the hotels to be sure that we didn't mistype something in here about time/distance estimates.<br /> <br /> Cambridge (ideal for MIT events):<br /> <br /> * [http://www.cambridgeresidenceinn.com/|Cambridge Residence Inn by Marriott] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $199)<br /> * [http://www.kendallhotel.com/| Kendall Hotel] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line, (ask for the MIT rate, currently $185)<br /> * Harding House B&amp;B - 20 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> * [http://www.marriott.com/hotels/travel/boscy-courtyard-boston-cambridge| Courtyard Marriott, Cambridge]- 20-25 minute walk to Stata Center, 10 minute to Central T stop on the Red Line (for on-line reservations, use Corp. Promo Code: MT2)<br /> <br /> <br /> Boston (better for 75 Francis Street, BWH):<br /> <br /> * The Inn at Longwood Medical/Best Western Boston - ~2 minutes to BWH main campus, 20 min walk to 1249 Boylston (cab ride would be $5)<br /> * Omni Parker - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Park Plaza - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Lenox - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Hilton Copley<br /> <br /> Boston (better for 1249 Boylston, BWH):<br /> <br /> * Commonwealth Hotel, Kenmore Square, right next to Kenmore T stop. ~10 min walk to 1249. (To get the preferred rate for Brigham visitors, use the code MASCO)</div>

Dkauf https://www.na-mic.org/w/index.php?title=Boston_Hotels&diff=51410 2010-04-13T12:53:19Z

<p>Dkauf: </p> <hr /> <div>Here are some hotels in Boston that are conveniently located to various NA-MIC events. Most of the information here is mostly verified by NA-MIC folk who have stayed at these hotels, but please double check with the hotels to be sure that we didn't mistype something in here about time/distance estimates.<br /> <br /> Cambridge (ideal for MIT events):<br /> <br /> * [http://www.cambridgeresidenceinn.com/|Cambridge Residence Inn by Marriott] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> * [http://www.kendallhotel.com/| Kendall Hotel] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line, (ask for the MIT rate, currently $185)<br /> * Harding House B&amp;B - 20 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> * [http://www.marriott.com/hotels/travel/boscy-courtyard-boston-cambridge| Courtyard Marriott, Cambridge]- 20-25 minute walk to Stata Center, 10 minute to Central T stop on the Red Line (for on-line reservations, use Corp. Promo Code: MT2)<br /> <br /> <br /> Boston (better for 75 Francis Street, BWH):<br /> <br /> * The Inn at Longwood Medical/Best Western Boston - ~2 minutes to BWH main campus, 20 min walk to 1249 Boylston (cab ride would be $5)<br /> * Omni Parker - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Park Plaza - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Lenox - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Hilton Copley<br /> <br /> Boston (better for 1249 Boylston, BWH):<br /> <br /> * Commonwealth Hotel, Kenmore Square, right next to Kenmore T stop. ~10 min walk to 1249. (To get the preferred rate for Brigham visitors, use the code MASCO)</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25332 2008-05-20T20:20:51Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B Please click here to reserve.]This rate is good only through June 1.<br /> <br /> Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

Dkauf https://www.na-mic.org/w/index.php?title=Boston_Hotels&diff=25314 2008-05-20T20:01:21Z

<p>Dkauf: </p> <hr /> <div>Here are some hotels in Boston that are conveniently located to various NA-MIC events. Most of the information here is mostly verified by NA-MIC folk who have stayed at these hotels, but please double check with the hotels to be sure that we didn't mistype something in here about time/distance estimates.<br /> <br /> &lt;br /&gt; Cambridge (ideal for MIT events):<br /> <br /> <br /> <br /> * [http://www.cambridgeresidenceinn.com/|Cambridge Residence Inn by Marriott] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> * [http://marriottcambridge.com/|Boston Marriott Cambridge]- 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> <br /> * [http://www.kendallhotel.com/| Kendall Hotel] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line,<br /> * Harding House B&amp;B - 20 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> * [http://www.marriott.com/hotels/travel/boscy-courtyard-boston-cambridge| Courtyard Marriott, Cambridge]- 20-25 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> <br /> <br /> Boston (better for BWH):<br /> <br /> * The Inn at Longwood Medical/Best Western Boston - ~2 minutes to BWH main campus, 20 min walk to 1249 Boylston (cab ride would be $5)<br /> * Omni Parker - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Park Plaza - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Lenox - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Hilton Copley<br /> * Commonwealth Hotel, Kenmore Square, right next to Kenmore T stop. ~10 min walk to 1249.</div>

Dkauf https://www.na-mic.org/w/index.php?title=Boston_Hotels&diff=25312 2008-05-20T20:00:42Z

<p>Dkauf: </p> <hr /> <div>Here are some hotels in Boston that are conveniently located to various NA-MIC events. Most of the information here is mostly verified by NA-MIC folk who have stayed at these hotels, but please double check with the hotels to be sure that we didn't mistype something in here about time/distance estimates.<br /> <br /> &lt;br /&gt; Cambridge (ideal for MIT events):<br /> <br /> <br /> <br /> * [http://www.cambridgeresidenceinn.com/|Cambridge Residence Inn by Marriott] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> * [http://marriottcambridge.com/|Boston Marriott Cambridge]- 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> <br /> * [http://www.kendallhotel.com/| Kendall Hotel] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line,<br /> * Harding House B&amp;B - 20 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> * [http://www.marriott.com/hotels/travel/boscy-courtyard-boston-cambridge/| Courtyard Marriott, Cambridge]- 20-25 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> <br /> <br /> Boston (better for BWH):<br /> <br /> * The Inn at Longwood Medical/Best Western Boston - ~2 minutes to BWH main campus, 20 min walk to 1249 Boylston (cab ride would be $5)<br /> * Omni Parker - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Park Plaza - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Lenox - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Hilton Copley<br /> * Commonwealth Hotel, Kenmore Square, right next to Kenmore T stop. ~10 min walk to 1249.</div>

Dkauf https://www.na-mic.org/w/index.php?title=Boston_Hotels&diff=25311 2008-05-20T19:59:29Z

<p>Dkauf: </p> <hr /> <div>Here are some hotels in Boston that are conveniently located to various NA-MIC events. Most of the information here is mostly verified by NA-MIC folk who have stayed at these hotels, but please double check with the hotels to be sure that we didn't mistype something in here about time/distance estimates.<br /> <br /> &lt;br /&gt; Cambridge (ideal for MIT events):<br /> <br /> <br /> <br /> * [http://www.cambridgeresidenceinn.com/|Cambridge Residence Inn by Marriott] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> * [http://marriottcambridge.com/|Boston Marriott Cambridge]- 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> <br /> * [http://www.kendallhotel.com/| Kendall Hotel] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line,<br /> * Harding House B&amp;B - 20 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> * [http://www.marriot.com/boscy| Courtyard Marriott, Cambridge]- 20-25 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> <br /> <br /> Boston (better for BWH):<br /> <br /> * The Inn at Longwood Medical/Best Western Boston - ~2 minutes to BWH main campus, 20 min walk to 1249 Boylston (cab ride would be $5)<br /> * Omni Parker - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Park Plaza - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Lenox - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Hilton Copley<br /> * Commonwealth Hotel, Kenmore Square, right next to Kenmore T stop. ~10 min walk to 1249.</div>

Dkauf https://www.na-mic.org/w/index.php?title=Boston_Hotels&diff=25308 2008-05-20T19:58:21Z

<p>Dkauf: </p> <hr /> <div>Here are some hotels in Boston that are conveniently located to various NA-MIC events. Most of the information here is mostly verified by NA-MIC folk who have stayed at these hotels, but please double check with the hotels to be sure that we didn't mistype something in here about time/distance estimates.<br /> <br /> &lt;br /&gt; Cambridge (ideal for MIT events):<br /> <br /> <br /> <br /> * [http://www.cambridgeresidenceinn.com/|Cambridge Residence Inn by Marriott] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> * [http://marriottcambridge.com/|Boston Marriott Cambridge]- 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> <br /> * [http://www.kendallhotel.com/|Kendall Hotel] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line,<br /> * Harding House B&amp;B - 20 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> * [http://www.marriot.com/boscy|Courtyard Marriott, Cambridge]- 20-25 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> <br /> <br /> Boston (better for BWH):<br /> <br /> * The Inn at Longwood Medical/Best Western Boston - ~2 minutes to BWH main campus, 20 min walk to 1249 Boylston (cab ride would be $5)<br /> * Omni Parker - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Park Plaza - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Lenox - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Hilton Copley<br /> * Commonwealth Hotel, Kenmore Square, right next to Kenmore T stop. ~10 min walk to 1249.</div>

Dkauf https://www.na-mic.org/w/index.php?title=Boston_Hotels&diff=25307 2008-05-20T19:57:43Z

<p>Dkauf: </p> <hr /> <div>Here are some hotels in Boston that are conveniently located to various NA-MIC events. Most of the information here is mostly verified by NA-MIC folk who have stayed at these hotels, but please double check with the hotels to be sure that we didn't mistype something in here about time/distance estimates.<br /> <br /> &lt;br /&gt; Cambridge (ideal for MIT events):<br /> <br /> <br /> <br /> * [http://www.cambridgeresidenceinn.com|Cambridge Residence Inn by Marriott] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> * [http://marriottcambridge.com|Boston Marriott Cambridge]- 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line (ask for the MIT rate; currently $239)<br /> <br /> * [http://www.kendallhotel.com/|Kendall Hotel] - 5-7 minute walk to Stata Center, 1 minute to Kendall T stop on the Red Line,<br /> * Harding House B&amp;B - 20 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> * [http://www.marriot.com/boscy|Courtyard Marriott, Cambridge]- 20-25 minute walk to Stata Center, 10 minute to Central T stop on the Red Line<br /> <br /> <br /> Boston (better for BWH):<br /> <br /> * The Inn at Longwood Medical/Best Western Boston - ~2 minutes to BWH main campus, 20 min walk to 1249 Boylston (cab ride would be $5)<br /> * Omni Parker - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Park Plaza - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Lenox - ~5 minute walk to the Green line, which gets you to Kenmore square for 1249 Boylston<br /> * Hilton Copley<br /> * Commonwealth Hotel, Kenmore Square, right next to Kenmore T stop. ~10 min walk to 1249.</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25298 2008-05-20T19:35:03Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B | Please click here to reserve.]This rate is good only through June 1.<br /> <br /> Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25297 2008-05-20T19:34:18Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B| Please click here to reserve.]This rate is good only through June 1.<br /> <br /> Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25296 2008-05-20T19:33:16Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B| Please click here to reserve.]Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25295 2008-05-20T19:32:49Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B| Please use this link to reserve:] Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25294 2008-05-20T19:29:48Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. You should use this link to reserve: [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B| LeMeridien booking link] Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25291 2008-05-20T19:29:21Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. You should use this link to reserve: [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B|LeMeridien booking link] Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25289 2008-05-20T19:25:14Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. You should use this link to reserve: [[http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B]] Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

Dkauf https://www.na-mic.org/w/index.php?title=2008_Summer_Project_Week&diff=25286 2008-05-20T19:23:44Z

<p>Dkauf: /* Logistics */</p> <hr /> <div>Back to [[Engineering:Programming_Events|Programming/Project Events]]<br /> <br /> [[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]<br /> <br /> == Logistics ==<br /> <br /> '''Dates:''' June 23-27, 2008<br /> <br /> '''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A &amp; B: 34-401A &amp; 34-401B]].<br /> <br /> <br /> '''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to &quot;Massachusetts Institute of Technology&quot; and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139<br /> <br /> If you are attending for one day only, the registration fee is not required.<br /> <br /> '''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. You should use this link to reserve: [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&amp;key=4FD1B] Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> <br /> ([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br /> <br /> ==Introduction to NA-MIC Project Week==<br /> <br /> NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). <br /> The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend. <br /> <br /> * NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br /> * Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.<br /> * This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].<br /> * NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.<br /> * NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.<br /> * NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.<br /> * External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.<br /> * Everyone should '''bring a laptop'''. We will have four projectors.<br /> * About half the time will be spent working on projects and the other half in project related discussions.<br /> * You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> ** 9:00-9:45am: NA-MIC Software Process <br /> ** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]] <br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** noon lunch<br /> **2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]<br /> ** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> <br /> # [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY. <br /> # [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams<br /> # [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded &quot;collaborations with NCBC&quot; leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups. <br /> # [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.<br /> # By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## 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)<br /> ## 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.)<br /> ## 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)<br /> # 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...<br /> <br /> == A History in Wiki Links ==<br /> <br /> A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].<br /> <br /> == Projects ==<br /> <br /> ===DBP II===<br /> These are projects by the new set of DBPS:<br /> #[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br /> ##Add Projects for this DBP here...<br /> #[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br /> ##Add Projects for this DBP here...<br /> <br /> ===Structural Analysis===<br /> <br /> ===Diffusion Image Analysis===<br /> <br /> ===Calibration/Validation===<br /> <br /> ===NA-MIC Kit - Slicer 3===<br /> <br /> ===External Collaborations===<br /> #[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)<br /> #[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)<br /> <br /> ===Non-Medical Collaborations===<br /> <br /> ==Attendee List==<br /> # Ron Kikinis, BWH<br /> # Gary Christensen, The University of Iowa<br /> # Jeffrey Hawley, Gary Christensen's student<br /> # Kate Raising, Gary Christensen's student<br /> # Nathan Fritze, Gary Christensen's student<br /> # Paul Song, Gary Christensen's student<br /> # Cheng Zhang, Gary Christensen's student<br /> # Ying Wei, Gary Christensen's student<br /> # Nathan Burnette, The University of Iowa<br /> # Steve Pieper, Isomics, Core 2/6<br /> # Dana C. Peters, BIDMC Harvard Medical<br /> # Jason Taclas, BIDMC Harvard Medical<br /> # Nicole Aucoin, BWH, Core 2<br /> # Will Schroeder, Kitware, Cores 2/4<br /> # Sebastien Barre, Kitware, Core 2<br /> # Julien Jomier, Kitware, Core 2<br /> # Luis Ibanez, Kitware, Core 2<br /> # Curtis Lisle, KnowledgeVis, Core 2<br /> # Katie Hayes, BWH, Core 2<br /> # Randy Gollub, MGH, Core 5<br /> # Clement Vachet, UNC, Core 3<br /> # Casey Goodlett, Utah, Core 1<br /> # Jeffrey Grethe, UCSD, Core 2<br /> # Marco Ruiz, UCSD, Core 2<br /> # Zhen Qian, Rutgers University<br /> # Jinghao Zhou, Rutgers University<br /> # Luca Antiga, Mario Negri Institute<br /> # Adam Wittek, The University of Western Australia<br /> # Grand Joldes, The University of Western Australia<br /> # Jamie Berger, The University of Western Australia<br /> # Serdar Balci, MIT, Core 1<br /> # Bryce Kim, MIT, Core1<br /> # Vincent Magnotta, The University of Iowa<br /> # Tina Kapur, BWH, Core 6<br /> # Carling Cheung, Robarts Research Institute / The University of Western Ontario<br /> # Danielle Pace, Robarts Research Institute / The University of Western Ontario<br /> # Sean Megason, Dept of Systems Biology, Harvard Medical School<br /> # Alex Gouaillard, Dept of Systems Biology, Harvard Medical School<br /> # Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School<br /> # Arnaud Gelas, Dept of Systems Biology, Harvard Medical School<br /> # Sonia Pujol, Surgical Planning Laboratory, BWH<br /> # Bjoern Menze, (then) Surgical Planning Laboratory, BWH<br /> # Alex Yarmarkovich, Isomics, Core 2<br /> # Sylvain Bouix, BWH, Core 3<br /> # Chris Churas, UCSD, Core 2<br /> # John Melonakos, Georgia Tech, Core 1<br /> # Yi Gao, Georgia Tech, Core 1<br /> # Tauseef Rehman, Georgia Tech, Core 1<br /> # Clare Poynton, MIT, Core 1<br /> <br /> ==Pictures==</div>

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