Difference between revisions of "Robarts Training Session"
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==Course Description== | ==Course Description== | ||
The NA-MIC Kit is a free open-source software platform for biomedical researchers and algorithm developers working in the fields of medical image analysis, visualization and image-guided therapy. This NA-MIC Kit Software Workshop is a two-day interactive course allowing scientists and trainees to learn about the NA-MIC Kit, including 3D Slicer, The Visualization Toolkit (VTK), The Insight Toolkit (ITK) and CMake. Participants will receive hands-on training in the end-user applications and software libraries, making this course applicable to both clinical users interested in using the software for their image analysis and visualization tasks, and software developers considering using the NA-MIC Kit as their software platform. | The NA-MIC Kit is a free open-source software platform for biomedical researchers and algorithm developers working in the fields of medical image analysis, visualization and image-guided therapy. This NA-MIC Kit Software Workshop is a two-day interactive course allowing scientists and trainees to learn about the NA-MIC Kit, including 3D Slicer, The Visualization Toolkit (VTK), The Insight Toolkit (ITK) and CMake. Participants will receive hands-on training in the end-user applications and software libraries, making this course applicable to both clinical users interested in using the software for their image analysis and visualization tasks, and software developers considering using the NA-MIC Kit as their software platform. | ||
+ | |||
+ | ==Pictures from the Event== | ||
+ | <gallery perrow="3" widths="200px"> | ||
+ | Image:London_TerryIntro.jpg | Introduction by Terry | ||
+ | Image:London_SteveTeaching.jpg| Steve teaching | ||
+ | Image:London_Guitar.jpg| Guitar anyone? | ||
+ | Image:London_WorkingAway.jpg| Hard at work | ||
+ | Image:London_Visitors.jpg | Some unexpected visitors | ||
+ | Image:London_GroupShot.jpg | The group | ||
+ | </gallery> | ||
==Course Faculty== | ==Course Faculty== | ||
− | * Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School | + | * Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School |
− | |||
* Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School | * Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School | ||
+ | * Kathryn Hayes, M.S.E., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School | ||
* Danielle Pace, B.CmpH, Robarts Research Institute and The University of Western Ontario | * Danielle Pace, B.CmpH, Robarts Research Institute and The University of Western Ontario | ||
+ | * Steve Pieper, Ph.D., Isomics Inc. | ||
+ | * Junichi Tokuda, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School | ||
==Local Hosts== | ==Local Hosts== | ||
Line 16: | Line 26: | ||
==Logistics== | ==Logistics== | ||
− | * Dates: October 15-16, 2008 | + | * Dates: Wednesday, October 15 - Thursday, October 16, 2008 |
− | * Venue: Room 100, London Hall, 1421 Western Road, The University of Western Ontario, London, Ontario, Canada | + | * Venue: Room 100, London Hall, 1421 Western Road, [http://www.uwo.ca The University of Western Ontario], London, Ontario, Canada |
− | * [http://www.geography.uwo.ca/campusmaps/images/map/westernandaffiliates.pdf Map] | + | * [http://communications.uwo.ca/about/map.htm The University of Western Ontario on Google Maps] |
+ | * [http://communications.uwo.ca/about/directions.htm Driving directions to The University of Western Ontario] | ||
+ | * [http://www.geography.uwo.ca/campusmaps/images/map/westernandaffiliates.pdf Map of campus] | ||
+ | * [http://www.uwo.ca/parking/map.html Parking map] | ||
+ | ** Parking is available in either the "Huron Flats Lot" or "Althouse Lot" and is $4.00 (coin) per entry. Please note that the front desk of London Hall does not have change available for parking. | ||
+ | ** There is a pathway leading from the Huron Flats parking lot to London Hall. Althouse Lot is located behind Perth Hall on the opposite side of Western Road to London Hall. | ||
==Registration== | ==Registration== | ||
+ | |||
+ | '''<span style="background-color: red">Registration for this event is now closed.</span>''' | ||
+ | |||
+ | [[NA-MIC_Training_Workshop_Robarts_Institute_Oct2008_Participants| List of participants]] | ||
+ | |||
* In order to maintain a close participant-faculty ratio, space is extremely limited. | * In order to maintain a close participant-faculty ratio, space is extremely limited. | ||
* Please register with Sandra Noble-Topham via email (snt [at] imaging.robarts.ca) by Friday, September 26, 2008. Please include your: | * Please register with Sandra Noble-Topham via email (snt [at] imaging.robarts.ca) by Friday, September 26, 2008. Please include your: | ||
Line 33: | Line 53: | ||
==Course Requirements== | ==Course Requirements== | ||
* To participate in this interactive workshop, attendees are required to bring their own laptop with the tutorial software and sample datasets pre-installed. | * To participate in this interactive workshop, attendees are required to bring their own laptop with the tutorial software and sample datasets pre-installed. | ||
+ | |||
+ | ==Sponsors== | ||
+ | <gallery perrow="6"> | ||
+ | Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing] | ||
+ | Image:OICRlogo.jpg|[http://www.oicr.on.ca Ontario Institute for Cancer Research] | ||
+ | Image:RobartsResearchLogo.jpg|[http://imaging.robarts.ca Imaging Research Laboratories, Robarts Research Institute] | ||
+ | Image:Nac.png|[http://nac.spl.harvard.edu/ Neuroimage Analysis Center] | ||
+ | Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy] | ||
+ | Image:Logo_CIMIT.png|[http://www.cimit.org CIMIT] | ||
+ | </gallery> | ||
==Agenda== | ==Agenda== | ||
− | * | + | Arrival: Tuesday, October 14 |
+ | {| border="1" cellpadding="5" | ||
+ | |- style="background:#ebeced; color:black" align="left" | ||
+ | | style="width:20%" | '''Time''' | ||
+ | | style="width:40%" | '''Wednesday, October 15 | ||
+ | | style="width:40%" | '''Thursday, October 16 | ||
+ | |- | ||
+ | | style="background:#ffffdd; color:black"| Breakfast | ||
+ | | style="background:#ccdd97; color:#522200"| '''Breakfast''' (8:00-8:30) | ||
+ | | style="background:#ccdd97; color:#522200"| '''Breakfast''' (8:00-8:30) | ||
+ | |- | ||
+ | | style="background:#ffffdd; color:black"| Morning Session 1 | ||
+ | | style="background:#b4d597; color:#522200"| | ||
+ | *08:30-08:45''' Welcome''' (Fenster, Peters, Pieper) | ||
+ | *08:45-9:00 Overview of NA-MIC [[media:NA-MIC_2008.ppt|(Slides by Kikinis) (Hata)]] | ||
+ | *09:00-10:00 '''Engineering methodology''' (Hata) | ||
+ | ** Extreme programming | ||
+ | ** What is a software engineering methodology, do I need one? | ||
+ | ** The components of the NA-MIC kit software engineering tools: ITK, VTK, CMAKE, CTEST, CPACK, Dashboards | ||
+ | |||
+ | ** [[media:Engineering_Methodology_-_2008_June_Workshop_Germany.ppt|Extreme Programming, CMake, CPack (Slides by Barre)]] | ||
+ | ** [[media:Na-MIC-Germany-CTestCDash.ppt|CTest and Dashboard (Slides by Jomier)]] | ||
+ | ** [http://www.itk.org/ItkSoftwareGuide.pdf ITK] (Jomier) [[media:Na-MIC-Germany-ITK.ppt|(Slides by Jomier)]] | ||
+ | ** [http://vtk.org VTK] [[media:VTK_-_2008_June_Workshop_Germany.ppt|(Slides by Barre)]] | ||
+ | ** [http://kwwidgets.org KWWidgets] [[media:KWWidgets_-_2008_June_Workshop_Germany.ppt|(Slides by Barre)]] | ||
+ | ** [[Media:NA-MIC-AHM08-BatchMake.ppt|Batchmake]] [[media:Na-MIC-Germany-BatchMake.ppt|(Slides by Jomier)]] | ||
+ | |||
+ | | style="background:#b4d597; color:#522200"| | ||
+ | |||
+ | |||
+ | * 8:30 - 9:15 [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''IGT Workflows''' using neurosurgical planning as an example (Pace)] | ||
+ | ** Diffusion Tensor (Part 2) | ||
+ | * 9:15 - 10:00 [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning '''MR-Guided Prostate Interventions''' (Pace)] | ||
+ | |- | ||
+ | | style="background:#ffffdd; color:black"| Coffee Break | ||
+ | | style="background:#ccdd97; color:#522200"| '''Coffee Break''' (10:00-10:30) | ||
+ | | style="background:#ccdd97; color:#522200"| '''Coffee Break''' (10:00-10:30) | ||
+ | |- | ||
+ | | style="background:#ffffdd; color:black"| Morning Session 2 | ||
+ | | style="background:#b4d597; color:#522200"| | ||
+ | * 10:30 - 11:00 '''XNAT''' (Pieper) [[media:Pieper-XNAT-2008-06-16.ppt|(Slides)]] | ||
+ | *11:00 - 12:30 '''Slicer3''' (Pieper) | ||
+ | ** Overview and Features [[media:Slicer-Overview-Features-London-2008-10-15.ppt|(Slides)]] | ||
+ | ** Architecture and Implementation [[media:Slicer-Architecture-Implementation-London-2008-10-15.ppt|(Slides)]] | ||
+ | | style="background:#b4d597; color:#522200"| | ||
+ | * 10:30 - 11:30 [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial '''I/O to trackers, devices, and scanners: OpenIGTLink''' (Pace)] | ||
+ | * 11:30 - 12:00 '''Slicer interactive modules and programming resources''' (Pieper) [[media:Slicer-Interactive-Modules-London-2008-10-16.ppt|(Slides)]] | ||
+ | |- | ||
+ | | style="background:#ffffdd; color:black"| | ||
+ | | style="background:#ccdd97; color:#522200"| '''Lunch''' (12:30-1:30) | ||
+ | | style="background:#ccdd97; color:#522201"| '''Lunch''' (12:00-1:00) | ||
+ | |- | ||
+ | | style="background:#ffffdd; color:black"| Afternoon Session 1 | ||
+ | | style="background:#b4d597; color:#522200"| | ||
+ | * 1:30 - 4:00 '''Slicer3 user training''' (SPujol) | ||
+ | ** [[media:3DVisualization_SoniaPujol_Canada2008.ppt | 3D Visualization]] (SPujol) | ||
+ | ** [[media:AutomaticSegmentation_SoniaPujol_Canada2008.ppt| Automatic Segmentation]] (SPujol) | ||
+ | | style="background:#b4d597; color:#522200"| | ||
+ | * '''Programming in Slicer3''' (SPujol) | ||
+ | ** 1:00 - 1:30 Introduction to the new execution model | ||
+ | ** 1:30 - 2:30 [[media:Programming_NA-MIC_Kit_SoniaPujol_Canada2008.ppt |Programming into Slicer3 ]](Part 1) | ||
+ | |- | ||
+ | | style="background:#ffffdd; color:black"| Coffee Break | ||
+ | | style="background:#ccdd97; color:#522200"| Coffee Break (4:00-4:30) | ||
+ | | style="background:#ccdd97; color:#522200"| Coffee Break (2:30-3:00) | ||
+ | |- | ||
+ | | style="background:#ffffdd; color:black"| Afternoon Session 2 | ||
+ | | style="background:#b4d597; color:#522200"| | ||
+ | * 4:30 - 4:45 | ||
+ | ** [[media:SlicerIGTOverview.ppt|'''Slicer 3 IGT capabilities''']] (15 min. Hata) | ||
+ | ** [[IGT:ToolKit|The IGT Toolkit]] | ||
+ | ** Concept, Architecture, Design | ||
+ | ** Application specific modules: Neuro, MRIg Prostate, Cardiac 3D US | ||
+ | * 4:45 - 6:00 [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''IGT Workflows''' using neurosurgical planning as an example (Pace)] | ||
+ | ** Image registration and segmentation (Part 1) | ||
+ | | style="background:#b4d597; color:#522200"| | ||
+ | * '''Programming in Slicer3''' (SPujol) | ||
+ | ** 3:00-5:00 [[media:Programming_NA-MIC_Kit_SoniaPujol_Canada2008.ppt |Programming into Slicer3]] (Part 2) | ||
+ | *5:00-6:00 '''Migrating to the NA-MIC Kit:''' Discussion and Conclusion | ||
+ | |- | ||
+ | |||
+ | |} | ||
==Pre-workshop Preparation List== | ==Pre-workshop Preparation List== | ||
− | * | + | The workshop is a series of hands-on sessions. <span style="background-color: yellow">All participants should complete the [http://www.na-mic.org/Wiki/index.php/Training:RobartsResearchInstitute2008_Workshop_Prerequisite '''Developer Prerequisites'''] |
+ | in advance of the workshop. </span> This includes both building Slicer '''from source''', building the '''additional software''' and '''downloading the datasets'''. | ||
+ | * Note: '''<span style="background-color: yellow"> Building Slicer can take up to 2 hours.</span>''' | ||
+ | * We recommended the following configuration: Windows XP, Linux (x86 or x86_64), Mac OS (ppc or Intel), 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory. | ||
+ | * Please contact the [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Slicer Users mailing list] for support and questions related to the software. |
Latest revision as of 18:43, 3 November 2010
Home < Robarts Training SessionContents
Course Description
The NA-MIC Kit is a free open-source software platform for biomedical researchers and algorithm developers working in the fields of medical image analysis, visualization and image-guided therapy. This NA-MIC Kit Software Workshop is a two-day interactive course allowing scientists and trainees to learn about the NA-MIC Kit, including 3D Slicer, The Visualization Toolkit (VTK), The Insight Toolkit (ITK) and CMake. Participants will receive hands-on training in the end-user applications and software libraries, making this course applicable to both clinical users interested in using the software for their image analysis and visualization tasks, and software developers considering using the NA-MIC Kit as their software platform.
Pictures from the Event
Course Faculty
- Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
- Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
- Kathryn Hayes, M.S.E., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
- Danielle Pace, B.CmpH, Robarts Research Institute and The University of Western Ontario
- Steve Pieper, Ph.D., Isomics Inc.
- Junichi Tokuda, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
Local Hosts
- Aaron Fenster, Ph.D., Director, Ontario Institute for Cancer Research Imaging Pipeline Platform
- Terry Peters, Ph.D., Robarts Research Institute and The University of Western Ontario
Logistics
- Dates: Wednesday, October 15 - Thursday, October 16, 2008
- Venue: Room 100, London Hall, 1421 Western Road, The University of Western Ontario, London, Ontario, Canada
- The University of Western Ontario on Google Maps
- Driving directions to The University of Western Ontario
- Map of campus
- Parking map
- Parking is available in either the "Huron Flats Lot" or "Althouse Lot" and is $4.00 (coin) per entry. Please note that the front desk of London Hall does not have change available for parking.
- There is a pathway leading from the Huron Flats parking lot to London Hall. Althouse Lot is located behind Perth Hall on the opposite side of Western Road to London Hall.
Registration
Registration for this event is now closed.
- In order to maintain a close participant-faculty ratio, space is extremely limited.
- Please register with Sandra Noble-Topham via email (snt [at] imaging.robarts.ca) by Friday, September 26, 2008. Please include your:
- Full Name
- Email address
- Telephone number
- Lab supervisor
- University Name
- Current status (Masters Candidate, PhD candidate, undergraduate, staff member or principal investigator)
- Any dietary restrictions
Course Requirements
- To participate in this interactive workshop, attendees are required to bring their own laptop with the tutorial software and sample datasets pre-installed.
Sponsors
Agenda
Arrival: Tuesday, October 14
Time | Wednesday, October 15 | Thursday, October 16 |
Breakfast | Breakfast (8:00-8:30) | Breakfast (8:00-8:30) |
Morning Session 1 |
|
|
Coffee Break | Coffee Break (10:00-10:30) | Coffee Break (10:00-10:30) |
Morning Session 2 |
| |
Lunch (12:30-1:30) | Lunch (12:00-1:00) | |
Afternoon Session 1 |
|
|
Coffee Break | Coffee Break (4:00-4:30) | Coffee Break (2:30-3:00) |
Afternoon Session 2 |
|
|
Pre-workshop Preparation List
The workshop is a series of hands-on sessions. All participants should complete the Developer Prerequisites in advance of the workshop. This includes both building Slicer from source, building the additional software and downloading the datasets.
- Note: Building Slicer can take up to 2 hours.
- We recommended the following configuration: Windows XP, Linux (x86 or x86_64), Mac OS (ppc or Intel), 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory.
- Please contact the Slicer Users mailing list for support and questions related to the software.