Difference between revisions of "2008 June Workshop Germany"

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(137 intermediate revisions by 11 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
*Still tentative, approval pending
 
  
*When: June 16/17
+
==Introduction==
*Where: Germany, specific location TBD
+
This event is a hands-on workshop about the NA-MIC kit. The workshop is intended for participants from within Germany and it was sponsored by the DFG. The target audience for this workshop are scientists with an engineering background who are considering using the NA-MIC kit as their software platform for research. The NA-MIC kit consists of free open source software without restrictions on use and without a give-back requirement. The NA-MIC kit is well-suited for both academic and commercial activities.
  
== Venue and Logistics==
+
The participants will receive an overview of the software libraries, the end-user applications, and documentation that comprise the NA-MIC kit. The curriculum is '''hands-on''' which means that participants are required to attend the workshop with a suitable laptop, preloaded with the software and sample data as specified below. Attendance is limited in order to ensure quality interactions between the faculty and participants.
The workshop will take place at the [http://www.ihk-muenchen.de/trz/trz/inhalte/Westerham/index.html IHK Akademie Westerham] on June the 16th and 17th, 2008 which is [http://maps.google.de/maps?f=q&hl=de&geocode=&q=ihk+akademie+westerham&sll=47.911308,11.826535&sspn=0.006357,0.013475&ie=UTF8&ei=LVXiR7XCKJGC3AKO5aXsDQ&sig2=6FMUFysSnMQylBd70Em9dw&cd=1&cid=47908296,11830927,18245121051090319374&li=lmd&z=14&t=m located] south-east of Munich. Currently our plan is to arrive already on Sunday the 15th such that the workshop can start on time on Monday morning.
 
  
All participants will receive a letter of invitation from the DFG. Besides the program the letter will contain a form that need to be filled out and sent back to the DFG in order to get reimbursed for travel and accommodation costs.
+
= Pictures from the Event =
 +
<gallery perrow="4" widths="150px">
 +
Image:Munich2008-Venue.jpg | The IHK Akademie
 +
Image:Munich2008-workshop.jpg| At work
 +
Image:NAMIC-MUNICH2008.JPG|The group
 +
Image:NAMIC-MUNICH2008_2.JPG|Having fun with the robot
 +
Image:Munich2008-Danielle.jpg | Danielle teaching
 +
Image:Munich2008-Seb.jpg | Sebastien teaching
 +
</gallery>
  
=Introduction=
+
Coincidentally we were there during the [[Media:Munich2008-WatchingEuro2008.mov | Euro2008 tournament.]]
This curriculum is intended as an introduction for scientists with engineering background who are considering using the NA-MIC kit as their software platform for research. The NA-MIC kit consists of free open source software without restrictions on use and without a give-back requirement. The NA-MIC kit is suited for academic or commercial activities.
 
  
The curriculum provides an overview over the technologies, toolkits and applications which are available in the NA-MIC kit. It is a hands-on curriculum and will require participants to attend with a suitable laptop, preloaded with software and sample data.
+
==Sponsors==
 +
<gallery perrow="4" widths="150px">
 +
Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
 +
Image:CAMP_logo_blue.png|[http://wwwnavab.in.tum.de/WebHome Computer Aided Medical Procedures, TU Munich]
 +
Image:DFG zweizeilig sw.jpg|[http://www.dfg.de/ DFG]
 +
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:LogoBIRN.jpg|[http://www.nbirn.net/ BIRN]
 +
Image:Logo_CIMIT.png|[http://www.cimit.org CIMIT]
 +
Image:Isip.jpg|[http://www.intelli-si.org/index_e.html Intelligent Surgical Instrument Project, Japan]
  
==Prerequisites==
 
*This workshop is a hands-on workshop!
 
*A working knowledge of C++ is a prerequisite for benefiting from the full curriculum.
 
* You will be expected bring a computer with you with a minimum of 1 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory. The NA-MIC kit is running on Linux, Windows XP and Mac OSX.
 
  
=Application=
+
</gallery>
Due to the fact that the workshop is mainly supported by the [http://www.dfg.de/ DFG] only applications of German citizens can be taken into account. Multiple applications from single institutes are possible but the primary intention is to achieve a wide spread distribution over many institutes. Finally each person attending will have to pay xxx for participating.
 
  
The applications should include:
 
* Cover letter
 
** Field of reaserch/work
 
** Previous experiences with the NA-MIC kit
 
** Expectations of the participant
 
* Currivulum vitae
 
  
=Schedule=
+
*June 15-17, [http://www.ihk-muenchen.de/trz/trz/inhalte/Westerham/index.html IHK Akademie Westerham]
* March - Web site, Call for application
 
* April - announcement in Nassir's talk
 
* April 20 - deadline for application, selection Workshop
 
* May 5 - DFG deadline for list of participants
 
* Workshop: (arrival on the 15th) 16 and 17
 
 
 
=Requirement=
 
  
 
=Program=
 
=Program=
* Engineering methodology:
+
Arrival: Sunday, June 15
 +
{| border="1" cellpadding="5"
 +
|- style="background:#ebeced; color:black" align="left"
 +
| style="width:20%" | '''Time'''
 +
| style="width:40%" | '''Monday, June 16'''
 +
| style="width:40%" | '''Tuesday, June 17'''
 +
|-
 +
| style="background:#ffffdd; color:black"| 08.00-08.30
 +
| style="background:#ccdd97; color:#522200"| Breakfast
 +
| style="background:#ccdd97; color:#522200"| Breakfast
 +
|-
 +
| style="background:#ffffdd; color:black"| 08.30-10.00
 +
| style="background:#b4d597; color:#522200"|
 +
*08.30-08.45 Welcome (Navab, Kikinis)
 +
** Overview over [[media:NA-MIC_2008.ppt|NA-MIC]]
 +
*08.45-10.00 Engineering methodology: (Jomier, Barre)
 
** Extreme programming
 
** Extreme programming
 
** What is a software engineering methodology, do I need one?
 
** What is a software engineering methodology, do I need one?
 
** The components of the NA-MIC kit software engineering tools: CMAKE, CTEST, CPACK, Dashboards
 
** The components of the NA-MIC kit software engineering tools: CMAKE, CTEST, CPACK, Dashboards
==Day 1==
+
** [[media:Engineering_Methodology_-_2008_June_Workshop_Germany.ppt|(Barre's Slides)]]
* Welcome (Navab, Kikinis)
+
** [[media:Na-MIC-Germany-CTestCDash.ppt|(Jomier's Slides)]]
* How to use ITK, VTK, XNAT and Batchmake (Jomier, Barre)
+
| style="background:#b4d597; color:#522200"|
** [http://www.itk.org/ItkSoftwareGuide.pdf ITK]
+
* 08.30-10.00 Slicer3 IGT
** [http://public.kitware.com/VTK/index.php VTK]
+
** [[media:SlicerIGTOverview.ppt|Slicer 3 IGT capabilities]] (15 min. Hata)
** [http://www.xnat.org XNAT]
+
*** [[IGT:ToolKit|The IGT Toolkit]]
** [[Media:NA-MIC-AHM08-BatchMake.ppt|Batchmake]]
+
*** Concept, Architecture, Design
 +
*** Application specific modules: Neuro, MRIg Prostate, Cardiac 3D US
 +
** [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning IGT Workflows] using Neurosurgical Planning as an Example (60 min, hands-on tutorial, by Pace)
  
* [[media:2008_NA-MIC_AHM_Slicer3.ppt|Slicer 3 introduction & capabilities]] (Pieper, Pujol)
+
|-
** [[media:Slicer_3-beta-2007-01-10.ppt|Slicer 3 architecture]]
+
| style="background:#ffffdd; color:black"| 10.00-10.30
** [[Media:Slicer3Training LoadingAndVisualization.ppt|Loading, Visualization]]
+
| style="background:#ccdd97; color:#522200"| Coffee Break
** [[Slicer3:EM|The EM segmenter in Slicer]]
+
| style="background:#ccdd97; color:#522200"| Coffee Break
 +
|-
 +
| style="background:#ffffdd; color:black"| 10.30-12.30
 +
| style="background:#b4d597; color:#522200"|
 +
* How to use ITK, VTK, XNAT and Batchmake
 +
** [http://www.itk.org/ItkSoftwareGuide.pdf ITK] (Jomier) [[media:Na-MIC-Germany-ITK.ppt|(Slides)]]
 +
** [http://vtk.org VTK] (Barre) [[media:VTK_-_2008_June_Workshop_Germany.ppt|(Slides)]]
 +
** [http://kwwidgets.org KWWidgets] (Barre) [[media:KWWidgets_-_2008_June_Workshop_Germany.ppt|(Slides)]]
 +
** [http://www.xnat.org XNAT] (Pieper) [[media:Pieper-XNAT-2008-06-16.ppt|(Slides)]]
 +
** [[Media:NA-MIC-AHM08-BatchMake.ppt|Batchmake]] (Jomier) [[media:Na-MIC-Germany-BatchMake.ppt|(Slides)]]
 +
| style="background:#b4d597; color:#522200"|
 +
* Slicer 3 IGT continued
 +
** [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial I/O to trackers, devices, and scanners: OpenIGTLink] ( 45 min, Hands-on, by Pace)
 +
** [[LEGO_IGT_and_Medical_Robotics_Tutorial|Lego robot tutorial]] as an example of robot control (45 min, Demonstration, by Pace)
 +
***Participants do not need to download this tutorial software
 +
** [https://www.slicer.org/wiki/Slicer3:Volume_Rendering_With_Cuda CUDA-based volume rendering] (15 Min, Demonstration, by Hata, [[media:slicerIGTCUDA.ppt|Slides]])
 +
***Clinical needs, approach
 +
|-
 +
| style="background:#ffffdd; color:black"| 12.30-13.30
 +
| style="background:#ccdd97; color:#522200"| Lunch
 +
| style="background:#ccdd97; color:#522200"| Lunch
 +
|-
 +
| style="background:#ffffdd; color:black"| 13.30-15.00
 +
| style="background:#b4d597; color:#522200"|
 +
*Slicer3 (Pieper)
 +
** Overview and Features [[media:Slicer-Overview-Features-Munich-2008-06-16.ppt|(Slides)]]
 +
** Architecture and Implementation [[media:Slicer-Architecture-Implementation-Munich-2008-06-16.ppt|(Slides)]]
 +
| style="background:#b4d597; color:#522200"|
 +
*Plug-ins for Slicer 3 (Pujol):
 +
** [[Media:ProgrammingIntoSlicer3_SoniaPujol_Munich2008.ppt‎ |Introduction: ]]Plug-ins as a way to interface external programs (Pujol)
 +
** [[Media:ProgrammingIntoSlicer3_SoniaPujol_Munich2008.ppt‎ |Programming into Slicer3: ]] How-to make a "hello world" plug-in - Part 1 (Pujol)
 +
|-
 +
| style="background:#ffffdd; color:black"| 15.00-15.30
 +
| style="background:#ccdd97; color:#522200"| Coffee Break
 +
| style="background:#ccdd97; color:#522200"| Coffee Break
 +
|-
 +
| style="background:#ffffdd; color:black"| 15.30-18.00
 +
| style="background:#b4d597; color:#522200"|
 +
* [[Media:3DVisualization_SoniaPujol_Munich2008.ppt|3D Visualization]](Pujol)
 +
* [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt‎ | EM Segmentation ]] (Pujol)
 +
| style="background:#b4d597; color:#522200"|
 +
* Plug-ins continued (Pujol)
 +
**[[Media:ProgrammingIntoSlicer3_SoniaPujol_Munich2008.ppt‎ |Programming into Slicer3: ]] How-to make a "hello world" plug-in - Part 2 (Pujol)
 +
* 17.30-18.00 Registration in Slicer 3 [[media:Na-MIC-Germany-Registration.ppt|(Slides)]] ‎(Jomier)
 +
|-
 +
| style="background:#ffffdd; color:black"| 18.00-19.00
 +
| style="background:#b4d597; color:#522200"|
 +
* [http://www.mitk.org MITK] [[media:2008_NA-MIC_MITK.pdf|(slides)]] (Wolf, Neuhaus, Nolden, Maleike, Zelzer, all at [http://www.dkfz-heidelberg.de/en/mbi/index.html DKFZ]). MITK is an application framework that leverages the [[NA-MIC-Kit|NA-MIC kit]].
 +
| style="background:#b4d597; color:#522200"|
 +
* 18.00-18.15 Closing remarks (Navab, Kikinis)
 +
|-
 +
| style="background:#ffffdd; color:black"| 19.00-open
 +
| style="background:#ccdd97; color:#522200"| Dinner
 +
| style="background:#ccdd97; color:#522200"| Dinner
 +
|}
  
==Day 2==
+
= Prerequisites: Hardware and Software=
* Slicer 3 IGT capabilities (Hata, Pace)
 
** Workflow engine
 
** Real-time behavior
 
** I/O to trackers, devices, and scanners
 
*** Synchronization
 
*** Output to alternative display devices, e.g. HMDs
 
** Slicer demon
 
** [[LEGO_IGT_and_Medical_Robotics_Tutorial|Lego robot tutorial]] as an example of robot control
 
** Registration in the Slicer environment
 
  
* Plug-ins for Slicer 3 (Pujol)
+
*'''Participants are required to install the NA-MIC kit components on their laptop in preparation for the workshop.''' Please follow the [http://www.na-mic.org/Wiki/index.php/Training:Workshop_Prerequisite '''Workshop Prerequisite instructions'''] to build Slicer3 and download the datasets.
** Introduction: Plug-ins as a way to interface external programs
+
 
** [[2008_Winter_Project_Week_Plug-ins_for_Slicer3|How-to make a hello world plug-in]]
+
Note: Building Slicer3 can take up to 2 hours.
 +
We recommend a minimum of 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory. Windows XP, Linux (x86 and x86_64) and Darwin (ppc and x86) are supported.
 +
 
 +
* Image Guided Therapy tutorial software and datasets:
 +
** [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning IGT Workflows using Neurosurgical Planning]:  Download the tutorial slides and the tutorial dataset
 +
** [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial I/O to trackers, devices, and scanners: OpenIGTLink]:  Install the OpenIGTLink module and the tracker simulator; download the tutorial slides, the abdominal atlas and the tool model
  
= Prerequisites: Hardware and Software=
 
* [http://www.slicer.org/ Slicer 3]
 
* [http://www.cmake.org/HTML/index.html CAMKE]
 
* Working [http://www.itk.org/HTML/Download.htm ITK] environment
 
* Working [http://www.vtk.org/get-software.php VTK] environment
 
* Common test database - TBD
 
  
 
=Faculty=
 
=Faculty=
Line 85: Line 142:
 
# Sonia Pujol
 
# Sonia Pujol
 
# Danielle Pace
 
# Danielle Pace
# Sebastian Barre
+
# Sebastien Barre
 
# Julien Jomier
 
# Julien Jomier
  
=Local Host=
+
*Local Host: Nassir Navab
# Nassir Navab
+
 
 +
=Venue and Logistics=
 +
The workshop will take place at the [http://www.ihk-muenchen.de/trz/trz/inhalte/Westerham/index.html IHK Akademie Westerham] on June the 16th and 17th, 2008 which is [http://maps.google.de/maps?f=q&hl=de&geocode=&q=ihk+akademie+westerham&sll=47.911308,11.826535&sspn=0.006357,0.013475&ie=UTF8&ei=LVXiR7XCKJGC3AKO5aXsDQ&sig2=6FMUFysSnMQylBd70Em9dw&cd=1&cid=47908296,11830927,18245121051090319374&li=lmd&z=14&t=m located] south-east of Munich. Faculty and participants are expected to arrive at the venue on Sunday the 15th to allow the workshop to begin on time on Monday morning.
 +
 
 +
All participants will receive a letter of invitation from the DFG. In addition to the workshop program the letter will contain a form that needs to be filled out and sent back to the DFG in order to get '''reimbursed for travel and accommodation costs'''.
 +
 
 +
==Information on Public Transport for Local Travel==
 +
 
 +
In regard to the ticket you need for local travel: you have two options depending on the size of the traveling group. You can either go for a partner day ticket (18 €, all zones/''Gesamtnetz'') or a single day ticket (10 €, all zones/''Gesamtnetz'').
 +
 
 +
'''Coming from the [http://en.wikipedia.org/wiki/Munich_International_Airport Munich Airport]'''
  
=Planning meeting=
+
When going to the subway station at the airport you can choose between any of the two subways, either '''S1''' (west route) or '''S8''' (east route) though the '''S8''' is probably beneficial in terms of journey time (approx. 35 minutes).
  
==T-con==
+
With both trains you should travel to the station '''Ostbahnhof'''.
Phone: (001) 1-218-936-1100,
 
PIN: 23869 #
 
  
==Minutes==
+
At '''Ostbahnhof''' you need to change to the '''S6''' (direction '''Giesing''') and leave the train at the terminal stop '''Kreuzstraße'''.
#[[Jun-Germany/022608tcon | Feb 26, 2008 T-con]]
 
#[[Jun-Germany/030508tcon | March 5, 2008 T-con]]
 
#[[Jun-Germany/031708tcon | March 17, 2008 T-con]]
 
#[[Jun-Germany/032408tcon | March 24, 2008 T-con, Nassier on-site]]
 
  
=Sponsors=
+
''Coming from the Central Station''
<gallery>
+
 
Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
+
At central station you can directly enter the '''S6''' (direction '''Karlsplatz/Stachus''' or '''Marienplatz''') and leave the train at the terminal stop '''Kreuzstraße'''. The traveling time is around 50 minutes.
Image:Nac.png|[http://nac.spl.harvard.edu/nac Neuroimage Analysis Center]
+
 
Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy]
+
''The last meters''
Image:LogoBIRN.jpg|[http://www.nbirn.net/ BIRN]
+
 
</gallery>
+
At '''Kreuzstraße''' you need to change into a regional express (e.g. RB30239, RB30245, RB30247, direction '''Bad Aibling''') which you will leave at the first stop in '''Westerham'''. This final train trip requires an extra ticket which costs around 2€.

Latest revision as of 17:00, 10 July 2017

Home < 2008 June Workshop Germany


Introduction

This event is a hands-on workshop about the NA-MIC kit. The workshop is intended for participants from within Germany and it was sponsored by the DFG. The target audience for this workshop are scientists with an engineering background who are considering using the NA-MIC kit as their software platform for research. The NA-MIC kit consists of free open source software without restrictions on use and without a give-back requirement. The NA-MIC kit is well-suited for both academic and commercial activities.

The participants will receive an overview of the software libraries, the end-user applications, and documentation that comprise the NA-MIC kit. The curriculum is hands-on which means that participants are required to attend the workshop with a suitable laptop, preloaded with the software and sample data as specified below. Attendance is limited in order to ensure quality interactions between the faculty and participants.

Pictures from the Event

Coincidentally we were there during the Euro2008 tournament.

Sponsors


Program

Arrival: Sunday, June 15

Time Monday, June 16 Tuesday, June 17
08.00-08.30 Breakfast Breakfast
08.30-10.00
  • 08.30-08.45 Welcome (Navab, Kikinis)
  • 08.45-10.00 Engineering methodology: (Jomier, Barre)
    • Extreme programming
    • What is a software engineering methodology, do I need one?
    • The components of the NA-MIC kit software engineering tools: CMAKE, CTEST, CPACK, Dashboards
    • (Barre's Slides)
    • (Jomier's Slides)
  • 08.30-10.00 Slicer3 IGT
10.00-10.30 Coffee Break Coffee Break
10.30-12.30
12.30-13.30 Lunch Lunch
13.30-15.00
  • Slicer3 (Pieper)
15.00-15.30 Coffee Break Coffee Break
15.30-18.00
18.00-19.00
  • MITK (slides) (Wolf, Neuhaus, Nolden, Maleike, Zelzer, all at DKFZ). MITK is an application framework that leverages the NA-MIC kit.
  • 18.00-18.15 Closing remarks (Navab, Kikinis)
19.00-open Dinner Dinner

Prerequisites: Hardware and Software

  • Participants are required to install the NA-MIC kit components on their laptop in preparation for the workshop. Please follow the Workshop Prerequisite instructions to build Slicer3 and download the datasets.

Note: Building Slicer3 can take up to 2 hours. We recommend a minimum of 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory. Windows XP, Linux (x86 and x86_64) and Darwin (ppc and x86) are supported.


Faculty

  1. Ron Kikinis
  2. Steve Pieper
  3. Noby Hata
  4. Sonia Pujol
  5. Danielle Pace
  6. Sebastien Barre
  7. Julien Jomier
  • Local Host: Nassir Navab

Venue and Logistics

The workshop will take place at the IHK Akademie Westerham on June the 16th and 17th, 2008 which is located south-east of Munich. Faculty and participants are expected to arrive at the venue on Sunday the 15th to allow the workshop to begin on time on Monday morning.

All participants will receive a letter of invitation from the DFG. In addition to the workshop program the letter will contain a form that needs to be filled out and sent back to the DFG in order to get reimbursed for travel and accommodation costs.

Information on Public Transport for Local Travel

In regard to the ticket you need for local travel: you have two options depending on the size of the traveling group. You can either go for a partner day ticket (18 €, all zones/Gesamtnetz) or a single day ticket (10 €, all zones/Gesamtnetz).

Coming from the Munich Airport

When going to the subway station at the airport you can choose between any of the two subways, either S1 (west route) or S8 (east route) though the S8 is probably beneficial in terms of journey time (approx. 35 minutes).

With both trains you should travel to the station Ostbahnhof.

At Ostbahnhof you need to change to the S6 (direction Giesing) and leave the train at the terminal stop Kreuzstraße.

Coming from the Central Station

At central station you can directly enter the S6 (direction Karlsplatz/Stachus or Marienplatz) and leave the train at the terminal stop Kreuzstraße. The traveling time is around 50 minutes.

The last meters

At Kreuzstraße you need to change into a regional express (e.g. RB30239, RB30245, RB30247, direction Bad Aibling) which you will leave at the first stop in Westerham. This final train trip requires an extra ticket which costs around 2€.