View source for MICCAI2007 ITK.Slicer3.ProgrammersTutorial

= ITK and Slicer 3 Programmers course =

Quote from Ross: "Given the promise of Slicer 3 and and the success of ITK, I think we could easily pitch an ITK/Slicer-3 toturial (at the programmer level, not just the application level), with a focus on a certain set of applications such as segmentation and DTI.  I think this would attract a lot of people from the MICCAI crowd."
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== Organization ==

10th International Conference on Medical Image Computing and Computer Assisted Intervention, Sydney Austriala

Monday October 29th, 2007

<br />http://www.miccai2007.org/program/

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ALL TEXT BELOW IS COPIED FROM 2005 CONFERENCE WILL BE UPDATED SHORTLY
== Context ==

ITK is an open-source software toolkit for performing registration and segmentation. ITK is implemented in C++. ITK is cross-platform, using the CMake build environment to manage the configuration process. In addition, an automated wrapping process generates interfaces between C++ and interpreted programming languages such as Tcl, Java, and Python. This enables developers to create software using a variety of programming languages. ITK's C++ implementation style is referred to as generic programming (i.e., using templated code). Such C++ templating means that the code is highly efficient, reusable, and that many software problems are discovered at compile-time, rather than at run-time during program execution. Because ITK is an open-source project, developers from around the world can use, debug, maintain, and extend the software. ITK uses a model of software development referred to as extreme programming. Extreme programming collapses the usual software creation methodology into a simultaneous and iterative process of design-implement-test-release

== Objectives of the course ==

This intensive course aims both at giving a brief introduction to ITK for new and potential users, as well as in-depth details on advanced ITK programming for ITK developers. Moreover, a special session will be dedicated to the link between ITK and different medical image viewers. The course will include plenary presentation by specialists from Kitware Inc. (http://www.kitware.com) as well as hands-on exercises on real, practical problems in medical imaging.

== Organization ==

The course is organised by the Signal Processing Institute (ITS) of the Swiss Federal Instittue of Technology (EPFL), Lausanne, Switzerland (http://itswww.epfl.ch), under the direction of Prof. Jean-Philippe Thiran. It is supported by the European Network of Excellence (NoE) SIMILAR (http://www.similar.cc) on multimodal interfaces.

== Instructors ==

* Luis Ibanez, Kitware Inc,
* Steve Pieper of Isomics, Inc,

Isomics Inc. is the company in charge of the Dissemination core of the National Alliance for Medical Image Computing (NAMIC).

Kitware Inc. is the company responsible for the maintenance of the ITK toolkit, and dedicated to providing professional consulting services about ITK and other open-source packages, including VTK, CMake and ParaView.

= Program =

[[Media:EPFL.jpg|Picture of the group at the EPFL workshop]]

== Wednesday, October 5th 2005 ==

* 9:00 - 9:30 [http://itk.epfl.ch/ppt/intro_thiran.ppt Introduction by Jean-Philippe Thiran]
* 9:30 - 10:30 ITK Introduction and Architecture (Ibanez: Presentation: [[Media:Insight-Architecture.ppt|Insight-Architecture]])
* 10:30 - 11:00 Coffee Break
* 11:00 - 12:00 ITK Design Patterns and Frameworks (Ibanez: Presentation: [[Media:Insight-DesignPatterns.ppt|Insight-DesignPatterns]])

* 12:00 - 12:30 Hands on exercices (hoe) (Ibanez)
* 12:30 - 13:30 Lunch
* 13:30 - 13:50 NAMIC Introduction - NAMIC Kit (Ron Kikinis: [[Media:NAMIC-Overview-Lausanne-10-05-2005.ppt|NA-MIC Overview]])
* 13:50 - 14:50 Writing an ITK filter (hoe) (Ibanez: Presentation: [[Media:Insight-Writing-a-New-Filter.ppt|Insight-Writing-a-New-Filter]])

* 14:50 - 16:20 3D [[Media:SlicerTraining-NAMIC-1_V1.1.ppt|Slicer Demonstration ]], [[Media:NA-MIC-2005-10-05-Slicer-Overview.ppt|Slicer Overview]] (Pieper)
* 16:20 - 16:50 Coffee break

* 16:50 - 17:20 The Insight Journal - Open Access (Ibanez: Presentation: [[Media:Insight-OpenScience.ppt|Insight-OpenScience]])

* 17:20 - 19:00 Poster Session

== Thursday, October 6th 2005 ==

* 8:30 - 10:00 Multi-threading (course + hoe) (Ibanez: Presentation: [[Media:Insight-MultiThreading.ppt|Insight-MultiThreading]])

* 10:00 - 10:30 Testing Environment (CTest,Dart) (Ibanez: Presentation: [[Media:Insight-SoftwareProcess.ppt|Insight-SoftwareProcess]])

* 10:30 - 11:00 Coffee Break
* 11:00 - 12:00 Optimization: Inlining, Functors, Metaprogramming (Ibanez)
* 12:00 - 13:00 Lunch

* 13:00 - 13:45 [[Media:NA-MIC-2005-10-05-Slicer-Architecture.ppt| Architecture, Slicer Modules]] [[Media:NA-MIC-2005-10-05-Slicer-ITK.ppt|Accessing ITK from VTK, use in Slicer,]] [[Media:NA-MIC-2005-10-05-GenericReader2.ppt|Generic Reader]] (Pieper)

* 13:45 - 14:30 [[Media:Slicer_DTMRI_V1.1.ppt| Tensor Imaging and Fiber Tracking ]] (Pieper)

* 14:30 - 15:30 New classes, ITK Road Map (Ibanez)

* 15:30 – 16:00 Coffee Break

* 16:00 – 17:30 Iterators, Adaptors, Calculators + open discussion (Ibanez)

== Friday, October 7th 2005 ==

* 8:30 - 9:30 Registration Framework (Ibanez: Presentation: [[Media:Insight-Registration.ppt|ITK Image Registration]])
* 9:30 - 10:30 Writing an Image Metric (hoe) (Ibanez)

* 10:30 - 11:00 Coffee Break

* 11:00 - 12:00 Writing a Transform (hoe) (Ibanez)
* 12:00 - 13:00 Lunch
* 13:00 - 14:00 Deformable Registration (+discussion) (Ibanez)
** [[Media:Insight-DeformableRegistration-BSplines.ppt|ITK Image Deformable Registration BSplines]]
** [[Media:Insight-DeformableRegistration-FEM.ppt|ITK Image Deformable Registration FEM]]
** [[Media:Insight-DeformableRegistration-Demons.ppt|ITK Image Deformable Registration Demons]]

* 14:00 - 15:00 Segmentation Methods (Ibanez: Presentation: [[Media:Insight-Segmentation.ppt|ITK Segmentation]])
* 15:00 - 16:00 Practical Case : Brain Tumor (Ibanez)
* 16:00 - 17:00 Practical Case : Abdominal Aortic Aneurysm (Ibanez)

== Exercises Source Code ==

The source code of the hands-on exercises is contained in the following zip file.

[[Image:ITKCourseExercises.zip|Image:ITKCourseExercises.zip]]

= Open Discussions and Attendant Projects =

[[Dissemination:EPFL_Workshop_2005_Attendant_Projects|Open Discussions and Attendants Projects]]

= Venue and accommodation =

Lausanne is a beautiful city in the heart of western Switzerland on the shores of Lake Geneva. It is easy to reach from anywhere – by road (the A1/E25 and A9/E27 motorways), by rail (both the Swiss Federal Railway network and the French TGV Paris-Milan line) and by air (just 40 miles from Geneva-Cointrin International Airport). Lausanne is also close to many popular excursion destinations such as Montreux and Chillon Castle, Zermatt and the Matterhorn, the Jungfrau and Lucerne, the historical hamlet of Gruyères, the Les Diablerets Glacier, the Vaud Alps and the famous French resort of Chamonix.

A list of selected hotels will be provided. Moreover, low cost student accommodation will be proposed.

= Registration =

Registration and registration fees: will be published later on http://itk.epfl.ch Attendance will be limited. Potential participants are invited to send already an email to JP.Thiran@epfl.ch for declaring their interest and receiving updated information when available.

For more information: Please visit regularly our web page: http://itk.epfl.ch

= Course Preparation =

Please download the 3D Slicer XX binaries for your platform by following the links here:

http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

Binaries are available for windows, linux, mac and solaris.

Please also get the following data sets that we will use for the hands on exercises: