Difference between revisions of "SlicerNagoyaJune2009Workshop"

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(17 intermediate revisions by one other user not shown)
Line 4: Line 4:
 
<gallery perrow="4" widths="150px">
 
<gallery perrow="4" widths="150px">
 
Image:Isip.jpg|[http://www.intelli-si.org/index_e.html Intelligent Surgical Instrument Project, Japan]
 
Image:Isip.jpg|[http://www.intelli-si.org/index_e.html Intelligent Surgical Instrument Project, Japan]
 +
Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy]
 
Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
 
Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
−
Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy]
 
 
Image:NISTlogo.gif|[http://eng.nitech.ac.jp Nagoya Institute of Technology]
 
Image:NISTlogo.gif|[http://eng.nitech.ac.jp Nagoya Institute of Technology]
  
 
</gallery>
 
</gallery>
  
−
= Parent Conference =
 
−
[http://www.caos-international.org/2009/ CAOS 2009], [http://www.caos-international.org/2009/index.php?tab=4&item=4 Workshop Announcement]
 
  
−
== Syllabus ==
 
−
The 4 hour course is divided into three sections: an introduction on the concepts of 3D visualization, an experimental hands-on training session using an MR DICOM dataset of the brain and a CT DICOM dataset of the abdomen, and
 
−
This workshop provides an introduction for orthopaedic surgeons to the basics of viewing and interacting with DICOM volumes in 3D using the Slicer software.
 
  
−
[[Media:CAOS2009_SlicerWorkshop.pdf  | CAOS 2009 Slicer Workshop announcement (pdf) ]] [[Media:CAOS2009_SlicerWorkshop.doc  | (Word)]]
+
== Learning Objectives ==
 +
The learning objectives of the workshop are to understand the basic functions of slicer in the context of image guided therapy, open igt link, programming methods to develop customized interface panel in Slicer.  
  
−
== Learning Objectives ==  
+
== Pre-requisit ==
−
The learning objectives of the workshop are (a) to enhance interpretation of DICOM images through the use of 3D visualization, (b) to gain experience with interactive assessment of complex anatomical structures (c) to present current directions of open-source computer graphics applications in Radiology. After completion of the workshop, participants will be able to visualize and analyze their own datasets within the 3DSlicer platform.  
+
The participants are expected to have account in SVN account for Intelligent-SI project.
 +
Programming environment - Compilation environment for Slicer including appropriate compiler and SVN client.
  
 
== Course Faculty ==
 
== Course Faculty ==
−
* Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Department of Radiology, Brigham and Women's Hospital, Boston, MA
+
* Nobuhiko Hata, Ph,D, Associate Professor of Radiology, Brigham and Women's Hospital
−
* Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Department of Radiology, Brigham and Women's Hospital, Boston, MA
+
 
−
* Kathryn Hayes, M.S.E,Surgical Planning Laboratory, Harvard Medical School, Department of Radiology, Brigham and Women's Hospital, Boston, MA
 
−
* Wendy Plesniak, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Department of Radiology, Brigham and Women's Hospital, Boston, MA
 
  
 
== Logistics and Registration ==
 
== Logistics and Registration ==
−
*Date: Wednesday June 17, 2009
+
*Date: Tuesday June 16, 2009
−
*Time: 2 PM - 5:30 PM
+
*Time: 10AM - 5:30 PM
−
*Location: 1249 Boylston St., Boston MA.
+
*Location: Nagoya Institute of Technology
−
*[http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street Directions] The venue is walking distance from the Conference facility. 
+
*Participants are required to come with their own computer (PC, Linux or MacOS) with '''a 3D Slicer compiled''' (see below for instruction).
−
*Participants are required to come with their own computer (PC, Linux or MacOS).
+
*Bring your own lunch and snacks.
−
*Attendance is limited to 25 participants. To sign-up for this event, please register on the [http://www.caos-international.org/2009/index.php?tab=4&item=2 CAOS registration website]  with your contact information: name, title, affiliation and address.
 
  
−
==Tentative Agenda==   
+
== Agenda==   
−
** 1:45 PM - 2:00 PM Preliminary session: Software and data installation trouble shooting
+
** 11:00 AM - 11:30 AM Noby Hata arrives.
−
** 2:00 PM - 2:30 PM Overview of NA-MIC tool-kit and the Slicer 3 platform (Ron Kikinis)
+
** 11:30 PM - 12:00 PM Introduction to Slicer in IGT (slide).
−
** 2:30 PM - 3:30 PM Hands-on Session 1: 3D Data Loading and Visualization (Sonia Pujol)
+
** 12:00 PM - 1:00 PM Lunch on your own. Confirming compilation, SVN co/ci.
−
** 3:30 PM - 3:45 PM Coffee-break
+
** 1:00 PM - 2:30 PM OpenIGTLink I/F converting STL model,joint, vtkModel (understanding MRML)
−
** 3:45 PM - 4:30 PM Hands-on Session 2: Data Saving (Sonia Pujol)
+
** 3:00 PM - 4:30 PM OpenIGTLink custom software, changing MRML and model property based on OpenIGTLink input (sphere changing color)
−
** 4:30 PM - 5:00 PM Clinical Applications in Orthopaedic Surgery (TBN)
+
** 4:30 PM - 6:00 PM Customized GUI, skeleton generator, loadable module
−
** 5:00 PM - 5:30 PM Discussion
+
** 6:00 PM - 7:00 PM Hata-Mori-Hayashi meeting on BrainLab-Slicer integration
 +
** 7:00 PM  PM Noby Hata leaves to Nagoya Airport
  
 
= '''Pre-Workshop Preparation''' =
 
= '''Pre-Workshop Preparation''' =
−
The workshop is a series of hands-on sessions. <span style="background-color: yellow">Please complete the following tasks
+
*The workshop is a series of hands-on sessions. <span style="background-color: yellow">Please complete the following tasks in advance of the workshop.</span>
−
in advance of the workshop.</span>
 
  
−
Please allow yourself ample preparation time.  Depending on network connection and configuration of your laptop it may take anywhere from 10 to 60 minutes to complete these download and installation tasks.   
+
*Please allow yourself ample preparation time.  Depending on network connection and configuration of your laptop it may take anywhere from 10 to 60 minutes to complete these download and installation tasks.   
  
−
The following components of the NA-MIC kit will be used during the workshop.  
+
*The following components of the NA-MIC kit will be used during the workshop.  
  
 
* 1. '''Slicer3''': software application  
 
* 1. '''Slicer3''': software application  
Line 58: Line 52:
 
='''Slicer3 Software''' =
 
='''Slicer3 Software''' =
  
−
Please install the version of Slicer3 appropriate to the platform you'll be working on during the workshop
+
*Please follow the instruction at https://www.slicer.org/wiki/Slicer3:Build_Instructions#Building_the_3.4_release, check out the latest slicer from the SVN repository, and compile 3D Slicer.
−
 
 
−
* Windows XP: [http://www.na-mic.org/Slicer/Download/Snapshots/win32/Slicer3-3.2.2008-08-20-win32.exe Slicer3-3.2.2008-08-20-win32.exe]
 
−
* Mac OSX Darwin PPC: [http://www.na-mic.org/Slicer/Download/Snapshots/darwin-ppc/Slicer3-3.2.2008-08-20-darwin-ppc.tar.gz Slicer3-3.2.2008-08-20-darwin-ppc.tar.gz]
 
−
* Mac OSX Darwin Intel: [http://www.na-mic.org/Slicer/Download/Snapshots/darwin-x86/Slicer3-3.2.2008-08-20-darwin-x86.tar.gz Slicer3-3.2.2008-08-20-darwin-x86.tar.gz]
 
−
* Linux x86: [http://www.na-mic.org/Slicer/Download/Snapshots/linux-x86/Slicer3-3.2.2008-08-20-linux-x86.tar.gz Slicer3-3.2.2008-08-20-linux-x86.tar.gz]
 
−
* Linux x86-64: [http://www.na-mic.org/Slicer/Download/Snapshots/linux-x86_64/Slicer3-3.2.2008-08-20-linux-x86_64.tar.gz Slicer3-3.2.2008-08-20-linux-x86_64.tar.gz]
 
−
 
 
−
Recommended 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.
 
  
−
Note: Apple Mac OS X
+
*Go to Slicer Training page http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training and finish the following tutorials.
 +
**1.1   Data Loading and 3D Visualization in Slicer3
 +
**1.3    Manual segmentation with 3D Slicer
 +
**1.4    Affine and Deformable Registration in Slicer 3
  
−
For Mac OS 10.4.10 (Tiger) install X11 from the OS disk 1 (not installed by default on new machines).  
+
=Course Material=
 +
*Open IGT Link [http://www.na-mic.org/Wiki/index.php/OpenIGTLink]
 +
*Downloading models and images [http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training]
 +
**"Data Loading and 3D Visualization in Slicer3 "
  
−
For Mac OS 10.5 (Leopard) visit the [http://xquartz.macosforge.org/trac/wiki xquartz website] and install xquartz.
+
*"svn co https://www.nitrc.org/svn/slicer3examples/trunk/Slicer3ExampleModules Slicer3ExampleModules"
 +
* https://www.slicer.org/wiki/Slicer3:Loadable_Modules:HOWTO
 +
* http://www.na-mic.org/Wiki/index.php/Slicer3:SkeletonGenerator
  
−
='''Datasets'''=
+
=Contact=
−
Please download the following datasets for the hands-on sessions:
 
−
*Linux/Mac/Windows:
 
−
** The [[media:SlicerSampleVisualization-2009-02-24.zip | SlicerSampleVisualization]] will be used for the hands-on sessions.
 
−
** The [[media:Patient1.zip | RSNA dataset ]] contains examples of 3D reconstructions of anatomical structures of the abdomen.
 
  
 
Please contact the [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Slicer Users mailing list] for support and questions related to the software.
 
Please contact the [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Slicer Users mailing list] for support and questions related to the software.
  
 
Back to [[Events|Events]]
 
Back to [[Events|Events]]

Latest revision as of 18:07, 10 July 2017

Home < SlicerNagoyaJune2009Workshop

3D Visualization Workshop

Sponsors


Learning Objectives

The learning objectives of the workshop are to understand the basic functions of slicer in the context of image guided therapy, open igt link, programming methods to develop customized interface panel in Slicer.

Pre-requisit

The participants are expected to have account in SVN account for Intelligent-SI project. Programming environment - Compilation environment for Slicer including appropriate compiler and SVN client.

Course Faculty

  • Nobuhiko Hata, Ph,D, Associate Professor of Radiology, Brigham and Women's Hospital


Logistics and Registration

  • Date: Tuesday June 16, 2009
  • Time: 10AM - 5:30 PM
  • Location: Nagoya Institute of Technology
  • Participants are required to come with their own computer (PC, Linux or MacOS) with a 3D Slicer compiled (see below for instruction).
  • Bring your own lunch and snacks.

Agenda

    • 11:00 AM - 11:30 AM Noby Hata arrives.
    • 11:30 PM - 12:00 PM Introduction to Slicer in IGT (slide).
    • 12:00 PM - 1:00 PM Lunch on your own. Confirming compilation, SVN co/ci.
    • 1:00 PM - 2:30 PM OpenIGTLink I/F converting STL model,joint, vtkModel (understanding MRML)
    • 3:00 PM - 4:30 PM OpenIGTLink custom software, changing MRML and model property based on OpenIGTLink input (sphere changing color)
    • 4:30 PM - 6:00 PM Customized GUI, skeleton generator, loadable module
    • 6:00 PM - 7:00 PM Hata-Mori-Hayashi meeting on BrainLab-Slicer integration
    • 7:00 PM PM Noby Hata leaves to Nagoya Airport

Pre-Workshop Preparation

  • The workshop is a series of hands-on sessions. Please complete the following tasks in advance of the workshop.
  • Please allow yourself ample preparation time. Depending on network connection and configuration of your laptop it may take anywhere from 10 to 60 minutes to complete these download and installation tasks.
  • The following components of the NA-MIC kit will be used during the workshop.
  • 1. Slicer3: software application
  • 2. Datasets: pre-computed MR datasets

Slicer3 Software

Course Material

  • Open IGT Link [1]
  • Downloading models and images [2]
    • "Data Loading and 3D Visualization in Slicer3 "

Contact

Please contact the Slicer Users mailing list for support and questions related to the software.

Back to Events

Retrieved from "https://www.na-mic.org/w/index.php?title=SlicerNagoyaJune2009Workshop&oldid=97757"