Difference between revisions of "Events:Slicer Workshop August 2009"

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== Course Syllabus ==  
 
== Course Syllabus ==  
The purpose of this tutorial is to provide the members of the research community with a practical experience of the image processing, 3D visualization, and Image-Guided Therapy capabilities of the Open Source 3D Slicer software platform. 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.
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The purpose of this [http://www.ibmisps-worldcongress.org/precongress.asp IBMISPS 2009 pre-congress course] is to provide the members of the research community with a practical experience of the image processing, 3D visualization, and Image-Guided Therapy capabilities of the Open Source 3D Slicer software platform. 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.
  
 
== Course Faculty ==
 
== Course Faculty ==
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Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
 
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
  
*Lauren O'Donnell, Instructor in Radiology, Harvard Medical School
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*Lauren O'Donnell, Ph.D., Instructor in Radiology, Harvard Medical School
 
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
 
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
  
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Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
 
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
  
*Haying Liu, M.S.E.
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*Haiying Liu, M.Eng., M.Sc.
 
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
 
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
  
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===Morning: Introduction to Slicer===
 
===Morning: Introduction to Slicer===
 
*  9:00 am - 9:10 am Preliminary session: Software and data installation trouble shooting
 
*  9:00 am - 9:10 am Preliminary session: Software and data installation trouble shooting
*  9:10 am - 9:30 am [[media:Slicer3_Introduction_SoniaPujol_NationalCancerInstitute_August15_2008.ppt| Slicer3 Overview and Applications]] (Sonia Pujol)
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*  9:10 am - 9:30 am [[Media:Slicer3 Introduction IBMISPS2009 SoniaPujol.pdf | Slicer3 Overview and Applications ]](Sonia Pujol)
*  9:30 am - 10:30 am Hands-on Session 1: [[media:3DVisualization_SoniaPujol_NationalCancerInstitute_August15_2008.ppt‎| Data Loading and 3D Visualization]] (Sonia Pujol)
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*  9:30 am - 10:30 am [[Media:Slicer3Course_DataLoadingAndVisualization_IBMISPS2009_SoniaPujol.pdf | Hands-on Session 1: Data Loading and 3D Visualization ]](Sonia Pujol)
 
* 10:30 am - 10:45 am Coffee-break
 
* 10:30 am - 10:45 am Coffee-break
* 10:45 am - 11:30 am Hands-on Session 2: [[media:3DVisualization_SoniaPujol_NationalCancerInstitute_August15_2008.ppt‎| Data Saving]] (Sonia Pujol)
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* 10:45 am - 11:30 am [[Media:Slicer3Course_DataLoadingAndVisualization_IBMISPS2009_SoniaPujol.pdf | Hands-on Session 2: Data Saving ]](Sonia Pujol)
 
* 11:30 am - 12:00 pm Discussion and Conclusion
 
* 11:30 am - 12:00 pm Discussion and Conclusion
 
* 12:00 -1pm Lunch Break
 
* 12:00 -1pm Lunch Break
  
 
===Afternoon: Introduction to Slicer IGT===
 
===Afternoon: Introduction to Slicer IGT===
*1:00 - 1:30 pm [[media:SlicerIGTOverview.ppt|'''Introduction: Why Slicer 3 for your IGT research? An example from BWH BrainLab collaboration''']] (15 min. Hata)  
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*1:00 - 1:30 pm [[media:Slicer-IGT-Overview-IBMSPSAug2009.ppt|'''Introduction: Why Slicer3 for your IGT research? An overview of Slicer3 for IGT.''']] (15 min. O'Donnell)  
* 1:30 - 4:00 pm [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''Neurosurgical Planning and Guidance by Slicer"]
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* 1:30 - 4:00 pm [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''Neurosurgical Planning and Guidance by Slicer''']
**Module 1-3 (1:30-2:45 pm)
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**Module 1-3 (1:30-2:45 pm) (K. Hayes)
 
# Loading and visualizing anatomical MRI data
 
# Loading and visualizing anatomical MRI data
 
# Incorporating fMRI data using image registration and thresholding
 
# Incorporating fMRI data using image registration and thresholding
 
# Creating a 3D model of the tumour volume
 
# Creating a 3D model of the tumour volume
 
* 2:45 - 3:00 pm Coffee-break
 
* 2:45 - 3:00 pm Coffee-break
**Module 4-6 (3:00-4:00 pm)
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**Module 4-6 (3:00-4:00 pm) (H. Liu)
 
# Predicting the locations of brain structures using image registration and a brain atlas
 
# Predicting the locations of brain structures using image registration and a brain atlas
 
# Incorporating brain fiber tractography from diffusion weighted images
 
# Incorporating brain fiber tractography from diffusion weighted images
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** Linux x86-64: Slicer3-3.4.2009-05-21-linux-x86_64.tar.gz
 
** Linux x86-64: Slicer3-3.4.2009-05-21-linux-x86_64.tar.gz
  
The [http://www.slicer.org/slicerWiki/index.php/Slicer3:Downloads instructions for installing the Slicer3 program ] describe the different steps of the procedure on Mac OS, Linux and Windows.
+
The [https://www.slicer.org/wiki/Slicer3:Downloads instructions for installing the Slicer3 program ] describe the different steps of the procedure on Mac OS, Linux and Windows.
  
 
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.
 
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.
  
*Data to download: Please install the [http://www.slicer.org/slicerWiki/index.php/Image:Slicer3VisualizationDataset.zip Slicer3VisualizationDataset].
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*Data to download: Please install the [https://www.slicer.org/wiki/Image:Slicer3VisualizationDataset.zip Slicer3VisualizationDataset].
  
  
 
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]
 
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

Latest revision as of 17:07, 10 July 2017

Home < Events:Slicer Workshop August 2009

Course Title

776px-Flyer SlicerWorkshop August2009.png

Introduction to Opensource Software Slicer and its Application to Image-Guided Therapy

Course Syllabus

The purpose of this IBMISPS 2009 pre-congress course is to provide the members of the research community with a practical experience of the image processing, 3D visualization, and Image-Guided Therapy capabilities of the Open Source 3D Slicer software platform. 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.

Course Faculty

  • Sonia Pujol, Ph.D., Instructor in Radiology, Harvard Medical School

Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

  • Lauren O'Donnell, Ph.D., Instructor in Radiology, Harvard Medical School

Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

  • Kathryn Hayes, M.S.E.

Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

  • Haiying Liu, M.Eng., M.Sc.

Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

Logistics

  • Date: Tuesday, August 25, 2009
  • Time: 9am - 4pm
  • Location: 1249 Boylston Street, Boston MA (Directions)
  • Participants are required to come with their own computer (PC, Linux or MacOS).
  • Registration is on a first-come, first-served basis and space is limited to 15 participants.

To register to this event, please send an e-mail to slicer-training at bwh.harvard.edu with your name, affiliation, contact information and the characteristics of the laptop you'll be bringing to the workshop.


Agenda

Morning: Introduction to Slicer

Afternoon: Introduction to Slicer IGT

  1. Loading and visualizing anatomical MRI data
  2. Incorporating fMRI data using image registration and thresholding
  3. Creating a 3D model of the tumour volume
  • 2:45 - 3:00 pm Coffee-break
    • Module 4-6 (3:00-4:00 pm) (H. Liu)
  1. Predicting the locations of brain structures using image registration and a brain atlas
  2. Incorporating brain fiber tractography from diffusion weighted images
  3. Annotating the preoperative plan and saving the scene

Preparation for the Workshop

Please complete the following items prior to the course. Support will be provided as requested

  • Software Installation: Please install the newest Slicer3.4 release appropriate to the computer you will be bringing to the workshop:
    • Windows: Slicer3-3.4-2009-05-21-win32.exe
    • Mac OSX Darwin PPC: Slicer3-3.4.2009-05-21-darwin-ppc.tar.gz
    • Mac OSX Darwin Intel: Slicer3-3.4.2009-05-21-darwin-x86.tar.gz
    • Linux x86: Slicer3-3.4.2009-05-21-linux-x86.tar.gz
    • Linux x86-64: Slicer3-3.4.2009-05-21-linux-x86_64.tar.gz

The instructions for installing the Slicer3 program describe the different steps of the procedure on Mac OS, Linux and Windows.

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.


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