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. | |
| − | |||
| − | 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. | ||
== Course Faculty == | == Course Faculty == | ||
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*Kathryn Hayes, M.S.E. | *Kathryn Hayes, M.S.E. | ||
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA | Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA | ||
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== Logistics == | == Logistics == | ||
*Date: Tuesday, August 25, 2009 | *Date: Tuesday, August 25, 2009 | ||
*Time: 9am - 4pm | *Time: 9am - 4pm | ||
| − | *Location: 1249 Boylston Street, Boston MA | + | *Location: 1249 Boylston Street, Boston MA ([http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street Directions]) |
*Participants are required to come with their own computer (PC, Linux or MacOS). | *Participants are required to come with their own computer (PC, Linux or MacOS). | ||
== Agenda == | == Agenda == | ||
| − | + | ===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) |
| − | * 9:10 am - 9:30 am [[media:Slicer3_Introduction_SoniaPujol_NationalCancerInstitute_August15_2008.ppt| 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) |
| − | * 9:30 am - 10:30 am Hands-on Session 1: [[media:3DVisualization_SoniaPujol_NationalCancerInstitute_August15_2008.ppt| 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) | * 10:45 am - 11:30 am Hands-on Session 2: [[media:3DVisualization_SoniaPujol_NationalCancerInstitute_August15_2008.ppt| Data Saving]] (Sonia Pujol) | ||
* 11:30 am - 12:00 pm Discussion and Conclusion | * 11:30 am - 12:00 pm Discussion and Conclusion | ||
| − | * 12: | + | * 12:00 -1pm Lunch Break |
| − | + | ===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) | |
| − | *1:00-1: | + | * 1:30 - 4:00 pm [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''Neurosurgical Planning and Guidance by Slicer"] |
| − | * 1:30 - 4:00 [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) |
| − | **Module 1-3 (1:30-2:45) | ||
# 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 | + | * 2:45 - 3:00 pm Coffee-break |
| − | **Module 4-6 (3:00-4:00) | + | **Module 4-6 (3:00-4:00 pm) |
| − | #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 | ||
# Annotating the preoperative plan and saving the scene | # Annotating the preoperative plan and saving the scene | ||
| − | |||
| − | |||
== Preparation for the Workshop == | == Preparation for the Workshop == | ||
Revision as of 20:16, 3 April 2009
Home < Events:Slicer Workshop August 2009Contents
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.
Course Faculty
- Sonia Pujol, Ph.D., Instructor in Radiology, Harvard Medical School
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA
- Noby Hata, Ph.D, Assistant Professor 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
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).
Agenda
Morning: Introduction to Slicer
- 9:00 am - 9:10 am Preliminary session: Software and data installation trouble shooting
- 9:10 am - 9:30 am Slicer3 Overview and Applications (Sonia Pujol)
- 9:30 am - 10:30 am Hands-on Session 1: Data Loading and 3D Visualization (Sonia Pujol)
- 10:30 am - 10:45 am Coffee-break
- 10:45 am - 11:30 am Hands-on Session 2: Data Saving (Sonia Pujol)
- 11:30 am - 12:00 pm Discussion and Conclusion
- 12:00 -1pm Lunch Break
Afternoon: Introduction to Slicer IGT
- 1:00 - 1:30 pm Introduction: Why Slicer 3 for your IGT research? An example from BWH BrainLab collaboration (15 min. Hata)
- 1:30 - 4:00 pm Neurosurgical Planning and Guidance by Slicer"
- Module 1-3 (1:30-2:45 pm)
- Loading and visualizing anatomical MRI data
- Incorporating fMRI data using image registration and thresholding
- Creating a 3D model of the tumour volume
- 2:45 - 3:00 pm Coffee-break
- Module 4-6 (3:00-4:00 pm)
- Predicting the locations of brain structures using image registration and a brain atlas
- Incorporating brain fiber tractography from diffusion weighted images
- 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 release appropriate to the computer you will be bringing to the workshop:
- Windows: Slicer3-3.2.2008-08-08-win32.exe
- Mac OSX Darwin PPC: Slicer3-3.2.2008-08-08-darwin-ppc.tar.gz
- Mac OSX Darwin Intel: Slicer3-3.2.2008-08-08-darwin-x86.tar.gz
- Linux x86 Slicer3-3.2.2008-08-08-linux-x86.tar.gz
- Linux x86-64 Slicer3-3.2.2008-08-08-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.
- Data to download: Please install the tutorial dataset SlicerSampleVisualization.tar.gz.
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