Difference between revisions of "User:Noby"
From NAMIC Wiki
| Line 1: | Line 1: | ||
| − | + | M==Course Title== | |
| + | [[Image:776px-Flyer SlicerWorkshop August2009.png|right|500 px]] | ||
| + | Introduction to Opensource Software Slicer and its Application to Image-Guided Therapy | ||
| − | + | == 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 | ||
| + | |||
| + | *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 ([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). | ||
| + | *'''Registration is on a first-come, first-served basis and space is limited to 15 participants'''. | ||
| + | <span style="background-color: yellow"> '''To register to this event, please send an e-mail to slicer-training at bwh.harvard.edu''' </span> with your name, affiliation, contact information and the characteristics of the laptop you'll be bringing to the workshop. | ||
| + | |||
| + | |||
| + | |||
| + | == 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 [[Media:Slicer3 Introduction IBMISPS2009 SoniaPujol.pdf | Slicer3 Overview and Applications ]](Sonia Pujol) | ||
| + | * 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 | ||
| + | * 10:45 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 | ||
| + | * 12:00 -1pm Lunch Break | ||
| + | |||
| + | ===Afternoon: Introduction to Slicer IGT=== | ||
| + | *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'''] | ||
| + | **Module 1-3 (1:30-2:45 pm) (K. Hayes) | ||
| + | # 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) (H. Liu) | ||
| + | # 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 [http://www.slicer.org/pages/Special:SlicerDownloads 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 [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. | ||
| + | |||
| + | 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]. | ||
| + | |||
| + | |||
| + | Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events] | ||
Revision as of 02:49, 9 February 2010
M==Course Title==
Introduction to Opensource Software Slicer and its Application to Image-Guided Therapy
Contents
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
- 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
- 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 Slicer3 for your IGT research? An overview of Slicer3 for IGT. (15 min. O'Donnell)
- 1:30 - 4:00 pm Neurosurgical Planning and Guidance by Slicer
- Module 1-3 (1:30-2:45 pm) (K. Hayes)
- 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) (H. Liu)
- 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 Slicer3.4 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.
- Data to download: Please install the Slicer3VisualizationDataset.
Back to NA-MIC Events
