Difference between revisions of "Events:UCLA-Slicer-Training-11-2010"
m (Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/") |
|||
| (8 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
== Logistics == | == Logistics == | ||
| + | {| class="wikitable2" border="1" cellpadding="8" cellspacing="1" | ||
| + | | style="width:25%" |[[Image:NAMIC.jpg]] | ||
| + | | style="width:25%" |[[Image:Logo_nac.gif]] | ||
| + | | style="width:25%" |[[Image:NCIGTlogo.gif]] | ||
| + | | style="width:25%" |[[Image:Catalyst_logo_final.jpg|150px]] | ||
| + | |} | ||
Location: Neuroscience Research Building (NRB), Room 470, UCLA campus. | Location: Neuroscience Research Building (NRB), Room 470, UCLA campus. | ||
| Line 9: | Line 15: | ||
== Agenda == | == Agenda == | ||
*9:00-10:00 am Computer setup assistance by the instructors | *9:00-10:00 am Computer setup assistance by the instructors | ||
| − | *10:00-10:30 am Introduction to NA-MIC and the Slicer community (Ron Kikinis) | + | *10:00-10:30 am [[media:Kikinis-NA-MIC-2010-09-20.ppt|Introduction to NA-MIC]] and [[media:Kikinis-Slicer Community-2010-09-20.ppt|the Slicer community]] (Ron Kikinis) |
*10:30-12:15 pm [[media:Slicer3_DataLoadingAndVisualization_UCLA2010_SoniaPujol.pdf | Data Loading and 3D Visualization ]](Sonia Pujol) | *10:30-12:15 pm [[media:Slicer3_DataLoadingAndVisualization_UCLA2010_SoniaPujol.pdf | Data Loading and 3D Visualization ]](Sonia Pujol) | ||
*12:15-1:00 pm Lunch | *12:15-1:00 pm Lunch | ||
*1:00-2:15 pm [[media:ManualRegistration_UCLA2010.pdf | Image Registration ]] and [[media:InteractiveEditorTutorial_UCLA2010_SoniaPujol.pdf | Interactive Editing ]](Sonia Pujol) | *1:00-2:15 pm [[media:ManualRegistration_UCLA2010.pdf | Image Registration ]] and [[media:InteractiveEditorTutorial_UCLA2010_SoniaPujol.pdf | Interactive Editing ]](Sonia Pujol) | ||
| − | *2:15-2:45 pm Atlas-Based Classification (Marcel Prastawa) | + | *2:15-2:45 pm [[media:NAMIC-ABC-UCLA-08Nov2010.ppt|Atlas-Based Classification]] (Marcel Prastawa) |
*2:45-3:00 pm [[media:TBIDataAnalysis_SoniaPujol.pdf | TBI Cases]] (Sonia Pujol)[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C31 TBI Registration Case Library] | *2:45-3:00 pm [[media:TBIDataAnalysis_SoniaPujol.pdf | TBI Cases]] (Sonia Pujol)[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C31 TBI Registration Case Library] | ||
*2:45-3:00 pm Questions from the Audience and Discussion (Ron Kikinis/Sonia Pujol) | *2:45-3:00 pm Questions from the Audience and Discussion (Ron Kikinis/Sonia Pujol) | ||
| Line 22: | Line 28: | ||
This format is used in Slicer to represent the necessary information about a DWI image volume, its anatomical orientation, and all the DWI-specific acquisition parameters for estimating the diffusion tensors. A detailed description of the Nrrd file format usage for DWI images and DTI data can be found [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format here]. | This format is used in Slicer to represent the necessary information about a DWI image volume, its anatomical orientation, and all the DWI-specific acquisition parameters for estimating the diffusion tensors. A detailed description of the Nrrd file format usage for DWI images and DTI data can be found [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format here]. | ||
| − | The [ | + | The [https://www.slicer.org/wiki/Modules:DicomToNRRD-3.6 DicomToNrrd module] in Slicer can be used to convert Dicom data into Nrrd. A detailed [https://na-mic.org/w/images/7/77/SlicerTraining9_DTI-FromDicomToNrrd.ppt tutorial] describes how to construct a nhdr file from a set of images, which can be in Dicom or in other format such as Nifti, and a list of known gradients, using the Teem Library. |
== Local Organizer== | == Local Organizer== | ||
| Line 45: | Line 51: | ||
* Mac Darwin: [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20-darwin-x86] | * Mac Darwin: [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20-darwin-x86] | ||
| − | Please download the [[media:Slicer3VisualizationDataset.zip | 3D Visualization dataset]], [ | + | Please download the [[media:Slicer3VisualizationDataset.zip | 3D Visualization dataset]], [https://www.slicer.org/wiki/File:EditorTutorialDataset.zip Editor dataset], and [http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Registration dataset] in preparation for the workshop. |
== Slicer3 Training Survey == | == Slicer3 Training Survey == | ||
| + | [http://www.surveymonkey.com/s/GZDXKXQ Please click here to take the Slicer3 Training Survey] | ||
| − | [http://www. | + | == Slicer Community == |
| − | + | Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] for questions and feature requests related to the software. | |
| − | |||
[[Events#2010|Back to Events 2010]] | [[Events#2010|Back to Events 2010]] | ||
Latest revision as of 18:27, 10 July 2017
Home < Events:UCLA-Slicer-Training-11-2010Contents
Logistics
|
|
|
|
Location: Neuroscience Research Building (NRB), Room 470, UCLA campus.
Date: Monday November 8, 2010
Registration: To sign-up for this event, please fill in the registration form and send it by e-mail to Jack Van Horn, PhD [jack.vanhorn at loni.ucla.edu] before Friday November 5.
Agenda
- 9:00-10:00 am Computer setup assistance by the instructors
- 10:00-10:30 am Introduction to NA-MIC and the Slicer community (Ron Kikinis)
- 10:30-12:15 pm Data Loading and 3D Visualization (Sonia Pujol)
- 12:15-1:00 pm Lunch
- 1:00-2:15 pm Image Registration and Interactive Editing (Sonia Pujol)
- 2:15-2:45 pm Atlas-Based Classification (Marcel Prastawa)
- 2:45-3:00 pm TBI Cases (Sonia Pujol)TBI Registration Case Library
- 2:45-3:00 pm Questions from the Audience and Discussion (Ron Kikinis/Sonia Pujol)
Notes on the Nrrd file format
The Nrrd file format, which is part of the NA-MIC kit, accurately represents N-dimensional raster information for scientific visualization and medical image processing. This format is used in Slicer to represent the necessary information about a DWI image volume, its anatomical orientation, and all the DWI-specific acquisition parameters for estimating the diffusion tensors. A detailed description of the Nrrd file format usage for DWI images and DTI data can be found here.
The DicomToNrrd module in Slicer can be used to convert Dicom data into Nrrd. A detailed tutorial describes how to construct a nhdr file from a set of images, which can be in Dicom or in other format such as Nifti, and a list of known gradients, using the Teem Library.
Local Organizer
- Jack Van Horn, PhD, Laboratory of Neuro Imaging, UCLA School of Medicine
Teaching Faculty
- Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
- Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
- Nobuhiko Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
- Marcel Prastawa, Ph.D., Scientific Computing and Imaging Institute, University of Utah
Preparation for the Workshop
The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers. All participants are required to come with their own laptop computer and install the software and datasets prior to the event.. A minimum of 1 GB of RAM (2 GB if possible) and a dedicated graphic accelerator with 64mb of on board graphic memory are required.
Please install the Slicer3.6.1 version appropriate to the laptop computer you'll be bringing to the tutorial:
- Windows: Slicer3-3.6.1-2010-08-23-win32.exe
- Linux 64: Slicer3-3.6.1-2010-08-23-linux-x86_64
- Linux 32: Slicer3-3.6.1-2010-08-20-linux-x86
- Mac Darwin: Slicer3-3.6.1-2010-08-20-darwin-x86
Please download the 3D Visualization dataset, Editor dataset, and Registration dataset in preparation for the workshop.
Slicer3 Training Survey
Please click here to take the Slicer3 Training Survey
Slicer Community
Participants are invited to join the Slicer user and Slicer developer community for questions and feature requests related to the software.
Back to Events 2010
