Iowa-March-20-2012-Slicer-Workshop
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Contents
Training Faculty
- Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA
- Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA
- Demian Wasserman, Ph.D., Brigham and Women's Hospital, Boston, MA
- Andrey Fedorov, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA
- Hans Johnson, Ph.D., University of Iowa, Iowa City, IA
- Vince Magnotta, Ph.D., University of Iowa, Iowa City, IA
- David Welch, University of Iowa, Iowa City, IA
- Eric Axelson, University of Iowa, Iowa City, IA
- Joy Matsui, University of Iowa, Iowa City, IA
Logistics
- Date: Tuesday March 20th and Wednesday March 21st, 2012
- Location: Information Commons West (2nd floor), Hardin Library, University of Iowa, Iowa City
- File:3D slicer training 2012-final.pdf
- Slicer version: Slicer 4 - please be sure to use these versions:
Note: not all steps of the tutorials can be completed on 32bit operating systems due to memory limitations.
Please download and install Slicer to your laptop before the event.
Workshop Instructions
- Step1: Download the 4 archive datasets on the workshop workstation (memory stick)
- Step2: Create a new directory called 'workshopData' in your home directory
- Step3: Copy the 4 archive datasets in the directory workshopData
- Step4: Unzip all archive datastes
Tentative Agenda
| Time | Tuesday, March 20, 2012 | |
| 9:00-9:10 AM | Welcome (Ron Kikinis) | |
| 9:10-9:55 AM | Slicer Basics (Sonia Pujol) | |
| 9:55-10:45 AM | DTI Tutorial: From DWI images to tracts (Sonia Pujol) | |
| 10:45-11:00 AM | Coffee Break | |
| 11:00-12:15 PM | Neurosurgical Workflow (Sonia Pujol) | |
| 12:15-1:30 PM | Lunch | |
| 1:30-3:00 PM | XNAT, Registration (Hans Johnson) | |
| 3:00-3:30 PM | Coffee Break | |
| 3:30-5:00 PM | BWH QIN project: Quantitiative MRI of prostate cancer as a biomarker and guide for treatment: Presentation and Slicer demo (Andrey Fedorov) | |
| Time | Wednesday, March 21, 2012 | |
| 09:00-10:30 AM | Programming in Slicer4: The Hello Python tutorial (Sonia Pujol/Andrey Fedorov/Demian Wassermann) | |
| 10:30-10:45 AM | Coffee Break | |
| 10:30 AM-11:30 AM | SimpleITK with Slicer (Hans Johnson) | |
| 11:30-12:00 PM | Concluding Remarks and Feedback | |
| 1:00-5:00 PM | DWI Discussion (Demian Wassermann) (By invitation only) | QIN Discussion (Andriy Fedorov) (By invitation only) |
Note: 3rd Tuesday of the month 11AM until 1PM Iowa time is the time of monthly QIN working group TCONs (Image Analysis and Bioinformatics WGs). Some of the Iowa QIN members and Andrey Fedorov (BWH QIN) will need to attend those calls.
BWH/Iowa QIN/AIM meeting (March 22)
Agenda to be finalized by Milan Sonka, based on email communication of BWH and Iowa teams
Items of interest (Reinhard Beichel):
- AIM - general overview + discussion (~1 h)
- Discussion of BWH QIN use-case (~30 min)
- Discussion of Iowa QIN use-case - H&N (~1-2 h)
- Discussion of Iowa bioinformatics infrastructure setup: XNAT, databases, application to Iowa use cases (~30 min)
- AIM/Slicer project - overview + discussion: 2D/3D/4D objects, AIM toolkit concept vs. specific use-case implementation, ... (~2h)
- Slicer 4 - module development, GUI design, future directions, development support, etc. (~1-2h; I'm not sure if this will be covered by other presentations and who would be the right person for this)
Andrey's sugested items
1) Slicer 4.0 status and future (~30 min -- beyond what will be covered by the general workshop program, Fedorov) * what is currently available * what is being actively developed and should be available soon * it would help if Iowa collect specific set of questions according to your needs 2) AIM 3.0 overview (~1 hr, Fedorov + Iowa AIM experts) * concepts and motivation for structured reporting * AIM * alternatives (e.g., DICOM SR) * available support: user-level tools, toolkits * limitations 3) Slicer/AIM integration plans and status (~30 min, Fedorov) * connection with the existing Slicer functionality * supported annotation types * user-level workflow * limitations 4) BWH QIN use case (~30-45 min, Fedorov) * research questions of our interest * kinds of data being analyzed * processing workflows * use of Slicer * applicability of AIM 5) Iowa QIN use case (~1 hr, Iowa) * I would like to learn specifically about Iowa bioinformatics infrastructure (use of XNAT, other components) 6) Brainstorming/discussion of AIM applicability, alternatives (~1hr) 6) Focused discussion for developers, as Reinhard suggested (~1-2 hr), need to coordinate with the general program events to avoid duplication)
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