Iowa-March-20-2012-Slicer-Workshop

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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

Laptop Instructions

If you are bringing a laptop to the training session, please download and install the correct Slicer binary before the event. Also, consider downloading the datasets in the Data Instructions section below before the session.

You can find the correct pre-built executable for your system below:

Note: not all steps of the tutorials can be completed on 32bit operating systems due to memory limitations.

Workshop Instructions

  • Step 1: (On the USB) Delete the directory Home->Data
  • Step 2: Create a new directory called 'workshopData' in your home directory
  • Step 3: Download the 4 archive datasets on the workshop workstation (Right-click->Save Link As->Choose 'workshopData' directory->Okay)
  • Step 5: Unzip all archive datasets into 'workshopData'
  • Step 6: (Personal laptop) If not done already, download the correct Slicer4 binary file (see Laptop Instructions above)

For USB participants: All tutorials except SimpleITK with Slicer, will be using the 'Slicer' icon. The SimpleITK with Slicer will be using the 'Slicer-ITKv4' icon.

Agenda

Time Tuesday, March 20, 2012
9:00-9:10 AM 3D Slicer, a Platform for Medical Image Computing (Ron Kikinis)
9:10-9:55 AM ‎ Data Loading and 3D Visualization (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 (Sonia Pujol) (Andriy Fedorov.Demian Wassermann)
10:30-10:45 AM Coffee Break
10:30 AM-11:30 AM SimpleITK with Slicer (Hans Johnson) SimpleITK page
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)

Slicer4 Training Survey

Click here to take the Slicer4 Training Survey

BWH/Iowa QIN/AIM meeting (March 22)

  • 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.
  • Wednesday 3/21

· 1:00 pm - 5:00pm - 4016 SC, 1501-B SC - Informal discussions

o It would be great to arrive at some consensus what to present as a preferred future steps to the U01 group on Th


o 1:00pm - 4016 SC - get together, fine-tune schedule – ALL (Bauer, Beichel, Braun, Brown, Fedorov, Kikinis (?), Sonka, Wahle, Watharkar)

o 1:15pm - AIM/Slicer - technical description, toolkit, DICOM SR relationships – Fedorov, Beichel, Bauer + whoever else wants to participate

o 2:00pm - Slicer 4.0 status – Fedorov, Beichel, Bauer + whoever else wants to participate

o 2:40pm – 1501-B SC - Demo of Iowa Slicer usage – Beichel, Bauer, Fedorov + whoever else wants to participate

o 3:20pm - Slicer/AIM integration plans and status - Fedorov, Beichel, Bauer + whoever else wants to participate

o 4:00pm – 4016 SC - XNAT at Iowa – Wahle, Fedorov, Beichel, Braun, Brown + whoever else wants to participate


· 6:00 – dinner


Thursday 3/22

· 9:00am – Radiation Oncology tour - Bayouth

· 9:30am - Radiation Oncology conf. room 01600 PFP - Overview of Slicer, Overview of AIM, DICOM SR, linkages, etc. – Recommendation to Iowa U01 which way to go è outcome of Wed technical discussion – Fedorov (DICOM-SR and the role of Siemens?)

· 10:15am - Discussion of BWH QIN use-case – Fedorov, Kikinis

· 10:45am - Iowa QIN use-case - H&N – Buatti, Beichel, Bayouth, Sunderland

· 11:30am – XNAT infrastructure, bioinformatics – outcomes of Wed discussions in light of the BWH and Iowa use cases – Braun, Brown

· 12:00 Lunch

· 1:00pm AIM/DICOM-SR/Slicer project - more general overview + discussion - Fedorov

· 2:00pm Strategy for sharing data with BWH, Stanford – web page?, XNAT? - Fedorov, Beichel, Sunderland

· 3:00pm Conclusions and next steps – Buatti, all

· 3:30pm Focused discussion for developers – address remaining and newly occurred problems based on Th program – Beichel, Fedorov

· 4:30pm Leave for airport

· 6:20pm Flight from CID


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