2011 Winter Project Week:Breakout Slicer with Ron

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Moderator: Ron Kikinis

Introduction

• This is an advanced topic presentation on Slicer abilities. The intention is to familiarize the NA-MIC community with Slicer abilities.
• You have mastered the introductions and you are hungry for more.... :)
  • This means that we expect you to at least have worked through the Core Tutorials before this class.
• Ron and the creators of modules will show you advanced capabilities in Slicer 3.6

Logistics

• What: Advanced capabilities in Slicer
• Who: All the new DBP engineers, all the participants new to NA-MIC
• When: Monday afternoon: 3pm through 5pm
• Where: Room XXXX

Data

• Image data used
• 

  Case 40 from the fMRI neurosurgery data set on central.xnat.org

• 

  T1 Weighted SPGR image

• 

  T2 weighted Bzero image derived from the DWI acquisition

• 

  FLAIR image

• 

  SPGR after injection of Gd

• 

  DTI color by orientation overlayed over T2 baseline

Preliminary Program

• 10 minutes or less per segment
• Comply with Rons Rules for Tools

• Registration (Dominik Meier, Hans Johnson)
  • Register everything to the SPGR data: complete. Data, transforms and instructions available here: Reg.Lib Case 33
  • additional info: basic concept and outline of DTI registration (cookbook) on FAQ
    • List of special caveats pertaining to DTI registration and resampling
    • overview of all DTI cases currently in the registration case library
    • similar cases that required different approaches Case 29: DWI -> T2 -> T1 (direct to T1 fails), Case 03: low resol. & anisotropy require resampling, masking & manual initial alignment, Case 27: anisotropy required prior DWI resampling prior to conversion
  • Resample as needed (DTI, T2 Baseline):
    • transforms available here: Reg.Lib Case 33
• Compareview (Jim Miller)
• Scenesnapshots (Wendy Plesniak, Alex Yarmarkovic)
• Simple measurements and fiducials (Nicole Aucoin)
• Interactive editor (Steve Pieper)
• Fast segmenters: Fast Marching, RSS, GrowCutSegment (Andrey Fedorov, Yi Gao, Harini Veeraraghavan)
  • preliminary scene from Andrey (details to be added)
• DTI processing (Alex Yarmarkovic, Demian Wasserman)
• Volume Cropping (Andrey Fedorov)
• Keyboard and mouse shortcuts (Steve Pieper)
• Volume Rendering (Yanling Liu/Alex Yarmarkovic)
• EM segmentation (Kilian Pohl)

Attendees

1. Ron Kikinis
2. Steve Pieper
3. UCLA DBP Engineer: Andrei Irimia
4. Iowa DBP Engineer: Mark Scully
5. MGH DBP Engineer:
6. Utah DBP Engineer: Josh Cates
7. Utah DBP Student: Josh Blauer
8. Utah DBP PI: Rob MacLeod
9. Utah DBP Student: Chris Gloschat