2011 Winter Project Week:Breakout Slicer with Ron

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Moderator: Ron Kikinis


  • 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


  • 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: Main Event Room


Preliminary Program

  • Registration (Dominik Meier, Hans Johnson)
    • Update: revised dataset and Slicer Scenes for demo here:Media:RegDemo_AHM11.zip‎
    • focusing on DTI only: issues
      • T1 is too high resolution to resample DTI into (will cause memory problems); use subsampled version T1_sub instead.
      • initial misalignment is regional only, BSpline portion is sufficient (no affine required)
      • masking is required for successful registration: BRAINSfit requires two masks: moving mask for the DTI_base we get from the initial DTI_estimation; for the fixed mask T1_sub we use the same one but resampled (T1_sub_mask).
      • BRAINSfit registration will take ca. 90seconds with default settings and parameters as suggested below
      • BRAINSfit parameters: fixed volume: T1_sub, moving volume: DTI_base; check: "include BSpline Registration Phase"; output: Slicer BSpline Transform : create new; output image volume: create new; output image pixel type: short; Registration parameters: number of grid subsdivisions; = 7,5,5 ; Control of mask processing: check ROI; input fixed mask = T1_sub_mask; input moving mask: DTI_maskj
    • DTI resampling is done via ResampleDTI Volume module. Parameters
      • Input Volume: DTI, Output Volume: create new; Reference Volume: "T2-sub"; Transform Node: Bspline Xform produced by BRAINSfit, check output-to-input" box.
    • for the procedures to register everything to the T1 (incl. contrast, FLAIR, T2) , see here: Reg.Lib Case 33
    • Resample as needed (DTI, T2 Baseline):
  • Compareview (Jim Miller)
  • Scenesnapshots (Wendy Plesniak, Alex Yarmarkovich) Sample scene (large) including scene snapshots: fMRICase040.zip
  • Simple measurements and fiducials (Nicole Aucoin) Sample scene and data with snapshots for fiducials, seeding, measurements
    • Fiducials tutorial and Data
      • Adding and Deleting Fiducials
      • Editing Fiducials
      • Display properties
      • Linking (control key+mouse move) and jumping slices (right click in table)
      • Passing Fiducials to Command Line modules
      • Fiducial Seeding
    • Measurements
      • Ruler (put down two fiducials, Control-m to make a ruler)
      • Angle
      • Constraining to slices or models
  • Interactive editor (Steve Pieper)
  • Fast segmenters: Fast Marching, RSS, GrowCutSegment (Andrey Fedorov, Yi Gao, Harini Veeraraghavan)
    • Fast Marching demo scene
      • inner part of the tumor segmented from SPGR
      • outer part of the tumor segmented from post-Gad
      • WM and GM segmented from N4-processed SPGR (WM segmentation of the original SPGR volume is included, note under-segmented WM in the skull base)
      • all segmentations were done using FastMarching, fiducials are included for each of the segmentations
      • no fine-tuning of the fiducial locations was done -- this is an example result one can get almost right away
      • rule of thumb in placing fiducials: try to cover uniformly the volume you are trying to segment; this is particularly important for large structures like WM/GM
    • RSS demo scene
      • Segment the inner part of the tumor from SPGR using RSS
  • DTI processing (Alex Yarmarkovich, Demian Wasserman)
  • Volume Cropping (Andrey Fedorov)
  • Keyboard and mouse shortcuts (Steve Pieper)
  • Volume Rendering (Yanling Liu/Alex Yarmarkovich/Curtis Lisle)
  • EM segmentation (Kilian Pohl)


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