Physiology & function



Daniel Haehn

Steve pieper

  • CEO at Isomics, Inc.
  • Chief Architect of 3D Slicer
  • VIZBI Veteran

http://slicer.org

Daniel haehn

  • Research Software Developer
  • Contributor to 3D Slicer
  • WebGL Enthusiast

FNNDSC

http://slicedrop.com

Webgl?

brain camera!

MR Scanner at BCH Waltham *
* Nadine Gaab, BCH

MRI Data

Typically
  • ~1mm resolution
  • 256x256x170 vx dimensions
    (for Neuroimaging)
  • ~20 MB

multi modality imaging

Combined structural MR, 2D and 3D Segmentations as well as DTI Fiber Tracking
MEG response overlay on 3D Segmentation *
* Banu Ahtam, BCH

Fetal MRI

Problem: Motion

Fetal MRI: Diagnostic

28 weeks, pathologic
28 weeks, healthy atlas *
After Motion Correction
* Atlas data from Imperial College

2d visualization

  • Window/Level
  • Corner Annotations
  • Pseudo Color
  • Lightbox view

2d visualization

label maps


Automatic or Manual Segmentation

3d visualization

3d visualization

volume rendering

  • Ray Casting
    • Summation (simulated X-Ray)
    • Maximum Intensity Projection
    • Shaded Surface Display
Fused PET-CT Volume Rendering *
* Joris Heuberger, University Hospital of Geneva
Exposure Render: Photo-realistic Volume Rendering (CUDA) *
* Thomas Kroes, TU Delft

3d visualization

Surfaces

Left Brain Hemisphere
with Curvature overlay *
* Rudolph Pienaar, BCH
  • Triangulation of 2D Label Maps
  • Material properties, Lighting, Opacity
  • Overlays
Cerebral Aneurysm modeled with clipping plane *
* Luca Antiga, Orobix Srl.

3d visualization

fiber tracking (DTI)

Tumor with surrounding Brainfibers *
* Ron Kikinis, BWH
'

registration

Alignment of Images

  • Patient specific
    • Scans over time (4D)
    • Disease Tracking *

* Andrey Fedorov, BWH
  • Group-based
    • Comparison Studies
    • Atlas Alignment

software

software

Free Downloads

file formats

  • Volume Data
    • DICOM
    • .NII, .NII.GZ, .NRRD, .MGH, .MGZ
  • Surface Meshes
    • .VTK, .VTP, .STL, .OBJ
    • SMOOTHWM, .INFLATED, .SPHERE, .PIAL ...
  • Fiber Tracks
    • .TRK, .STL, .VTK

demos

demos

slice:DROP


http://slicedrop.com

demos

knee atlas


http://demos.goxtk.com/knee_atlas/

demos

brain atlas


http://demos.goxtk.com/brain_atlas/

demos

Semantic Movies


http://gallantlab.org/semanticmovies/ Huth, Nishimoto, Vu and Gallant (2012), "A continuous semantic space describes the representation of thousands of object and action categories across the human brain", Neuron 2012

demos

stackdrop


http://stackdrop.org

demos

fetal mri


http://fetalmri.org

demos

3d slicer webGl export


https://github.com/xtk/SlicerWebGLExport

demos

An easy-to-use WebGL library

						var r = new X.renderer3D();
r.init();

// .. load a .VTK mesh
var m = new X.mesh();
m.file = 'skull.vtk';

// add it ..
r.add(m);

// .. render it
r.render();
					
http://goXTK.com

future

zSpace Virtual Holographic Display
http://zspace.com
  • Virtual Reality / Augmented Reality
    • Human-Computer Interaction
  • GPU Computing using WebCL!
  • Higher Resolution, larger Data
Oculus Rift VR headset
http://oculusvr.com
Leap Motion Controller
http://leapmotion.com

thank you

http://danielhaehn.com/p/vizbi2013