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3D Slicer & NA-MIC: Overview and Applications. Steve Pieper, PhD. Acknowledgments.

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3d slicer na mic overview and applications

3D Slicer & NA-MIC:Overview and Applications

Steve Pieper, PhD


  • F. Jolesz, R. Kikinis, C. Tempany, P. Black, S. Wells, CF. Westin, M. Halle, N. Hata, T. Kapur, A.Tannenbaum, M. Shenton, E. Grimson, P.Golland, W.Schroeder, J. Miller, N. Aucoin, K. Hayes, S. Barre, W. Plesniak, R. Gollub, S. Pujol and many more….

Overall goal for na mic
Overall Goal for NA-MIC

  • Why Medical Research?

    • To Help Patients!

How to make this happen
How to Make this Happen?

  • Enable World-Class Biomedical Research

  • Develop a Comprehensive Platform

  • Create a Community of Developers and Users

  • Ensure Maximum Reusability of Software

Autism development
Autism Development

  • Correlate Localized Brain Development with Observed Behavioral Characteristics of Autism

  • Structural and Diffusion Imaging at 2yo and 4yo

  • Cortical Thickness and Subcortical Volume Metrics

Blue: Growth

Red: Atrophy

Green: No Change

Images: Hazlett et al


  • Structural and Diffusion to Discover Disruptions Correlated with Symptoms

  • First Generation DBP

    • Regional Analysis of FA Based on Manual Tract Identification

  • Second Generation DBP

    • Stochastic Tractography, Improved Metrics, Registration

Images Ngo et al.

Prostate disorders
Prostate Disorders

  • Segmentation tool for Brachytherapy Planning and Biopsy

  • Navigation for Biopsy

  • Future FUS and Robot Applications

Haker SJ, Mulkern RV, Roebuck JR, Barnes AS, Dimaio S, Hata N, Tempany CM.: Magnetic resonance-guided prostate interventions. Top Magn Reson Imaging. 2005 Oct;16(5):355-68.

Lupus lesions
Lupus Lesions

  • Automatic Analysis of White Matter Abnormalities in Neuropsychiatric SLE (Lupus)

  • About 1.5 Million Americans with Lupus, Underlying Pathologic Processes Unknown – Possibly Vascular

Hypointense on T1

Hyperintense T2

Hyperintense on FLAIR

Images: Bockholt et al

Patient specific finite element model development
Patient-Specific Finite Element Model Development

  • Iowa: Kiran H. Shivanna, Vincent A. Magnotta, Nicole M. Grosland,

  • NA-MIC: Steve Pieper, Curt Lisle

  • Automate the generation of high quality hexahedral meshes

  • Inclusion of soft tissues such as cartilage

  • Automated Segmentation

  • Validation

  • Published / Accepted

    • Devries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning. Skeletal Radiol. 2008 Jan;37(1):35-42. Epub 2007 Oct 25.

    • Gassman EE, Powell SM, Kallemeyn NA, DeVries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM, Automated Bony Region Identification Using Artificial Neural Networks: Reliability and Validation Measurements. Skeletal Radiology (accepted / online).

  • Grant funding NIH

    • R21 (EB001501)

    • R01 (EB005973)

Alcohol and stress

Chlorocebus aethiops (vervet)

Alcohol and Stress

  • Primate (Rhesus and Vervet) Models to Study the Effect of Chronic Alcohol Self-Administration on Brain Structure and Function

  • Compare Mother-Reared vs. Nursery-Reared

  • Apply Automated Segmentation Tools to Assess Cortical and Subcortical Regions (EMSegmenter, Pohl et al)

* Rhesus template and atlas graciously provided by Martin Styner and collaborators

Images: Wyatt et al

Image guided therapy igt
Image Guided Therapy (IGT)

  • Is the active visualization of medical images to aid in decision making during a procedure.

  • Allows physician to

    • See Beyond the Surface

    • DefineTargets

    • Control the Interventions

  • Enables new procedures, decreases invasiveness, optimizes resection

Dimaio SP, Archip N, Hata N, Talos IF, Warfield SK, Majumdar A, Mcdannold N, Hynynen K, Morrison PR, Wells WM 3rd, Kacher DF, Ellis RE, Golby AJ, Black PM, Jolesz FA, Kikinis R.: Image-guided neurosurgery at Brigham and Women's Hospital.IEEE Eng Med Biol Mag. 2006 Sep-Oct;25(5):67-73


Provided by Archip, Warfield

Alignment of all pre-operative datasets to the intra-operative images achieved during the neurosurgery.

Archip N, Clatz O, Whalen S, Kacher D, Fedorov A, Kot A, Chrisochoides N, Jolesz F, Golby A, Black PM, Warfield SK. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage. 2007 Apr 1;35(2):609-24

Liver lesion treatment
Liver Lesion Treatment

  • Needle Placement for CT-Guided Radio Frequency Ablation (RFA)

    • Unresectable Hepatocellular Carcinoma (HCC) and Liver Metastases

  • Open Source Environment

    • Slicer3 and IGSTK

  • Automated Liver Segmentation

  • Path Planning Tools for Multiple Overlapping Lesions

  • Validation on Swine Model

Images: Cleary et al

Na mic governance
NA-MIC Governance

Software Sharing:


  • …software should be freely available …

  • …permit the commercialization of enhanced or customized versions …

  • …include the ability of researchers outside the center and its collaborating projects to modify the source code and to share modifications …

Bsd style license
BSD Style License

  • Open Source

  • No license fees

  • No restriction on use

    • Clinical and commercial uses do not require our permission

  • No guarantees

    • User is responsible for making sure that the software works, we promise nothing. Same for compliance with all regulations.

    • E.g. if you want to use our software for clinical trials, you have to apply for the proper authorizations at your institution

  • NO requirement to give your code back to open source (NOT viral).

    • You can contribute code back to us, if you want to do that and it is our decision if we will accept it.

  • Acknowledge our contribution

  • See http://www.slicer.org for more information

Foss a public highway
FOSS – A Public Highway…

  • Open-source is like a Public Road System

    • Provides Infrastructure for a Variety of Uses

    • Driveways can Lead to Anything:

      • a Public Park

      • a Private Facility

        FOSS= Free Open Source Software

Provided by Pieper, Kikinis

Na mic a network of peers


BWH: Ron Kikinis, (Overall PI)

Core 1 Algorithms

Utah: Ross Whitaker (Core 1 PI)

MIT: Eric Grimson

UNC: Guido Gerig

MGH: Bruce Fischl, Dave Kennedy

GaTech: Allen Tannenbaum

Core 2 Engineering

Kitware: Will Schroeder (Core 2 PI)

GE: Jim Miller

Isomics: Steve Pieper

UCSD: Mark Ellisman

UCLA: Art Toga

Core 3 DBP 2004-2007

BWH: Martha Shenton

Dartmouth: Andy Saykin

UCI: Steve Potkin

UofT: Jim Kennedy

DBP 2007

UNC: H. Cody

BWH: M. Kubicki

Mind Institute: J. Bockolt

Queens University: G. Fichtinger

Core 4 Service

Kitware: Will Schroeder

Core 5 Training

MGH: Randy Gollub

Core 6 Dissemination

Isomics: Steve Pieper, Tina Kapur

Core 7 Management

BWH: S. Manandhar

NA-MIC: A Network of Peers

Provided by Pieper, Kikinis

Dissemination and training
Dissemination and Training

  • National and International Events


  • All Materials on Wiki

  • Project Weeks

    • Full Week Each Summer

    • ½ Week at Winter AHM

  • Workshops

    • MICCAI 2005, 2006, 2007, 2008..

    • OHBM, RSNA, Munich, NCI…

What is 3d slicer
What is 3D Slicer?

  • Reference NA-MIC Kit Implementation

  • A platform for image analysis and visualization

  • Current Releases 2.7 and 3.0

    • 2.7 most features and documentation

    • 3.0 focus of current activity

  • A freely-downloadable program

    • Source code and executables available for Windows, Linux, and Mac OS X

  • Slicer is a research platform:

    • NOT an FDA approved medical device

    • NOT finished – some parts will work better than others

Slicer features
Slicer Features

  • I/O:

    • Image: DICOM, NIfTI, Analyze, Meta, NRRD, MGZ...

    • Surface: vtk, vtp, stl, freesurfer, fiber bundle

  • Coordinate Systems: Patient-Referenced Data

  • Visualization: Volume Rendering, Surfaces, Slices Planes, Clipping, Volume Overlays...

  • Filtering: Denoising, Nonlinear/Aniostropic Smoothing, Format Conversion

  • Registration: Multimodal (e.g. CT/MR), Rigid, Affine, BSpline. Apply Transforms to other volumes.

More slicer features
More Slicer Features

  • Segmentation: Manual Editor, Semi-Automated (Region Growing), Statistical Classifiers, Atlas Based

  • Diffusion Imaging: DICOM Import, Tensor Tools, Tractography

  • Quantification: Volume Measurements, Points, Lines

  • Real-time: Networked Trackers and Volume I/O

  • And more...

    • Meshing, Fiducials, Batch Processing, Remote Data I/O,

Integrated scene
Integrated Scene

  • XML-Based MRML File Stores Scene Description

    • Volumes (Images, Label Maps)

    • Models

    • Hierarchical Affine Transforms

    • Scene Data (Cameras, Colors, Fiducials, etc).

  • Manipulated in World Coordinates based on Patient RAS (Right-Anterior-Superior)

Provided by N. Archip et al