Surgical Planning Laboratory -1- Brigham and Womens Hospital Slicer 3 Tutorial The SPL Abdominal Atlas Ion-Florin Talos, M.D.

Slides:

Advertisements

Similar presentations

NA-MIC National Alliance for Medical Image Computing Slicer Advanced Training 11: Registration Sonia Pujol, Ph.D. Surgical Planning Laboratory.

Advertisements

Pujol S, Gollub R -1- National Alliance for Medical Image Computing Data Loading and Visualization Sonia Pujol, PhD Randy Gollub, MD, PhD Slicer3 Training.

Surgical Planning Laboratory -1- Brigham and Womens Hospital Slicer Tutorial 7 Saving Data Sonia Pujol, Ph.D. Randy Gollub, M.D.,

Pujol S, Gollub R -1- National Alliance for Medical Image Computing Stochastic Tractography Module Tri Ngo Slicer3 Training Compendium.

Surgical Planning Laboratory -1- Brigham and Womens Hospital Diffusion Tensor Imaging Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.

NCIGT NIH National Center for Image-Guided Therapy System Test for the Integration of Brainlab, BioImage Suite and Slicer3 Haiying.

Slicer3 for developers – Sonia Pujol, Ph.D. -1- National Alliance for Medical Image Computing Programming into Slicer3 Sonia Pujol, Ph.D. Surgical Planning.

Pujol S, Gollub R -1- National Alliance for Medical Image Computing Data Loading and Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard.

Surgical Planning Laboratory -1- Brigham and Womens Hospital Diffusion Tensor Imaging: from Dicom to Nrrd Sonia Pujol, Ph.D. Randy.

NA-MIC National Alliance for Medical Image Computing Slicer3 Tutorial Atlas Registration & Label Merging Dominik Meier, Ron Kikinis February.

Surgical Planning Laboratory -1- Brigham and Womens Hospital Converting DTI data into Nrrd file format Sonia Pujol, Ph.D. Gordon.

-1- iGyne1.0 Tutorial Xiaojun Chen, Ph.D. and iGyne Team Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School Surgical Planning.

NA-MIC National Alliance for Medical Image Computing Slicer3 Tutorial Manual Registration Dominik Meier, Ron Kikinis January 2010.

NA-MIC National Alliance for Medical Image Computing © 2010, All Rights Reserved Diffusion Tensor Imaging Tutorial Sonia Pujol, Ph.D.

Image Guided Therapy in Slicer3 Planning for Image Guided Neurosurgery Nobuhiko Hata, Ph.D. Slicer3 Training Compendium Neurosurgery Tutorial, N. Hata.

Image Guided Therapy in Slicer3

Slicer3 Training Compendium Pohl K, Konukoglu E, Fedorov A Measuring Volume Change in Tumors Kilian M. Pohl, Ph.D. Ender Konugolu, Ph.D. Andriy Fedorov,

NA-MIC National Alliance for Medical Image Computing Slicer3 Tutorial Manual Registration Dominik Meier, Ron Kikinis January 2010.

NA-MIC National Alliance for Medical Image Computing Slicer3 Tutorial Manual Registration Dominik Meier, Ron Kikinis January 2010.

Tokuda, J National Alliance for Medical Image Computing NA-MIC© 2010, ARR Connecting IGT Device with OpenIGTLink Junichi Tokuda, PhD Slicer3 Training Compendium.

National Alliance for Medical Image Computing © 2010, All Rights Reserved Sonia Pujol, PhD Slicer3Minute Tutorial Sonia.

Pohl K, Konukoglu E, Fedorov A National Alliance for Medical Image Computing NA-MIC© 2010, ARR Measuring Volume Change in Tumors Kilian M Pohl, PhD Ender.

National Alliance for Medical Image Computing © 2010, ARR Sonia Pujol, PhD Slicer3Minute Tutorial Slicer3 minute tutorial.

NA-MIC National Alliance for Medical Image Computing Diffusion Tensor Imaging tutorial Sonia Pujol, PhD Surgical Planning Laboratory.

NA-MIC National Alliance for Medical Image Computing © 2010, All Rights Reserved Diffusion Tensor Imaging Tutorial Sonia Pujol, Ph.D.

Data Loading & and Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School National Alliance for Medical Image Computing Neuroimage.

PublicConsultingGroup.com October 15 th Data File Upload Demonstration October 2007.

1 StarPanel How To Create a Panel and More. 2 Presentation Overview: What are Panels and How They work How to : Create a panel Add a patient to a panel.

Delegated Admin Tool Edit User Profile Training Module.

NA-MIC National Alliance for Medical Image Computing Connected Threshold Image Filter Salma Bengali, Alan Morris, Josh Cates, Rob.

NA-MIC National Alliance for Medical Image Computing CARMA Inhomogeneity Correction Filter Alan Morris, Eugene Kholmovski, Josh Cates,

NA-MIC National Alliance for Medical Image Computing [Tutorial Name] [List of authors] [Institution] [ of the first author]

Slicer4Minute Tutorial Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR

Addition 1’s to 20.

Test B, 100 Subtraction Facts

Slicer User Training 101 IGT Edition Haiying Liu Nobuhiko Hata.

Slicer Welcome Tutorial

Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Training 1 Loading and Viewing Data Sonia Pujol, Ph.D. Randy.

Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Training 1: Loading and Viewing Data.

NA-MIC National Alliance for Medical Image Computing Interactive Editor tutorial Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard.

-1- Pujol S et al. National Alliance for Medical Image Computing 3D Visualization of FreeSurfer Data Sonia Pujol, Ph.D. Silas Mann, B.Sc. Randy Gollub,

© NIH National Center for Image-Guided Therapy, 2011 Tumor Segmentation from DCE-MRI with the SegmentCAD module Vivek Narayan, Jayender Jagadeesan Brigham.

-- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium.

-1- 3DSlicer Quantitative Medical Imaging Session: Quick Overview and PET/CT Analysis Jeffrey Yap, Ph.D. Ron Kikinis, M.D. Randy Gollub, M.D., Ph.D Wendy.

NA-MIC National Alliance for Medical Image Computing Fiducials Nicole Aucoin Brigham and Women's Hospital

-1- 3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing 3D Visualization Sonia Pujol, Ph.D. Surgical.

Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Training 10 EMAtlasBrainClassifier Sonia Pujol, Ph.D. Randy.

Pujol S., Plesniak, W. -1- National Alliance for Medical Image Computing Neuroimage Analysis Center Harvard CTSC Slicer3 minute tutorial Sonia Pujol, PhD.

Sonia Pujol, PhD National Alliance for Medical Image Computing © 2010, ARR.

PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium.

Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Training 1 Loading and Viewing Data Sonia Pujol, Ph.D. Randy.

Image Guided Therapy in Slicer3 Planning for Image Guided Neurosurgery Nobuhiko Hata, Ph.D. Slicer3 Training Compendium Neurosurgery Tutorial, N. Hata.

NA-MIC National Alliance for Medical Image Computing Diffusion Tensor Imaging tutorial Sonia Pujol, PhD Surgical Planning Laboratory.

Sonia Pujol, PhD -1- National Alliance for Medical Image Computing Neuroimage Analysis Center Diffusion Tensor Imaging tutorial Sonia Pujol, Ph.D. Surgical.

Surgical Planning Laboratory -1- Brigham and Women’s Hospital 3DSlicer Hands-on session Sonia Pujol, Ph.D.

Standard Response Evaluation Criteria in Solid Tumors (RECIST) using 3D Slicer Slicer3 Training Compendium Jeffrey Yap, PhD Ron Kikinis, MD Wendy Plesniak,

Standard Response Evaluation Criteria in Solid Tumors (RECIST) using 3D Slicer Slicer3 Training Compendium Image here. Jeffrey Yap, PhD Wendy Plesniak,

Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Tutorial 4 Module: DTMRI Data: Sample Slicer DTI Sonia Pujol,

3D Visualization Sonia Pujol, Ph.D. Instructor of Radiology

Fiber Bundle Volume Measurement

shapeAnalysisMANCOVA_Wizard

3D Visualization of FreeSurfer Data

The SPL Abdominal Atlas

Slicer 3 Tutorial The SPL Abdominal Atlas

Tumor Segmentation from DCE-MRI with OpenCAD

Igyne Tutorial Xiaojun Chen, Ph.D.1 Jan Egger, Ph.D., Ph.D.1

Automatic SPHARM Shape Analysis in 3D Slicer

Interactive Editor tutorial

Presentation transcript:

Surgical Planning Laboratory Brigham and Womens Hospital Slicer 3 Tutorial The SPL Abdominal Atlas Ion-Florin Talos, M.D.

Surgical Planning Laboratory Brigham and Womens Hospital Acknowledgments NIH P41RR (Neuroimage Analysis Center) NIH U54EB (NA-MIC)

Surgical Planning Laboratory Brigham and Womens Hospital Disclaimer It is the responsibility of the user of 3DSlicer to comply with both the terms of the license and with the applicable laws, regulations and rules.

Surgical Planning Laboratory Brigham and Womens Hospital Material Slicer 3 Atlas data set CT Labels 3D-models

Surgical Planning Laboratory Brigham and Womens Hospital Learning Objectives Loading the atlas data Creating and displaying customized 3D-views of anatomy

Surgical Planning Laboratory Brigham and Womens Hospital Prerequisites Slicer Training Slicer 3 Training 1: Loading and Viewing Data

Surgical Planning Laboratory Brigham and Womens Hospital Overview Part 1: Loading the Abdominal Atlas Data Part 2: Creating and Displaying Customized 3D anatomical Views

Surgical Planning Laboratory Brigham and Womens Hospital Loading the Abdominal Atlas Data Slicer can load: Anatomic grayscale data (CT, MRI) …………………………………………. Label maps…………………………… 3D-Models……………………………… MRML Scenes ……………………….

Surgical Planning Laboratory Brigham and Womens Hospital Loading the Atlas Data Select File -> Load Scene In the pop-up window, select the file named Abdominal_Atlas2008.mrml, then click Open

Surgical Planning Laboratory Brigham and Womens Hospital 3D-models Loading the Atlas Data CT with overlaid label maps

Surgical Planning Laboratory Brigham and Womens Hospital Overview Part 1: Loading the Brain Atlas Data Part 2: Creating and displaying customized 3D anatomical views

Surgical Planning Laboratory Brigham and Womens Hospital Creating customized 3D-Views By taking advantage of the ability to selectively display 3D-models, customized 3D-views of anatomy can be created

Surgical Planning Laboratory Brigham and Womens Hospital Customized 3D-Views

Surgical Planning Laboratory Brigham and Womens Hospital Creating customized 3D-Views (1) Select the Models module Select the Display tab From the pull-down menu, select the models of interest, then click the checkbox, in order to make them visible in the 3D-view; to remove models from the 3D-view, uncheck the box

Surgical Planning Laboratory Brigham and Womens Hospital Creating customized 3D-Views (2) Select the Data module Click Create Scene Snapshot; when prompted, select a name for your customized 3D-view (e.g. Portal Circulation)

Surgical Planning Laboratory Brigham and Womens Hospital Creating customized 3D-Views (3) To switch between different customized 3D-views select the view you wish to display from the pull-down menu, then clickRestore