brain surgery navigation with live tractography

Slides:



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

Understanding Your Laptop A scavenger hunt designed to help you get to know your new computer.
Slicer4Minute Tutorial Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School Slicer4Minute - Sonia Pujol, Ph.D. NA-MIC ARR
NA-MIC National Alliance for Medical Image Computing Slicer3 Tutorial / Registration Library: Case 03 - DTI aligning low-resolution diffusion.
Once download completes, click “Open Folder” Uncheck the box “Close this dialog box when download completes” Save the file in a location easy to find.
Downloading, Installing, and Working with Dropbox.
Slicer Welcome Tutorial
NA-MIC National Alliance for Medical Image Computing Slicer Tutorial Module: DTMRI Data: Dartmouth DTI May 26-27, 2005.
Pohl K, Konukoglu E -1- National Alliance for Medical Image Computing Measuring Volume Change in Tumors Kilian M Pohl, PhD Ender Konugolu Slicer3 Training.
-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,
SlicerRT Hands-on tutorial Csaba Pinter Laboratory for Percutaneous Surgery, Queen’s University, Canada.
NA-MIC National Alliance for Medical Image Computing shapeAnalysisMANCOVA_Wizar d Lucile Bompard, Clement Vacher, Beatriz Paniagua, Martin.
DTIAtlasBuilder Adrien Kaiser Neuro Image Research and Analysis Laboratories University of North Carolina at Chapel Hill A tool to create an atlas from.
EEC-693/793 Applied Computer Vision with Depth Cameras Lecture 13 Wenbing Zhao
Trouble-shooting Tips Georgia Bulldogs I can receive, but not send messages  If you can successfully receive messages, but can’t send.
Downloading defined: Downloading is the process of copying a file (such as a game or utility) from one computer to another across the internet. When you.
Using the iPad as of 9/1/15. Learning Target: To learn how to navigate and use my iPad. Success Criterion: I can complete at least half of the items on.
Workflow based Slicer IGT Module : Tutorial Andinet Enquobahrie, PhD Kitware Inc December, 2008.
-1- 3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing 3D Visualization Sonia Pujol, Ph.D. Surgical.
MyBLAST standalone installation Lab of Systems Biology & Network Biology website Download link. 1.Click the Download link.
Historic Digimap service Ancient Roam Screen share Historic Download Questions Historic Digimap.
Downloading and Installing Autodesk Revit 2016
Setting up and getting going with…. MIT App Inventor.
NA-MIC National Alliance for Medical Image Computing Slicer3 Tutorial: Registration Library Case 14 Intra-subject Brain PET-MRI fusion.
Downloading and Installing Autodesk Inventor Professional 2015 This is a 4 step process 1.Register with the Autodesk Student Community 2.Downloading the.
Click your mouse to continue. The Office Shortcut Bar The Office Shortcut Bar contains program buttons that, when clicked, start new documents or start.
CMPF124: Basics Skills for Knowledge Workers Manipulating Windows GUI.
NA-MIC National Alliance for Medical Image Computing Using Annotations in Slicer 4.0 Yong Zhang, Kilian Pohl June 2010.
NA-MIC National Alliance for Medical Image Computing Slicer3 Tutorial: Registration Library Case 15 AC-PC Alignment Dominik Meier, Ron.
Common Computer Problems. Freezing Problem: My computer won't do anything. Solution: Make sure your computer is turned on, plugged in, and there is no.
Sonia Pujol, PhD -1- National Alliance for Medical Image Computing Neuroimage Analysis Center Diffusion Tensor Imaging tutorial Sonia Pujol, Ph.D. Surgical.
VMWare Workstation Installation. Starting Vmware Workstation Go to the start menu and start the VMware Workstation program. *Note: The following instructions.
NA-MIC National Alliance for Medical Image Computing Slicer3 Tutorial Nonrigid Atlas Registration Dominik Meier, Ron Kikinis February.
Using Audacity Let’s get Started Open Audacity. Getting started…
Troubleshooting Dashhawk Issues. Here's what you have to do to have the DashHawk run properly Go to the ACTUAL PROGRAM file (not the short cut)
Surgical Planning Laboratory -1- Brigham and Women’s Hospital Slicer Tutorial 4 Module: DTMRI Data: Sample Slicer DTI Sonia Pujol,
WHAT ARE THE STEPS TO CONNECT MY HP DESKJET 3520 TO WI-FI?
Microsoft Word 2016 Lesson 2.
EEC-693/793 Applied Computer Vision with Depth Cameras
ODMAP Level 2 access.
3D Visualization Sonia Pujol, Ph.D. Instructor of Radiology
Technology Staff Development, April 2011
Installing Citrix Receiver
Fiber Bundle Volume Measurement
Dropbox Basics.
Hillsborough Community College
EEC-693/793 Applied Computer Vision with Depth Cameras
How to Set Up and Use Your Filimin Long Distance Touch Lamp
ODMAP Level 2 access.
3D Slicer hands-on tutorial
Opening an Existing File
shapeAnalysisMANCOVA_Wizard
Offline software installation
Sometimes, you may require or wish to print from your iPhone 6/6s/7 (plus), but it would be little difficult to print from an iPhone 6/6s/7 (Plus) directly,
Technical expert studying and writing helpful articles on antivirus and other security products.
EEC-693/793 Applied Computer Vision with Depth Cameras
Microsoft Windows 2000 Professional
RR RR Problems Along With Solutions For iPhone And iPad Toll Free ( )
3D Modelling with Tinkercad
Macrosystems EDDIE: Getting Started + Troubleshooting Tips
McKesson Radiology Clinical Reference Viewer (CRV)
Microsoft Word 2010 Lesson 2 Revised February 14, 2011 Fixed Slide 4
Microsoft Word 2010 Lesson 2 Word Lesson 2 presentation prepared by Kathy Clark (Southside H.S. IT Academy Teacher at Chocowinity, NC). Content from Microsoft.
3D Visualization of FreeSurfer Data
Macrosystems EDDIE: Getting Started + Troubleshooting Tips
Microsoft Word 2010 Lesson 2.
EEC-693/793 Applied Computer Vision with Depth Cameras
Macrosystems EDDIE: Getting Started + Troubleshooting Tips
Macrosystems EDDIE: Getting Started + Troubleshooting Tips
Skills Sheet: ‘Using the 3D viewer’
Presentation transcript:

brain surgery navigation with live tractography SlicerIGT tutorial 2017 brain surgery navigation with live tractography

Prerequisites This tutorial can be completed without any previous tutorials, but the following tutorials are recommended before this one Slicer4 Minute Tutorial from https://www.slicer.org/wiki/Documentation/4.8/Tr aining SlicerIGT tutorials from http://www.slicerigt.org/wp/user-tutorial/

Install Slicer Visit http://download.slicer.org/ Download Slicer version 4.8 (blue buttons) for your operating system Run the downloaded installer Start up Slicer 1

Install Slicer extensions 1. click 2. Find and install these extensions: SlicerIGT, Sequences, SlicerDMRI 6. click 3. click 4. click 5. click 7. click

Approve restart of Slicer (if asked) 1. check 2. click

Verify extensions installed

Download tutorial data Visit the tutorial website: http://www.slicerigt.org/wp/smit-2017-tutorial/ Download the tutorial data ZIP file Unzip the contents (e.g. in your home folder)

Open dialog

1 2 2 2 3

1

About the loaded data SkullCtModel.stl: Segmentation from CT scan of the plastic skull model loaded as model MRI.nrrd: Magnetic resonance image of a person. (not the same one the plastic model was based on) loaded as a scalar volume DTIVolume.nhdr: Diffusion tensor image (from a third person) loaded as a tensor volume All three are already roughly registered (overlap)

1 2

Try 2D interactions Mouse wheel – change slice Mouse right button drag – zoom Mouse middle button drag – panning Mouse left button drag – intensity windowing Try 3D interactions Mouse left button drag – rotations Mouse wheel – zoom Mouse middle button drag – panning

1 2 select

1. see 2. Press once You won’t see anything after you press this button, but don’t worry.

2. see 1 3 4. Right click 4 Rename to “StylusTip”

Double-click to rename new transform 1. Right-click on Scene 2 Double-click to rename new transform

1 2 3

Connect to the PLUS computer If you are not connected yet… Connect to SlicerIGT2 WiFi (or SlicerIGT1, but that is slower) Password: slicerigt There will be no internet, just local network

1. see 5. Should turn ON 2 4. Check Active 3. type: 192.168.0.2

3. Drag and drop nodes to create this transform hierarchy 2. see 1 3. Drag and drop nodes to create this transform hierarchy

Checkpoint 01

1 2 3. select

Under 1 mm RMSE is acceptable now 4 1 2 3 (optional) 5. visualize blue stick WAIT! 6 WAIT! 7 Make sure to start pivot calibration when the physical tool is pivoting Start pivot calibration again until the blue stick rotates around its tip 8 see Under 1 mm RMSE is acceptable now

1

5 rename to “ReferenceToRas” 2 see 1 3 right-click 4 6 drag and drop 5 rename to “ReferenceToRas” RAS is usually our patient coordinate system

1 2 3. select

New name “ReferencePoints” 1. see 2 3 New name “ReferencePoints” 4. Create “RasPoints” 5. select

Make sure this button is unchecked when interacting with 3D viewer! 1

Set up 3D viewer like this 1 3 2

Set up 3D viewer like this 1 3 2

Set up 3D viewer like this 1 3 2

Set up 3D viewer like this 1 3 2

Set up 3D viewer like this 1 3 2

Set up 3D viewer like this 1 3 2 4. See “3”

Checkpoint 02

this button (called “From”), a new point will be created in 1 When you press this button (called “From”), a new point will be created in this list (called “From”) 2. Select “StylusTipToStylus” 3. Wait for presenter’s signal before pressing this button

See select uncheck See

Very important to reset before starting a new registration! Troubleshooting How to redo one point Delete How to reset registration 2. see 1 Very important to reset before starting a new registration! 3

Checkpoint 03

1 2 3. Volume Reslice Driver

1 2

2. see 1 5. see 3 4

2. Back to Volume Reslice Driver 1. module history 2. Back to Volume Reslice Driver

Checkpoint 04

2. see 1 3

3. double-click each coordinate and set to zero 1 2. click anywhere 3. double-click each coordinate and set to zero

1 result 2. drag and drop “F” here

1 2. double-click 3 4

1 double-click 2

Tractography Seeding

see result 1 2 3