HataBCDSTalk2010 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:04:34Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Noby: /* Recommended reading before the class */

2010-10-01T10:36:53Z

Noby at 10:24, 1 October 2010

2010-10-01T10:24:44Z

Noby at 10:21, 1 October 2010

2010-10-01T10:21:17Z

Noby at 10:15, 1 October 2010

2010-10-01T10:15:36Z

Noby: Created page with '=Lecturer= Nobuhiko Hata, PhD ([http://www.spl.harvard.edu/pages/People/noby Dr. Hata's personal web page]) Assistant Professor of Radiology, Harvard Medical School Director, S…'

2010-10-01T09:55:26Z

Created page with '=Lecturer= Nobuhiko Hata, PhD ([http://www.spl.harvard.edu/pages/People/noby Dr. Hata's personal web page]) Assistant Professor of Radiology, Harvard Medical School Director, S…'

New page

=Lecturer=
Nobuhiko Hata, PhD ([http://www.spl.harvard.edu/pages/People/noby Dr. Hata's personal web page])

Assistant Professor of Radiology, Harvard Medical School

Director, Surgical Navigation and Robotics Laboratory (www.snrlab.org)

=Lab date/time/location=
*3:00- 5:00pm, March 19, 2008
*Direction http://www.spl.harvard.edu/pages/Directions

==Background:==

[[Image:robot.png|200px]]
[[Image:slicer.png|200px]]

In comparison to other medical imaging modalities, magnetic resonance imaging (MRI) has clear advantages in its volumetric scanning capabilities, tissue discrimination and the detailed delineation of anatomic features. Additionally, MR imaging has unique potential capabilities for functional physiologic imaging and temperature mapping. These features of MR imaging motivated the development of intraoperative MR imaging (IMRI) for guidance of biopsy, thermal ablation and other surgical procedures. The major application of IMRI has been neurosurgical cases, including biopsy, drainage and tumor ablation. Other applications include liver biopsy and sinus endoscopic surgery.

There are many benefits in using pre-operatively obtained MRI as part of an analysis of imagery from IMRI. For example, IMRI has some limitations in its imaging capability in comparison to pre-operative MRI from conventional diagnostic MR scanner, since requirements for interventional use (for example, the use of surface coils for good access) have some impact on the imaging capability. After performing a registration that determines the proper spatial relationship between the pre-operative MRI and IMRI, one could compare and determine whether changes in tissue structure have occurred. For instance, this would be extremely useful in evaluating the extent of tumor.

We can further appreciate the benefit of pre-operative image, if we can co-register imagery from other modalities than MRI. Currently, we can register computed tomography (CT), T1- and T2-weighted MRI: magnetic resonance angiography (MRA), single photon emission computed tomography (SPECT). Incorporation of these images can provide information that can not be deduced from regular MRI.
In general, utilizing pre- and intra-operative image registration would allow a surgeon to more precisely identify and avoid critical structures and more accurately locate pathological tissues during a procedure.

In this laboratory course, we will present our approach to register pre-operative image to intra-operative MRI and use co-registered images to navigate neurosurgeries. We will first outline the registration method through maximization of mutual information. Then, the comprehensive accuracy study of the registration and clinical application of the method are introduced. In the clinical application section, we will introduce our engineering and computational setup to achieve online and near real-time registration and navigation in an inerventional MRI scanner.
An example scenario

===Recommended reading before the class===
The following papers describe a number of IMRI applications currently under development at the Surgical Planning Laboratory. Please read the paper on neurosurgery and be familiar with the other applications.

'''Image-guided Neurosurgery at Brigham and Women’s Hospital'''
http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=294

'''MR-guided prostate interventions'''
http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1225

'''Current status and future potential of MRI-guided focused ultrasound surgery'''
http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1244

'''MRI-guided cryotherapy'''
http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1247

===Recommended exercise before the class===

If you are interested in learning how we process pre-operative images in preparation for MRI-guided therapy, download the free software slicer following the instructions in the "Slicer 101" page below.
http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

Among the courses available in the web page, we suggest you take the following topics..
*Data Loading and Visualization
*Data Saving
*Manual Segmentation
*Level-Set Segmentation
*Automatic Brain Segmentation
*Registration

==On the day of the lab....==

===Introduction===
We will present the overview of the MRI-guided therapy and technologies involved in it.
===Pre-operative diagnostic imaging===
*fMRI, CT, MRI, DT-MRI, PET, CT

===Surgical Planning===
*preoperative imaging
*registration
*planning

===Surgical Navigation===
*Patient-to-image registration
Q. What is the patient-to-image registration? What kind of mathematical process is involved in the patient-to-image registration?
Q. What is Target Registration Error, Fiducial Registration Error, and Fiducial Localization error?
[[media:west1.zip]]

*Tracking device (optical and EM)
*Guidance

===MRI-guided Therapy===
*What if we can take intra-operative image (demo)

Q. What is the difference between pre-operative image guided therapy and intra-operative image guided therapy?
Q. How would you solve the problem that intra-operative MRI has inherently less quality than pre-operative images?
Q. What are the main clinical applications in MRI-guided therapy?

==Homework problems==

===Problems we address in the demo===
#What is the patient-to-image registration? What kind of mathematical process is involved in the patient-to-image registration?
#What is Target Registration Error, Fiducial Registration Error, and Fiducial Localization error?
#What is the difference between pre-operative image guided therapy and intra-operative image guided therapy?
#What is the benefit of MRI-guided intra-operative image guided therapy?
#How would you solve the problem that intra-operative MRI has inherently less quality than pre-operative images?
#What are the main clinical applications in MRI-guided therapy?

===Open questions===
#What is the benefit of medical imaging for guiding and navigating surgery?
#What are the technologies involved in image guided therapy? List and briefly describe them in the order of workflow.
#From PubMed, find three interesting paper on MRI-guided therapy and summarize them. (Hint: the review papers on this topic can be found in the Feb 2008 issue of Journal Magnetic Resonance Imaging)
#What do you think is an unchallenged clinical target in MRI-guided therapy? (Hint: moving organs, soft tissue organs, tubular organs). Specify needs in the treatment and benefit of using MRI for guidance and monitoring.

@@ Line 38: / Line 38: @@
 *Try a tutorial on Slicer
-**Go to the tutorial page http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training
+**Go to the tutorial page https://www.slicer.org/wiki/Slicer_3.6:Training
 *Try the tutorial in the top two rows, namely "Slicer3Minute Tutorial" and "Slicer3Visualization Tutorial"

@@ Line 24: / Line 24: @@
 =Recommended reading before the class=
-*PBS secret of Brain Anatomy .Very very very good program series. Strongly suggested.
+*PBS Series Secret of Brain Anatomy . A bit old, but good portal page to start with.
 **http://www.pbs.org/wnet/brain/3d/index.html
 =Recommended exercise before the class=

@@ Line 6: / Line 6: @@
-==Speaker Bio==
+=Speaker Bio=
 Nobuhiko Hata was born in Kobe, Japan. He received the B.E. degree in precision machinery engineering in 1993 from School of Engineering, The University of Tokyo, Tokyo, Japan, and the M.E. and the Doctor of Engineering degrees in precision machinery engineering in 1995 and 1998 respectively, both from Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.  He is currently an Associate Professor of Radiology, Harvard Medical School and Technical Director of Image Guided Therapy Program, Brigham and Women’s Hospital. He started his career at Brigham and Women’s Hospital initially as a research fellow in 1995, then became Instructor of Radiology in 2000 and Assistant Professor of Radiology in 2005, all at Department of Radiology.  In 2008, He founded a research group called Surgical Navigation and Robotics Laboratory, under Image Guided Therapy Program.In the Image Guided Therapy Program and Surgical Navigation and Robotics Laboratory, he continues to work on medical image processing and robotics in image-guided surgery.  His major achievements include neurosurgical navigation combined with ultrasound imaging, surgical robot for magnetic resonance imager, and motion-adaptable surgical robot for image-guided therapy.  More importantly, he developed key technology in many “the first” therapy in MRI-guided therapy; MR-guided prostate biopsy, MR-guided laser ablation therapy of brain tumor, and MR-guided microwave ablation therapy of liver tumor. In total, he has co-authored 49 original articles and have been involved in 11 federal and non-federal grants during the course of his research career.
-=Lab date/time/location=
+=Lecture date/time/location=
 * Oct 7, 2010, 11:45- ,
 *Location TBD
@@ Line 22: / Line 22: @@
-===Recommended reading before the class===
+=Recommended reading before the class=
 =Recommended exercise before the class=

@@ Line 19: / Line 19: @@
 *The participants will learn the basics and principles of medical imaging (CT, ultrasound, MRI)
 *The participants will learn the utility of medical imaging in diagnostic medicine
-*The learners can
+*The learners can  basic anatomy of brain and its primary function.
 ===Recommended reading before the class===
@@ Line 37: / Line 38: @@
-===Recommended exercise before the class===
+=Recommended exercise before the class=
 *Download 3D Slicer/Install it in your computer
@@ Line 52: / Line 53: @@
-===Problems we address in the demo===
+=Problems we address in the class=
-#What is the patient-to-image registration? What kind of mathematical process is involved in the patient-to-image registration?
+#Describe MRI in short. What is it?
-#What is Target Registration Error, Fiducial Registration Error, and Fiducial Localization error?
+#What is the utility of MRI?
-#What is the difference between pre-operative image guided therapy and intra-operative image guided therapy?
+#Where is The Primary Motor Cortex? What is its function?
-#What is the benefit of MRI-guided intra-operative image guided therapy?
+#How do you visualize The Corticospinal Tract? What is the computational methods used?
-#How would you solve the problem that intra-operative MRI has inherently less quality than pre-operative images?
+#What does The Visual System consist of?

@@ Line 2: / Line 2: @@
 Nobuhiko Hata, PhD ([http://www.spl.harvard.edu/pages/People/noby Dr. Hata's personal web page])
-Assistant Professor of Radiology, Harvard Medical School
+Associate Professor of Radiology, Harvard Medical School
 =Lab date/time/location=
-*3:00- 5:00pm, March 19, 2008
+* Oct 7, 2010, 11:45- ,
-*Direction http://www.spl.harvard.edu/pages/Directions
+*Location TBD
+==Learning objective==
 [[Image:robot.png|200px]]
 [[Image:slicer.png|200px]]
-−
+*The participants will learn the basics and principles of medical imaging (CT, ultrasound, MRI)
-In comparison to other medical imaging modalities, magnetic resonance imaging (MRI) has clear advantages in its volumetric scanning capabilities, tissue discrimination and the detailed delineation of anatomic features. Additionally, MR imaging has unique potential capabilities for functional physiologic imaging and temperature mapping. These features of MR imaging motivated the development of intraoperative MR imaging  (IMRI) for guidance of biopsy, thermal ablation and other surgical procedures. The major application of IMRI has been neurosurgical cases, including biopsy, drainage and tumor ablation. Other applications include liver biopsy and sinus endoscopic surgery.
+*The participants will learn the utility of medical imaging in diagnostic medicine
+*The learners can
 ===Recommended reading before the class===
@@ Line 43: / Line 35: @@
 '''MRI-guided cryotherapy'''
 http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1247
 ===Recommended exercise before the class===
-If you are interested in learning how we process pre-operative images in preparation for MRI-guided therapy, download the free software slicer following the instructions in the "Slicer 101" page below.
+*Download 3D Slicer/Install it in your computer
-http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
+** Go to the down load page http://www.slicer.org/pages/Special:SlicerDownloads
+**Select "stable" releases, select your OS (Windows or Mac Intel), and select the latest release
+**After the downloading the installation file, click it and start an installation of the software.
-*Tracking device (optical and EM)
+*Try a tutorial on Slicer
-*Guidance
+**Go to the tutorial page http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training
-   Q. What is the difference between pre-operative image guided therapy and intra-operative image guided therapy?
+*[Optional] If you are comfortable using Slicer, try loading and visualizing Brain Atlas (http://www.na-mic.org/publications/item/view/1265). This will most likely be used in the lecture for demonstration.
 ===Problems we address in the demo===