Difference between revisions of "Training:OHBM2007 Training Workshop"

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(69 intermediate revisions by 7 users not shown)
Line 1: Line 1:
=== June 9, 2007*** Note change in date- this is confirmed, it is the day before the official OHBM meeting starts in the same venue as the OHBM meeting ===
+
[[Image:Photo 060907 002.jpg|thumb|right|350px| The workshop in full swing.]]
 +
= Satellite Workshop Goals =
 +
 
 +
* To educate attendees in the fundamentals of Diffusion Tensor Imaging (DTI) data required to make informed decisions about how to analyze their own DTI data.<br />
 +
* To provide tutorials on DTI data validation and management (including how to put your image data into NRRD format, an emerging standard endorsed by the NA-MIC and BIRN* communities).<br />
 +
* To provide hands on tutorials in the use of NA-MIC DTI analysis tools.<br />
 +
* To establish contact between NA-MIC Tookit experts (users and developers) and basic and clinical researchers in the global neuroimaging community.<br />
  
== Workshop Goals ==
 
  
* To provide attendees with critical background education in the fundamentals of Diffusion Tensor Imaging data required to make informed decisions about how to analyze their own DTI data.
 
* To provide tutorials on DTI data validation and management (including how to put your image data into NRRD format).
 
* To provide hands on tutorials in the use of NA-MIC DTI analysis tools (including the Slicer DTI module).
 
* To establish contact between NA-MIC Tookit experts (users and developers) and basic and clinical researchers in the global neuroimaging community.
 
* To provide complementary material to what is being taught in the OHBM DTI Educational course to follow.
 
  
 
== Workshop Logistics ==
 
== Workshop Logistics ==
  
* The workshop at the Sheraton Hotel that is hosting the [http://www.humanbrainmapping.org/ OHBM Conference] on the day before the meeting, June 10, 2007 in Chicago.
+
* June 9, 2007, 8:00 AM- 5:00 PM<br />
* We anticipate that approximately 45-50 graduate students, research fellows, junior faculty, research assistants and post-doctoral trainees from among the fields of clinical neuroscience (Psychiatry, Psychology, Neurology) as well as Radiology, and Computer Science will attend.
+
* The workshop is being held in the Michigan Room at the Sheraton Hotel that is hosting the [http://www.humanbrainmapping.org/index.php?src=gendocs&ref=HBM2007_Home&category=Main| 13th Annual Meeting of the Organization for Human Brain Mapping OHBM2007 Conference] in Chicago, IL. <br />
 +
 
 +
* Enrollment is limited to approximately 45-50 attendees due to the highly interactive format of the workshop. 
 +
 
 +
*The material is targeted for an audience of graduate students, research fellows, junior faculty, research assistants and post-doctoral trainees from among the fields of clinical neuroscience (Psychiatry, Psychology, Neurology) as well as Radiology, and Computer Science.
 +
 
 +
==Registration==
 +
* '''To register, send an e-mail to Katie Mastrogiacomo (kmast at bwh.harvard.edu)'''.  Please include your contact information including full spelling of your name, degree, current institution, preferred email address for communication, your educational background and training and your reason for attending.  We would also appreciate it if you would indicate the characteristics of the computer you will be using for the workshop (OS, RAM, Processor).
  
== Workshop Faculty ==
+
* A deposit is required to hold your place in the workshop.  Please mail a check or money order for $50.00 US made out to "Brigham and Women's Hospital, NA-MIC project" to Katie Mastrogiacomo, Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital, Room L1-050, 75 Francis Street, Boston, MA 02115.
 +
 
 +
* Your deposit will be returned to you at the Workshop.  If you are unable to attend after registering and give us 48 hours advance notice, your deposit will be returned, otherwise you will forfit this earnest money.
  
* Guido Gerig
+
* Questions about logistics should be addressed to to Katie Mastrogiacomo (kmast at bwh.harvard.edu, or 617-732-7389).  Questions about content of the Workshop should be addressed  to Randy Gollub (rgollub at partners.org).
* Ross Whitaker (?)
 
* Randy Gollub
 
* Sonia Pujol
 
* Steve Pieper
 
* Katie Hayes
 
  
== Preparation for Workshop -- ''Important Information for all attendees'' ==
+
* '''This Workshop is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics'''.
  
Prerequisites for workshop: Read introductory materials to read in advance.
 
  
Please do these installations now.
+
== Workshop Faculty ==
  
All attendees are required to complete the following items prior to the workshop. Support will be provided as requested.
+
* Guido Gerig, PhD, University of North Carolina
 +
* [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
 +
* [[User:Pieper|Steve Pieper, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
 +
* Anastasia Yendiki, PhD, Harvard Medical School (Martinos Center, Department of Radiology, Massachussets General Hospital)
 +
* [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
 +
* Katie Hayes, Brigham and Women's Hospital Surgical Planning Laboratory
  
# Software Installation:
+
== Preparation for Workshop -- ''Important Information for all attendees'' ==
  
# Data to Download:
+
Suggested background reading for workshop:<br />
  
<br /> We will be happy to assist anybody who may encounter difficulties in the installation process. As first point of contact, send an email to the NAMIC-developers mailing list which will be closely monitored by NA-MIC Tookit experts. Because we will focus on how to use the application(s) during the workshop not on how to install it, please do the install before you arrive.
+
* Le Bihan D, Mangin JF, Poupon C, et al. Diffusion tensor imaging:. concepts and applications. J Magn Reson Imaging 2001;13:534–546 [http://www.meteoreservice.com/PDFs/JMRI_DTI.PDF [pdf download]]
 +
* Westin CF, Maier SE, Mamata H, Nabavi A, Jolesz FA, Kikinis R., Processing and Visualization for Diffusion Tensor MRI. Medical Image Analysis, 6(2)::93-108, June 2002 [http://lmi.bwh.harvard.edu/papers/papers/westinMEDIA02.html [pdf dowload]]
 +
* S. Mori and P.C.M. van Zijl, Fiber tracking: principles and strategies – a technical review. NMR in Biomedicine, 15(7-8):468-480, 2002 [[Media:Mori-intro-2002.pdf| [pdf download]]]<br /><br />
  
<br />
+
<span style="background-color: yellow">'''This is hands-on training. All participants must come with their own computer and install our software and data. Windows XP, Linux or MacOS 10.4 computers are supported. A minimum of 1 GB of RAM (2 GB if possible) and a dedicated graphic accelerator with 64mb of on board graphic memory are recommended.'''</span><br />
  
== Draft Agenda (subject to modifications by Workshop providers, trainees please do not edit this section) ==
+
Please complete the following items prior to the workshop.
 +
* <span style="background-color: orange">'''Software Installation'''</span><nowiki>: Please install the newest release of the Slicer program </nowiki>[https://www.slicer.org/wiki/Slicer:Slicer2.6_Getting_Started Slicer2.6] appropriate to Operating System of the computer you will be bringing to the workshop.
 +
'''NOTE:''' Intel based Macs will be supported on an experimental basis. Mac users please be sure to install the X11 application (available from the Mac OS X install disks).
  
=== '''8:00 AM - 5 PM''' ===
+
'''NOTE:''' ''Windows Vista is not supported at this time.''
  
* 8:00 - 8:45 AM (Optional) What is DTI?  Introduction to and working with DTI file formats (Sonia Pujol)
+
* <span style="background-color: orange">'''Download Data'''</span><nowiki>: Please install the tutorial datasets </nowiki>[http://share.spl.harvard.edu/share/birn/public/software/tutorial-with-dicom.zip tutorial-with-dicom.zip], [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.zip]], [[Media:Dwi-dicom.zip|dwi-dicom.zip]].
* 9:00 - 9:15 AM Goals of Workshop, Introduction to the NA-MIC Kit, and People-Introductions (Randy Gollub)
+
<br /> We will be happy to assist anybody who may encounter difficulties in the installation process. As first point of contact, send an email to the NAMIC-developers mailing list which will be closely monitored by NA-MIC Tookit experts. Because we will focus on how to use the application(s) during the workshop not on how to install it, please do the install before you arrive. Most people find that the installation can be completed without difficulties. If you need any hands on assistance after making attempts to complete this on your own with email support, please arrive early (8:00 AM).
* 9:15 - 10:45 '''DTI data characterization & clinical applications (Guido Gerig/Randy Gollub)'''
+
<br />
* 10:45-11:00 Break
 
* 11:00 - 12:00 '''Getting to Know DTI really, really well- tensors, glyphs and more''' (Ross Whitaker*)
 
* 12:00 - 1:00 Lunch on own
 
* 1:00- 1:15 '''Hands-on Session 1''' (Sonia Pujol) Getting your DTI into the NRRD format
 
* 1:15- 2:00 '''Hands-on Session 2''' (Guido Gerig) Introductory DTI tools for data exploration and characterization
 
* 2:00-3:00 '''Hands-on Session 3''' (Sonia Pujol) Slicer DTI tractography tool
 
* 3:00- 3:15 Coffee Break on own
 
* 3:15 - 4:30 '''Hands-on Session 4''' (Guido Gerig/Randy Gollub/Ross Whitaker) DTI data statistical analysis and interpretation
 
* 4:30 - 5:00 Users feedback - input from participants about this Workshop
 
  
 +
== Agenda ==
 +
=== '''8:30 AM - 5 PM''' ===
 +
* 8:30 - 8:40 AM '''Goals of Workshop''' (Randy Gollub)
 +
* 8:40 - 9:20 AM '''Introduction to DTI: what it is, how it is used clinically and its future potential''' (Randy Gollub) [http://wiki.na-mic.org/Wiki/images/5/56/Intro-DTI-Workshop-OHBM2007.ppt Slides]
 +
* 9:20 - 10:15 '''Mathematical and physical foundations of DTI''' (Anastasia Yendiki) [http://wiki.na-mic.org/Wiki/images/8/8f/Dti_namic_yendiki.ppt Slides]
 +
* 10:15 -10:30 Coffee Break
 +
* 10:30 - 11:45 '''Getting to Know DTI really, really well- tensors, glyphs and more''' (Guido Gerig) [[Media:DTI_intro_tutorial_06_09.ppt | Slides ]]
 +
* 11:45 - 1:00 Lunch on own
 +
* 1:00 - 2:00 '''Clinical applications''' (Guido Gerig/Randy Gollub) [[Media:Clinical_Use_HBM_06_09_07.ppt | Slides ]]
 +
* 2:00 - 3:00 '''Hands-on Session 1- Slicer and NA-MIC DTI tools part 1''' (Sonia Pujol/Randy Gollub/Steve Pieper/Katie Hayes) ([[media:DTI_HandsOnTraining_OHBM2007_SPujol_final.ppt | slides]])
 +
* 3:00 - 3:15 Coffee Break
 +
* 3:15 - 4:30 '''Hands-on Session 2- Slicer and NA-MIC DTI tools part 2''' (Sonia Pujol/Randy Gollub/Steve Pieper/Katie Hayes)
 +
* 4:30 - 4:40 Ongoing NA-MIC Development Activities (Steve Pieper - [[media:Pieper-Slicer3-OHBM-2007-06-09.ppt | slides]])
 +
* 4:40 - 5:00 Users feedback - input from participants about this Workshop
 
<br />
 
<br />
 +
 +
==To learn more about the NA-MIC Toolkit==
 +
Please visit our [[Slicer:Workshops:User_Training_101| Slicer 101]] Wiki page

Latest revision as of 18:07, 10 July 2017

Home < Training:OHBM2007 Training Workshop
The workshop in full swing.

Satellite Workshop Goals

  • To educate attendees in the fundamentals of Diffusion Tensor Imaging (DTI) data required to make informed decisions about how to analyze their own DTI data.
  • To provide tutorials on DTI data validation and management (including how to put your image data into NRRD format, an emerging standard endorsed by the NA-MIC and BIRN* communities).
  • To provide hands on tutorials in the use of NA-MIC DTI analysis tools.
  • To establish contact between NA-MIC Tookit experts (users and developers) and basic and clinical researchers in the global neuroimaging community.


Workshop Logistics

  • Enrollment is limited to approximately 45-50 attendees due to the highly interactive format of the workshop.
  • The material is targeted for an audience of graduate students, research fellows, junior faculty, research assistants and post-doctoral trainees from among the fields of clinical neuroscience (Psychiatry, Psychology, Neurology) as well as Radiology, and Computer Science.

Registration

  • To register, send an e-mail to Katie Mastrogiacomo (kmast at bwh.harvard.edu). Please include your contact information including full spelling of your name, degree, current institution, preferred email address for communication, your educational background and training and your reason for attending. We would also appreciate it if you would indicate the characteristics of the computer you will be using for the workshop (OS, RAM, Processor).
  • A deposit is required to hold your place in the workshop. Please mail a check or money order for $50.00 US made out to "Brigham and Women's Hospital, NA-MIC project" to Katie Mastrogiacomo, Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital, Room L1-050, 75 Francis Street, Boston, MA 02115.
  • Your deposit will be returned to you at the Workshop. If you are unable to attend after registering and give us 48 hours advance notice, your deposit will be returned, otherwise you will forfit this earnest money.
  • Questions about logistics should be addressed to to Katie Mastrogiacomo (kmast at bwh.harvard.edu, or 617-732-7389). Questions about content of the Workshop should be addressed to Randy Gollub (rgollub at partners.org).
  • This Workshop is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics.


Workshop Faculty

  • Guido Gerig, PhD, University of North Carolina
  • Randy Gollub, MD, PhD, Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
  • Steve Pieper, PhD, Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
  • Anastasia Yendiki, PhD, Harvard Medical School (Martinos Center, Department of Radiology, Massachussets General Hospital)
  • Sonia Pujol, PhD, Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
  • Katie Hayes, Brigham and Women's Hospital Surgical Planning Laboratory

Preparation for Workshop -- Important Information for all attendees

Suggested background reading for workshop:

  • Le Bihan D, Mangin JF, Poupon C, et al. Diffusion tensor imaging:. concepts and applications. J Magn Reson Imaging 2001;13:534–546 [pdf download]
  • Westin CF, Maier SE, Mamata H, Nabavi A, Jolesz FA, Kikinis R., Processing and Visualization for Diffusion Tensor MRI. Medical Image Analysis, 6(2)::93-108, June 2002 [pdf dowload]
  • S. Mori and P.C.M. van Zijl, Fiber tracking: principles and strategies – a technical review. NMR in Biomedicine, 15(7-8):468-480, 2002 [pdf download]

This is hands-on training. All participants must come with their own computer and install our software and data. Windows XP, Linux or MacOS 10.4 computers are supported. A minimum of 1 GB of RAM (2 GB if possible) and a dedicated graphic accelerator with 64mb of on board graphic memory are recommended.

Please complete the following items prior to the workshop.

  • Software Installation: Please install the newest release of the Slicer program Slicer2.6 appropriate to Operating System of the computer you will be bringing to the workshop.

NOTE: Intel based Macs will be supported on an experimental basis. Mac users please be sure to install the X11 application (available from the Mac OS X install disks).

NOTE: Windows Vista is not supported at this time.


We will be happy to assist anybody who may encounter difficulties in the installation process. As first point of contact, send an email to the NAMIC-developers mailing list which will be closely monitored by NA-MIC Tookit experts. Because we will focus on how to use the application(s) during the workshop not on how to install it, please do the install before you arrive. Most people find that the installation can be completed without difficulties. If you need any hands on assistance after making attempts to complete this on your own with email support, please arrive early (8:00 AM).

Agenda

8:30 AM - 5 PM

  • 8:30 - 8:40 AM Goals of Workshop (Randy Gollub)
  • 8:40 - 9:20 AM Introduction to DTI: what it is, how it is used clinically and its future potential (Randy Gollub) Slides
  • 9:20 - 10:15 Mathematical and physical foundations of DTI (Anastasia Yendiki) Slides
  • 10:15 -10:30 Coffee Break
  • 10:30 - 11:45 Getting to Know DTI really, really well- tensors, glyphs and more (Guido Gerig) Slides
  • 11:45 - 1:00 Lunch on own
  • 1:00 - 2:00 Clinical applications (Guido Gerig/Randy Gollub) Slides
  • 2:00 - 3:00 Hands-on Session 1- Slicer and NA-MIC DTI tools part 1 (Sonia Pujol/Randy Gollub/Steve Pieper/Katie Hayes) ( slides)
  • 3:00 - 3:15 Coffee Break
  • 3:15 - 4:30 Hands-on Session 2- Slicer and NA-MIC DTI tools part 2 (Sonia Pujol/Randy Gollub/Steve Pieper/Katie Hayes)
  • 4:30 - 4:40 Ongoing NA-MIC Development Activities (Steve Pieper - slides)
  • 4:40 - 5:00 Users feedback - input from participants about this Workshop


To learn more about the NA-MIC Toolkit

Please visit our Slicer 101 Wiki page