Difference between revisions of "Training:OHBM2007 Training Workshop"
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| + | [[Image:Photo 060907 002.jpg|thumb|right|350px| The workshop in full swing.]] | ||
= Satellite Workshop Goals = | = 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 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 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 | + | * 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 /> | * To establish contact between NA-MIC Tookit experts (users and developers) and basic and clinical researchers in the global neuroimaging community.<br /> | ||
| Line 11: | Line 12: | ||
* June 9, 2007, 8:00 AM- 5:00 PM<br /> | * June 9, 2007, 8:00 AM- 5:00 PM<br /> | ||
| − | * 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| | + | * 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. | * 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. | *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== | ==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, 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). | + | * '''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. | * 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. | ||
| Line 28: | Line 28: | ||
* '''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'''. | * '''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 == | == Workshop Faculty == | ||
| Line 33: | Line 34: | ||
* Guido Gerig, PhD, University of North Carolina | * 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: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 (Brigham and Women's 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]], Harvard Medical School (Brigham and Women's 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 | * Katie Hayes, Brigham and Women's Hospital Surgical Planning Laboratory | ||
| − | |||
| − | |||
| − | |||
== Preparation for Workshop -- ''Important Information for all attendees'' == | == Preparation for Workshop -- ''Important Information for all attendees'' == | ||
| − | + | Suggested background reading for workshop:<br /> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | * 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 /> | ||
| − | + | <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 /> | |
| + | 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). | ||
| − | + | '''NOTE:''' ''Windows Vista is not supported at this time.'' | |
| + | * <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]]. | ||
| + | <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). | ||
<br /> | <br /> | ||
| − | == Agenda == | + | == Agenda == |
| − | + | === '''8:30 AM - 5 PM''' === | |
| − | === '''8: | + | * 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] | |
| − | * 8:30 - 8: | + | * 10:15 -10:30 Coffee Break |
| − | * 8: | + | * 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 ]] |
| − | * 9: | + | * 11:45 - 1:00 Lunch on own |
| − | * 10:15-10:30 Coffee Break | + | * 1:00 - 2:00 '''Clinical applications''' (Guido Gerig/Randy Gollub) [[Media:Clinical_Use_HBM_06_09_07.ppt | Slides ]] |
| − | * 10:30 - 11: | + | * 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) |
| − | * 1:00- 2:00 ''' | + | * 4:30 - 4:40 Ongoing NA-MIC Development Activities (Steve Pieper - [[media:Pieper-Slicer3-OHBM-2007-06-09.ppt | slides]]) |
| − | * 2:00-3:00 '''Hands-on Session | + | * 4:40 - 5:00 Users feedback - input from participants about this Workshop |
| − | * 3:00- 3:15 Coffee Break | ||
| − | * 3:15 - 4:30 '''Hands-on Session | ||
| − | * 4:30 - 5:00 Users feedback - input from participants about this Workshop | ||
| − | |||
<br /> | <br /> | ||
| − | + | ==To learn more about the NA-MIC Toolkit== | |
| − | ==To learn more about NA-MIC== | + | 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
Contents
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
- June 9, 2007, 8:00 AM- 5:00 PM
- The workshop is being held in the Michigan Room at the Sheraton Hotel that is hosting the 13th Annual Meeting of the Organization for Human Brain Mapping OHBM2007 Conference in Chicago, IL.
- 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.
- Download Data: Please install the tutorial datasets tutorial-with-dicom.zip, SlicerSampleDTI.zip, dwi-dicom.zip.
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
