Training:DTI Workshop - Revision history

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

2017-07-10T18:07:10Z

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

Melonakos at 19:35, 6 November 2008

2008-11-06T19:35:06Z

Andy: Update from Wiki

2006-12-18T13:31:00Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:30:59Z

Update from Wiki

New page

=== Spring 2006: scheduled for Friday, May 26 ===

Local Organizer's at UNC Computer Science:

Guido Gerig, gerig at cs.unc.edu and Casey Goodlett, gcasey at cs.unc.edu

<br /> Logistical support provided by:

Sylvain Gouttard, Research Associate in Neuroimaging Laboratory (919 843 9497)

To register for this workshop, please send an email with your contanct information to "sylvain_gouttard@yahoo.fr" with subject: "NA-MIC DTI Workshop". He will add your name and affiliation to our list [[Training:DTI_Workshop_Spring_2006_Attendee_List|[Attendee List]]].

== 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 formats and management (including how to create Nrrd headers for your data).
* 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 local clinical and basic science research collaborators in the Durham/Chapel Hill/Raleigh neuroimaging community.
* To obtain feedback on this NA-MIC DTI Workshop prior to its delivery in Chicago, IL at the Human Brain Mapping meeting in June 2007.

== Workshop Logistics ==

* Venue: UNC Chapel Hill, Department of Computer Science, Sitterson Hall, Lecture Room SN 011. For directions go to this link [http://www.cs.unc.edu/General/Directions/ [Direcions]] [[Media:Sitterson.gif| [Map UNC Sitterson Hall]]].
* Enrollment is limited to the first 50 registrants.
* The program is geared to train graduate students, research fellows, junior faculty, research assistants and post-doctoral trainees. We welcome enrollees from the Departments of Psychiatry, Psychology, Radiology, and Computer Science at UNC-CH, Duke and other institutions.

== Workshop Faculty ==

* Guido Gerig, PhD
* Ross Whitaker, PhD
* [[User:Randy|Randy Gollub, MD, PhD]], MGH
* [[User:Gcasey|Casey Goodlett]], UNC
* [[User:Pieper|Steve Pieper, PhD]], BWH

== Preparation for Workshop -- ''Important Information for all attendees'' ==

Prerequisites for workshop: Introduction materials:

* 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]]]

All participants must come with their own PC, Linux or MacOS 10.4 laptop computer. Please complete the following items PRIOR to the workshop.

* Software Installation: Please install the newest version of the Slicer program [[Slicer:Slicer2.6_Getting_Started|Slicer2.6 ]] appropriate to the computer you will be bringing to the workshop.
* Data to Download: Please install the tutorial data [http://share.spl.harvard.edu/share/birn/public/software/tutorial-with-dicom.zip tutorial-with-dicom.zip], [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.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 NAMIC 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. If you need any hands on assistance after making attempts to complete this on your own with email support, please arrive early (8:30 AM).

<br />

== Final Agenda ==

=== '''9:00 AM - 4 PM''' ===

* 9:00 - 9:10 AM Goals of Workshop, Introduction to the NA-MIC Kit, and People (Randy Gollub)
* 9:10 - 10:40 '''DWI data characterization (neuroanatomy, physics)''' (Guido Gerig)
* 10:40-10:50 Coffee Break
* 10:50 - 11:50 '''Getting to Know DTI really, really well- tensors, glyphs and more''' (Ross Whitaker)
* 11:50 - 1:20 Lunch on own
* 1:20- 1:40 '''Hands-on Session 1: Creating a Nrrd header for your DWI data (coordinate and file format issues)''' (Randy Gollub)
* 1:40- 3:00 '''Hands-on Session 2: Slicer DWI analysis tool tutorial''' (Randy Gollub)
* 3:00- 3:10 Coffee Break
* 3:20 - 3:50 '''Clinical Applications of DWI''' (Guido Gerig)
* 3:50 - 4:00 Users feedback - input from participants about this Workshop

<br /> Back to [[Training:Main|Training:Main]]

@@ Line 43: / Line 43: @@
 All participants must come with their own PC, Linux or MacOS 10.4 laptop computer. Please complete the following items PRIOR to the workshop.
-* Software Installation: Please install the newest version of the Slicer program [http://www.slicer.org/slicerWiki/index.php/Slicer:Slicer2.6_Getting_Started Slicer2.6] appropriate to the computer you will be bringing to the workshop.
+* Software Installation: Please install the newest version of the Slicer program [https://www.slicer.org/wiki/Slicer:Slicer2.6_Getting_Started Slicer2.6] appropriate to the computer you will be bringing to the workshop.
 * Data to Download: Please install the tutorial data [http://share.spl.harvard.edu/share/birn/public/software/tutorial-with-dicom.zip tutorial-with-dicom.zip], [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.zip ]] and [[Media:Tensor_data.zip|TensorData.zip]].
 * FiberTracking/FiberViewer Download: [http://www.ia.unc.edu/dev/download/fibertracking/index.htm FiberTracking] [http://www.ia.unc.edu/dev/download/fiberviewer/index.htm FiberViewer] Tutorials: [http://www.ia.unc.edu/dev/tutorials/FiberTracking-1.2/manual.htm FiberTracking Manual] [http://www.ia.unc.edu/dev/tutorials/FiberViewer/index.htm FiberViewer Manual] Data: [[Media:DTI_Test.zip| Test DTI data]]

@@ Line 43: / Line 43: @@
 All participants must come with their own PC, Linux or MacOS 10.4 laptop computer. Please complete the following items PRIOR to the workshop.
-* Software Installation: Please install the newest version of the Slicer program [[Slicer:Slicer2.6_Getting_Started|Slicer2.6 ]] appropriate to the computer you will be bringing to the workshop.
+* Software Installation: Please install the newest version of the Slicer program [http://www.slicer.org/slicerWiki/index.php/Slicer:Slicer2.6_Getting_Started Slicer2.6] appropriate to the computer you will be bringing to the workshop.
 * Data to Download: Please install the tutorial data [http://share.spl.harvard.edu/share/birn/public/software/tutorial-with-dicom.zip tutorial-with-dicom.zip], [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.zip ]] and [[Media:Tensor_data.zip|TensorData.zip]].
 * FiberTracking/FiberViewer Download: [http://www.ia.unc.edu/dev/download/fibertracking/index.htm FiberTracking] [http://www.ia.unc.edu/dev/download/fiberviewer/index.htm FiberViewer] Tutorials: [http://www.ia.unc.edu/dev/tutorials/FiberTracking-1.2/manual.htm FiberTracking Manual] [http://www.ia.unc.edu/dev/tutorials/FiberViewer/index.htm FiberViewer Manual] Data: [[Media:DTI_Test.zip| Test DTI data]]

@@ Line 44: / Line 44: @@
 * Software Installation: Please install the newest version of the Slicer program [[Slicer:Slicer2.6_Getting_Started|Slicer2.6 ]] appropriate to the computer you will be bringing to the workshop.
-* Data to Download: Please install the tutorial data [http://share.spl.harvard.edu/share/birn/public/software/tutorial-with-dicom.zip tutorial-with-dicom.zip], [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.zip ]].
+* Data to Download: Please install the tutorial data [http://share.spl.harvard.edu/share/birn/public/software/tutorial-with-dicom.zip tutorial-with-dicom.zip], [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.zip ]] and [[Media:Tensor_data.zip|TensorData.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 NAMIC 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. If you need any hands on assistance after making attempts to complete this on your own with email support, please arrive early (8:30 AM).
 == Final Agenda ==
@@ Line 57: / Line 56: @@
 * 9:00 - 9:10 AM Goals of Workshop, Introduction to the NA-MIC Kit, and People (Randy Gollub)
-* 9:10 - 10:40 '''DWI data characterization (neuroanatomy, physics)''' (Guido Gerig)
+* 9:10 - 10:40 '''[[Media:MR-DTI-GG-s.ppt| DWI data characterization (neuroanatomy, physics) ]]''' (Guido Gerig)
 * 10:40-10:50 Coffee Break
-* 10:50 - 11:50 '''Getting to Know DTI really, really well- tensors, glyphs and more''' (Ross Whitaker)
+* 10:50 - 11:50 '''[[Media:DTI_intro_tutorial_May06.ppt|Getting to Know DTI really, really well- tensors, glyphs and more ]]''' (Ross Whitaker)
 * 11:50 - 1:20 Lunch on own
-* 1:20- 1:40 '''Hands-on Session 1: Creating a Nrrd header for your DWI data (coordinate and file format issues)''' (Randy Gollub)
+* 1:20- 2:40 '''Hands-on Session 1: [[Media:Slicer_DTMRI_Training4.ppt| Slicer DWI analysis tool tutorial ]]''' (Randy Gollub)
-* 1:40- 3:00 '''Hands-on Session 2: Slicer DWI analysis tool tutorial''' (Randy Gollub)
+* 2:40- 3:00 '''Hands-on Session 2: [[Media:SlicerTraining8-NrrdFileFormat.ppt|Creating a Nrrd header for your DTI data (coordinate and file format issues)]]''' (Randy Gollub)
 * 3:00- 3:10 Coffee Break
-* 3:20 - 3:50 '''Clinical Applications of DWI''' (Guido Gerig)
+* 3:20 - 3:50 '''[[Media:Clinical_Use.ppt| Clinical Applications of DWI ]]''' (Guido Gerig)
 * 3:50 - 4:00 Users feedback - input from participants about this Workshop
 <br /> Back to [[Training:Main|Training:Main]]