Dissemination:Workshop May 26-27 2005 - Revision history

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

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

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2008-11-06T19:20:20Z

Andy: Update from Wiki

2006-12-18T19:39:12Z

Update from Wiki

New page

== Some Pictures from the Workshop ==

* [[Media:Panorama1.jpg| a "stitched" mosaic]]

== Workshop Goals ==

* To provide hands-on training in NAMIC Toolkit applications to clinical researchers.
* To establish contact between NAMIC Tookit experts (users and developers) and clinical researchers of the NAMIC community.
* To obtain feedback on how the NAMIC Toolkit applications satisfy the needs of the clinical research being carried out in NAMIC

<br />

== Workshop Logistics ==

* [[Dissemination:Workshop_May26-27_2005_Logistics|Location, Hotels, Airport Information, and Driving Directions]]
* [[Dissemination:Workshop_May26-27_2005_Feedback|Attendee Feedback -- Attendees, please provide feedback here.]]

== Workshop Participants ==

* [[Dissemination:Workshop_May26-27_2005_Attendee_List|List of Participants]]

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

All attendees are required to complete the following items prior to the workshop. Support will be provided as requested.

# Mailing List: Please ensure that you are on the mailing list [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-dissemination namic-dissemination].
# Software Installation: Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to the computer you will be bringing to the workshop, the tutorial guide for Slicer, the generic sample data set. This material is located in [[Slicer:Slicer2.5_Getting_Started|Slicer 2.5 Getting Started: Software & Sample Data ]].
# Also, go to this link [[Training:Resources_and_Information|Loading-Dartmouth-NAMIC-DTI]] and download the powerpoint presentation that will guide you through the process of accessing Dartmouth specific data sets from the BIRN portal.

* '''The documentation refers to a protocol file to be obtained from Dartmouth - this available here. Save [[Media:NAMIC-Dartmouth-2b12g-Volume.doc| this protocol file]] as slicer2/Modules/vtkDTMRI/data/NAMIC-Dartmouth-2b12g-Volume''' in your slicer distribution.

# Data to Download:
## Get the Tutorial Data with Dicom pointed to at the getting started page [http://share.spl.harvard.edu/share/birn/public/software/tutorial-with-dicom.zip [1]]
## Get this extra set of interoperative data [[Media:Mrt-images.zip| mrt-images.zip]]
## Get this data for testing registrations [[Media:Reg-sample.zip|reg-sample.zip]]
## Get this data for fMRI demonstrations: [[Media:FMRI-demo-short.zip|short sequence for small memory machines]] [[Media:FMRI-demo-long.zip|longer data sequence.]]
## Get this data for DTI demonstrations: [http://slicerl.bwh.harvard.edu/tmp/dtiviz.tar.gz dtiviz.tar.gz ]

<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. We will focus on how to use the application(s) during the workshop, so please do the install before you arrive.

== Agenda ==

Note: The computer room does not permit food, so we will be wandering downstairs to the [[http://www.dartmouth.edu/~dds/text/novackcafe.shtml|Novak Cafe]] for lunch and coffee breaks.

=== '''Day 1:noon-6pm''' ===

* 12:00 - 12:15 Goals of Workshop, Introduction to the NAMIC Kit, and People-Introductions (Ron Kikinis)
* 12:15 - 1:00 Lunch (If you had trouble downloading and/or installing Slicer 2.5 or the sample data sets, we will help you- but don't come hungry because you will miss lunch!)
* Confirm user accounts and data download
* '''1pm-5pm End-User Slicer Training'''
** Introduction (Steve Pieper) [[Media:Slicer-Overview.ppt| Overview Slides for Background (will not be presented in detail)]]
** 1:00 - 2:00 Hands-on Session 1 (Sonia Pujol, RLG-B/U) [[Media:SlicerTraining-NAMIC-1.ppt|Hands-on Session 1 Slides]], ([[Media:Laura_NAMIC_slide.ppt|Laura intro]],[[Media:AdamCohenNAMIC.ppt|Adam intro]], [[Media:Mark_NAMIC_slide.ppt|Mark intro]])
*** User Interface Overview
*** Loading Data (Volumes, Models, Scenes)
*** Viewing Images and Models (Structural MRI)
* 2:00 - 2:15 User Experiences and Applications - Segmentation (Sylvain Bouix) [[Media:01-IntroSegmentation.ppt|(slides)]]
* Hands-on Session 2 (Steve Pieper and Sylvain Bouix) [[Media:Slicer_Segmentation_Tutorial.ppt|(slides)]]
** Manual Segmentation with the Editor (SP)
** Model Making (SP)
* 3:00 - 3:15 Break
* 3:15 - 4:45 Break
** Segmentation Foundations (Sandy Wells) [[Media:NAMICSegFoundations.ppt|(slides)]]
** Voxel Classification with EMSegment (SB) [[Media:02-EMmanual.ppt|(slides)]]
** Level Set Segmentation (SB) [[Media:03-LevelSet.ppt|(slides)]]
* 4:45 - 6:15 Hands-on Session 3 (Steve Pieper) [[Media:Volume-Registration.ppt|Registration Slides]]
** Manual Registration (SP)
** Registration Foundations (Sandy Wells) [[Media:NAMICSReg-IntroEtc-sw.ppt|(slides)]]
** Automatic Registration (SP)
*** ITK-based Rigid Registration, Resampling Volumes (SP)
*** vtkAG - nonrigid Registration (SP)
** Atlas Based Segmentation with vtkAG and EMSegment (SB) [[Media:04-AtlasEMSeg.ppt|(slides)]]
** Measuring Image Statistics (SB) [[Media:05-MeasureVol.ppt|(slides)]]

=== ''' Day 2:8am-3pm ''' ===

* 8:00 - 8:15 Review and Questions
* 8:15 - 8:45 Introduction to DTI (Sylvain Bouix, Mark Dreusicke) [[Media:06-IntroDTI.ppt|(slides)]]
* 8:45 - 9:15 White Matter Neuroanatomy using Tractography (Jim Fallon)[[Media:NAMIC_Fallon_Dartmouth_post.ppt|(slides)]]
* 9:15 - 11:30 Hands on DTI Analysis Using Slicer(Tina Kapur) [[Media:Slicer_DTMRI_Tutorial_Dartmouth_Data.ppt| Slicer DTMRI Module Slides]]
** Loading Data
** Tensor Conversion
** Scalar Fields (FA, ColorByOrientation)
** 10:00 - 10:15 Break
** Tractography
** ROI Analysis (Mark D.)
* 11:30 - noon DTI Use Cases and User Experiences Discussion (Tina Kapur)
** Harvard Schiz Group
** Dartmouth Feedback / Needs
** University of Toronto
* noon - 1:00 Lunch
* 1:00 - 2:00 fMRI in Slicer (Steve Pieper and Sandy Wells)
** Statistical Foundations (SW)[[Media:NAMICfMRIintro.ppt|(slides)]]
** Interval Browser (SP) [[Media:IbrowserAndFMRIengine-03-23-05.ppt|IBrowser and fMRI Engine Design Slides]]
** fMRIEngine (SP) [[Media:Analyzing-fMRI-Data-Short.ppt|Small Data Version Slides]], [[Media:Analyzing-fMRI-Data.ppt|Large Data Version Slides]]
*** Block Design (detailed discussion)
*** Event Related (overview)
* 2:00 - 3:00 Discuss Results Wrap up (Ron Kikinis)
** End User Needs / Priorities
** Ideas for Future Dissemination and Training Activities

== [[Dissemination:Workshop_May_26-27_2005UseCaseDiscussion|User Feedback Discussion]] ==

@@ Line 25: / Line 25: @@
 # Mailing List: Please ensure that you are on the mailing list [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-dissemination namic-dissemination].
-# Software Installation: Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to the computer you will be bringing to the workshop, the tutorial guide for Slicer, the generic sample data set. This material is located in [http://www.slicer.org/slicerWiki/index.php/Slicer:Slicer2.5_Getting_Started Slicer 2.5 Getting Started: Software & Sample Data].
+# Software Installation: Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to the computer you will be bringing to the workshop, the tutorial guide for Slicer, the generic sample data set. This material is located in [https://www.slicer.org/wiki/Slicer:Slicer2.5_Getting_Started Slicer 2.5 Getting Started: Software & Sample Data].
 # Also, go to this link [[Training:Resources_and_Information|Loading-Dartmouth-NAMIC-DTI]] and download the powerpoint presentation that will guide you through the process of accessing Dartmouth specific data sets from the BIRN portal.