Training:MIND Institute Workshop Spring 2006 - Revision history

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

2017-07-10T18:07:23Z

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

Melonakos at 19:32, 6 November 2008

2008-11-06T19:32:12Z

Andy: Update from Wiki

2006-12-18T13:16:46Z

Update from Wiki

New page

== Organization ==

MIND Host:

* Jeremy Bockholt

NA-MIC Lead:

* Sonia Pujol
* Katie Hayes (technical support)

== Workshop Participants ==

Clinical and biomedical science researchers interested in training in 3DSlicer, an open-source medical imaging data visualization and analysis software tool and ITK, an open-source software toolkit for performing segmentation and registration.

Some [[Training:The_MIND_Institute_Training_Workshop_April_2006_pictures|pictures ]] from the workshop are available.

== Workshop Logistics ==

* The two days workshop will be held on April 10-11 in room 1025 at the MIND Institute, New Mexico.

To get there, go to the far north entrance at 1101 Yale Blvd NE (Domenici Hall) and get a parking permit from the receptionist. Follow the signs leading to room 1025, which is the large conference room going south from the reception desk off of the main atrium.

* Recommended accomodations at
** Hilton Albuquerque
** (505) 884-2500
** (800) 274-6835
** (505) 880-1196
** 1901 University Blvd NE
** Albuquerque, NM 87102
** let them know you are attending a UNM conference to get a discounted rate
* To sign-up for this event, send an e-mail to Sonia Pujol (spujol at bwh.harvard.edu) with your contact information and any specific training requests.
* All participants must come with their own PC, LINUX or MacOS 10.4 laptop computer with the Slicer software and demonstration data sets loaded.
* Confirmed Attendees (we would like to have 15-20 total)

# H. Jeremy Bockholt (The MIND Institute)
# Deidre Devier (The MIND Institute)
# Arvind Caprihan (New-Mexico Resonance)
# Julia Stephen (The MIND Institute)
# Stefan Posse (The MIND Institute)
# Josef Ling (The MIND Institute)
# Andy Mayer (The MIND Institute)
# Maria Ashna (The MIND Institute)
# Sumner Williams (The MIND Institute)
# Jill Fries (The MIND Institute)
# Jon Carmignani (The MIND Institute)
# Diana Krenz (The MIND Institute)
# Mark Scully (The MIND Institute)
# Ranee Barrow (The MIND Institute)
# Steve Altobelli (New-Mexico Resonance)
# Rob Roach (University of New-Mexico)
# Hans Johnson (University of Iowa)
# Ronald Pierson (University of Iowa)
# Carolina Montalvo (Memorial Sloan-Kettering Cancer Center)
# Halley Eisenberg (Memorial Sloan-Kettering Cancer Center)
# Rebecca England (University of New-Mexico)
# Chuck Gasparovic (University of New-Mexico)

== 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.

# 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:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]], [[Media:BrainAtlasClassifier2.zip|BrainAtlasClassifier.zip]] and [[Media:LoRes_8Ch_1.5T.zip| The Mind Institute dataset LoRes_8Ch1.5T.zip]].

= Draft Agenda =

== Day 1 ==

'''Slicer Workshop (Sonia Pujol, BWH) 8:30 AM - 5 PM '''

* 8:30 - 9:00 Preliminary session: checking for software and data installation.
* 9:00 - 9:30 Goals of Workshop, Introduction to the NAMIC Kit - People-Introductions
* 9:30 - 11:15 '''Slicer Basics - Hands-on Session 1: [[Media:SlicerTraining1LoadingAndViewingData.ppt|Loading and Viewing Data ]] '''(Sonia Pujol)
** Slicer Interface Overview
** Loading Data: Volumes, Models, Scenes
** Interacting with Images and Models
* 11:15 - 11:30 Coffee-break
* 11:30 - 12:30 '''Slicer Basics - Hands-on Session 2: [[Media:SlicerTraining7SavingData.ppt| Saving Data ]]''' (Sonia Pujol)
** Saving Volumes
** Saving Models
** Saving Scenes
* 12:30 - 2:00 '''Lunch Break'''
* 2:00 - 3:00 '''Slicer Advanced - Hands-on Session 3 '''(Sonia Pujol)

# [[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| vtkFreeSurferReaders Module ]]
# intro to the [[Media:Slicer_DTMRI_Training4.ppt| DT-MRI module ]] and fMRI capabilities

* 3:00 - 3:15 Coffee-break
* 3:15 - 4:15 '''Slicer Advanced - Hands-on Session 4: [[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt| EMBrainAtlasClassifier ]] '''(Sonia Pujol)

# Expectation Maximization Segmentation tutorial

* 4:15 - 4:45 '''Specific questions from users and [http://www.surveymonkey.com/s.asp?u=423161702497 users feedback]'''
* 4:45 - 5:00 '''Conclusion '''

== Day 2 ==

'''Preparation'''

''"Those who succeed do so because they have already acted''<br />''Those who failed do so because they act too late"''

'''Please follow the instructions given [[Training:ITK|here]] to prepare for this workshop. '''

As in previous workshops, we need all participants to have completed installation of ITK on their machines, as well as the exercises provided in the training section.''''''

<br />''' ITK (Luis Ibanez - Kitware) 9:00 AM - 5 PM '''

* ** 9:00 - 10:00 ITK Introduction and Architecture (Ibanez: Presentation: [[Media:Insight-Architecture.ppt|Insight-Architecture]])
** 10:00 - 12:00 Registration Framework (Ibanez: Presentation: [[Media:Insight-Registration.ppt|ITK Image Registration]])
** 12:00 - 1:00 Lunch
** 1:00 - 2:00 Segmentation Methods (Ibanez: Presentation: [[Media:Insight-Segmentation.ppt|ITK Segmentation]])
** 2:00 - 3:30 Break
** 3:30 - 5:00 Writing an ITK filter (hoe) (Ibanez: Presentation: [[Media:Insight-Writing-a-New-Filter.ppt|Insight-Writing-a-New-Filter]])

* 5:00 - 5:30 Conclusion

@@ Line 61: / Line 61: @@
 All attendees are required to complete the following items prior to the workshop. Support will be provided as requested.
-# 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:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]], [[Media:BrainAtlasClassifier2.zip|BrainAtlasClassifier.zip]] and [[Media:LoRes_8Ch_1.5T.zip| The Mind Institute dataset LoRes_8Ch1.5T.zip]].