NAMIC Wiki - User contributions [en]

File:Favicon.ico

2019-11-13T12:11:48Z

Grundlett: Any file uploaded here will automatically become the site favicon

== Summary ==
Any file uploaded here will automatically become the site favicon

File:Logo.png

2019-11-13T12:10:56Z

Grundlett: Any file uploaded here will replace the wiki logo automatically.

== Summary ==
Any file uploaded here will replace the wiki logo automatically.

NAMIC Wiki:Bureaucrats

2018-05-18T15:49:41Z

Grundlett: Created page with "Bureaucrats have the most authority in the wiki. They can provide/revoke Administrator privileges."

Bureaucrats have the most authority in the wiki. They can provide/revoke Administrator privileges.

NAMIC Wiki:Administrators

2018-05-18T15:30:12Z

Grundlett: minor "help" text about the confirmacount-notify setting in LocalSettings.php

Administrators of this wiki will review new account requests. After you confirm your email address, a message with your request will be sent to the group for review.

User:Grundlett

2017-10-17T21:06:30Z

Grundlett: create a new page after db repair

I'm Greg Rundlett, President and Principal Consultant of eQuality-Technology. If you notice any problems with this wiki, please let site administrators know; and you're welcome to send email to info@eQuality-Tech.com

CMF Workshop Cleveland 2013

2017-07-10T18:27:09Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable"
| style="width:25%" |[[Image:NAMIC.jpg]]
| style="width:25%" |[[Image:CWRU.png]]
| style="width:25%" |[[Image:MU.jpg|150px]]
| style="width:25%" |[[Image:UNC_uni.jpg]]
|}

==Hands on Workshop - 3D Registration - Joint Cephalometric Experts ==

== Introduction ==
This workshop will highlight new developments in publicly available software for image superimpositions in Dental applications.
3D image analysis continue to mandate a multidisciplinary collaborative team including clinician researchers, software engineers and computer science experts.
This hands-on workshop for Cranio Maxillo Facial applications will be held prior to the [https://www.eventbrite.com/event/5257003840 Joint Cephalometric Experts Group 2013] at the Bolton Brush Growth Study Center, Cleveland, OH.
This work was supported by the National Institute Of Dental & Craniofacial Research of the National Institutes of Health under Award Number R01DE024450. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health

==Date and Location==
Wednesday November 20th , 1:00-‐5:00 pm, at the Case Western Reserve University School of Dental Medicine.

==Workshop Content==

12:00pm Trouble shoot any problem attendees may have had downloading the software from the website. Please do your best to download the software ahead of time.

1:00pm Introductory presentations:(20 Mins each )

• 3D image analysis: an overview.
• 3D registration: voxel based, surface to surface, point to point: bone remodeling and displacement in relative superimposition.
• 3D data: A chair side perspective.
2:00pm Hands-‐on workshop: (3 hours)- See information on [https://sites.google.com/a/umich.edu/dentistry-image-computing/Clinical-Applications/3d-registration---longitudinal-and-across-subjects 3D registration - longitudinal and across subjects] webpage.

• How to load CBCT and Surface models in new CMFreg module in Slicer 4.3 open source software.
• How to correct for differences in CBCT acquisition at different time points in Slicer 4.3.
• How to register the images and save them as surface models in Slicer
• How to visualize meshes overlays in Slicer

==Presenters==

• Lucia Cevidanes, Ph.D. DDS, University of Michigan

• Tung Nguyen, DDS, University of North Carolina at Chapel Hill

• Beatriz Paniagua, Ph.D., University of North Carolina at Chapel Hill

• Vinicius Boen, Computer Programmer, University of Michigan

==Preparation for the workshop==

The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.
All participants are required to come with their own laptop computer (rather be MAC OS X) and install the software and datasets prior to the event. Slicer requires 1GB of RAM absolute minimum, with more highly recommended. Common data sets may require 4GB or more RAM for processing. A fast graphics card or GPU that supports OpenGL is also recommended.

Slicer is built and tested on many hardware and software platforms. 3D Slicer runs on Microsoft Windows XP, Vista, and Windows 7; Mac OS X versions 10.5 (Leopard), 10.6 (Snow Leopard), and 10.7 (Lion); and a variety of Linux distributions.

==Software==
[http://www.itksnap.org/pmwiki/pmwiki.php ITKsnap] - Semi-automatic segmentation tool and visualization

3D Slicer4.3 Nightly- Visualization and analysis tool ([http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2013-11-13-win-amd64.exe&checksum=0e5b20a0f2bd8ec23119226119f086e5 Windows 64bits], [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2013-11-13-macosx-amd64.dmg&checksum=813db2f41c47f8f30bdc27adf2babca6 Mac OS X], [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2013-11-13-linux-amd64.tar.gz&checksum=1d75cf40339eb7e1832fed723d263676 Linux])

Download [https://sites.google.com/a/umich.edu/dentistry-image-computing/home-1/3d_registration_joint-_cephalometric-_experts/cmfreg-download-tutorial CMFreg Extension in Slicer4.3]

Check out the [https://sites.google.com/a/umich.edu/dentistry-image-computing/Clinical-Applications/3d-registration---longitudinal-and-across-subjects CMFreg voxel based registration Tutorial]

Check out the others [https://sites.google.com/a/umich.edu/dentistry-image-computing/home-1/3d_registration_joint-_cephalometric-_experts/cmf-modules-tutorial CMFreg Tutorials]

==Data==
[https://na-mic.org/w/images/e/e8/Data_ITKsnap.zip ITKsnap segmentation]

[https://na-mic.org/w/images/4/47/Data_Slicer3.zip Slicer4 visualization]

[http://www.slicer.org/slicerWiki/images/c/c1/CMFregData.zip CMFreg registration]

==Other Resources==
[http://www.nitrc.org/ Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)]

[http://www.ncbi.nlm.nih.gov/pubmed?term=spharm%20pdm%20styner SPHARM-PDM publications in PubMed]

[https://www.slicer.org/wiki/Main_Page Slicer user orientation]

[https://www.slicer.org/wiki/Documentation/4.3/Training Slicer tutorials]

ChangeTracker

2017-07-10T18:27:09Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

<div class="floatright">__TOC__</div>

= Overview =

''THIS PAGE IS UNDER CONSTRUCTION -- CHECK BACK OFTEN!''

'''ChangeTracker''' is a 3D Slicer GUI module for monitoring slowly evolving tumors. This page will host the relevant information about ChangeTracker.

= What's New =
*Jan 25, 2009, use of 3d box widget with tumor volume rendering for ROI selection
*Jan 12, 2009, New visualization features integrated
*Jan 4-9, 2009, ChangeTracker project on NA-MIC AHM/Programming Week at Salt Lake City. See summary and results [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_ChangeTracker here]
*Dec 27, 2008, DiameterEstimator tool is available for automatic estimation of tumor diameter from the binary image

=Background=

=User information / Tutorials=

* Detecting subtle change in pathology: [https://na-mic.org/w/images/8/8b/Slicer3Training_ChangeTracker.ppt slides], [https://na-mic.org/w/images/1/19/ChangeTracker-Tutorial-Data.zip data]
* ChangeTracker module documentation page on Slicer Wiki [http://wiki.slicer.org/slicerWiki/index.php?title=Modules:ChangeTracker-Documentation here]

=Technical details=

=Bugs / Known issues=

* during "Analysis type step", Slicer crashes if "Analyze" button is hit more than once
* registration of a new volume node with the scene results in update of the slice views: ''Resolved: this appeared to be due to a lacking functionality in SliceCompositeNode, which invoked PropagateVolumeUpdate() on image load. This functionality can now be controlled via the DoPropagatVolumeUpdate in SliceComposite MRML node''
* incorrect setting of the registration parameters results in registration producing empty volume, no error messages from the module: ''Resolved: committed a fix to CommandLineModuleLogic to update the module node status correctly to indicate the error, if module entry point returns non-zero. TODO: update ChangeTracker logic to account for this change''
* need to investigate reproducibility of registration and impact of the random seed initialization: ''Linear registration updated with metric seed reinitialization''
* investigate reasons for segfault with the weird dataset from Yanling: ''Resolved (?): data is intrinsically very difficult to align. Registration must be solved prior to using ChangeTrcker''
* check and clean up file output procedures (..-TG directories)

=Feature requests/Features under development=

* multi-color volume rendering for tumor growth results: DONE
* use ''Compare view'': DONE
* 3d box widget for ROI selection DONE
* analysis of multiple time points
* testing IN PROGRESS
* improved tumor segmentation to exclude prominent non-tumor regions (vessels, scull, falx)
* Jean-Jacques Lemaire: would be nice to combine growth results with the 3D rendering of the estimated tumor volume
* Jean-Jacques Lemaire: improve user interface for tumor boundary identification -- something missing in the existing tools; would like to see better robustness of segmentation
* Ron wish list: get user input for inside/outside locations of points for tracked structure, use this for threshold selection and initial segmentation; ROI centering; sync ROI scales colors with the 3d box colors; review naming conventions for intermediate volumes; allow for separate show/hide functionality for 3d box and volume rendering; link compare views; support scene snapshots; fix bottom layout panel random popup issue
* graceful error handling

=Use cases=

* Meningioma growth analysis
* [http://wiki.na-mic.org/Wiki/index.php/ChangeTracker:Lupus_DBP Longitudinal lesion analysis for Lupus DBP]

=People=

* Ron Kikinis
* Kilian Pohl
* Andriy Fedorov

=Funding=

=Publications=

# E.Konukoglu, W.M.Wells, S.Novellas, N.Ayache, R.Kikinis, P.M.Black, K.M.Pohl. Monitoring Slowly Evolving Tumors. Proc. of 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2008, pp.812-815 [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1430 link]

= Contact =
Please contact [[User:Fedorov| Andriy Fedorov]] for further information.

2016 Winter Project Week/Breakout Sessions/SlicerExtensions Birds of a Feather

2017-07-10T18:27:09Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

=Slicer Extensions=
==Moderator ==
Steve Pieper

== Goal ==

This will be a "birds of a feather" session for current and potential developers of Slicer extensions to share ideas and experiences. Among other things, we will discuss what the right boundaries are between Slicer Core and Extensions, the types of needs there are across current/future Extensions, and whether we should have a hierarchy of dependencies between Extensions.

==Attendees==
All interested extension developers are encouraged to attend. The following people are active extension developers and are encouraged to participate.

[https://na-mic.org/w/images/6/63/SlicerRT_Extension_Pinter.pptx Csaba Pinter], Andras Lasso, Raul San Jose Estepar, Jorge Onieva, [https://na-mic.org/w/images/0/0c/SlicerExtensions_CMFteam.pdf Beatriz Paniagua], Andrey Fedorov, Eric Moult, Lauren O'Donnell, Isaiah Norton, Greg Sharp, Erich Bremer

== Preparation ==

Extension developers should be prepared to discuss their development plans, particularly if they have any requirements for the Slicer core that can be used to prioritize discussions for the Thursday afternoon discussion of development in the Slicer core.

[http://www.na-mic.org/Wiki/index.php/File:SlicerDMRIU01.pdf SlicerDMRIU01]

Events:2011-06-15-Robarts-Slicer-Workshop

2017-07-10T18:27:09Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable"
| colspan="3"|[[Image:BIRC.gif]]
|-
| style="width:33%" |[[Image:NAMIC.jpg‎]]
| style="width:33%" |[[Image:Logo_nac.gif‎]]
|style="width:33%" |[[Image:NCIGTlogo.gif]]

|}

== Introduction ==
[[Image:BIRC Workshop Canada June2011.jpg|300 px]][[Image:2011_June_UWO_BIRC_SlicerTraining_BRAINSFit.jpg|300px]][[Image:2011_June_UWO_BIRC_SlicerTraining_OpenIGTLink.jpg|300px]]

A Slicer tutorial will be hosted by the Biomedical Imaging Research Centre (BIRC) of the University of Western Ontario, London, Canada, on Wednesday, June 15, 2011. The primary objective of this event is to introduce users to the Slicer environment, as well as to illustrate the ability to integrate with ITK and Python modules. The concept of interfacing Slicer with imaging and tracking systems using Open IGTLink will also be discussed. The event will be held in Room MSB 148, Schulich School of Medicine and Dentistry, University of Western Ontario. This course will be followed at 5:30pm by a BIRC Seminar "Open Source Platforms for Collaborative Research - Examples from 3D Slicer" delivered by Dr Ron Kikinis. The seminar will take place in Auditorium A of University Hospital, on the University campus.

== Faculty ==
*[http://www.spl.harvard.edu/~kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
*[http://lmi.bwh.harvard.edu/~spujol/ Sonia Pujol, Ph.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
*[http://www.spl.harvard.edu/~tokuda Junichi Tokuda, Ph.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
*[http://www.kitware.com/company/team/pace.html Danielle Pace, M.ESc], Kitware Inc., Chapel Hill, NC

==Local Organizer==
*[http://www.robarts.ca/terry-peters Terry Peters, Ph.D.], Biomedical Imaging Research Centre, University of Western Ontario, London, Canada

== Agenda ==
*8:00-8:25 am Computer setup assistance by the instructors
*8:25-8:30 am Welcome and presentation of day activities (Ron Kikinis)
*8:30-9:45 am Hands-on session 1: [[media:Slicer3_DataLoadingAndVisualization_BIRCWorkshop_June2011_SoniaPujol.pdf | Data Loading and 3D Visualization ]] (Sonia Pujol)
*9:45-10:15 am Coffee Break
*10:15-11:15 am Hands-on session 2: [[media:Slicer3_BRAINSFITRegistration_DPace_June2011_final.pdf | Registration and resampling using Brainsfit: Rigid, Affine and Non-rigid ]] (Danielle Pace)
*11:15-12:30 Hands-on session 3: [[media:WhiteMatterExplorationNeurosurgicalPlanning_BIRCWorkshop_June2011_SoniaPujol.pdf‎ |White Matter Exploration for Surgical Planning]] (Sonia Pujol)
*12:30-13:30 Lunch Break
*13:30-14:45 Hands-on session 4:[[media:ProgrammingIntoSlicer-HelloPythonTutorial_BIRCWorkshop2011_SoniaPujol.pdf | Python based modules to Slicer: The Hello Python Programming Tutorial ]](Sonia Pujol)
*14:45-15:30 Hands-on session 5: [https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf Slicer to devices] (Junichi Tokuda)
*15:30-15:45 Coffee Break
*15.45-16:30 Demonstration of Slicer4 and the Skeletongenerator (Junichi Tokuda)
*16:15-16:30 Questions from the audience and concluding remarks
*17:30-19:00 BIRC Lecture: Ron Kikinis, MD: [[Events:Robarts-2011-06-15|3D Slicer]] "Open Source Platforms for Collaborative Research - Examples from 3D Slicer." <br> Location: Auditorium A, University Hospital.

== Logistics ==
*Date: June 15, 2011
*Workshop Location: Room MSB 148, Schulich School of Medicine and Dentistry, University of Western Ontario [[media:Westernandaffiliates.pdf ‎| Click here for the campus map]]
*BIRC Seminar location: Auditorium A, University Hospital, on the University campus

*'''Registration''': To sign-up for this event, please fill in the [[media:RegistrationForm_SlicerWorkshop_RobartsResearchInstitute_June15_2011.doc‎ | registration form]] and send it by e-mail to Katie Mastrogiacomo (kmast at bwh.harvard.edu) before June 7.

== Room Configuration - Fisher Conference Room ==

24 port switch, wireless, two LCD projectors and screens, 6 power strips available for additional power.

== Preparations ==

*Hardware<span style="background-color: yellow"> The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.
All participants are required to come with their own laptop computer and install the software and datasets prior to the event.</span> A minimum of 1 GB of RAM (4 GB is better) and a graphic accelerator with 64mb (512MB is better) of on-board graphic memory are required. Shared memory graphics boards have significantly poorer performance.

*<span style="background-color: cyan">'''UPDATE: New version of Slicer to download'''
Software installation: Please install the S'''licer3.6.3-2011-06-07 version''' appropriate to the laptop computer you'll be bringing to the workshop
* Windows: [http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]
* Linux 64: [http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]
* Linux 32: [http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz]
* Mac Darwin: [http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]

*Datasets and Tutorials:
{| style="color:green" border="1"
|Tutorial || Data
|-
| [[media:Slicer3_DataLoadingAndVisualization_BIRCWorkshop_June2011_SoniaPujol.pdf| Data Loading and 3D Visualization]]|| [[media:Slicer3VisualizationDataset.zip | 3D Visualization dataset]]
|-
|‎[[media:WhiteMatterExplorationNeurosurgicalPlanning_BIRCWorkshop_June2011_SoniaPujol.pdf‎ |White Matter Exploration for Surgical Planning]] || [[media:WhiteMatterExplorationData.zip‎| White Matter Exploration dataset]]
|-
| [[media:ProgrammingIntoSlicer-HelloPythonTutorial_BIRCWorkshop2011_SoniaPujol.pdf | Python based modules to Slicer: The Hello Python Tutorial ]]|| [[media:HelloPython.zip | HelloPython dataset]]
|-
| [https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLinkIF Tutorial] ||
|-
| [[media:Slicer3_BRAINSFITRegistration_DPace_June2011_final.pdf | BRAINSFIT Registration]] || [[media:Slicer3_BRAINSFITRegistration.zip | BRAINSFIT Registration dataset]]
|-
|}

== Slicer Community ==
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] prior to the workshop, for questions and feature requests related to the software.

For questions related to the workshop, please send an e-mail to Sonia Pujol (spujol at bwh.harvard.edu).

== Slicer3 Training Survey ==

[http://www.surveymonkey.com/s/GZDXKXQ Click here to take the Slicer3 Training Survey]

== Registrants ==
# Kamyar Abhari, Biomedical Imaging Research Centre at the University of Western Ontario
# Mariam Afshin, UWO
# Del Archer, Parallax Innovations Inc.
# Ali Asadian, UWO
# Joseph Awad, Biomedical Imaging Research Centre at the University of Western Ontario
# Hamid Azimian, CSTAR, UWO
# Mahdi Azizian, CSTAR
# Srikanth Bhattad, UWO
# Adam Blais, Biomedical Imaging Research Centre at the University of Western Ontario
# Susan Buchanan, Biomedical Imaging Research Centre at the University of Western Ontario
# Daniel Cho , Biomedical Imaging Research Centre at the University of Western Ontario
# Derek Cool, Biomedical Imaging Research Centre at the University of Western Ontario
# Stephen Costella, Biomedical Imaging Research Centre at the University of Western Ontario
# Andrew Curtis, Biomedical Imaging Research Centre at the University of Western Ontario
# Tharindu De Silva, Biomedical Imaging Research Centre at the University of Western Ontario
# Ryan Divigalpitiya, UWO/Baines Center for Translational Cancer Research
# Maria Drangova, Biomedical Imaging Research Centre at the University of Western Ontario
# John Drozd, Biomedical Imaging Research Centre at the University of Western Ontario
# Abelardo Escoto, CSTAR
# Mehdi Esteghamatian, UWO
# Lori Gardi, UWO
# Eli Gibson, Biomedical Imaging Research Centre at the University of Western Ontario
# Jeremy Gill, Parallax Innovations Inc.
# Maged Goubran, Biomedical Imaging Research Centre at the University of Western Ontario
# Reza Heydarian, Biomedical Imaging Research Centre at the University of Western Ontario
# Samaneh Kazemifar, Biomedical Imaging Research Centre at the University of Western Ontario
# Jeff Kempe, LHSC
# Iman Khalaji, UWO
# Ali Khan, Biomedical Imaging Research Centre at the University of Western Ontario
# Miranda Kirby, Biomedical Imaging Research Centre at the University of Western Ontario
# Pencilla Lang, UWO
# Fraser Le Ber, CSTAR
# Feng Li, Biomedical Imaging Research Centre at the University of Western Ontario
# Hao Li, CSTAR
# Harry Marshall, LRHI
# Lindsay Mathew, Biomedical Imaging Research Centre at the University of Western Ontario
# Brandon Miles, UWO
# John Moore, Biomedical Imaging Research Centre at the University of Western Ontario
# Michael Naish, UWO
# Nima Najmaei, UWO
# Hamid Neshat, Biomedical Imaging Research Centre at the University of Western Ontario
# Haroon Oqab, UWO
# Amir Owrangi, Biomedical Imaging Research Centre at the University of Western Ontario
# Grace Parraga, UWO
# Rajni Patel, UWO
# Ivailo Petrov, Biomedical Imaging Research Centre at the University of Western Ontario
# Terry Peters, Biomedical Imaging Research Centre at the University of Western Ontario
# Bon Ryu, Biomedical Imaging Research Centre at the University of Western Ontario
# Brendan Santyr, Biomedical Imaging Research Centre at the University of Western Ontario
# Maysam Shahedi, Biomedical Imaging Research Centre at the University of Western Ontario
# Arefin Shamsil, UWO
# Harish Sharma, UWO
# Igor Solovey, Biomedical Imaging Research Centre at the University of Western Ontario
# Feng Su, UWO
# Sarah Svenningsen, Biomedical Imaging Research Centre at the University of Western Ontario
# Ali Tavallaei, Biomedical Imaging Research Centre at the University of Western Ontario
# Trevor Thang, UWO
# Jian Wang, UWO
# Aaron Ward, UWO
# Andrew Wheatley, Biomedical Imaging Research Centre at the University of Western Ontario
# Ran Xu, CSTAR
# Kevin Yang, Biomedical Imaging Research Centre at the University of Western Ontario
# Timothy Yeung, UWO

Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

2017 Winter Project Week/2017TutorialContest

2017-07-10T18:27:09Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
Sonia Pujol, Ph.D., Director of Training, Neuroimage Analysis Center

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" |
Objective:
! style="text-align: left; width:27%" |
Approach and Plan:
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* The primary purpose of the Winter 2017 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer.
|

* The contest provides members of the medical image computing and radiology research community a methodology and a framework for developing step-by-step tutorials on advanced image analysis methods.
|

*[http://www.na-mic.org/Wiki/index.php/2017_Tutorial_Contest '''Winter 2017 Tutorial Contest''']
#[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerPathology Slicer Pathology] (Erich Bremer/Andriy Fedorov)
#[[Media:SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx| Simple Python Tool for Quality Control of DWI data (Laurent Chauvin)]]
#[https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM (Beatriz Paniagua)]
#[https://na-mic.org/w/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing] (Csaba Pinter)
#[[Media:ROSIGTLTutorial_Tokuda_Jan2017.pptx| Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink (Junichi Tokuda)]]
#[[Media:Fiber_Bundle_Volume_Measurement.pptx|Fiber Bundle Volume Measurement]], [[Media:FiberVolume_data.zip| tutorial data]] (Shun Gong)

Winner: Csaba Pinter won the contest and was awarded $250 by Kitware Inc

Judges:
**Rebekka Lauer, Humboldt-University, Berlin
**Parvin Mousavi, Brigham and Women's Hospital
**Peter Anderson
**Hongtao Zhang, Hebei General Hospital
**Michael Chae, Monash University

|}

DBP:Harvard:DTIROI

2017-07-10T18:27:09Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

* Cingulum Bundle: (N=30 SZ; N=42 Ctrl)
** Reference: [https://na-mic.org/w/images/e/ec/Kubicki_CB.pdf Kubicki M, Westin CF, Nestor PG, Wible CG, Frumin M, Maier SE, Kikinis R, Jolesz FA, McCarley RW, Shenton ME. Cingulate fasciculus integrity disruption in schizophrenia: a magnetic resonance diffusion tensor imaging study. Biol Psychiatry. 2003 Dec 1;54(11):1171-80. Erratum in: Biol Psychiatry. 2004 Mar 15;55(6):661.]
* Fornix: (N=24 SZ; N=31 Ctrl)
** Reference (note: abstract only, #256): [https://na-mic.org/w/images/7/74/Kuroki_2004_abstract_only.pdf Kuroki N, Kubicki M, Nestor PG, McCarley RW, Park HJ, Levitt JJ, Woolston S, Frumin M, Niznikiewicz M, Westin CF, Maier SE, Shenton ME. Fornix Integrity and Hippocampal Volume in Schizophrenia. Biol Psychiatry 2004;55:72S.]

CMF Workshop Cleveland 2014

2017-07-10T18:27:08Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable"
| style="width:25%" |[[Image:NAMIC.jpg]]
| style="width:25%" |[[Image:CWRU.png]]
| style="width:25%" |[[Image:MU.jpg|150px]]
| style="width:25%" |[[Image:UNC_uni.jpg]]
|}

==Pre- Joint Cephalometric Experts Imaging Hands-on Workshop ==

== Introduction ==
This workshop will highlight new developments in publicly available software for image analysis and imaging based research for Dental applications.
3D image analysis continue to mandate a multidisciplinary collaborative team including clinician researchers, software engineers and computer science experts.
This hands-on workshop for Cranio Maxillo Facial applications will be held prior to the [http://www.eventbrite.com/e/joint-cephalometric-experts-group-2014-tickets-12027212717?aff=es2&rank=0 Joint Cephalometric Experts Group] at the Bolton Brush Growth Study Center, Cleveland, OH. This work was supported by the National Institute Of Dental & Craniofacial Research of the National Institutes of Health under Award Number R01DE024450. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health

==Date and Location==
Wednesday November 5th , 1:00-‐5:00 pm, at the Case Western Reserve University School of Dental Medicine.

==Workshop Content==

*1:00 – 2:00pm

- General presentation of the different '''open source dental tools''' [[File:ClevelandPresentation.pdf]] – ''Lucia Cevidanes''

- Presentation '''EasyClip''' – ''Julia Lopinto''

- Presentation '''Angle Measurement''' – ''Julia Lopinto''

- Presentation '''Pick'nPaint''' – ''Lucie Macron''

- Installation of software: '''ITK-SNAP (version 2.4)''' and '''Slicer-4.3.1'''

Problems for the installation of Slicer because a new version was just upload on the website and with this version the extension presented during the workshop can’t be installed.

----

The different presentations started with a presentation and a demonstration of the use of the tool
The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.

*2:00 – 3:00pm
- Dicom files - They are different from the gipl files – ''Lucia Cevidanes''

----

*3:00 – 3:30pm
- Gipl files – ''Antonio Ruella''

----

*3:30 – 4:00pm
- Scan already approximated – ''Antonio Ruella''

----

*4:00 – 4:30pm
- CB segmentation – ''Antonio Ruella''

----

*4:30 – 5:00pm
- CB registration – ''Antonio Ruella''

==Presenters==

* '''Lucia Cevidanes''' , ''Ph.D, DDS, University of Michigan''
luciacev@umich.edu

* '''Antonio Ruella''', ''Ph.D, DDS, MS, University of Michigan''
antonioruellas@yahoo.com.br

* '''Marcelo Gomes''', ''DDS, MS, University of Michigan''
marceloregisgomes@hotmail.com

* '''Liliane Gomes''', ''DDS, MS, PhD student, University of Michigan''
lilianerosas@hotmail.com

* '''Marilia Yatabe''', ''DDS, MS, PhD student, University of Michigan''
msyatabe@umich.edu

* '''Lucie Macron''', ''Computer Programmer intern, University of Michigan''
luciemac@umich.edu

* '''Julia Lopinto''', ''Computer Programmer intern, University of Michigan''
jlop@umich.edu

==Preparation for the workshop==

The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.
All participants are required to come with their own laptop computer and install the software and datasets prior to the event. A minimum of 1 GB of RAM (4 GB is better) and a graphic accelerator with 64mb (512MB is better) of on-board graphic memory is required. Shared memory graphics boards have significantly poorer performance.

==Software==
[https://na-mic.org/w/images/e/e8/Data_ITKsnap.zip ITKsnap segmentation]

[https://na-mic.org/w/images/4/47/Data_Slicer3.zip Slicer4 visualization]

==Data==
[https://drive.google.com/a/umich.edu/folderview?id=0Bz1Z-9rzZGPEV0M4eWJEeUhrb3c&usp=sharing_eid&tid=0Bz1Z-9rzZGPESEhhV3hlNFdZaHc Folder 1: Dicom files - They are different from the gipl files]

[https://drive.google.com/a/umich.edu/folderview?id=0Bz1Z-9rzZGPEQWJzN29BMnR2WW8&usp=sharing_eid&tid=0Bz1Z-9rzZGPESEhhV3hlNFdZaHc Folder 2: gipl files]

[https://drive.google.com/a/umich.edu/folderview?id=0Bz1Z-9rzZGPEYWE4QWRXUk5JNjg&usp=sharing_eid&tid=0Bz1Z-9rzZGPESEhhV3hlNFdZaHc Folder 3: Scan already approximated]

[https://drive.google.com/a/umich.edu/folderview?id=0Bz1Z-9rzZGPEOEVFWmVRUVpRQWM&usp=sharing_eid&tid=0Bz1Z-9rzZGPESEhhV3hlNFdZaHc Folder 4: CB segmentation]

[https://drive.google.com/a/umich.edu/folderview?id=0Bz1Z-9rzZGPESi1pQzVkQWFFckk&usp=sharing_eid&tid=0Bz1Z-9rzZGPESEhhV3hlNFdZaHc Folder 5: CB registration]

[https://drive.google.com/a/umich.edu/folderview?id=0Bz1Z-9rzZGPESUNRVERaY0JnXzQ&usp=sharing_eid&tid=0Bz1Z-9rzZGPESEhhV3hlNFdZaHc Folder 5a: segm Max and MD T1]

[https://drive.google.com/a/umich.edu/folderview?id=0Bz1Z-9rzZGPEWEp3ZWhkYTU4MVk&usp=sharing_eid&tid=0Bz1Z-9rzZGPESEhhV3hlNFdZaHc Folder 6: Models - CB registration]

[https://www.youtube.com/channel/UCQUtGe5KrpBt2k4mrNeHeUQ/videos DCBIA Videos - Tutorial videos for the image analysis tools]

==Other Resources==
[http://www.nitrc.org/ Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)]

[http://www.ncbi.nlm.nih.gov/pubmed?term=spharm%20pdm%20styner SPHARM-PDM publications in PubMed]

[https://www.slicer.org/wiki/Main_Page Slicer user orientation]

[https://www.slicer.org/wiki/Documentation/4.3/Training Slicer tutorials]

==Participant List==
#Toni Magni
#Vicente Hernandez-Soler
#Anwar Alhazmi
#Bo Amornporncharoen
#Michael Mouroulanos
#Ipsit Patra
#Pritesh Parmar
#Domenico Dalessandri
#Alex Vo
#Manuel Lagravere
#Nicholas Dietrich
#Ahmed Ghoneima
#Mohamed Bazina

Events:UCSF-Slicer-Training-11-2010

2017-07-10T18:27:08Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

[[Image:UCSF_Event1.jpg|thumb|300px|Class photo 1]]
[[Image:UCSF_Event2.jpg|thumb|300px|Class photo 2]]
[[Image:UCSF_Event3.jpg|thumb|300px|Cable car]]

{| class="wikitable2" border="1" cellpadding="8" cellspacing="1"
| colspan="4"|[[image:UCSF-Logo.png|300px|center]]
|-
| style="width:25%" |[[Image:NAMIC.jpg‎]]
| style="width:25%" |[[Image:Logo_nac.gif‎]]
| style="width:25%" |[[Image:NCIGTlogo.gif]]
| style="width:25%" |[[Image:Catalyst_logo_final.jpg|150px]]
|}

== Logistics ==

Location: [http://www.radiology.ucsf.edu/china-basin-imaging UCSF (3rd floor) China basin campus]

Date: Tuesday November 9, 2010

'''Registration''': To sign-up for this event, please fill in the [[media:RegistrationForm_SlicerWorkshop_UCSF_Nov9_2010.doc‎ | registration form]] and send it by e-mail to Jason Crane, PhD [jason.crane at ucsf.edu] before Friday November 5.

== Agenda ==
*8:45-9:00 am Computer setup assistance by the instructors
*9:00-9:15 am Welcome and Goals of the Workshop (Ron Kikinis/Sonia Pujol)
*9:15-9:45 am [[media:Kikinis-NA-MIC-2010-09-20.ppt|Introduction to NA-MIC]] and [[media:Kikinis-Slicer Community-2010-09-20.ppt|the Slicer community]] (Ron Kikinis)
*9:45-10:45 am [[media:Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf‎ | Data Loading and 3D Visualization ]] (part1)(Sonia Pujol)
*10:45-11:00 am Coffee break
*11:00-11:45 am [[media:Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf‎ | Data Loading and 3D Visualization ]] (part 2) (Sonia Pujol)
*11:45 am-1:00 pm Lunch
*1:00-2:00 pm [[media:ManualRegistration_UCSF2010_DominikMeier.pdf | Image Registration ]] (Sonia Pujol)
*2:00-3:00 pm [[media:DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf‎ | Diffusion Tensor Imaging Analysis: from DWI to DTI data ]](Sonia Pujol)
*3:00-3:15 pm Coffee Break
*3:15-4:15 pm [[media:DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf‎ | Diffusion Tensor Imaging Analysis: from DTI data to 3D fiber bundles ]] (Sonia Pujol)
*4:15-4:30 pm MR Spectroscopy module in Slicer (Jason Crane)
*4:30-5:00 pm Questions from the audience and concluding remarks

== Notes on the Nrrd file format==

The Nrrd file format, which is part of the NA-MIC kit, accurately represents N-dimensional raster information for scientific visualization and medical image processing.
This format is used in Slicer to represent the necessary information about a DWI image volume, its anatomical orientation, and all the DWI-specific acquisition parameters for estimating the diffusion tensors. A detailed description of the Nrrd file format usage for DWI images and DTI data can be found [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format here].

The [https://www.slicer.org/wiki/Modules:DicomToNRRD-3.6 DicomToNrrd module] in Slicer can be used to convert Dicom data into Nrrd. A detailed [https://na-mic.org/w/images/7/77/SlicerTraining9_DTI-FromDicomToNrrd.ppt tutorial] describes how to construct a nhdr file from a set of images, which can be in Dicom or in other format such as Nifti, and a list of known gradients, using the Teem Library.

== Local Organizers==
*Jason Crane, PhD, Department of Radiology and Biomedical Imaging, UCSF
*Sarah Nelson, PhD, Department of Radiology and Biomedical Imaging, UCSF
*Daniel Rubin, MD, MS, Department of Radiology, Stanford University

== Teaching Faculty==
*[http://www.spl.harvard.edu/pages/People/kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
*[http://lmi.bwh.harvard.edu/~spujol Sonia Pujol, Ph.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
*[http://www.spl.harvard.edu/~noby Nobuhiko Hata, Ph.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School

== Preparation for the Workshop ==

<span style="background-color: yellow"> The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.
All participants are required to come with their own laptop computer and install the software and datasets prior to the event.</span>. A minimum of 1 GB of RAM (2 GB if possible) and a dedicated graphic accelerator with 64mb of on board graphic memory are required.

Please install the '''Slicer3.6.1''' version appropriate to the laptop computer you'll be bringing to the tutorial:
* Windows: [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23-win32.exe]
* Linux 64: [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23-linux-x86_64]
* Linux 32: [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20-linux-x86 ]
* Mac Darwin: [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20-darwin-x86]

Please download the [[media:Slicer3VisualizationDataset.zip | 3D Visualization dataset]],[http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Registration dataset] and [[media:DiffusionDataset.zip| Diffusion dataset]] in preparation for the workshop.

== Slicer3 Training Survey ==

[http://www.surveymonkey.com/s/GZDXKXQ Click here to take the Slicer3 Training Survey]

== Slicer Community ==
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] for questions and feature requests related to the software.

[[Events#2010|Back to Events 2010]]

2014 Project Week Breakout Session: DICOM

2017-07-10T18:27:08Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

== Purpose ==

Overall discussion of DICOM in slicer and related projects.

== Agenda ==
* Introduction - Steve (5 minutes)
* 3D Slicer DICOM Module - Alireza (10 minutes)
** Recent improvements
** Plans
* DICOM RT - Andras, Csaba - (10 minutes) ([https://na-mic.org/w/images/5/53/DICOM-RT_NAMIC2014Jun.pptx slides])
* Recent developments related to DICOM - Andrey, Steve (15 minutes)
** SR, DSR, SEG, RWVM, Parameter Maps...
** "2.25.UUID"
** [http://www.dclunie.com/dicom-status/status.html#BaseStandard2013 DICOM xml docbook]
** [https://fedorov.cloudant.com/dicom_search/.site/index.html DICOMSearch site]
*** source code: https://github.com/QIICR/DICOMSearch
* [http://dcmjs.org dcmjs] - Steve, Jc (10 minutes) ([https://github.com/jcfr/namic_projectweek_2014-06-24_dcmjs slides])
* Discussion and other topics of interest to the community
** How to create ''correct'' derived DICOM objects (e.g. how to wrap CLI modules to export valid DICOM).

== Remote participation ==

We will be holding a google hangout as part of this breakout session. Anyone interested in joining, please contact Steve or Andrey so we can email you the hangout link.

Signed up so far:
* David Clunie, PixelMed Publishing
* Michael Onken, Offis / OpenConnections GMBH

== Other reference material ==

* Standardized radiology reports and DICOM structured reports
** http://www.radreport.org/ and https://rsna.org/Reporting_Initiative.aspx ?
** http://medical.nema.org/dicom/2013/output/pdf/part16.pdf

DataFusion

2017-07-10T18:27:08Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

*3D Slicer can register/fuse volumes
* Data to use for this tutorial
**[https://na-mic.org/w/images/a/aa/Reg-sample.zip 1.5T Data]
**[https://na-mic.org/w/images/5/5c/Mrt-images.zip .5T Data]
**These are data sets from the same subject, taken on two different scanners
***1.5 Tesla diagnostic MR scanner (low resolution for better interactivity)
***0.5 Tesla intraoperative MR scanner
*PPT about the [[media:NAMICSReg-IntroEtc-sw.ppt |scientific background]]
*[[media:Volume-Registration.ppt | Tutorial]] with step-by-step instructions.

2013 Summer Project Week:Patient hierarchy

2017-07-10T18:27:08Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SlicerRT_0.10_PatientHierarchy_ProstateEntLoaded.png|Initial GUI
</gallery>

==Key Investigators==
* Queen's: Csaba Pinter, Andras Lasso
* Isomics: Steve Pieper

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Discussing the progress about the Patient Hierarchy module and implement further enhancements and utilisations.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

The approach is to have a mechanism that maps the DICOM hierarchy to be used within Slicer. This involves visualizing and editing the loaded DICOM hierarchy, connecting the data objects that are connected on a DICOM level, and utilizing this knowledge for the widest imaginable manner.

The plan for the project week is to give a short demo of the current functionality and solicit feedback, then continuing to work on implementation.

Consider renaming options for this feature ('patient' being inappropriate for mice, for example). "Subject Hierarchy" is a current candidate name.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

*Patient Hierarchy module shows the hierarchy, enables reparenting and adding from outside the Patient Hierarchy. Also facilitates grouped toggling of visualization, deformation, and exporting
**[https://na-mic.org/w/images/6/6f/Pinter_SlicerRt_PatientHierarchy_Introduction_NA-MIC_2013_Summer.pptx Presentation]
*Some steps toward utilization of Patient Hierarchy has been implemented (SlicerRT [https://www.assembla.com/spaces/slicerrt/tickets/278#/activity/ticket: #278])
*Roadmap and plan for generalizing to Subject Hierarchy and its integration into Slicer core
**[http://www.na-mic.org/Wiki/index.php/2013_Summer_Project_Week_Breakout_Session:RT#Patient_Hierarchy Meeting minutes]

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer Loadable Module inside the SlicerRT extension. In the long term, integrating this functionality in the Slicer core would be desirable.

==References==
* [https://www.slicer.org/wiki/Documentation/Nightly/Modules/PatientHierarchy Patient Hierarchy module in SlicerRT]
* [https://www.assembla.com/spaces/slicerrt/tickets SlicerRT issue tracking system]

Events:RSNA 2010

2017-07-10T18:27:08Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

__TOC__

{| class="wikitable" border="1" cellpadding="8" cellspacing="1"
| colspan="4"|[[Image:RSNA2010-logo.jpg]]
|-
| style="width:25%" |[[Image:NAMIC.jpg‎]]
| style="width:25%" |[[Image:Logo_nac.gif‎]]
| style="width:25%" |[[Image:NCIGTlogo.gif]]
| style="width:25%" |[[Image:Catalyst_logo_final.jpg|200px]]
|}

<br>

<gallery widths="300px" perrow="3">
Image:RSNA2010_visualization_tutorial_attendees1.jpg|Slicer visualization tutorial
Image:RSNA2010_visualization_tutorial_attendees2.jpg|Slicer visualization tutorial
Image:RSNA2010_CTSC_tutorial_attendees.jpg|Slicer CTSC tutorial
Image:RSNA2010_CTSC_tutorial_netbook.jpg|We ran out of RSNA computers, and one of the attendees downloaded and installed Slicer on his netbook!
Image:RSNA2010_booth_staff1.jpg|At the Slicer booth in Quantitative Imaging Reading Room
Image:RSNA2010_booth_staff2.jpg|At the Slicer booth
</gallery>

= NA-MIC and NAC at RSNA =

==Introduction==
The '''[[media: 3DVisualization_SoniaPujol_KittShaffer_RSNA2010.pdf‎ | 3D Interactive Visualization of DICOM Images for Radiology Applications]]''' course is offered by the National Alliance for Medical Image Computing (NA-MIC) in conjunction with the Neuroimage Analysis Center (NAC) at the [http://rsna2010.rsna.org 96th Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA 2010)].

As part of the outreach missions of these NIH funded National Centers, we have developed an offering of freely available, multi-platforms open source software to enable medical image analysis research. The course along with the tutorial 3D Visualization datasets aim to introduce translational clinical scientists to the capabilities of the 3D Slicer software.

==Logistics ==
*Date: Monday November 29, 2010
*Time: 2:30-4:00 pm
*Location: S401CD, McCormick Place, Chicago, Illinois
*Course: IA22

==Learning Objectives==

* Enhance interpretation of DICOM images through the use of computer-assisted 3D visualization,
* Enhance the understanding of the correlation of the segments of the liver with the surrounding vascular anatomy,
*Introduce cutting-edge open-source computer graphics applications for Radiology.

==Abstract==

Three-dimensional visualization of the anatomy is being made possible through the combined emergence of technological breakthroughs in Radiology hardware and increasingly sophisticated software tools for medical image analysis.

For the past six years, the National Alliance for Medical Image Computing (NA-MIC), one of the seven National Centers for Biomedical Computing, part of the NIH Roadmap for medical research, has converted some of the major scientific advances made by the biomedical imaging community into open-source software tools, contributing fasten the deployment of cutting-edge visualization techniques on a national and international scale.

As part of the NA-MIC toolkit, the 3D SLICER open-source software has been developed as a technology delivery platform for clinical researchers. 3D SLICER has become a multi-institution effort to share the latest advances in image analysis with the scientific and clinical community. To foster the translation of NA-MIC technology to clinical research applications, the NA-MIC Training Core has developed a series of workshop and tutorials using the 3DSLICER software.

This workshop is an introduction to the basics of viewing and interacting with DICOM volumes in 3D using the SLICER software. The 90 minute course is divided into two sections: the first part introduces the concepts of 3D visualization through an hands-on training session using two MR DICOM datasets of the brain and 3D reconstructed models of cerebral structures; the second part guides the user through the exploration of abdominal structures using a series of models, which include the segments of the liver, reconstructed from DICOM images of three clinical cases. Interactions with the 3D models are fostered by a series of ten radiological tasks to accomplish by the participants. Detailed answers to the tasks are provided during the workshop as the instructors guide the audience through the 3D visualization settings to enhance the understanding of the complexity of the anatomical structures involved.

== Instructors ==
*Author/Presenter: Kitt Shaffer MD, PhD
*Author/Presenter: Sonia Marie-Aurore Pujol PhD
*Author/Presenter: Randy L. Gollub MD, PhD
*Andriy Fedorov, PhD
*Wendy Plesniak, PhD
*Ron Kikinis, MD

== How to sign up ==
* [http://rsna2010.rsna.org/attendees.cfm Online registration and course enrollment ]

= CTSA at RSNA =

==Introduction==
The '''Quantitative Medical Imaging for Clinical Research and Practice''' course is offered by the Clinical Translational Science Award (CTSA) Consortium at the [http://rsna2010.rsna.org 96th Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA 2010)].

As part of the outreach missions of these cooperating institutions, we will offer a presentation and hands-on demonstration using freely available, multi-platforms open source software to enable medical image analysis research. The course along with the tutorial and datasets aim to introduce translational clinical scientists to the capabilities of the 3D Slicer software.

==Logistics ==
*Date: Tuesday, November 30 2010
*Time: 10:30 AM - 12:00 PM
*Location: S401CD, McCormick Place, Chicago, Illinois
*Course: IA31

==Learning Objectives==
* Enhance interpretation of medical images through the use of 3D visualization,
* Gain experience with interactive, quantitative assessment of complex anatomical structures,
* Present current directions of quantitative imaging as a biomarker in clinical trials.

==Abstract==
Technological breakthroughs in medical imaging hardware and the emergence of increasingly sophisticated image processing software tools permit the visualization and display of complex anatomical structures with increasing sensitivity and specificity.

This workshop will begin with an introductory presentation of state-of-the-art, clinical examples of quantitative imaging biomarkers for diagnosis and clinical trial outcome measures. Cases from multiple imaging modalities and from multiple organ systems will be highlighted to illustrate the depth and breath of this field. Participants will then be led through a series of tutorials on the basics of viewing and processing DICOM volumes in 3D using 3D SLICER (www.SLICER.org). Specific hands-on demonstrations will focus on basic use of 3D Slicer software, quantitative measurements from PET/CT studies, and volumetric analysis of meningioma.

== Instructors ==
* Author/Presenter: Randy L. Gollub MD, PhD
* Author/Presenter: Katarzyna J. Macura MD, PhD
* Author/Presenter: Jeffrey T. Yap PhD
* Author/Presenter: Ron Kikinis MD
* Author/Presenter: Valerie Humblet
* Author/Presenter: Wendy Plesniak PhD

== Tutorial Materials ==
* [https://na-mic.org/w/images/d/d4/Combined-RSNA2010-CTSA.ppt Combined tutorial slides (ppt) ]
* [https://na-mic.org/w/images/3/33/Slicer_data-RSNA2010-CTSA.zip Tutorial datasets ]

== How to sign up ==
* [http://rsna2010.rsna.org/attendees.cfm Online registration and course enrollment ]

= 3D Slicer at RSNA =

== Quantitative Imaging Reading Room Exhibit==

Title: '''3D Slicer: An Open Source Application for Registration, Segmentation, Quantitative Analysis, and Visualization of Biomedical Image Data'''
* Focus: Interactive Editor, Volume Rendering, Tools for Quantitative Analysis

== Exhibitors ==
* A Fedorov
* K. Hayes
* W. Plesniak
* R. Kikinis
* V. Humblet

"Meet the Experts" sessions for this exhibit will be held on the following dates/times:
* Monday November 29 (12:15-1:15pm)
* Wednesday December 1 (12:15-1:15pm)
* Thursday December 2 (12:15 - 1:15pm)

== Logistics ==
The Quantitative Imaging Reading Room will be located in the Lakeside Learning Center (Hall E) of McCormick Place Convention Center, Chicago. The Lakeside Learning Center will be open according to the following schedule:
* Sunday, Nov. 28, 8:00am – 6:00pm
* Monday-Thursday, Nov. 29-Dec. 2, 7:00am – 10:00pm
* Friday, Dec. 3, 7:00am – 12:45pm

Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

== (Plannning Log) ==

[http://www.na-mic.org/Wiki/index.php/RSNA2010.PlanningLog RSNA planning]

CaBIG.DICOM.Viewer

2017-07-10T18:27:07Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

== Logistics ==
* August 20, 11am (EDT)
* Conference call
** Phone number: 1-800-704-9804
** Contact stephen.aylward@kitware.com for participants code.

== Attendees ==
* Ron Kikinis
* Eliot Siegel
* Larry Clarke
* Paul Mulhern
* Carl Jaffe
* Keyvan Farahani
* Bob Nordstrom
* Steve Pieper
* Stephen Aylward

== Background ==

=== Related Links ===
* [http://mircwiki.rsna.org/index.php?title=DICOM_Viewer MIRC DICOM Viewer]
* [http://www.na-mic.org/ NAMIC Website]
* [https://na-mic.org/w/images/d/d6/2007WS3DSlicer.ppt Radiology Workstation Module for Slicer3]
* [http://wiki.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Lightbox Lightbox in Slicer3]
* [http://www.slicer.org/ Slicer]

=== Initial Emails ===
Subject: FW: MIRC DICOM Viewer Question
Date: Sun, 5 Aug 2007 11:46:54 -0400
From: Mulhern, Paul <mulhern_paul@BAH.COM>
Reply-To: mulhern_paul@BAH.COM
To: CABIG_IMAGE-L@LIST.NIH.GOV
Message from Eliot Siegel:

Dear members of the imaging workspace:

If you get a chance, I was wondering if you could do us a favor in
support of our MIRC teaching file software. We're hoping to add a free
DICOM viewer to the MIRC teaching file software without having to
develop one from scratch. If you get a chance would you please check
out John Perry's Wiki site and let me know if you have any ideas. The
Wiki page is http://mircwiki.rsna.org/index.php?title=DICOM_Viewer.
Please let me know if you have any ideas. Thanks so much in advance!

Warm regards,
Eliot

From: Ron Kikinis MD
Sent: Monday, August 06, 2007 7:33 AM
To: Clarke, Laurence (NIH/NCI) [E]
Subject: [Fwd: [Fwd: FW: MIRC DICOM Viewer Question]]

Larry,

There is a lot of potential leverage in improving the interoperability
between Slicer and CaBIG (e.g. for NCIGT, NAMIC and NAC efforts). Slicer
is already listed as a dicom viewer for NCIA (as you know) and we have a
tutorial on how to use the current product release of slicer for viewing
NCIA images (www.slicer.org).

The new version of slicer (Slicer3) allows a closer integration with the
CaBIG framework with relatively little incremental effort. for that
version, we are already working on a first generation of a radiology
centric display.

Has there been any change in the procedures or do I just write an email
to Eliot?

Ron

=== caBIG Initiative ===

From http://grants.nih.gov/grants/guide/pa-files/PAR-07-426.html

caBIG™ provides a different infrastructure for tool and data federation than BIRN does. caBIG™ has developed strategic infrastructure that depends on open source software and on using commercial software where appropriate to provide interoperability, to connect users and tools through a grid infrastructure, and to provide researchers with grid-enabled applications. The software tools support basic, clinical, and translational research functions. It is expected that providing the capability for researchers to use caBIG-enabled applications will remove the technological barriers to sharing data on the grid. Ultimately, the goal of caBIG™ is to connect the research community from bench scientists to clinical researchers and on to the Food and Drug Administration. A key part of the caBIG™ strategy is to use well-defined standards for data exchange and to develop a core vocabulary so that results from multiple experiments or data streams can be compared. caBIG™ tools and infrastructure components are freely available on the caBIG™ web site (https://caBIG.nci.nih.gov).

The caBIG™ interfaces cover four distinct areas: programming and messaging interfaces, information models, vocabularies/ontologies and terminologies, and data elements. To assist developers that wish to build systems that can leverage this infrastructure, the caBIG™ Compatibility Guidelines (https://cabig.nci.nih.gov/guidelines_documentation/ ) have been created. The guidelines recognize four levels of maturity, based on the degree of interoperability that the system can support starting with Legacy (not interoperable) through Bronze, Silver and Gold (fully interoperable using the caBIG™ infrastructure). This FOA is targeted at systems that can be made interoperable at the “Gold” maturity level, so that they can have the broadest benefit to the research community.

Gold level information systems interoperate using the caGrid infrastructure (https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/ ) that provides the formalized grid architecture and specifications for this level of interoperability. The caGrid infrastructure is layered on existing grid technologies such as Globus Toolkit and leverage several existing middleware components including the National Cancer Institute Center for Bioinformatics (NCICB) caCORE infrastructure (http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/ ) and the Ohio State University Mobius middleware. The caGrid infrastructure contains many innovative features augmenting these core components. These features include a robust grid security infrastructure, innovative metadata management services and workflow management systems for service orchestration. The caGrid distribution also includes an integrated development environment (IDE) tool called Introduce, which simplifies the construction of new “Gold” compatible systems. The use of caGrid infrastructure and tools does not require any specialized hardware, and is supported on most commonly available platforms.

There are two key registration steps that must be undertaken for a system to become part of caGrid. The first step involves registration of an information model and associated semantic annotations, expressed in the Unified Modeling Language (UML), into the Cancer Data Standards Repository, or caDSR (http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr ). The caDSR is a metadata registry where all caBIG data semantics are maintained and referenced. The caDSR derives its semantics from ontology and terminology sources that are approved for use in caBIG, but is not itself an ontology management system. Rather, it is a metadata registry for caBIG information models. Tools and live support are available to assist with UML model registration. Once an information model is registered, the system can then be added to the actual caGrid data and analysis federation. This requires that the system be exposed as a "service" on caGrid using the Introduce tool referred to above. Introduce assists with the process of wrapping and registering a service with the main caGrid Index Service registry.

Once registered, a service becomes available to all authorized users of caGrid. Currently available caGrid services can be found on a prototype caGrid portal site, still under development, which can be found here: http://cagrid-portal.nci.nih.gov/portal . In addition to the portal, more sophisticated scientific research applications that leverage caGrid are also under development.

2016 Summer Project Week/Auditory Display

2017-07-10T18:27:07Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*David Black, University of Bremen, Fraunhofer MEVIS
*Sarah Frisken, BWH/HMS
*Christian Hansen, Uni Magdeburg
*Longquan Chen, BWH/HMS
* Tamas Ungi
* Rocio Lopez
* Elvis Chen
*Julian Hettig

==Related Work==
Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see

*VIDEO: [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy, with BWH/HMS and with Slicer][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link]
*VIDEO: [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion, with Univeristy of Magdeburg]
*VIDEO: [https://www.youtube.com/watch?v=gCg5nJSI2pY Auditory Display for Liver Resection] [http://www.ncbi.nlm.nih.gov/pubmed/23192891 Paper]
*[http://ioi.cs.uni-bremen.de/?page_id=780 Towards Uncertainty-Aware Auditory Display for Surgical Navigation (CARS 2016)]
*D. Black, J. Al Issawi, C. Rieder, and H. Hahn. Enhancing medical needle placement with auditory display. In Mensch & Computer 2013: Interaktive Vielfalt, pages 289–292, 2013. [https://na-mic.org/w/images/7/7d/Curac2013_dblack_Auditory_support_for_Navigated_Radiofrequency_Ablation_FINAL.pdf PDF ]

==Possible application areas / IDEAS==
*Acquiring 3D data sets for US, did we acquire all we need?
* Uncertainty in navigation information
*Brain / Structure Shift
* reduce complexity of displays by offloading to audio
*Depth cues for 3D data (shown on 2D screens)
*coverage of needle in US

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Explore possibilities of auditory display for intraoperative use
* Find opportunities for extending existing projects with auditory display
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* common sound synthesis software: [https://puredata.info PureData], [https://cycling74.com/products/max/ Max], or [http://supercollider.github.io/ SuperCollider] DOWNLOAD PUREDATA EXTENDED>>> [https://puredata.info/downloads/pd-extended here]
* Test program for Puredata to listen for incoming OSC messages: [http://wiki.na-mic.org/Wiki/images/8/81/Test_incoming_OSC.zip link]
* libraries for OpenSoundControl include C++: [http://liblo.sourceforge.net/ liblo], Python: [http://das.nasophon.de/pyliblo/ PyLiblo]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Existing methods for intraoperative navigation guidance already implemented in [https://puredata.info Puredata], see [https://www.dropbox.com/s/6wfrklm8by4fx29/Dual-frequency-feedback.mov?dl=0 for ureteroscopy][http://wiki.na-mic.org/Wiki/index.php/File:Dual-frequency-feedback.mov download link], [https://www.dropbox.com/s/35rvm7kx30hwl08/WirbelBeispielMitAudio.mov?dl=0 for ablation needle insertion]
* Tried out iplementing liblo library for OSC messages, this workson Mac but not well on Windows.
* Switched to python-based library, which works well. Rocio tried this out but not enough time to integrate with their existing apps.
* Friendly contact between groups who are interested in working together (Rocio, Tamas, Elvis, Longquan)

*[[Code from Jay Jagadeesan for OgenIGTLink]], [https://na-mic.org/w/images/3/3d/ReceiveClient.cxx.zip here as zip.]
*Only for Linux and Mac system, as the "lo" library has some build issue with visual studio. For windows user, it is recommended to use the python version of lo [http://das.nasophon.de/pyliblo/ Python library for lo]
*[http://www.na-mic.org/Wiki/index.php/File:AudioSimulator.zip A small lo simulator from Longquan Chen]
** This simulator use the lo library, sends note to the local/remote server running PD-Extended.
** Instructions about how to build and test the program is written in the readme.txt file
</div>
</div>

Events:RSNA 2010 CTSA

2017-07-10T18:27:07Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable2" border="1" cellpadding="8" cellspacing="1"
| style="width:25%" |[[Image:NAMIC.jpg‎]]
| style="width:25%" |[[Image:Logo_nac.gif‎]]
| style="width:25%" |[[Image:NCIGTlogo.gif]]
| style="width:25%" |[[Image:Catalyst_logo_final.jpg|200px]]
|}

= CTSA at RSNA =

==Introduction==
The '''Quantitative Medical Imaging for Clinical Research and Practice''' course is offered by the Clinical Translational Science Award (CTSA) Consortium at the [http://rsna2010.rsna.org 96th Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA 2010)].

As part of the outreach missions of these cooperating institutions, we will offer a presentation and hands-on demonstration using freely available, multi-platforms open source software to enable medical image analysis research. The course along with the tutorial and datasets aim to introduce translational clinical scientists to the capabilities of the 3D Slicer software.

==Logistics ==
*Date: Tuesday, November 30 2010
*Time: 10:30 AM - 12:00 PM
*Location: S401CD, McCormick Place, Chicago, Illinois
*Course: IA31

==Learning Objectives==
* Enhance interpretation of medical images through the use of 3D visualization,
* Gain experience with interactive, quantitative assessment of complex anatomical structures,
* Present current directions of quantitative imaging as a biomarker in clinical trials.

==Abstract==
Technological breakthroughs in medical imaging hardware and the emergence of increasingly sophisticated image processing software tools permit the visualization and display of complex anatomical structures with increasing sensitivity and specificity.

This workshop will begin with an introductory presentation of state-of-the-art, clinical examples of quantitative imaging biomarkers for diagnosis and clinical trial outcome measures. Cases from multiple imaging modalities and from multiple organ systems will be highlighted to illustrate the depth and breath of this field. Participants will then be led through a series of tutorials on the basics of viewing and processing DICOM volumes in 3D using 3D SLICER (www.SLICER.org). Specific hands-on demonstrations will focus on basic use of 3D Slicer software, quantitative measurements from PET/CT studies, and volumetric analysis of meningioma.

== Instructors ==
* Author/Presenter: Randy L. Gollub MD, PhD
* Author/Presenter: Katarzyna J. Macura MD, PhD
* Author/Presenter: Jeffrey T. Yap PhD
* Author/Presenter: Ron Kikinis MD
* Author/Presenter: Valerie Humblet
* Author/Presenter: Wendy Plesniak PhD

== Tutorial Materials ==
* [https://na-mic.org/w/images/d/d4/Combined-RSNA2010-CTSA.ppt Combined tutorial slides (ppt) ]
* [https://na-mic.org/w/images/3/33/Slicer_data-RSNA2010-CTSA.zip Tutorial datasets ]

== How to sign up ==
* [http://rsna2010.rsna.org/attendees.cfm Online registration and course enrollment ]

== (Plannning Log) ==

http://www.na-mic.org/Wiki/index.php/RSNA2010.PlanningLog

SDIWG:Meeting Minutes 20100528

2017-07-10T18:27:07Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

==NCBC Joint Working Group Meeting==

[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]

===Notes===
''Friday May 28, 2010: 2:30-3:30 PM EST''<br>
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br>
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br>
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b>

===Tcon DRAFT Agenda===

*Roll Call/Note-taker (Ivo) (5 min)
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)
*Status check on '''working groups''':
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. If you are interested, send [mailto:lysterp@mail.nih.gov Peter Lyster] a request for a copy of a paper on Biositemaps and BRO that was recently submitted with lead author Jessie Tennenbaum. Also, please try out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [https://na-mic.org/w/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].
**** Example: CCB Biositemap.RDF
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]
***** [https://na-mic.org/w/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]
***** [https://na-mic.org/w/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).
**** Example Pipeline workflows ([https://na-mic.org/w/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [https://na-mic.org/w/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [https://na-mic.org/w/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with [http://www.ncbcs.org/summary-cal.html NCBC RSS feeds for all centers]. Please check it out and provide feedback. (Joy)

<br>

===Minutes===
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 2010 Minutes]]
* Attendees: David Rubenson, Ivo Dinov, Karen Skinner, Susanne Churchill, Gil Omenn, Trish Whetzel, Will Schroeder, Zohara Cohen, Peter Lyster, Jeannette Schmidt, Zak Kohane.

* Peter/Zohara - [http://wiki.simtk.org/ncbcdisseminate/ dissemination efforts] / [http://www.ncbcs.org/cal.html NCBC Calendar]; [http://www.ncbcs.org/ NCBC web-page], [http://www.ncbcs.org/dbp_interactions.html DBP interactions] (access-stats, maps). How useful/used is the NCBC Calendar? Possible to add NCBC-Cal to Google/Personal Calendars.
** Email and Calendars are now low-maintenance.
** There are about 200 subscribers to this list (NCBC-Cal?)
* Peter: Merger/Symbiosis of DBP and Calendar efforts.

* Peter release of the [http://www.biositemaps.org/rds RDS (Resource Discovery System)].
* CTSA/Biositemaps WG continues to make progress. Released RDS V.2?
* Trish: latest efforts on [http://bioportal.bioontology.org/visualize/40656 BRO 3.1]. NCBC/CTSA collab - request from Pitt to include new regulatory branch - continually updated. Need to continue discussions on:
** Update existing Biositemaps.RDF files and account for deprecated RDF constructs. Auto updates?
** Extending the IM (Information model) to allow tool interoperability and comp-tool integration.
** (Trish) Added announcements to BRO?
** Send to Beth and Peter comments on RDS (2.0) functionality/operations/features.
** Karen S: Any stats on RDS usage yet? Peter: Dev team is NCBC/Pitt - none of them are on this call (Peter will check with them).
** BRO Paper (Jessie/Duke), in review.
* Peter: RDF extension Pipelining: Ivo suggested drafting some details on hands-on utilization of the Biositemaps.RDF extension enabling the tool interoperability.
* Peter: Action Items as above.
* Peter: NCBC Renewal apps (June 15 review; Council Review Sept).
** Susanne: Inter-interval/intermediate funding?
** No-cost extension apps (at least until the end of August/September) - check with program officer.
** Jeannette - assuming Aug/Sept (bridge?) difficult to plan.

===Action Items===
* TBD

Tests of Iowa Workshop tutorials

2017-07-10T18:27:07Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

[[Iowa 2012 Workshop Materials]]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Tutorial Data'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test Author & Comments/Mantis Links'''
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Lion || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Snow Leopard || 2012/03/18 ||2012-03-18 (r19639) || Sonia. OK.
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 32 || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP || 2012-03-17 || 3/18.12 || Steve<br>Everything works except turning on glyphs after label map seeding, which results in a crash due to lack of memory. Suggestion is to skip this step of the tutorial for users on win32. Another option is to only segment a single slice of the corpus in order to generate fewer tracts. Also it might help to delete the dwi volume after tensor estimation. When I did these steps I was able to complete all steps of the tutorial.
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux Unbuntu 64 || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug) || || ||
|-
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug)|| r19517 || 03/07/2012 ||
Nicole: <s>[http://na-mic.org/Bug/view.php?id=1793 1793]</s>. <s>[http://na-mic.org/Bug/view.php?id=1795 1795]</s>
|-
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 64b (package)|| r19577 || 03/13/2012 ||
Julien <br>pdf is 95MB !?!?<br>Page 22, Popup look is now different<br>Page 23, in red slice only the popup should still be up (didn't unpin)<br>Page 25: Diffusion Tensor Estimation has been renamed into DWI to DTI estimation<br>Page 25: dwi is already selected as Input DWI<br>Page 25: Minor Bug ! It stays "scheduled" for >5secs, not sure why<br>Page 26: Popup looks different now<br>Page 30: shouldn't labda1~labda2 >> lambda3 look more like a smarties ?<br>Page 32: typo connect ->connects<br>Page 36: Need to click on ">>" button first<br>Page 41: Bug ! After apply, the foreground image is reset to none, need to manually set it back to dti<br>Page 46: After selecting FractionalAnisotropy, Auto WL is automatically selected<br>Page 48: You might want to include screenshot of Link button again<br>Page 51: No need to move the mouse in 3D view, it automatically refreshes. If not, then a bug must be reported<br>Page 57: 1 bullet point has no . at the end(for information, there is no . in the other slides.<br>Page 60: Advice to use the right/left arrow keys to slice through?<br>Page 65: No axial slice displayed in 3D<br>Page 74: explain how to rename?<br>Page 78: explain to go to Annotation module again ?<br>Page 79: no need to turn off and on, it automatically refreshed when I placed the fiducial. If not, then a bug must be reported.<br>Page 81: explain where to place fiducial.<br>Page 82: Bug, it doesn't recompute automatically
|-
|-
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 64b (package) || 4.1.0-rc1-2012-03-17 <br> r19637 || 03/19/2012 ||
Benjamin - Work as expected <br> Setting a low (<4) scpacing value, in Glyphs, can turn your computer out of memories
|-
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux Unbuntu 64 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 || Benjamin - Work as expected <br> Setting a low (<4) scpacing value, in Glyphs, can turn your computer out of memories
|-
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OSX 10.7 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 || Jc - Work as expected
|-
|[https://na-mic.org/w/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP 32b || Slicer 4.1.0 rc1 (r19609) || 03/15/2012 ||
Julien <br>no link for the data mentioned in the tutorial<br>No mention to what Slicer version the tutorial is compatible with<br>Page1: Slicer Logo is 4.0, does it mean it's compatible with 4.0 ? no<br>Page 10: I have 100modules (from log messages dialog CTRL+0)<br>Page 19: typo: appears in the 2D viewer'''s'''<br>Page 22: Add "fit image to window" icon<br>Page 41: Odd black pixels in fa volume (see email)<br>Page 58: Add arrow to indicates how to change to yellow layout ?<br>Page 60: icon of the draw tool ? I first used the paint tool instead<br>Page 64: no "Minimum Length", only "Minimum Path Length". Bug ? why "Maximum Length" is not also "Maximum Path Length" ?<br>Page 64: Bug: why only Integration Step Length is (mm) but not others?<br>Page 66: Click on "Glyph" -> Crash (Slicer= 690Mo)
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Mac OS Lion || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Windows 7 64 || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset]|| Windows XP 32 || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Linux Ubuntu 64|| Slicer4.1rc1 || 03/19/2012 ||
Benjamin <br> p3 : Image has no link with this tutorial <br> p16 : The Directory HelloPython has two sub directories "code" and "data". Wrong path. <br> p21 : Add comment to warn the user about the indentation <br> p17 : Slicer layout change compare to the previous screenshot <br> p31 : We are not able to copy properly the text <br> p35 : helloPython sript path is ".../helloPython/code/" <br> p36: word "can" is written twice, and I already have 3 items in the sub menu "Exemples" <br> p48: The Directory HelloPython has two sub directories "code" and "data". Wrong path. <br> p50: Slicer layout change compare to the previous screenshot <br> p55: The last line should be on 1 line, or warn the user who may not know how work Python. <br> p59: Same as p48 and p16 <br> p61: Slicer layout change compare to the previous screenshot <br> p62: More explanation maybe - Up/Down - Left/Right - ?
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Linux Ubuntu 64 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 ||
Benjamin - Work as expected
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Windows 7 64b (package) || 4.1.0-rc1-2012-03-17 <br> r19637 || 03/19/2012 ||
Benjamin - Work as expected
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || MacOSX 10.7 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 ||
Jc - Work as expected
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Mac OS SnowLeopard || 2012.03.18|| 2012.03.18 || Sonia. OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Mac OS Lion || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Windows 7 64|| 4.1.0-rc1-2012-03-17 r19637 || March 19 || Julien<br>Page 13: Background is already correctly set<br>Page 14: circle on screenshot where to change current volume to "BaselineVolume" (DTIVolume selected by default) (+ typo, it's "BaselineVolume" not "Baseline Volume")<br>Page 24: You might want to mention that Grow Cut works in 3D<br>Page 31: grow cut button circle is off<br>Page 39: I don't have the axial slice visible in 3D view<br>Page 40: Didn't understand why positioning the mouse in the cystic part<br>Page 46: Give description for "Output Fiber Bundle"
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Windows XP 32|| version from tutorial page || March 19 || Steve<br>Worked as expected
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Linux Ubuntu 64 || 4.1rc1 || March 15 || Steve - worked great - few content comments sent to Sonia
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Linux Ubuntu 64 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 || Benjamin - worked as expected
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Windows 7 (package) || 4.1.0-rc1-2012-03-17 <br> r19637 || 03/19/2012 || Benjamin - worked as expected
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Mac OSX 10.7 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 || Jc - worked as expected
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization ]
||[[media:‎3DVisualizationData.zip| 3D Visualization dataset]] || Mac OS SnowLeopard || 2012-03-18 || 2012-03-18 (r19639) || Sonia. OK. Note: The Save Scene doesn't save the scene with the correction orientation e.g. if the user saves the scene with 3D viewer showing the 3D models in Superior orientation, the scene gets restore in Anterior orientation.
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎|3D Visualization dataset]] || Mac OS Lion || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Windows 7 64 || || || Julien<br>Page 47: Opacity could have been set from the tree view directly (last column)<br>Page 55 is a double<br>Page 56: no mention to check the Slice Intersection checkbox<br>Page 67 is a doublon<br>
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Windows XP 32 || 2012-03-17 || 3/18/12 || Steve<br> Everything worked as expected (32 bit windows build)
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Linux Ubuntu 64 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 ||
Benjamin - No Crash <br> Loading Scene - Image are not scaled all the time in the Slice views (random)-
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Windows 7 64b (package) || 4.1.0-rc1-2012-03-17 <br> r19637 || 03/19/2012 ||
Benjamin - No Crash <br> Loading Scene - Image are not scaled all the time in the Slice views (random)-
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Mac OSX 10.7 (package) || 4.1.0-rc1-2012-03-17 <br> r19635 || 03/19/2012 ||
Jc - <br> Crash at exit during the first part but can't reproduce <br> Loading Scene - Image are not scaled all the time in the Slice views (random)-
|-
|}

* [http://www.na-mic.org/Wiki/index.php/Slicer-4.1 Back to Slicer4.1 Feb 27 page]

UNC 2015

2017-07-10T18:27:07Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable"
|style="width:33%" |[[Image:NAMIC.jpg‎]]
|style="width:33%" |[[Image:NCIGTlogo.gif]]
|style="width:33%" |[[Image:Logo_nac.gif‎]]
|}
=Introduction=
The 3D Slicer UNC workshop is a full day course that will combine a series of lectures and hands-on sessions using the 3D Slicer software. The morning session will provide an introduction to the basics of data loading, 3D visualization and image registration. The afternoon session will focus on fundamental and practical aspects of Diffusion MRI analysis.

=Workshop Organizers=
* Sonia Pujol, Ph.D., Brigham and Women's Hospital, Harvard Medical School
* Martin Styner, Ph.D., University of North Carolina at Chapel Hill

=Local Host=
* Martin Styner, Ph.D., University of North Carolina at Chapel Hill

=Tentative Agenda=
*9:00-9:15 am Computer setup assistance by the instructors
*9:15-9:30 am Welcome and Goals of the Workshop (Martin Styner)
*9:30-10:00 am Introduction to the 3D Slicer software and community (Sonia Pujol)
*10:00-11:00 am Hands-on session 1: [https://na-mic.org/w/images/7/71/3DDataLoadingandVisualization_SoniaPujol_slicer4.4.pdf 3D Data Loading and Visualization (partI)](Sonia Pujol)
*11:00-11:15 am Coffee break
*11:15-12:15 pm Hands on session2: [[media:RegistrationTutorial_SoniaPujol_UNC2015.pdf | Image registration (Sonia Pujol)]]
*12:15-1:30 pm Lunch
*1:30 pm-2:15 pm [[media:DiffusionMRIanalysis Tutorial SoniaPujol UNC2015.pdf| An Introduction to Diffusion Tensor Imaging ]] (Sonia Pujol)
*2:15 pm-2:45 pm The DTI Prep Tool [[Media:2015-DTIPrep.pdf‎ | PDF Slides]] (Martin Styner/Francois Budin)
*2:45 pm -3:00 pm Coffee Break
*3:00-3:45 pm [[media:WhiteMatterExplorationTutorial_SoniaPujol_UNC2015.pdf‎ | White Matter exploration for Neurosurgical Planning (Sonia Pujol)]]
*3:45-4:30 pm 3D Slicer UNC demos (Martin Styner/Francois Budin) using DTI-Reg [[Media:2015-DTI-Reg-Tutorial.pptx.pdf | PDF Slides]], FiberViewerLight and DTIAtlasFiberAnalyzer
*4:30-5:00 pm Questions from the audience and concluding remarks

=Logistics=
* Date: Thursday June 11, 2015
* Location: Brooks Hall, FB 141
* Workshop Materials: The workshop will be a series of hands-on sessions using Slicer 4.4 and 4.3.1 release versions (http://slicer.org or http://slicer.kitware.com/midas3/slicerpackages/view) and the following datasets:
**[[Media:3DVisualizationData.zip | 3D Visualization Dataset]]
**[[Media:Dti_tutorial_data.zip‎ |Slicer DTI tutorial Dataset]]
**[[Media:SlicerWorkshop-UNC-20150611.zip | DTIPrep Diffusion Dataset]]
**[[Media:WhiteMatterExplorationData.zip|White Matter Exploration dataset]]
**[[Media:RegistrationData.zip|Registration dataset]]
* Registration: To register to the event, please fill in the [https://docs.google.com/a/cs.unc.edu/forms/d/1to_wiVc921cbgTYtqrJcB8xnlciLp6C8sAMGU8z3c7A/viewform online registration]. In case that the online registration does not work, you can also use the[[Media:RegistrationForm_SlicerWorkshop_UNC2015.doc‎| UNC registration form]] and send it to Alden Sharpe (ajsharpe at cs.unc.edu).
* Download an Ubuntu Virtual Machine with Slicer 4.4 [https://drive.google.com/file/d/0B024c-nPOGSdVW9jVW15U3YxMUU/view?usp=sharing here]

CTSC:Slicer handson.021810

2017-07-10T18:27:07Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]
<br>

{| class="wikitable2" border="1" cellpadding="8" cellspacing="1"
| style="width:25%" |[[Image:NAMIC.jpg‎]]
| style="width:25%" |[[Image:Logo_nac.gif‎]]
| style="width:25%" |[[Image:NCIGTlogo.gif]]
| style="width:25%" |[[Image:Catalyst_logo_final.jpg|200px]]
|}

==Logistics ==
*Date: Friday, February 18 2011 and Friday, March 11, 2011
*Time: 12:00 PM - 1:00 PM
*Location: Countway Library, room 403

==Learning Objectives==
* Enhance interpretation of medical images through the use of 3D visualization,
* Gain experience with interactive, quantitative assessment of complex anatomical structures,

==Abstract==
Technological breakthroughs in medical imaging hardware and the emergence of increasingly sophisticated image processing software tools permit the visualization and display of complex anatomical structures with increasing sensitivity and specificity.
Participants will then be led through a series of tutorials on the basics of viewing and processing DICOM volumes in 3D using 3D SLICER (www.SLICER.org). Specific hands-on demonstrations will focus on basic use of 3D Slicer software, quantitative measurements from PET/CT studies, and volumetric analysis of meningioma.

== Instructors ==
* Valerie Humblet, PhD
* Wendy Plesniak PhD
* Kathryn Hayes

== Agenda ==

*Slicer3 Minute tutorial
*Quantitative Measurement of Volumetric Change: ChangeTracker Tutorial
*Quantitative Measurements for Functional Imaging: PETCTFusion Tutorial

== Tutorial Materials ==
* [https://na-mic.org/w/images/d/d4/Combined-RSNA2010-CTSA.ppt Combined tutorial slides (ppt) ]
* [https://na-mic.org/w/images/3/33/Slicer_data-RSNA2010-CTSA.zip Tutorial datasets ]

== How to sign up ==
Please visit the [http://catalyst.harvard.edu/services/imagingcourses/workshops.html#workshop1 Harvard Catalyst website] for registration.

AHM2012-Slicer-Overview-and-Migration

2017-07-10T18:27:06Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

[[AHM_2012#Agenda|Back to AHM Schedule]]

'''Tuesday, January 10, 2012 8 to 10am'''
This session is for all developers planning to migrate existing slicer3 modules to slicer4 or start a new project from scratch in slicer4.

==Overview and Architecture==
* Steve (10 minutes) [[AHM2012-Slicer-Introduction|Introduction]]
** Capabilities
** Release Schedule
** Goals
** Ongoing Slicer4 projects and collaborations (NAC, NCIGT, CTK, Supplements...)
* Jc (10 minutes) [[AHM2012-Slicer-Architecture|Architecture]]
** Modularization Object Specialization
*** Qt Widgets <- CTK Widgets <- MRML Widgets <- Slicer Widgets
*** vtkObject <- MRMLLogic <- Module Logic
** Displayable Managers
** Views and Layouts

== Module Creation and Migration ==
* Steve (5 minutes) [https://www.slicer.org/wiki/Documentation/4.0/Developers/ModuleWizard Module Wizard]
* Jim (10 minutes)
** [[Media:Slicer4 CLI.ppt|CLI Modules]]
** Creating a CLI from existing C++ code
** Migrating CLI Modules to ITK version 4
* J2: Loadable Modules [[File:LoadableModules.pptx]] (20 minutes)
** Structure of a Loadable Module
** Specialization of Module Classes
** Integration with Designer
* Steve: [[AHM2012-Slicer-Python|Scripted Modules and Python Console]] (20 minutes)
** What is accessible via python
** Using the console (See [http://vimeo.com/33236047 J2's excellent demo video])
** Writing a Scripted Module
*** PythonQt interface
*** Logic with vtk/vtkITK/CLI Modules
*** Accessing MRML Data via numpy
** Refining the code and UI with slicerrc
** Limitations of python
* Demian: [[Whole-Brain-Tractography-Wizard|Whole Brain Tractography]] (10 minutes)
** Python wizard example
** Discussion of interactions among modules
** How to build on the dMRI module

== Testing Infrastructure ==
* Benjamin (20 minutes), [https://na-mic.org/w/images/e/ed/AHM-2012-SlicerTesting.pdf PDF]
** What is QtTesting/How it work.
** Tests for each widgets
** Limits : RenderWindow and GUI Testing
** Slicer integration [http://www.na-mic.org/Wiki/index.php/File:DemoTuto2Slicer.mpeg Demo]
** What's next ?

== Documentation ==
* Jc (10 minutes) [[AHM2012-Slicer-Documentation|Documentation]]
** How to write end user documentation for your module
** Source code naming and documentation style
** CMake documentaiton

== Extensions ==
* Jc (20 minutes) [[AHM2012-Slicer-Extension|Extension]]
** Writing an s4ext file
** Testing your extension
** How users will access your extension

2014 Winter Project Week:SubjectHierarchy

2017-07-10T18:27:06Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:SlicerRT 0.13 SubjectHierarchy ProstateEclipseLoaded.png|Screenshot of Subject Hierachy module
Image:Screenshot HuntingtonsLongitudinalInSubjectHierarchy.png|Huntington's longitudinal data in Sibject Hierarchy
</gallery>

==Key Investigators==
* Queen's: Csaba Pinter, Andras Lasso
* Isomics: Steve Pieper
* Kitware: Jean-Cristophe Fillion-Robin

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Review the current state of Subject Hierarchy
* Discuss features to develop and things to change
* Create roadmap for the integration

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* [http://www.na-mic.org/Wiki/index.php/AHM2014-SubjectHierarchy Breakout session]
** [https://na-mic.org/w/images/5/5e/SubjectHierarchy_NAMIC2014Jan.pptx Slides]
** [https://na-mic.org/w/images/6/6d/Subject_Hierarchy_-_Class_Diagram.png Detailed class diagram]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Subject hierarchy enhanced to better support handling Huntington's longitudinal data, [http://screencast.com/t/bIsTSFxkj video]
** Volumes subject hierarchy plugin handles labelmap and proper show/hide of volumes in the slice viewers
* Subject hierarchy module and mechanism presented in the breakot session, a lot of valuable feedback was given (see below)

</div>

== Received feedback ==
* DICOM back into SH? Derived vtkMRMLDICOMSubjectHierarchyNode class? For tags, UID, maybe levels?
* DICOM connections
** "All DICOM all the time" (@QIICR) means for import/export on disc, not in memory
** Tree vs DAG: Support DAGs? How to display them? "Infinite trees"?
** Update referenced UIDs and references when reparenting and the connections are known (plugins reparent method)
** Look at BioImageSuite (by Xenios) - User manual chapter 15 (page 193)
*** Connector lines in the tree are colored (indicate status of registration?)
* Export
** Override the selection made by the user to the most sensible one (if they select a contour, the RTSS is also selected)
** Determine mandatory tags for export
*** Stored in the plugins?
**** Maybe in XML or JSON templates that are read by the plugins?
**** Collect tags from plugin dependencies
** Use DICOM header widget with some changes (ctkDICOMObjectModel + ListWidget)
** Similar modalities to export (legacy, multiframe, enhanced) - separate plugins?
** Explicit representation of DICOM tags in Slicer in separate class?
** Ask for mandatory DICOM tags and connections (e.g. after conversion, resample, manual plugin selection)
* Use cases
** Neuro
*** Multiple modalities (different MR types)
*** Display tractography
*** Register volumes and indicate the registration status in the tree (in the icons)
** Data probe custom readout (e.g. dose)
** DICOM slice offset into the slice views
** Displayable manager customizable behavior
*** Scalar volume types e.g. multi-component vector volumes
*** Volume rendering transfer functions
* UIDs
** "2.25.hash" DICOM UIDs will be generated as new UIDs (perhaps even instead of MRML IDs in the future)
** What happens to the UIDs if we modify a node?
*** Create new SH node and move the data there?
** MIDAS url should be a SH storage node property? (Julien)
* Plugins
** Give confidence value of -1 if the node cannot be handled for sure?
** Per-structure labelmaps
** More abstraction: Qt, JavaScript etc. -> presentation managers
** Icon could be in the MRML node as a resource (string)
** Move core plugins into their corresponding modules after integration (Volumes, Transforms, Markups, etc.)
* Create dummy parents for loaded node if there is no parent (Study, Patient too)
* 'Unclaimed' section on the bottom of the tree instead of potential list? (Jim)
*Drag&drop would be difficult if there is a lot of nodes in the tree already
* Generate thumbnails as icons for volumes
* vtkSubjectHierarchyConstants -> vtkMRMLSubjectHierarchyConstants?
* qMRMLSortFilterPotentialSubjectHierarchyProxyModel be merged into qMRMLSortFilterSubjectHierarhcyProxyModel?
*Maybe a Q_PROPERTY controls their different behavior?
* Propagating / Overwriting attributes
*In the model, for example for "height" of an item
* Select and drag&drop multiple nodes from the potential list

== Reference ==
* [[2013_Summer_Project_Week:Patient_hierarchy|Summer Project Week page]]

Mapped Hexahedral Meshing

2017-07-10T18:27:06Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

'''Objective:'''

* Develop a tool for mapped meshing that will warp a template mesh onto a surface for a new subject
* Determine the limits that the warping algorithm will succeed and fail
* Apply these techniques to a sample of data to determine the reliability of the algorithm with respect to mesh quality

'''Progress:'''
* Previous work on this project was performed at the 2007 AHM - [https://na-mic.org/w/images/3/34/2007_AHM_Programming_Half_Week_MappedMesh.ppt Mapped Mesh 4 Block]
* Warped meshing framework has been developed using VTK and ITK using a finite element approach
**VTK
***Support the reading and writing of meshes (vtkUnstructuredGrid) and surfaces (vtkPolyData)
***Distance measures between the deforming mesh and the subject surface
***Initial registration - [http://www.vtk.org/doc/nightly/html/classvtkIterativeClosestPointTransform.html Iterative Closest Point] or [http://www.vtk.org/doc/nightly/html/classvtkProcrustesAlignmentFilter.html Procrustes]
**ITK
***Finite element framework used to warped the template mesh onto the subject surface
*Registration made hierarchical to speed up the registration process
**Requires multiple template meshes to exist
**This is readily supported using the interactive meshing tools by changing the average edge length
**Subsequent meshes are initialized using a thin plate splines
*Parameters allowed to vary at each level of the registration
**Iterations
**Young's Modulus
*Convergence based on distance between the warped template and the subject surface
**User specified convergence threshold in mm
**Convergence can be based on average or maximum distance
*Boundary conditions can be applied
**Center of the mesh - Holds the eight nodes closest to the center of the mesh fixed
**External - Applies boundary conditions to the mesh as they fall within a user specified tolerance of the subject surface
* Initial testing done by warping a cube mesh onto a sphere
**Evaluation:
***Distance between warped mesh and subject surface
***Mesh quality

'''Publications:'''
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.

'''Key Investigators:'''

* Iowa: Nicole Grosland, Vincent Magnotta, Ritesh Bafna

'''Links:'''
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]

'''Figures:'''

[[Image:MappedHexMeshSquareSphereInit.jpg|left|thumb|300px|Initial position of the cube template mesh and the sphere surface prior to registration using the itk::FEM mapped meshing algorithm]]

[[Image:MappedMeshCubeSphereQuality.jpg|left|thumb|325px|Mesh quality evaluation of the warped cube]]

[[Image:MappedMeshSquareSphere.jpg|left|thumb|300px|a)Position of the template cube mesh and surface after ICP registration. b) Resulting warped cube after itk::FEM mapped meshing. c) Distance map between the warped cube and the sphere surface]]

[[Image:MappedMeshProximalPhalanxTrial.jpg|left|thumb|300px|Initial attempt to apply mapped meshing algorithm to the proximal phalanx]]

Training:Slicer3.6 101 Test Table

2017-07-10T18:27:06Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

This table contains all the tests of the Slicer3.6 101 page tutorials.

*For Training Workshop specific module testing results, please refer to the [http://www.na-mic.org/Wiki/index.php/Journal_of_Slicer_Workshop_Tests Journal of Slicer Workshop Tests ]
*For previous module testing results for Slicer versions 3.6 and older, please refer to the [http://wiki.na-mic.org/Wiki/index.php/Journal_of_Slicer_Tests#Concept Journal of Slicer Tests]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|-
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]
|Mac Darwin|| 11-10-11 || OK (Tested by Daniel)
|-
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]
|Windows|| 11-10-11 || OK (Tested by Daniel)
|-
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]
|Linux 64|| 11-10-11 || OK (Tested by Daniel)
|-
| |[https://na-mic.org/w/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]
|Mac Darwin|| 06-10-11 || OK (Tested by Dominique)
|-
| |[https://na-mic.org/w/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]
|Windows|| 06-10-11 || OK (Tested by Dominique)
|-
| |[https://na-mic.org/w/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]
|Linux 64|| 06-10-11 || OK (Tested by Dominique)
|-
|[https://na-mic.org/w/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]
|Linux 32|| 06-10-11 || OK (Tested by Dominique)
|-
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]
|Mac Darwin|| 05-20-11 || OK (Tested by Dominique)
|-
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]
|Windows|| 05-13-11 || OK
|-
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]
|Linux 64|| 05-17-11 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz)]
|Linux 32|| 03-23-2011 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/e/e3/EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf EM Segmenter (Simple Mode)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz)]
|Linux 32|| 03-23-2011 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/darwin-x86/Slicer3-3.6.2-2010-11-03-darwin-x86.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-darwin-x86.tar.gz)]
|Mac Darwin|| 12-30-2010 || OK (Tested by Daniel)
|-
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/linux-x86/Slicer3-3.6.2-2010-11-03-linux-x86_64.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-linux-x86_64.tar.gz)]
|Linux 64|| 12-29-2010 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/linux-x86/Slicer3-3.6.2-2010-11-03-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-linux-x86.tar.gz)]
|Linux 32|| 12-29-2010 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
|Windows XP || 12-07-2010 || OK (Tested by SPujol)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86.tar.gz‎ | '''Linux 32''' (Slicer3-3.6.2-2010-12-03-linux-x86.tar.gz Linux-x32)]]
|Linux 32|| 12-07-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
|Windows XP || 12-04-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] |||[[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz‎ | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]
|Mac Darwin || 12-04-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz‎ | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]
|Linux 64|| 12-04-2010 || OK (Tested by Junichi)
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||11-2-2010 || All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||11-2-2010|| All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64|| 11-2-2010|| All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-win32.exe|| Win XP&7|| 11-2-2010|| All OK
|-
|[http://www.slicer.org/slicerWiki/images/6/67/PerkStationModule_TutorialContestSummer2010.pdf PERK Station Tutorial]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-25-2010||All OK
|-
|VMTK Centrelines Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-25-2010||All OK
|-
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-25-2010||All OK
|-
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-23-2010||All OK
|-
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-23-2010||All OK
|-
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-23-2010||All OK
|-
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-23-2010||All OK
|-
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK
|-
|VMTK Centrelines Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK
|-
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK
|-
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-21-2010||All OK
|-
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-21-2010||All OK
|-
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-21-2010||All OK
|-
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-21-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-21-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-20-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-12-2010||All OK
|-
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-12-2010||All OK
|-
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-12-2010||All OK
|-
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-12-2010||All OK
|-
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-12-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-12-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-11-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-11-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-11-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal Lesion Comparison] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-10-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal Lesion Comparison] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-06-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-06-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-06-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-06-2010||All OK
|-
|Robust Statistics Segmentation [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-29-2010||All OK; tutorial slide edits in progress
|-
|Robust Statistics Segmentation [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-29-2010||All OK; tutorial slide edits in progress
|-
|Robust Statistics Segmentation [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-29-2010||All OK; tutorial slide edits in progress
|-
|Atlas Label Merging & Surface Based Registration Tutorial [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||09-29-2010||All OK; tutorial slide edits in progress
|-
|Atlas Label Merging & Surface Based Registration Tutorial [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-27-2010||All OK; tutorial slide edits in progress
|-
|Atlas Label Merging & Surface Based Registration Tutorial [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-22-2010||All OK; tutorial slide edits in progress
|-
|Atlas Label Merging & Surface Based Registration Tutorial [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-22-2010||All OK; tutorial slide edits in progress
|-
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||09-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute][https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 |||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 |||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin |||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.12010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [https://www.slicer.org/wiki/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-

Questions, comments, and feedback can be sent to Sonia Pujol (spujol@bwh.harvard.edu)

Journal of Slicer Workshop Tests

2017-07-10T18:27:06Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

== '''Concept''' ==

This page will be used as a journal of tests for the Slicer workshops on four different platforms (Linux 32 and 64 bit, Mac Darwin, and Windows).

* Event: [[http://www.na-mic.org/Wiki/index.php/RSNA_2011 RSNA 2011 ]]
<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| Slicer4.0gamma2011-11-21 || Mac OSX Lion ||11/22/2011 || slide 39: when downloading the label layer, the foreground
disappeared, it needs to be reselected. slide 76: when using the compare viewer, I only have the option to
compare 2 views so I end up with 4 windows on the screen instead of 3. Every time I tried to go from lightbox
viewer to conventional viewer (last slide of the part 4), Slicer crashed. When I tried without data loaded to switch between the two I
have no problem, it seems linked to the dataset. Closing the scene at the end of part4 or part 5 of the tutorial causes Slicer to crash. (Valerie Humblet)
|-
|[[Media:RSNA2010_OsirixPanoramixDataset.zip | Abdominal CT scan with AAA (Osirix Panoramix Dataset)]]||Slicer4.0gamma2011-11-21||Mac OSX Lion||11/22/2011||cropping, volume rendering and GPU: OK, did not test annotations. No problem when closing the scene (Valerie Humblet)
|-
|[https://na-mic.org/w/images/7/79/RSNA2010_Prostate.zip Prostate data]||Slicer4.0gamma2011-11-21||Mac OSX Lion||11/22/2011||
|-
|[https://na-mic.org/w/images/2/28/RSNA2011_Prostate.zip Prostate data RSNA 2011 in progress]||Slicer4.0gamma2011-11-21||Mac OSX Lion||11/22/2011||Unable to unzip the file. It shows as .zip.download (Valerie Humblet)
|-
|[https://na-mic.org/w/images/3/33/Slicer_data-RSNA2010-CTSA.zip Quantitative imaging]||Slicer4.0gamma2011-11-23||Mac OsX Lion||11/23/2011||Slicer3 minutes: OK; PET/CT (using volumes and SUV computation): OK; Change tracker: Need to use the volume rendering module to view VOI widget in 3D viewer, does not appear automatically, close scene causes Slicer to crash (Valerie Humblet)
|-
|[https://na-mic.org/w/images/3/33/Slicer_data-RSNA2010-CTSA.zip Quantitative imaging]||Slicer4.0gamma2011-11-23||Windows 2008 32 bits Vista||11/23/2011||Slicer3 minutes: OK; PET/CT (using volumes and SUV computation): OK; Change tracker: Need to use the volume rendering module to view VOI widget in 3D viewer, does not appear automatically, close scene causes Slicer to crash (Valerie Humblet)
|-
|}

*'''Event''': [http://www.na-mic.org/Wiki/index.php/Events:2011-06-15-Robarts-Slicer-Workshop Robarts Institute workshop, Ontario, Canada]
* Datasets:
** [[media:Slicer3VisualizationDataset.zip | 3D Visualization dataset]]
** [[media:WhiteMatterExplorationData.zip‎| White Matter Exploration dataset]]
** [[media:HelloPython.zip | HelloPython dataset]]
** [[media:Slicer3_BRAINSFITRegistration.zip | BRAINSFIT Registration dataset]]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]|| [http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz] || Linux 32 || 06-08-2011 || OK on Ubuntu 10.10 32-bit (Junichi Tokuda)
|-
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-08-2011 || OK on Fedora 14 64-bit (Atsushi)
|-
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || || OK (Sonia Pujol)
|-
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]|| Windows XP || 06-09-2011 || OK (Junichi Tokuda)
|-
|[[media:Slicer3_DataLoadingAndVisualization_JHU2011_SoniaPujol.pdf |Data Loading and 3D Visualization]]||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]|| Windows 7 || 06-07-2011 || Laurent Chauvin
Slow on Windows 7 (64 bits).
First two times, Slicer crashed (first time when window opened after clicking Add Volume, second time when I tried to switch to Data module)
|-
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf‎ | Exploring peritumoral white matter fibers for neurosurgical planning ]]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz]|| Linux 32|| 06-08-2011 || OK on Ubuntu 10.10 (32-bit) (Junichi)
|-
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf‎ | Exploring peritumoral white matter fibers for neurosurgical planning ]]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-08-2011 || Atsushi
DTI volume was displayed with strange colors, or Slicer was crushed when I set Select the Scalar Mode to "Color By Orientation" on Fedora 14 64bit.
|-
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf‎ | Exploring peritumoral white matter fibers for neurosurgical planning ]]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || 06-09-2011 || OK (Sonia Pujol)
|-
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf‎ | Exploring peritumoral white matter fibers for neurosurgical planning ]]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]|| Windows XP || 06-08-2011 || OK (Junichi Tokuda)
|-
|[[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf‎ | Exploring peritumoral white matter fibers for neurosurgical planning ]]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe]|| Windows 7 || 06-07-2011 || Laurent Chauvin
Too slow to draw a line in grow cut mode (just points, but it's working.
One crash: Uncaught exception: bad allocation.
|-
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz] || Linux 32 || 06-08-2011 || OK on Ubuntu 10.10 (32-bit)(Junichi)
|-
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython ]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-09-2011 || Atsushi
When adding "inputVolume = scene.GetNodeByID(HelloPythonInputVolume)" to the source code, "Python HelloPython" was disappeared from the module list. So, I was not able to execute this module on Fedora 14 64bit. The binary version are Slicer3-3.6.3-2011-06-07-linux-x86_64 and Slicer3-3.6.3-2011-03-04-linux-x86_64.
|-
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython ]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || 06-09-2011 || OK (Sonia Pujol)
|-
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython ]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows XP || 06-09-2011 || OK (Junichi Tokuda)
|-
|[https://na-mic.org/w/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf HelloPython ]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows 7 || 06-08-2011 || Laurent Chauvin
Becareful when modifying HelloPython.py , Python is tab sensitive.
|-
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz] || Linux 32 || 06-07-2011 || OK on Ubuntu 10.10 (32-bit) (Junichi Tokuda)
|-
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-09-2011 || OK on Fedora 14 (64-bit) (Atsushi)
|-
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || || OK( Sonia Pujol)
|-
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows XP || 06-09-2011 || OK (Junichi Tokuda)
|-
|[https://na-mic.org/w/images/5/5a/OpenIGTLinkIFTutorial_Slicer3.6.3_JunichiTokuda_June2011.pdf OpenIGTLink]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows 7 || 06-07-2011 || Laurent Chauvin
|-
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86.tar.gz] || Linux 32 || 06-09-2011 || OK (Junichi Tokuda)
|-
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz Slicer3-3.6.3-2011-06-07-linux-x86_64.tar.gz]|| Linux 64 || 06-10-2011 || OK (Danielle Pace)
|-
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz Slicer3-3.6.3-2011-06-07-darwin-x86.tar.gz]|| Mac Darwin || || -when loading the scene, Slicer displays a warning that the users should ignore
-for visualizing the glyphs, you need to tell the participants to put DTI_iso in Bg viewer
- when select 'glyphs on display' with Scalar Mode 'Color by orientation', the glyphs are correctly displayed in the 3D viewer but all the 2D views are wrong
-registration and resampling test work on MacBook Pro (8GB RAM) (Sonia Pujol)
NOTE: Glyphs removed from tutorial (Danielle Pace)
|-
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows XP || 06-09-2011 || Error on final "Resample DTI Volume" step - Filed to allocat memory for image. (Junichi Tokuda)
|-
|[https://na-mic.org/w/images/f/f2/Slicer3_BRAINSFITRegistration_DPace_June2011.pdf BRAINSFIT Registration]
||[http://boggs.bwh.harvard.edu/slicer/Robarts-2011/Slicer3-3.6.3-2011-06-07-win32.exe Slicer3-3.6.3-2011-06-07-win32.exe] || Windows 7 || 06-09-2011 || Danielle Error on final "Resample DTI Volume" step - memory error, unable to allocate 77856768 elements of size 4 bytes
Laurent Chauvin: Unable to complete last step. Message: Completed with errors, but no more informations about error.
|-
|-

|}

*[http://www.na-mic.org/Wiki/index.php/Events:_Johns_Hopkins_University_Seminar_April_2011#Introduction JHU workshop April 5, 2011]
*[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Data Loading and 3D Visualization Data]
*[http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Data]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]|| [http://na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz] || Linux 32||04/4/11 || OK (Hayes)
|-
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]||[http://na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]|| Linux 64 || 04/1/11|| OK (SPujol)
|-
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]||[http://na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]|| Mac Darwin || 04/1/11||OK (SPujol)
|-
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]||[http://na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]|| Windows XP&7 || 04/4/11 || OK (Hayes)
|-
|[https://na-mic.org/w/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf Exploring peritumoral white matter fibers for neurosurgical planning ]
||[http://na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]|| Linux 32|| 04/04/11|| OK (Hayes)
|-
|[https://na-mic.org/w/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf Exploring peritumoral white matter fibers for neurosurgical planning ]
||[http://na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]|| Linux 64 || 04/1/11 || OK (SPujol)
|-
|[https://na-mic.org/w/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf Exploring peritumoral white matter fibers for neurosurgical planning ]
||[http://na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]|| Mac Darwin || 04/1/11|| OK (SPujol)
|-
|[https://na-mic.org/w/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf Exploring peritumoral white matter fibers for neurosurgical planning ]
||[http://na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]|| Windows XP&7 || 04/04/11 || OK (Hayes)
|-
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz] || Linux 32 || 04/04/11|| OK (Hayes)
|-
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]|| Linux 64 || 04/1/11||OK (SPujol)
|-
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]|| Mac Darwin || 04/1/11||OK (SPujol)
|-
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe] || Windows XP&7 || 04/04/11|| OK (Hayes)
|-
|}
<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 32|| 03/04/11 || Crashes when VTK models are rotated in 3D viewer (Hayes) (anago.nmr) [http://na-mic.org/Bug/view.php?id=1111 Bug Report]
|-
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || 03/04/11 || OK (Hayes) (panamint.nmr)
|-
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || 03/04/11 || Crashes when VTK models are rotated in 3D viewer (Hayes) (hima.nmr) [http://na-mic.org/Bug/view.php?id=1111 Bug Report]
|-
|[https://na-mic.org/w/images/2/2e/Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf Data Loading and 3D Visualization - UCSF Version]||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A || Testing Slicer3-3.6.3-2011-03-04 instead
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ]|| Linux 32|| N/A|| Waiting on completed slides (Hayes)
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || N/A || Waiting on completed slides (Hayes)
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || N/A|| Waiting on completed slides (Hayes)
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 ||N/A || Waiting on completed slides (Hayes)
|-
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 32 || N/A || Testing Slicer3-3.6.3-2011-03-04 instead
|-
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || N/A ||Testing Slicer3-3.6.3-2011-03-04 instead
|-
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin ||N/A ||Testing Slicer3-3.6.3-2011-03-04 instead
|-
|[https://na-mic.org/w/images/3/35/DiffusionMRITutorial_UCSF2010_SoniaPujol.pdf Diffusion Tensor Imaging - UCSF Version] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A|| Testing Slicer3-3.6.3-2011-03-04 instead
|-
|}
<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 32|| 03/03/11 || OK (Hayes) (anago.nmr)
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || 02/28/11 || OK, slides need updating (Hayes) (panamint.nmr)
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || 03/02/11 || Crashes when VTK models are rotated in 3D viewer (Hayes) (hima.nmr) [http://na-mic.org/Bug/view.php?id=1111 Bug Report]
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A || Testing UCSF slides instead
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ]|| Linux 32||N/A || Waiting on completed slides (Hayes)
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || N/A || Waiting on completed slides (Hayes)
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || N/A|| Waiting on completed slides (Hayes)
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A|| Waiting on completed slides (Hayes)
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 32 || 03/03/11 || OK (Hayes) (anago.nmr)
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Linux 64 || 02/28/11 || OK pending minor slide edits (Hayes) (panamint.nmr)
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Mac Darwin || 03/03/11 || OK (Hayes) (hima.nmr)
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/ 3.6.3-RC2 ] || Windows XP&7 || N/A || Testing UCSF slides instead
|-
|}

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 32|| 02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 64 || 02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Mac Darwin || N/A || Testing 3.6.3 RC2 instead (Hayes)
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Windows XP&7 || N/A || Testing 3.6.3 RC2 instead (Hayes)
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ]|| Linux 32|| 02/24/11|| Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
|| [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 64 || 02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Mac Darwin || N/A|| Testing 3.6.3 RC2 instead (Hayes)
|-
|Exploring peritumoral white matter fibers for neurosurgical planning
||[http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Windows XP&7 || N/A || Testing 3.6.3 RC2 instead (Hayes)
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 32 ||02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Linux 64 ||02/24/11 || Crashes on startup (Hayes) [http://www.na-mic.org/Mantis/view.php?id=934 Bug Report]
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Mac Darwin || N/A || Testing 3.6.3 RC2 instead (Hayes)
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] || [http://boggs.bwh.harvard.edu/slicer/3.6.3-RC1/ 3.6.3-RC1 ] || Windows XP&7 || N/A || Testing 3.6.3 RC2 instead (Hayes)
|
|-
|}

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt CTSA Tutorial Slides] || [[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz‎ | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]
||Mac ||12-03-2010 || OK (tested by SPujol)
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt CTSA Tutorial Slides] ||[[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz‎ | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]
||Linux 64|| 12-03-2010 || OK (tested by SPujol)
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt CTSA Tutorial Slides] ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
|Windows XP & Windows 7|| 12-03-2010 || OK (tested by SPujol)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
|Windows XP || 12-04-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] |||[[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz‎ | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]
|Mac Darwin || 12-04-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz‎ | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]
|Linux 64|| 12-04-2010 || OK (Tested by Junichi)
|-
|[https://www.slicer.org/wiki/File:InteractiveEditorTutorial_Slicer3.6-SoniaPujol.pdf Interactive Editor Slides] || [[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz‎ | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]

||Mac || 12-05-2010 || OK (Tested by Junichi)
|-
|[https://www.slicer.org/wiki/File:InteractiveEditorTutorial_Slicer3.6-SoniaPujol.pdf Interactive Editor Slides] ||[[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz‎ | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]
||Linux 64|| 12-04-2010 || OK (tested by SPujol)

|-
|[https://www.slicer.org/wiki/File:InteractiveEditorTutorial_Slicer3.6-SoniaPujol.pdf Interactive Editor Slides] ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
|Windows XP & Windows 7|| 12-04-2010 || OK (tested by SPujol)

|-
|[http://www.slicer.org/slicerWiki/images/c/c7/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Dec2010.pdf Diffusion Tensor Imaging Slides] || [[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz‎ | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]

|| Mac || 12-06-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/c/c7/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Dec2010.pdf Diffusion Tensor Imaging Slides] ||[[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz‎ | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]
||Linux 64|| 12-04-2010 || OK (tested by SPujol)

|-
|[http://www.slicer.org/slicerWiki/images/c/c7/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Dec2010.pdf Diffusion Tensor Imaging Slides] ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
|Windows XP & Windows 7|| 12-04-2010 || OK (tested by SPujol)

|-

|}

* [http://www.na-mic.org/Wiki/index.php/RSNA2010.PlanningLog '''RSNA 2010''' NAMIC Workshop November 29, 2010 ]
<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||11-2-2010 || All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||11-2-2010|| All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64|| 11-2-2010|| All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-win32.exe|| Win XP&7|| 11-2-2010|| All OK
|-
|}
<references/>

* [http://www.na-mic.org/Wiki/index.php/RSNA2010.PlanningLog '''RSNA 2010''' Quantitative Medical Imaging for Clinical Research and Practice November 30, 2010 ]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA09-WJP.ppt draft target tutorial slides] ||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||11-2-2010 || All OK
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA09-WJP.ppt draft target tutorial slides] || http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||11-2-2010|| All OK
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA09-WJP.ppt draft target tutorial slides] ||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64|| 11-2-2010|| All OK
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt Target tutorial slides] ||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||- || -
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt Target tutorial slides] || http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||- || -
|-
|[https://na-mic.org/w/images/4/4e/Combined-RSNA2010-CTSA.ppt Target tutorial slides] ||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64||- || -
|-
|}
<references/>
* [http://www.na-mic.org/Wiki/index.php/RSNA2010.PlanningLog '''RSNA 2010''' Quantitative Imaging Reading Room November 27-December 3, 2010 ]
<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
| [http://www.na-mic.org/Wiki/index.php/File:RSNA2010QIRR-LoopSlides.ppt QIRR Presentation] (presentation only, no tutorial) ||-- ||-- ||-- ||--
|}
<references/>

* [http://www.na-mic.org/Wiki/index.php/Events:UCLA-Slicer-Training-11-2010 - UCLA Workshop, Los Angeles, CA]
**[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Data Loading and 3D Visualization Data]
**[https://www.slicer.org/wiki/File:EditorTutorialDataset.zip Interactive Editor Data]
**[http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editing]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editing]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editing]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editing]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.12010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|}
<references/>

* [http://www.na-mic.org/Wiki/index.php/Events:UCSF-Slicer-Training-11-2010 - UCSF Workshop, San Francisco, CA]
**[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Data Loading and 3D Visualization Data]
**[https://www.slicer.org/wiki/File:EditorTutorialDataset.zip Interactive Editor Data]
**[http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.12010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|ABC module ?||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|}
<references/>

* [http://www.na-mic.org/Wiki/index.php/MICCAI_2010 - MICCAI 2010, Beijing, China]
** [http://www.na-mic.org/Wiki/index.php/File:HelloPython.zip Python Tutorial Data]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[http://www.na-mic.org/Wiki/index.php/File:ProgrammingIntoSlicer3.6.1_Python_SoniaPujol.pdf Programming in Slicer3 with Python]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||08-27-2010||All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:ProgrammingIntoSlicer3.6.1_Python_SoniaPujol.pdf Programming in Slicer3 with Python]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||08-27-2010||All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:ProgrammingIntoSlicer3.6.1_Python_SoniaPujol.pdf Programming in Slicer3 with Python]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||08-30-2010||All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:ProgrammingIntoSlicer3.6.1_Python_SoniaPujol.pdf Programming in Slicer3 with Python]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-30-2010||All OK
|-
|}
<references/>

* [http://www.na-mic.org/Wiki/index.php/Beijing_2010_NA-MIC_Workshop - PLA General Hospital Tutorial, Beijing China]
**[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Data Loading and 3D Visualization Data]
**[http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Tutorial Data]
**[http://www.slicer.org/slicerWiki/images/d/d1/Slicer-tutorial-neurosurgery.zip Neurosurgical Tutorial Data]
<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64|| 08-27-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32|| 08-27-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7|| 08-30-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin|| 08-30-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||08-27-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||08-27-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||08-30-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-30-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/b/ba/SlicerNeurosurgeryTutorial-3.6.1.ppt Neurosurgical Planning]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/b/ba/SlicerNeurosurgeryTutorial-3.6.1.ppt Neurosurgical Planning]||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-01-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/b/ba/SlicerNeurosurgeryTutorial-3.6.1.ppt Neurosurgical Planning]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/b/ba/SlicerNeurosurgeryTutorial-3.6.1.ppt Neurosurgical Planning]||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-01-2010||All OK
|-
|}
<references/>

* [http://www.na-mic.org/Wiki/index.php/2010-Slicer-UNCDuke August 11, 2010 - UNC Duke Workshop]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86_64.tar.gz Slicer3-3.6-2010-08-05] || Linux x64||08-08-2010 ||All OK
|-
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86.tar.gz Slicer3-3.6-2010-08-05] || Linux 32 ||08-08-2010||All OK
|-
|Data Loading and 3D Visualization||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-darwin-x86.tar.gz Slicer3-3.6-2010-08-05] ||Mac Darwin ||08-08-2010 ||All OK
|-
|Data Loading and 3D Visualization||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-win32.exe Slicer3-3.6-2010-08-05] || Windows XP ||08-08-2010 ||All OK
|-
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-win32.exe Slicer3-3.6-2010-08-05] || Windows 7 ||08-08-2010 ||All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86_64.tar.gz Slicer3-3.6-2010-08-05] ||Linux x64 ||08-08-2010 ||All OK with Thresholding tweak
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86.tar.gz Slicer3-3.6-2010-08-05] || Linux 32 ||08-08-2010 ||All OK with Thresholding tweak
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-05] || Windows XP ||08-09-2010 ||All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-05] ||Windows 7 ||08-09-2010 ||All OK
|-
|Interactive Editing ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-05] ||Mac Darwin||08-08-2010||All OK with Thresholding tweak
|-
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-05] ||Linux x64 || 08-08-2010||All OK
|-
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-05] ||Linux 32 ||08-08-2010||All OK
|-
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-05] ||Windows XP ||08-08-2010||All OK
|-
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-05] || Windows 7 ||08-08-2010|| All OK
|-
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-05] ||Mac Darwin || 08-08-2010||All OK
|-
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86_64.tar.gz Slicer3-3.6-2010-08-05] ||Linux x64 ||08-08-2010 ||All OK
|-
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-linux-x86.tar.gz Slicer3-3.6-2010-08-05] ||Linux 32 ||08-08-2010 ||All OK
|-
|Manual Registration|| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-win32.exe Slicer3-3.6-2010-08-05]||Windows XP || 08-08-2010||All OK
|-
|Manual Registration|| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-win32.exe Slicer3-3.6-2010-08-05] || Windows 7 || 08-08-2010||All OK
|-
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-05-darwin-x86.tar.gz Slicer3-3.6-2010-08-05] ||Mac Darwin ||08-08-2010 ||All OK
|-
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-02] || Linux x64|| 08-07-2010|| All OK
|-
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-03] || Linux 32 ||08-07-2010 ||All OK
|-
|Data Loading and 3D Visualization||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-04] ||Mac Darwin || 08-04-2010|| All OK
|-
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows XP || 08-08-2010||All OK
|-
|Data Loading and 3D Visualization ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows 7 || 08-08-2010||All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-02] ||Linux x64 || 08-05-2010||All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-03] || Linux 32 ||08-07-2010 ||All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows XP ||08-08-2010 || All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] ||Windows 7 ||08-08-2010 || All OK
|-
|Interactive Editing ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-04] ||Mac Darwin||08-04-2010 || All OK
|-
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-02] ||Linux x64 || 08-06-2010||All OK
|-
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-03] ||Linux 32 || 08-07-2010||All OK
|-
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] ||Windows XP ||08-08-2010 ||All OK
|-
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows 7 ||08-08-2010 ||All OK
|-
|Diffusion Tensor Imaging ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-04] ||Mac Darwin || 08-04-2010|| All OK
|-
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-02-linux-x86_64.tar.gz Slicer3-3.6-2010-08-02] ||Linux x64 || 08-07-2010||All OK
|-
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-linux-x86.tar.gz Slicer3-3.6-2010-08-03] ||Linux 32 ||08-07-2010 || All OK
|-
|Manual Registration || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03]||Windows XP ||08-08-2010 || All OK
|-
|Manual Registration || [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-03-win32.exe Slicer3-3.6-2010-08-03] || Windows 7 ||08-08-2010 || All OK
|-
|Manual Registration ||[http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6-2010-08-04-darwin-x86.tar.gz Slicer3-3.6-2010-08-04] ||Mac Darwin || 08-04-2010|| All OK
|-

|}
<references/>

* [http://www.na-mic.org/Wiki/index.php/2010-Slicer-StLouis July 1st,2010- StLouis Workshop] Use Slicer3.6 release (under construction)
<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6-2010-06-10-linux-x86_64.tar.gz Slicer3-3.6-2010-06-10] ||Linux x64 ||06-25-2010||All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6-2010-06-10-win32.exe Slicer3-3.6-2010-06-10] ||Windows XP&7 || 06-25-2010||All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6-2010-06-10-darwin-x86.tar.gz Slicer3-3.6-2010-06-10] ||Mac Darwin||06-25-2010||All OK
|-
|Interactive Editing || [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6-2010-06-10-linux-x86.tar.gz Slicer3-3.6-2010-06-10] || Linux x32|| 06-25-2010||All OK
|-
|Data Loading and 3D Visualization || [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6-2010-06-10-linux-x86_64.tar.gz Slicer3-3.6-2010-06-10] || Linux x64||06-11-2010||All OK
|-
|Data Loading and 3D Visualization || [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6-2010-06-10-win32.exe Slicer3-3.6-2010-06-10] ||Windows XP || 06-11-2010||All OK
|-
|Data Loading and 3D Visualization || [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6-2010-06-10-darwin-x86.tar.gz Slicer3-3.6-2010-06-10] ||Mac Darwin||06-11-2010||All OK
|-
|Data Loading and 3D Visualization || [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6-2010-06-10-linux-x86.tar.gz Slicer3-3.6-2010-06-10] || Linux x32] || 06-11-2010||All OK
|-
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6-2010-06-10-linux-x86_64.tar.gz Slicer3-3.6-2010-06-10] ||Linux x64 ||06-11-2010||All OK
|-
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6-2010-06-10-win32.exe Slicer3-3.6-2010-06-10] ||Windows XP || 06-11-2010 || All OK
|-
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6-2010-06-10-darwin-x86.tar.gz Slicer3-3.6-2010-06-10] ||Mac Darwin||06-11-2010||All OK
|-
|Diffusion Tensor Imaging || [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6-2010-06-10-linux-x86.tar.gz Slicer3-3.6-2010-06-10] || Linux x32 || 06-11-2010||All OK
|-
|Neurosurgical Planning|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6-2010-06-10-linux-x86_64.tar.gz Slicer3-3.6-2010-06-10] ||Linux x64 ||06-30-2010||All OK
|-
|Neurosurgical Planning|| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6-2010-06-10-win32.exe Slicer3-3.6-2010-06-10] ||Windows XP || 06-30-2010||All OK
|-
|Neurosurgical Planning|| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6-2010-06-10-darwin-x86.tar.gz Slicer3-3.6-2010-06-10] ||Mac Darwin||06-30-2010||All OK
|-
|Neurosurgical Planning|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6-2010-06-10-linux-x86.tar.gz Slicer3-3.6-2010-06-10] || Linux x32|| 06-30-2010||All OK
|-
|}
<references/>

Events:Dundee-Dec-2010

2017-07-10T18:27:05Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable2" border="1" cellpadding="8" cellspacing="1"
| colspan="5"|[[Image:Dundee-logo.gif|center]]
|-
| style="width:20%" |[[Image:NAMIC.jpg‎]]
| style="width:20%" |[[Image:Logo_nac.gif‎]]
| style="width:20%" |<br>[[Image:NCIGTlogo.gif]]
| style="width:20%" |<br>[[Image:Catalyst_logo_final.jpg|150px]]
| style="width:20%" |<br><br>[[Image:Logo CIMIT.png]]
|}

== Logistics ==
<big><big>This is a hands-on tutorial. You need a good laptop and you need to pre-install data and software. See below for more information.</big></big>
*Date: Monday December 6, 2010
*Location: Room, TBA, [http://www.imsat.org Institute for Medical Sciences and Technology], University of Dundee, Wislon House, 1 Wurzburg Loan, Dundee MediPark, Dundee DD2 1FD

== Agenda ==
* 9-9.30 Setup for those who had trouble with the installation
* 9.30-10.30 [https://na-mic.org/w/images/d/d4/Combined-RSNA2010-CTSA.ppt Combined tutorial slides (ppt) ]:
**Slicer3 Minute tutorial
**Quantitative Measurement of Volumetric Change: ChangeTracker Tutorial
**Quantitative Measurements for Functional Imaging: PETCTFusion Tutorial
**Please download the [[media:Slicer_data-RSNA2010-CTSA.zip | RSNA 2010 CTSA tutorial data ]] in preparation for the workshop.
*10.30-10.45 Break
*10.45-12.00 Interactive editor, DTI visualization
**Please download the [[media:Case-040-NeurofMRI-WithTransforms.zip| NeurofMRI Case 40]] in preparation for the workshop.
*12.00-13.00 Lunch
*13.00 IGT
**Demo of the OpenIGTLink simulator.
**How to connect your tracker to Slicer
**[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink Tutorial slides (ppt)].
**[http://wiki.slicer.org/slicerWiki/index.php/Modules:OpenIGTLinkIF-3.6-Simulators Link to the OpenIGTLink Data simulator].

== Teaching Faculty==
*[http://www.spl.harvard.edu/pages/People/kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School

== Registration ==
To sign-up for this event, please fill in the [[media:RegistrationForm_SlicerWorkshop_Dundee_Dec6_2010.doc | registration form]] send it by e-mail to Sonia Pujol, PhD [spujol at bwh.harvard.edu].

== Preparation for the Workshop ==

<span style="background-color: yellow"> The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.
All participants are required to come with their own laptop computer and install the software and datasets prior to the event.</span>. A minimum of 2 GB of RAM (4 GB if possible) and a dedicated graphic accelerator with 256MB of on-board graphic memory (512MB is better) are required.

Please install the '''Slicer3.6.2-2010-12-03 Nightly build version''' appropriate to the laptop computer you'll be bringing to the tutorial:

* [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
* [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz‎ | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz)]]
* [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86.tar.gz‎ | '''Linux 32''' (Slicer3-3.6.2-2010-12-03-linux-x86.tar.gz)]]
* [[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz‎ | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]

Please download the [[media:Slicer_data-RSNA2010-CTSA.zip | RSNA 2010 CTSA tutorial data ]] in preparation for the workshop.

== Slicer3 Training Survey ==
[http://www.surveymonkey.com/s/GZDXKXQ Please click here to take the Slicer3 Training Survey]

== Slicer Community ==
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] for questions and feature requests related to the software.
[[Events#2010|Back to Events 2010]]

MICCAI 2010

2017-07-10T18:27:05Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable"
| colspan="3"|[[Image:miccai2010logo.jpg]]
|-
|[[Image:NAMIC.jpg‎]]
|[[Image:Logo_nac.gif‎]]
|[[Image:NCIGTlogo.gif]]
|}

== From MICCAI Algorithms to Clinical Translational Tools: The NA-MIC Platform ==

'''Outline:''' [http://www.miccai2010.org/ MICCAI] offers a window on the technological breakthroughs in medical image computing, computer assisted interventions and surgical robotics that will allow for revolutionary progress in clinical care. A critical step to maximize the long-term positive impact of MICCAI algorithms is to foster their deployment, validation and concrete use by the clinical research community for whom they were developed.
The objective of the tutorial is to introduce the challenges inherent in delivering advanced medical imaging technologies (image processing, analysis and interventional capabilities) to end users for clinical translational research and to present solutions available in the National Alliance for Medical Image Computing (NA-MIC) open-source software toolkit. The day begins with an overview of the software components of the NA-MIC kit, followed by multiple example applications in current use for clinical research, with a final optional hands-on tutorial session that guides participants through the process of building, testing and deploying an exemplar algorithm using the NA-MIC open-source software toolkit.

Through concrete examples drawn from the translational research efforts of NA-MIC, this tutorial provides insights on practical approaches for bridging the gap between the scientific advances made by the biomedical imaging community and their widespread use in the clinical research community. By the end of the day course participants will know how to use the NA-MIC kit to facilitate greater use of their own algorithms by clinical end users.

== Organizers ==
*Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
*Guido Gerig, Ph.D., The Scientific Computing and Imaging Institute (SCI), University of Utah
*Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
*Martin Styner, Ph.D., Neuro Image Research and Analysis Laboratory, University of North Carolina

== Logistics ==

The tutorial will be held on Monday September 20, 2010 '''from 8:30 am to 6:00 pm in room 402A on the L4 level''' at the China National Convention Center (CNCC), No.7 Tianchen East Road, Chaoyang District, Beijing, China.

To register for the tutorial, please visit the [http://www.miccai2010.org/ MICCAI 2010 ] website.
== Tutorial format ==

The tutorial consists of lectures and an optional instructor-led hands-on session with the participants programming on their own laptop computers. A technical training staff will be providing one-to-one assistance as needed.

== Tutorial Faculty ==
*Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
*Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
*Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
*Guido Gerig, Ph.D.,The Scientific Computing and Imaging Institute (SCI), University of Utah
*Killian Pohl, Ph.D., Section for Biomedical Image Analysis, University of Pennsylvania
*Dinggang Shen, Ph.D., Radiology and BRIC, University of North Carolina School of Medicine
*Martin Styner, Ph.D., Neuro Image Research and Analysis Laboratory, University of North Carolina
*Stephan Aylward, Ph.D., Kitware, Inc.
*Xiaodong Tao, Ph.D., Visualization & Computer Vision, GE Research

== Tutorial Agenda ==
*8:45 am - 9:00 am: Introduction and goals of the workshop (Sonia Pujol)
*9:00 am - 9:15 am: [[media:Kikinis-NA-MIC-2010-09-20.ppt|Overview of the National Alliance for Medical Image Computing (NA-MIC)]] (Ron Kikinis)
*9:15 am - 9:45 am: [[media:NAMIC_Programming_Environment_MICCAI2010_SoniaPujol.pdf‎ | NA-MIC Programming Environment]] (Sonia Pujol)
*9:45 am - 10:15 am: [https://na-mic.org/w/images/1/15/NAMIC_Testing_MICCAI2010_XiaodongTao.pdf ‘Hardening’ your software with the NA-MIC kit, regression tests and dashboard ](Stephen Aylward/Xiaodong Tao)
*10:15 am - 10:30 am: Morning Tea/Coffee Break
*10:30 am - 11:00 am: [[media:BuildingBridgesBetweenSoftwarePlatforms_MICCAI2010_SoniaPujol.pdf‎ | Building bridges between complementary medical image analysis platforms (e.g. Freesurfer, BRAINS2, HAMMER) ]](Sonia Pujol)
*11:00 am - 11:30 am: [[media:Kikinis-How to work with NA-MIC-2010-09-20.ppt|How to participate in NA-MIC: collaboration grants, user and developer community (Kikinis)]]
*11:30 am - 12:00 pm: Exemplar Clinical Research Applications: Image-Guided Therapy (Hata)
*12:00 pm - 1:00 pm: Lunch
*1:00 pm - 3:00 pm: Exemplar Clinical Research Applications
**1:00 pm - 1:30 pm: Image Registration (Dinggang Shen)
**1:30 pm - 2:00 pm: Image Segmentation: [[media:MICCAI10-Tutorial-Pohl.pdf | EM Segmenter]] (Kilian Pohl) and Automatic Brain Segmentation [[media:NAMIC-ABC-MICCAI2010b.pdf‎ | ABC (Guido Gerig) ]]
**2:00 pm - 2:30 pm: [[media:2010_09_CortThick-NAMIC-MICCAI.pdf‎ | Cortical Thickness Measurements (Martin Styner) ]]
**2:30 pm - 3:00 pm: Diffusion Tensor Imaging (Sonia Pujol, Guido Gerig [[media:DTI_NAMIC-MICCAI2010.pdf | Gerig-Slides]])
*3:00 pm - 3:30 pm: Afternoon Tea/Coffee Break
*3:30 pm - 3:45 pm: [[media:Kikinis-Slicer Community-2010-09-20.ppt|Other examples from the community]] (Ron Kikinis)
*3:45 pm - 5:30 pm: Optional Hands-on Session: [[media:ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf‎ | Interfacing your MICCAI algorithm with the NA-MIC open-source toolkit: the ‘Hello Python’ tutorial ]](Sonia Pujol)
*5:30 pm - 6:00 pm: Open Discussion and one-on-one consultations for individual projects

== Preparation for the tutorial ==

In preparation for the optional hands-on session, please install the [http://www.slicer.org/pages/Special:SlicerDownloads Slicer3.6 release version] appropriate to the platform you'll be using, and the [[media:HelloPython.zip | HelloPython dataset]] Hardware minimum requirement: 2GB of main memory and graphics hardware acceleration with 256 MB of dedicated graphics memory (nvidia preferred).

[[media:MICCAI2010_T2tutorial_NAMIC_Draft_Tutorial_Notes.pdf| Draft Tutorial Notes]]

[[media:MICCAI2010_T2tutorial_NAMIC_flyer.pdf| Tutorial flyer]]

Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

CMF Workshop Cleveland 2012

2017-07-10T18:27:05Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable"
| style="width:25%" |[[Image:NAMIC.jpg]]
| style="width:25%" |[[Image:CWRU.png]]
| style="width:25%" |[[Image:MU.jpg|150px]]
| style="width:25%" |[[Image:UNC_uni.jpg]]
|}
== Introduction ==

This 3D software workshop for '''Open-source 3D Image Analysis in Dentistry''' is part of the Joint Cephalometric Experts Group 2012 that will be held from Wednesday, November 14-16, 2012 .

==Date==
*November 14, 2012 TBD 1pm - 5pm

==Tentative Agenda ==

12pm - 1pm Help and check software installations

1pm - 1.15pm Welcome

1.15pm - 1.45pm Beatriz Paniagua: Updates in Open Source Developments NAMIC [https://na-mic.org/w/images/7/7c/PaniaguaCWRU2012.pdf Slides]

1.45pm - 2.15pm Tung Nguyen: Registration and Superimposition techniques

2.15pm - 2.30pm Lucia Cevidanes: Updates in 3D Craniofacial research [https://na-mic.org/w/images/0/07/CevidanesCWRU2012.pdf Slides]

2.30pm - 5pm Open Discussion -- 1 on 1 with participants to help address their research questions

==Location==
Workshop will be held in the Bolton Brush Growth Study Center located on the third floor of the [https://maps.google.com/maps?q=school+of+dental+medicine+case+western+reserve+university+cleveland&hl=en&ll=41.505155,-81.603785&spn=0.008067,0.01929&sll=41.506247,-81.607046&sspn=0.008067,0.01929&hq=school+of+dental+medicine&hnear=CWRU+SDLE+Center,+10900+Euclid+Ave,+Cleveland,+Ohio+44106&t=m&z=16 School of Dental Medicine], in the Case Western Reserve University campus, Cleveland (OH).

JCEG2012 will take place in the Bolton Brush Conference Room DO3150. This workshop will be offered in the Enlow-Gould Room from 1-5pm. Enlow-Gould is the main seminar room for the Orthodontic Department and is located off the Orthodontics Clinic on the ground floor.

==Presenters==
*Lucia Cevidanes, Ph.D. DDS, University of Michigan
*Tung Nguyen, DDS, University of North Carolina at Chapel Hill
*Beatriz Paniagua, Ph.D., University of North Carolina at Chapel Hill

==Local host ==

Case Western Reserve University School of Dental Medicine, Cleveland (OH).
[http://dental.case.edu/faculty/hans.html Mark Hans, DDS, MSD]

==Logistics ==
* The registration for the workshop must be made in the Joint Cephalometric Experts Group 2012 website.

==Preparation for the workshop ==
'''The workshop combines oral presentations and 1 to 1 instructor-led open discussion session with the participants working on their own laptop computers with their own research data.'''
All participants are required to come with their own laptop computer with the software installed and their own datasets loaded prior to the event. A minimum of 1 GB of RAM (4 GB is better) and a graphic accelerator with 64mb (512MB is better) of on-board graphic memory are required. Shared memory graphics boards have significantly poorer performance.
*Software
** [http://www.itksnap.org/pmwiki/pmwiki.php ITKsnap] - Semi-automatic segmentation tool and visualization
**[http://www.slicer.org 3DSlicer] - Visualization and analysis tool
**[http://www.ia.unc.edu/dev/download/imagine/index.htm Imagine] - Registration tool (Download also [https://na-mic.org/w/images/7/70/ImaginePipelines.zip ImaginePipelines])
**[http://www.nitrc.org/projects/dentaltools/ Intensity Segmenter] - Intensity Segmenter v2 (Download also the example [https://na-mic.org/w/images/b/b8/Range.txt Range File])
*Participant Form for Open Discussion portion of the Workshop
**[https://na-mic.org/w/images/c/cb/ParticipantForm.docx Download] - <span style="background-color: cyan"> Please return filled and completed at beatriz_paniagua[at]med.unc.edu by Monday November 12th, 12pm EST </span>

==Other Resources==
*[http://www.na-mic.org/Wiki/index.php/CMF_Workshop_Cleveland Cleveland Workshop 2011 Materials]
*[http://www.nitrc.org/ Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)]
*[http://www.ncbi.nlm.nih.gov/pubmed?term=spharm%20pdm%20styner SPHARM-PDM publications in PubMed]
*[http://www.slicer.org/pages/UserOrientation Slicer user orientation]
*[https://www.slicer.org/wiki/Slicer_3.6:Training Slicer tutorials]

== Slicer Community ==
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] prior to the workshop, for questions and feature requests related to the software. For questions related to the Slicer community, please send an e-mail to Sonia Pujol (spujol[at]bwh.harvard.edu)

For questions related to the workshop, please send an e-mail to Lucia Cevidanes (cevidanl[at]dentistry.unc.edu), Beatriz Paniagua (beatriz_paniagua[at]med.unc.edu) or Tung Nguyen (nguyentu[at]dentistry.unc.edu).

== Slicer3 Training Survey ==

[http://www.surveymonkey.com/s/GZDXKXQ Click here to take the Slicer3 Training Survey]

== Participant List ==

# A. Ghoneima
# A. Mellion
# M. Lagravere
# A. Font Rytzner
# F. Samad
# S. Taher
# K. Gladstone
# F. Aljarki
# D. Knock
# C. Caballero
# K. Miyashita

Engineering:TCON 2010

2017-07-10T18:27:05Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

Back to [[TCON:Main|TCON:Main]], [[Events]]

==2010-12-16==

Attendees: Jim, Tina, Ron, Nicole, Greg, Curt, Daniel, Mark, Suyesh, Tamas

Agenda:

*Review registered attendee list, breakout sessions, and project list: http://wiki.na-mic.org/Wiki/index.php/AHM_2011
*Next tcon: Jan 6, 2011

==2010-12-09==

Attendees: Steve, Stephen, Jim, Xiadong, Nicole, Dominik, Mark Scully, Tina

*http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week

==2010-12-02==

Attendees: Ron, Jim, Steve, Stephen, Xiaodong, Andras, Tomas, Dan, Mark, Greg
Agenda:
Project week project review.

* Queens Projects: help porting to Qt - review of slicer4 beta.
** ProstateNav
** IGT Recording and Playback
* Iowa - has what they need
* MGH Medical Physics - debugging slicer on windows
* DicomToNrrd Converter
** new fixes for Siemens scanners
** project to refactor the code
** project to host testing data on midas

==2010-11-24==

Attendees: Ron, Steve, Stephen, Jeff, Jim, Dominik, Dan Marcus, Daniel H, Suarez <Germany>, Ross Whitaker, Guido Gerig

Agenda:
*Updates from Algorithms Core Retreat (Ross, Guido)
**DTI Breakout Session a must at the project week

==2010-11-10==

Attendees:

Agenda:

* Reports from [http://wiki.na-mic.org/Wiki/index.php/WidgetDesign2010 Widget Design Fiesta], maybe the Algorithm Core meeting
* Review NA-MIC Kit Internals projects for [http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week Project Week]

==2010-11-04==

No TCon due to [http://wiki.na-mic.org/Wiki/index.php/WidgetDesign2010 Widget Design Fiesta]

==2010-10-28==

Attendees: Jim, Tina, Will, Nicole, Wendy

Agenda:

*http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week
**First cut at engineering projects
**review upcoming thursday call allocations to different topics (DBP, Collaborations etc.)
* Slice view toggles (Jim, Nicole, Wendy) For Slicer 3.6 bug 1003
** in one viewer if in compare view, representation is that it's one slice node that governs that whole view, managed through lightbox mechanism, instead of slice node corresponding to a volume that has one slice, it has n slices in it. each of those n slices becomes a tile in one of the compare viewers. All slices will have same orientation in a single viewer. across viewers different slice nodes.
*** slice node to slice node to slice logic is one to one
*** slice node to slice controller widget is one to many: red viewer has a slice controller, but if show slices module there's a second one there (changes go via mrml slice node)
** get linked slice logics in sliceSWidget should return all slice logics that are linked under a certain context: if rgb views up, if get link slice logic, return all three. In compare view mode, the red in all the compare viewers have to be linked, but only if same orientation. Need context for getting linked slice logics.
*** future: link set node, here are the things that are linked and here are properties linked.
*** quick and dirty: add parameter to get linked * and pass what property
**** set of parameters that have no coordinate frame implications, and a set that does. boolean flag. slice location, zoom, pan, reset field of view, etc. set of things linked in rgb, then in compare view all those plus extra
** slice controller respects linking
* Building a module
** links against a subdirectory, there's a differnece in CMake between subdir (not guaranteed when added, deprecated) and add_subdirectory (goes in immediately)

==2010-10-21==

Attendees: Jim, Steve, Stephen, Tina, Dominik, Vince, Xiaodong, Harini

Agenda:
*Slicer 3.6.2
* Final Issues List https://www.slicer.org/wiki/Slicer3:3.6_Final_Issues

==2010-10-14==

Attendees: Jim, Tina, Vince, Dominik, Nicole, Wendy, Ron, Daniel, J2

Agenda
*Slicer 3.6.2
* http://wiki.na-mic.org/Wiki/index.php/WidgetDesign2010

==2010-10-07==

Attendees: Steve, Jim, Tina, Ron, Wendy, Daniel, Nicole, Dominik, Dan Marcus,

*[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues Slicer 3.6 debugging]
*[http://www.na-mic.org/Wiki/index.php/AHM_2011 AHM] (date change)
* [[Event:2011_Registration_Retreat]]
* [http://www.itk.org/Wiki/ITK_Release_4/Enhancing_Image_Registration_Framework ITKv4 Registration Refactoring]

==2010-09-30==
Attendees: Ron, Will, Stephen, Steve, Wendy, Daniel, Casey, Nicole, JC, Dominic, Tina, Kurt, Marco

[http://www.facebook.com/album.php?aid=91423&id=1185661914&l=94b6b77893 photos of Barcelona]

NA-MIC renewal
* Barcelona - brief description of CTK DICOM/Slicer integration
*[[2010-09-Leadership-Brainstorming#Computer_Science|Short term activities]]
*[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues Slicer 3.6 debugging]
* migration of Slicer and Na-mic websites
** Currently on Solaris machine, moving to Linux machine
** Ron will be sending email when this happens
* 2010-Slicer-Factory [[2010-Slicer-Factory| factory.slicer.org]]
** [http://www.na-mic.org/Wiki/index.php/2010-09-Leadership-Brainstorming#Service Service Short Term Service Activity]
* Need to fix the slicer dashboards:
** split slicer4 to dedicated dashboard with superbuild and Qt
** fix remaining failing tests (EMSegmenter, SparseFieldLevelSet, other sporadic failures...)
** fix test machines with no X server (thurmite)

==2010-09-23==
Attendees: Steve, Wendy, Tina, Jim

*DBP meeting (Monday ~11am at AHM) will be sent out by Katie M. this week
* Slicer and OpenIGTLink featured in NDI booth at MICCAI 2010 ([https://www.slicer.org/wiki/Slicer3:VisualBlog See slicer visual blog])

==2010-09-16==
Attendees: Jim, Tina, Wendy, Nicole, Dan, Dominik

*http://wiki.na-mic.org/Wiki/index.php/PeopleCycle2Staging

==2010-09-09==
Attendees: Jim, Stephen, Steve, Daniel, Nicole, Tina, Katie
*discussion about 3.6 versus 3.7 versus 4.0
**move to GIT will be deferred.
**discussion about svn for slicer 4
<pre>
Host TTL Numeric IP
www 7200 134.174.9.180
@ (None) 7200 134.174.9.180
* (All Others) 7200 134.174.9.180
ext.slicer.org 7200 75.101.141.190
i2b2.slicer.org 7200 184.73.243.106
mi2b2.slicer.org 7200 174.129.38.17
svn.slicer.org 7200 66.194.253.27
viewvc.slicer.org 7200 66.194.253.27
xnd.slicer.org 7200 75.101.141.190
</pre>
*Slicer 3.6 bug fixes. See: https://www.slicer.org/wiki/Slicer3:3.6_Final_Issues
*[[QtAugust2010#Draft_Timeline_.26_To-Do_list|Slicer 4 roadmap]]

Plan for Slicer4 nightly builds:
* Funding will hopefully resume next week
* Zack will create a new Slicer4 svn repository
* The Slicer3 trunk will become Slicer 3.7
* Nightly binaries will be built from the Slicer3 trunk
* Nightly builds will eventually switch over to Slicer4
* A dashboard for both Slicer3 and Slicer4 builds will be set up

* [[2010-Slicer-Factory|factory.slicer.org]]

==2010-09-02==

Attendees: Jim, Steve, Nicole, Wendy, Tina, Vince, Ron, Jay

* Discuss additional slicer layout options (Wendy, Jim, Steve, Ron)
<gallery>
file:Conventional-rotated-layout-2010.png|Layouts that use widescreen displays better (request from Ron)
file:Layout-Endoscopy-2010.jpg|three-3D-viewer display (request from Jay for kidney navigation IGT)
</gallery>

==2010-08-26==

==2010-08-19==
* Discussion of slicer 3.6.1/2
https://www.slicer.org/wiki/Slicer3:3.6_Final_Issues

==2010-08-13==
*No NA-MIC tcon this week (Event in progress: '''August 12-13:''' [[QtAugust2010| Review of Qt port]])

==2010-08-05==
Attendees: Xiaodong, Tina, Steve, Wendy, Nicole, Vince

Agenda:
*3.6.1 release update:
**http://wiki.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues
*Next week:
** '''August 11:''' [[2010-Slicer-UNCDuke|Slicer training event at UNC and Duke]]
** '''August 12-13:''' [[QtAugust2010| Review of Qt port]]

==2010-07-29==
Attendees: Steve, Jim, Nicole, Tina, Xiaodong, Wendy,

Agenda:
* discuss how to correctly remove display nodes if they become not needed after CLI invocation (this is just a hint for Nicole, we talked about this today, I will try to join around 3:45 --[[User:Fedorov|Fedorov]] 17:48, 29 July 2010 (UTC))
** usability level: what if there was something set on the output volume already? (Field of View)
** copy the input reference display node values inot the current output display node rather than creating a new one (if type is same)
** display node management is done when load volume back in
**if create new volume node (from a node selector), it doesn't create default display node automatically
**in command line module logic, store the information about what do you want to hook up (input volume display node id), and then in vtkSlicerApplication logic, when read things in set them up (around line 1570).
**if a display node should only be used by one thing (current implementation), in this rare case where change the type of the display node, remove the old display node node
**add method vtkMRMLScene to check if any displayable node references a given display node? Not necessary yet...
**every node has to be able to report everything it references (on vtkMRMLNode, see also UpdateReferenceID there)
**update the read data request with the reference display node and then put logic in the Slier application logic to deal with it, extend ReadDataRequest in vtkSlicerApplicationLogic.cxx

==2010-07-22==
Attendees: Xiaodong, Steve, Ron, Tina, Vince, Wendy, Katie

Agenda:
*http://wiki.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues

==2010-07-15==
Attendees: Jim, Xiaodong, Steve, Tina, Dominik, Vince, Wendy, Katie

*slicer 4 planning continues. next mtg+training session scheduled for aug 12-13 in chapel hill. details to appear on wiki soon.

==2010-07-08==
Attendees: Jim, Stephen, Nicole, Tina, Junichi, Xiaodong, Vince, Harini, Wendy

Agenda:
* Generalized plotting infrastructure in Slicer?
** Have DCE plotting infrastructure
** Also have [http://wiki.na-mic.org/Wiki/index.php/CTK_Transfer_function_widget CTK transfer function widget plotting]
** Need generalized base class for plots, upon which other specialized plotting can be based?
** 3D Slicer 4D Analysis Module has [https://www.slicer.org/wiki/Slicer3:2DPlotting 2D plotting]
** Nicole's wish list, based on use of scatter plots in population studies (one brain surface geometry file will have multiple scalars defined at each vertex) (see pages 70 and up [https://na-mic.org/w/images/4/4e/SlicerTraining6_vtkFreeSurferReaders.ppt here] where BLT was used):
*** highlight on mouse over a plotted point
*** toggle plotted point, or data set, visibility
*** legends: change text, colour, font, position for data set name, axis labels, chart title
*** print/save image to disk, export as table, postscript, pdf
*** set x/y axis variables (for example: input file has 10 values, allow selecting two to plot, and allow changing this at run time)
*** support plotting from multiple data sources
*** set plot symbol/colour/style to plot each data source
*** programmatic add/remove points from plot
*** on hover over a plotted point, pop up extra information about it (be able to associate extra info with a plotted point, for example if have a file that has an index, id, gender, age, val2, val1, when plot age versus val1, pop up id when hover over the point)
*** calculate average line through scatter plot
*** allow user to see values for all points

==2010-07-01==
Attendees: Xiadong, Nicole, Tina, Dominik

Agenda:
*[[2010_Summer_Project_Week|Project Week Summary]]
**(Katie is creating a Picasa album where we will use as a hopefully-persistent repository of photos)
*In Progress: [[2010-Slicer-StLouis|Slicer training event in St. Louis]]

==2010-06-23==

*[[2010_Summer_Project_Week|At Project Week]]

==2010-06-17==

Attendees: Katie, Jason White, Jim Barabas, Tamas, Xiaodong,Tina, Nicole, Steve, Vince, Luis, Sudhir Pathak (U Pittsburgh), Ron, Karl, Jim Miller, Marco, Hiro Yoshida

Agenda:
*Project Week Items
**Jason White project - transcranial ultrasound: [[2010_Summer_Project_Week_Intraoperative_Brain_Shift_Monitoring_Using_Shear_Mode_Transcranial_Ultrasound]]
**Sudhir project [[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data]]
**Karl Fracture [[2010_Summer_Project_Week_FractureClassification_Brainstorming]]

*'Record Set Explorer' version 0.6.2.alpha released
**Project site: http://www.gridwizardenterprise.org/rse/
**YouTube feature update video: http://www.youtube.com/watch?v=LWXannpfr6Y&hd=1

==2010-06-10==

Attendees: Jim, Tina, Dan, Tamas, Nicole, Wendy, Vince, Dominik, Jim Barabas, Katie, Luis, Hans

Agenda:
*project week review
*jim b's project
*Slicer 3.6 release
*http://www.slicer.org/
*Tutorial contest entries are due to Sonia Pujol on Monday

==2010-06-03==

Attendee: Jim, Tina, Wendy, Vince, Xioadong, Steve, Dan Marcus, Katie, Dominik, Sean Megason, Arnaud Gelas, Isaiah, Michel

Agenda:

*Project Week:
** In two weeks!
**75 registered attendees: [[2010_Summer_Project_Week#Attendee_List]]
**Review Projects/teams. Please note that deadline for completing project pages is BEFORE next week's TCON.
*Slicer Release http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues

Notes (discussing projects):
*community effort to make NA-MIC tools accessible to '''microscopy IA''' (Sean)
**[[Microscopy_Image_Analysis| Microscopy breakout session]]: standards, community needs.
**[[2010_Summer_Project_Week#Microscopy_Image_Analysis|Projects: detailed engineering efforts]]
**finding BWH investigators interested in microscopy: Liu, Yanling, SAIC-Frederick ; Lisle, Curtis, KnowledgeVis,
*[[Paraview_Support_for_Computational_Anatomy|Paraview]]: link via MRML or scene description file format w/o VTK dependencies. Which MRML node types should be supported.
*BrainLab-Aurora HybridNav (Isaiah Norton, A.Golby Lab): optical tracking system -> trying hybrid with AURORA, have both optical and EM tracking. Tool position history to track/document resection progress. -> add Dan Marcus (STEALTH -> openIGT) to project.
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise registration]]: (Ryan Eckbo); porting Matlab/C code into ITK -> Jim, Luiz
*removed ''Python'' & ''Execution models'' as project categories, fused into ''NA-MIC Kit Internals''
*Computer Aided Photodynamic Therapy: contacts?
*Slicer 3.6 release: last fixes: Editor, BRAINS, mutiple volume loading, DICOM series & XNAT, color LUT for generic use. New release scheduled June 10. If you know of critical issues please submit to http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:3.6_Final_Issues

==2010-05-27==
Atendees: Dan Marcus, Misha Milchenko, Tina, Nicole, Jim, Steve, Lorent, Greg, Wendy, Andre, Xiaodong, Leslie Holton, Tamas, Ron, Dominik

Agenda:
*OpenIGTLink discussion led by Junichi Tokuda. Agenda can be found in [[2010_Summer_Project_Week_Breakout_Session:OpenIGTLink| the OpenIGTLink breakout session page.]]
**Use case documentation/discussion can be found here: http://wiki.slicer.org/slicerWiki/index.php/Slicer3:BrainlabModule
*Problems with [http://en.wikipedia.org/wiki/Eclipse_(software) Eclipse] development

==2010-05-20==
Attendees: Jim, Tina, David Fuentes (MD Anderson), Dieter Hahn (Erlangen), Katie, Dominik, Xiaodong, Stephen, Andrej, Harini,Andrew Elliott (MD Anderson), Alex Z, Luis, Curt, Tamas (Queens), Nicole

Agenda:
*Discussion on adding Extensions to Slicer (led by Jim Miller). http://wiki.na-mic.org/Wiki/index.php/File:AHM2010-Plug-ins.ppt
** WebEx if needed https://emeetings.webex.com/emeetings/j.php?ED=135216267&UID=482060457&PW=NOGMwODUyMjM4

==2010-05-13==

Attendees: Sonia, Wendy, Ron, Tina, Katie, Haiying, Xiaodong, Nicole, Dominik, Vince, Marek, Andras, Tamas, Andrew Rauch, Ryan Eckbo (PNL), Mark Scully, Curt, Clement, Stephen, Harini, Isaiah, Luis Ibanez, Stuart

Agenda:
*Today's topic: Tutorial contest rules+discussion (http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest)
*QA discussion
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer-3.6-QA QA Wiki]
**[http://www.na-mic.org/Wiki/index.php/Journal_of_Slicer_Tests Journal of Slicer Tests]
*Next two weeks:
**May 20th -- How to interface external software with Slicer (Jim)
**May 27th --OpenIGTLink discussion (Junichi)

==2010-05-06==
Attendees: Jim, Steve, Curt, Tina, Xiaodong, Nicole, Vince, Harini, Dominik, Ron

Agenda:
*http://wiki.na-mic.org/Wiki/index.php/2010_Summer_Project_Week
**registration via credit card available, make sure to book hotel before June 1
**updated project page Wiki template [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template], includes "Delivery Mechanism" section
**Tuesday: Slicer Handson workshop from 10-12
**Wednesday: QA training session
**new [[2010_Summer_Project_Week#Projects|Projects]]
***registration:promote unsolved registration problems as project: e.g. Stanford group & knee MRI
***connect Python tools with execution model (NiPYPE)
***Slicer 4
*** femur fracture classification (Karl from Prof. Schubert's group), project placeholder added (Analysis)
***category for meshing efforts
*prospective first-time AHM attendees are welcome to attend the TCon, feel free to invite
*NA-MIC renewal: Supplemental Information needed: latest software releases
**Slicer 3.6
**ITK 3.18 (fixing DICOM parsing)
**VTK 5.6 (integration of GPU ray casting)
**XNAT 1.4 (webservices API)

==2010-04-27==

Attendees: Jim, Tina, Xiadong, Steve, Nicole, Ron, Wendy, Dan, Katie

Agenda:

*Please note that there will be two project-week specific tcons:
**May 13th - Sonia will lead the tutorial contest rules+discussion (http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest)
**May 27th -- Junichi will lead OpenIGTLink discussion
*Discussion of help text of command line modules. [[image:Help-characters.png|thumb|100px|right|discussion topic]]
*Review of slicer3.6 release plans and bug tracker.

==2010-04-22==

Attendees: Wendy, Nicole, Steve, Sonia, Ron, Dan, Dominik, Adam, J2, Jean-Christophe.

Agenda:

*QT tutorials/discussion with Adam Weinrich, Nokia.
** Review of Slicer tutorial structure (Sonia)
** Adam works on strategic accounts (advanced development for new applications) and on university outreach to encourage creation of new developers
** Kitware is a key account for Nokia
** Review of current state of Qt with Slicer (Steve, Jc, Julien)
** Best to stick with first hands on session on Monday afternoon (Adam).
** Topics to cover:
*** Adam: Motivation (examples of other applications), Designer, available widgets, signals&slots, coding style, implicit representation
*** J2/Jc: how to make a simple module, working with the rest of the slicer application (Tuesday afternoon).
** Qt Q&A lunch on Tuesday. Adam will check with Boston-based Qt developer group about attending.
** TODO: get a lecture hall for Monday afternoon? Tina will check with Donna.
*Note: May 27th is the OpenIGTLink discussion, led by Junichi Tokuda.

==2010-04-15==
Attendees: Xiadong, Harini, Tina, Steve, Dan Marcus, Vince, Ron, Dominik, Luis, Dave P, Katie, Alex Z, Marco

Agenda:
*Project Week Kickoff Call for Engineering
**[[2010_Summer_Project_Week]]
**Start listing Engineering Projects
**Project Page Template: Add Delivery Mechanism (Extension-cmdline or loadable, Built-in)
**Ideas for handling Project Week Planning/calls

==2010-04-08==

Attendees: Jim, Dan, Nicole, Tina, Wendy, Ron, Stephen Aylward

Agenda:
*Slicer Training Course in Iowa city tomorrow.
*Added breakout sessions/talks for the project week

==2010-04-01==
Attendees: Curt, Nicole, Katie, Wendy, Tina, Dominik, Vince, Steve, Dan Marcus, Luis
*Slicer 3.6 Feature freeze
*Project Week breakout session: QT, ITK, git,...

==2010-03-25==
Attendees: wendy, nicole, dominik, vince, tina, jim, dave, luis, katie, steve, ron, xiaodong, stephen, jj, jc, j2
* MIDAS Feedback from John M./Tina
*[https://www.slicer.org/wiki/Slicer3:3.6Release Slicer 3.6]
**Documentation
**testing and code coverage
**VTK status
*[https://www.slicer.org/wiki/Slicer4 Slicer 4.0]
**Community process (Stephen Aylward)
*** Superbuild status (Dave)
*** qt status (Julien)
*** Module acceptance process
**** From Nitrc
**** With Slicer
**Educating the community about the benefits of Qt (Steve Pieper)

''' Notes '''

* Slicer Extensions
** Reuse Statistics functionalities from MIDAS to report on downloads from
** http://ext.slicer.org/ext/trunk/
** Building Slicer extensions and submit them to the Slicer Dashboard
** Where are they located ? (it is described in the .s3ext files:)
*** http://ext.slicer.org/ext/trunk/12465-linux-x86_64/VmtkSlicerModule.s3ext
** Maybe build them only when their source code is actually modified ?
** Label extensions by a level of compliance with NAMIC practices ?
*** E.g. Gold, Silver, Bronze,... Coal.
**** '''Gold''': have > 80% coverage, 0 Valgrind errors, documentation and tutorial
**** '''Silver''': have > 70% coverage, < 10 Valgrind errors, and tutorial
**** '''Bronze''': have > 60% coverage, < 50 Valgrind errors, and tutorial
**** '''Coal''': have < 10% coverage, > 1000 Valgrind errors, no documentation, no tutorial
** Web of trust
*** Have gatekeepers who review the extension and label them accordingly.
*** Define a Testing procedure for Slicer 4.0. (Check lists)
** Community Support
*** Provide User Ratings (based on the Insight Journal / MIDAS functionality)
*** Use current MIDAS C++ API to Upload/Download data.
*** Create MIDAS Plugins to manage data / code for Slicer extensions
* Slicer Release 3.6
** VTK Release 5.6 : March 26th 2010
** Immediately after, switching Slicer to use VTK 5.6.
** Sorting out KWWidget issues on Windows 7 with VTK 5.6 (VTK CVS HEAD).
* Slicer Release 4.0
** Git: Conversion of CMake, VTK, Paraview
** Moving Slicer to Git ?
** ITK 4.0 will move to a clean Git repository (full reset of the history)
** Moving only Slicer modules that satisfy the '''Gold''' criteria.
** A2D2 Idea : port CLI modules to ITK 4.0
** Question about CLI modules in CTK for Slicer 4.0: Discovery process; making it cleaner by using Qt methods. But raise the concern of forcing a dependency on Qt (that not everybody may want).
*** Have specific mechanisms of discovery based on : Python, Qt, C++.
** MRML Refactoring ?
*** Jim suggests to add a dictionary-like organization to be able to query MRML nodes {by type,...}.
* Slicer Superbuild
** Dave reported on progress
*** Dealing with patches that getbuildtest.tcl applies to the third party libraries.
**** Difficulty of applying patches. Need for a multi-platform way of applying patches
**** Hosting git repositories with the patched versions of the third party libraries.
**** Use github ? create a "Slicer" user-account ?
**** CMake-ifying Python source tree ?
* Testing Modules and Extensions
** Hosting them in MIDAS
** Setting up Dashboard configuration to test modules as Slicer sub-projects
** Some CDash/CTest work is needed.
** Currently, sub-projects must be run from a common CTest script (the same of the host project).
** Needs to manage dependencies between extensions. (this can be done today with an XML file on CDash).
* Testing Submission Grouping
** Grouping {configure/build/test} submissions by Library and / or subdirectory
** Using CMake for generating labels that can be used later for grouping

==2010-03-18==
Attendees: Andriy (ran out of the room before he could take notes)
Nicole, Dominik Wendy, Steve, Stephen, Jim, Katie
* Andriy question about plots coming back from command line modules.
* Updated [[Downloads|Download page]]
** Images have been added.
** Lesion data still missing.
* Tracking downloads of extensions
** Use publication database? We can ask Julien next week.
** (See http://ext.slicer.org/ext/ for current layout - look in the trunk directory).
** Jim could use this functionality for renewal proposal
* DICOM Discussion
** https://www.slicer.org/wiki/DICOM:Database
** Drag and Drop image files?
** DICOM sorter (osirix is useful for this)
* Slicer3.6 release planning
** Next release of ITK (3.18) should be in a couple of weeks
** https://www.slicer.org/wiki/Slicer3:3.6Release

==2010-03-11==
Attendees: Dan, Tina, Vince, Xiaodong, Wendy, Nicole, Katie, Kurt, Dominic, John

* Updated [[Downloads|Download page]]
** Do we want to add images?
***Yes, please. And also to format this into a table. Thanks.

* XNAT Workshop (June 28-30)
** Include a NAMIC presentation? TBD
** http://nrg.wikispaces.com/2010+XNAT+Workshop

* OpenIGT and Medtronic Navigation
** Consider a joint grant to fund the development

* Ron can kill 18 birds with one stone.

==2010-03-04==
Attendees: jim, ron, nicole, vince, dan, katie, wendy, dominic, tina

* GetNodesByName leaking the collection from Tcl ( set foo [$::slicer3::MRMLScene GetNodesByName bar] )
* VTK GPU Mapper - Mac driver issue. But otherwise is working well with compositing. Dual 3D issue tabled for now.
* Store the Collapse of the SliceController in the Layout node?
* Should the layout of the modules (left verses right) be stored in the scene? Not for now.
* DICOM databases. See discussion on mailing list.
** DICOM Schemas. Jim tried searching for Osirix's schema. What about the XNAT schema? What about ClearCanvas?
** Extend Schemas for MRML, Project views, NRRD, VTK files, etc.

==2010-02-25==

Attendees: john, marco, dominik jim, steve, wendy, tina, nicole, ron, vince, dan, katie

* MIDAS handles - fixed
* GWE's RSE ("Record Set Explorer") version 0.6.1.alpha released:
** [http://www.gridwizardenterprise.org/rse/ Project site]
** [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube demo video]
*Slicer Release 3.6 Feature Freeze on April 1
*Japanese Slicer workshop in 2 weeks
*CTK workshop last week - went well

==2010-02-18==

Attendees: Jim, Steve, Wendy, Dan, Dominik, Katie, Nicole

* Discussion of whole body CT/MR data (Dan)
* Discussion of the [http://www.slicer.org/pages/Slicer_Community "Spit Kidney"]
* Dominik's registration case library data for download
* Discussion of download data for each module (like in ChangeTracker currently)
* Tutorials and Datasets
* Discussion of slicer 3.6 release schedule.

==2010-02-11==

Attendees: Jim, Katie, Curt, Casey, Tina, Xiaodong, Steve, Wendy, Dan, John, Dominik, Nicole

Agenda:
* NA-MIC data migration is complete and the Downloads page has been brought out to the Wiki sidebar (http://www.na-mic.org/Wiki/index.php/Downloads)
** Feedback is requested on the sidebar
** Feedback is requested on the Downloads page
** Feature request to track the downloads like it is done on the publication database. (Julien reports it is already available to administrators).
** Curt will work with John to add Meshing Module tutorial.
** Dominik will try putting some data in midas to see how much context can be added.
** John will check with Marek about Harvard data that had been on BIRN.
* Review of DBP2 webpages, which need updating
** Ron has contacted the parties directly
* Dan: XNAT workshop this summer (possibly June 28, 29, 30 in St. Louis)?
* Discussion of entry behavior on
* New Volume features from Xiaodong for viewing image sets in a directory (cool!)

==2010-02-04==

Attendees: Xiaodong, Tina, Casey, John, Dan, Vince, Stephen, Nicole

Agenda:
*http://www.na-mic.org/Wiki/index.php/Downloads
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]

DBP Tutorials should be listed at the top.
Software should point to Slicer and the NA-MIC Kit.
Data hosting is available on XNAT and Midas.

==2010-01-28==
Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey

Agenda
* data update (john m): Discussion of Data & Tutorials on the following page. Discussion of where to put the data (XNAT or Midas).
**example downloadable resources page: http://www.ncigt.org/pages/Downloads

*Iowa Data
**Visible Human Datasets https://mri.radiology.uiowa.edu//visible_human_datasets.html

*Project Sikuli from CSAIL
**Scripted UI interaction -- GUI testing http://groups.csail.mit.edu/uid/sikuli/

==2010-01-21==
Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan

* Update wiki pages in preparation for the review of the NA-MIC renewal

==2010-01-14==

Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron

* Discussion of [http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html parallel processing using ipython] for use with [[NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy|NA-MIC CT Colonography collaboration project]]. (confirmed).
** As a follow up people may be interested in the [http://www.enthought.com/training/webinars.php Enthought webinar on this topic 3pm eastern on Jan 22, 2010].
** Need real time processing speed. 10 fps for volume rendering. 5 minutes of image processing (down from 30 minutes)
** 512x512x1000 voxels
** GPU solutions or ipython solutions
** Python package for accessing to Slicer internals in a headless mode, i.e. run Slicer internals from Python instead of running Python from within Slicer
** iPython distinct from MPI (meet different needs)
** Microsoft interest in iPython
* Jim fell on the sword to take minutes
* Follow up information from Fernando about the new version of ipython in development:
** the docs for the in-testing ipython are at: http://ipython.scipy.org/doc/bzr.r1321/
** and downloads in various formats are at: http://ipython.scipy.org/dist/testing/
** ''Note:'' the files with .bzr.r1321 in the names are the relevant ones for today's call, NOT the 'nightly' ones.

Events:Manchester-Dec-2010

2017-07-10T18:27:05Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable2" border="1" cellpadding="8" cellspacing="1"
| colspan="5"|[[Image:UManchester-logo.jpg|center]]
|-
| style="width:20%" |[[Image:NAMIC.jpg‎]]
| style="width:20%" |[[Image:Logo_nac.gif‎]]
| style="width:20%" |<br>[[Image:NCIGTlogo.gif]]
| style="width:20%" |<br>[[Image:Catalyst_logo_final.jpg|150px]]
| style="width:20%" |<br><br>[[Image:Logo CIMIT.png]]
|}

== Logistics ==
<big><big>This is a hands-on tutorial. You need a good laptop and you need to pre-install data and software. See below for more information.</big></big>
*Date: Wednesday December 8, 2010
*Location: IBSE Library, Stopford Building, University of Manchester, Manchester, UK.
*Time 9-12

== Agenda ==
* 9-9.30 Setup for those who had trouble with the installation
* 9.30-10.30 [https://na-mic.org/w/images/d/d4/Combined-RSNA2010-CTSA.ppt Combined tutorial slides (ppt) ]:
**Slicer3 Minute tutorial
**Quantitative Measurement of Volumetric Change: ChangeTracker Tutorial
**Quantitative Measurements for Functional Imaging: PETCTFusion Tutorial
**Please download the [[media:Slicer_data-RSNA2010-CTSA.zip | RSNA 2010 CTSA tutorial data ]] in preparation for the workshop.
*10.30-10.45 Break
*10.45-12.00 Interactive editor, DTI visualization
**Please download the [[media:Case-040-NeurofMRI-WithTransforms.zip| NeurofMRI Case 40]] in preparation for the workshop.

== Teaching Faculty==
*[http://www.spl.harvard.edu/pages/People/kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School

==Registration ==
*To sign-up for this event, please fill in the [[media:RegistrationForm_SlicerWorkshop_Manchester_Dec8_2010.doc‎ | registration form]] and send it by e-mail to Sonia Pujol, PhD [spujol at bwh.harvard.edu].

== Preparation for the Workshop ==
<span style="background-color: yellow"> The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.
All participants are required to come with their own laptop computer and install the software and datasets prior to the event.</span>. A minimum of 2 GB of RAM (4 GB if possible) and a dedicated graphic accelerator with 256MB of on-board graphic memory (512MB is better) are required.

Please install the '''Slicer3.6.2-2010-12-03 Nightly build version''' appropriate to the laptop computer you'll be bringing to the tutorial:

* [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
* [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz‎ | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz)]]
* [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86.tar.gz‎ | '''Linux 32''' (Slicer3-3.6.2-2010-12-03-linux-x86.tar.gz)]]
* [[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz‎ | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]

Please download the [[media:Slicer_data-RSNA2010-CTSA.zip | RSNA 2010 CTSA tutorial data ]] in preparation for the workshop.

== Slicer3 Training Survey ==
[http://www.surveymonkey.com/s/GZDXKXQ Please click here to take the Slicer3 Training Survey]

== Slicer Community ==
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] for questions and feature requests related to the software.
[[Events#2010|Back to Events 2010]]

CMF Workshop Cleveland

2017-07-10T18:27:05Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable"
| style="width:25%" |[[Image:NAMIC.jpg]]
| style="width:25%" |[[Image:CWRU.png]]
| style="width:25%" |[[Image:MU.jpg|150px]]
| style="width:25%" |[[Image:UNC_uni.jpg]]
|}
== Introduction ==
This workshop will highlight the use of publicly available software for dental applications of 3D virtual models from Cone-beam CT volumes. The ability to visualize the face in 3D does not imply the ability to quantify growth or treatment changes. 3D structural shape analyses continue to mandate a multidisciplinary collaborative team including clinician researchers, shape analysis and statistical modeling experts.

This 3D software workshop for Cranio Maxillo Facial applications is part of the [http://jceg2011.eventbrite.com/ Joint Cephalometric Experts Group 2011] that will be held from Wednesday, November 9, 2011 at 6:30 PM - Friday, November 11, 2011 at 12:00 PM (ET) at Cleveland, OH.

==Date==
*November 9, 2011 9am - 5.30pm

==Tentative Agenda ==

9am - 10am USB delivery to attendees, data and software installation

10am - 10.20am Lucia Cevidanes / Tung Nguyen: Overview of 3D imaging applications, future development goals. Slicer application development in Orthodontics. [https://na-mic.org/w/images/7/7e/Cleveland_CMF_overview.pdf (Slides)]

10.20am -10.40am Beatriz Paniagua / Emerging methodologies in Image Analysis, NAMIC, NITRC [https://na-mic.org/w/images/e/ec/PaniaguaSlides.pdf (Slides)]

10.40am - 11.00am DICOM conversion [https://na-mic.org/w/images/6/62/CONVERT_DICOM.pdf (Slides)], surface models [https://na-mic.org/w/images/3/3c/Construct_surface_models.pdf (Slides)] and visualization in ITKsnap

11am - 11.20am Downsizing data [https://na-mic.org/w/images/7/70/ImaginePipelines.zip ImaginePipelines]

11.20am - 12.00am Familiarization with ITKsnap segmentations

12am - 1pm - LUNCH BREAK

1pm - 2pm Complete segmentation

2.00pm - 2.30pm CranialBase registration [https://na-mic.org/w/images/a/a2/Imagine_Downsizing_and_Registration.pdf (Slides)], Imagine vs CMFreg

2.30pm - 3.00pm Surface models vs Image models, surface formats

3.00pm - 3.30pm Slicer visualization, Slicer overview

3.30pm - 4pm Quantification options, MeshValmet using Closest Points

==Location==
Workshop will be held in the [http://maps.google.com/maps?q=+11240+Bellflower+Road+Cleveland,+Ohio+44106&hl=en&sll=41.506766,-81.647962&sspn=0.068519,0.154152&vpsrc=0&hnear=11240+Bellflower+Rd,+Cleveland,+Ohio+44106&t=w&z=16 George S. Dively Building], in the Case Western Reserve University campus, Cleveland (OH)

==Presenters==
*Lucia Cevidanes, Ph.D. DDS, University of Michigan
*Tung Nguyen, DDS, University of North Carolina at Chapel Hill
*Beatriz Paniagua, Ph.D., University of North Carolina at Chapel Hill

==Local host ==

Case Western Reserve University School of Dental Medicine, Cleveland (OH).
[http://dental.case.edu/faculty/hans.html Mark Hans, DDS, MSD]

==Logistics ==
* The registration for the workshop must be made in the [http://jceg2011.eventbrite.com/ Joint Cephalometric Experts Group 2011] website.

==Preparation for the workshop ==
*<span style="background-color: yellow"> The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.
All participants are required to come with their own laptop computer and install the software and datasets prior to the event.</span> A minimum of 1 GB of RAM (4 GB is better) and a graphic accelerator with 64mb (512MB is better) of on-board graphic memory are required. Shared memory graphics boards have significantly poorer performance.
*Software
** [http://www.itksnap.org/pmwiki/pmwiki.php ITKsnap] - Semi-automatic segmentation tool and visualization
**[http://www.slicer.org Slicer3] - Visualization and analysis tool
**[http://www.ia.unc.edu/dev/download/imagine/index.htm Imagine] - Registration tool
**[http://www.nitrc.org/projects/cmfreg CMF reg] - Slicer3 registration tool (under development)
*Data
**[https://na-mic.org/w/images/e/e8/Data_ITKsnap.zip ITKsnap segmentation]
**[https://na-mic.org/w/images/2/2a/Data_ImagineRegistration.zip Imagine registration]
**[https://na-mic.org/w/images/4/47/Data_Slicer3.zip Slicer3 visualization]
**[https://na-mic.org/w/images/b/b5/Data_MeshValmet.zip MeshValmet quantification]
** [https://na-mic.org/w/images/6/6d/DemoSPHARM.zip data] for the demo in Shape Correspondence <br>
** About the data: Pre and post corrective surgery CBCT (pre-V2, post-V8). The patient was diagnosed with a Class III malocclusion and the surgical procedure involved a mandibular retraction + maxillary advancement (The datasets will be also delivered to the attendees to the workshop using a USB storage device).

==Other Resources==
*Information about CMFApp: CMF application software (CMFapp) developed M.E. Müller Institute for Surgical Technology and Biomechanics, University of Bern, Switzerland, under the funding of the Co-Me network, http://co-me.ch and available to us under a collaborative agreement. Contact [http://www.bioeng.master.unibe.ch/content/faculty__staff/lecturers_n_z/mauricio_reyes/index_eng.html MauricioReyes] and Hyungmin Kim (hyungmin.kim[at]artorg.unibe.ch).
*[http://www.nitrc.org/ Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)]
*[http://www.ncbi.nlm.nih.gov/pubmed?term=spharm%20pdm%20styner SPHARM-PDM publications in PubMed]
*[http://www.slicer.org/pages/UserOrientation Slicer user orientation]
*[https://www.slicer.org/wiki/Slicer_3.6:Training Slicer tutorials]

== Slicer Community ==
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] prior to the workshop, for questions and feature requests related to the software. For questions related to the Slicer community, please send an e-mail to Sonia Pujol (spujol[at]bwh.harvard.edu)

For questions related to the workshop, please send an e-mail to Lucia Cevidanes (cevidanl[at]dentistry.unc.edu), Beatriz Paniagua (beatriz_paniagua[at]med.unc.edu) or Tung Nguyen (nguyentu[at]dentistry.unc.edu).

== Slicer3 Training Survey ==

[http://www.surveymonkey.com/s/GZDXKXQ Click here to take the Slicer3 Training Survey]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2017-07-10T18:27:04Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant#==
[http://projectreporter.nih.gov/project_info_description.cfm?aid=7599715&icde=7475498 R01AA016748]

==Key Personnel==
*Wake Forest University: Jim Daunais, Bob Kraft
*Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaoxing(Ginger) Li, Xiaojing Long
*NA-MIC: Kilian Pohl, Sandy Wells, Andriy Fedorov

==Funding Duration==
07/15/2009-03/31/2010

==Projects==
Active projects in this collaboration are:

=== Tutorials on using EMSegmenter to segment nonhuman primate images ===
#Slicer3 based tutorial
##[http://www.na-mic.org/Wiki/index.php/Image:EMSegment_TrainingTutorial.pdf Tutorial Slide Handouts (PDF)]
##[http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Atlas]
##[https://na-mic.org/w/images/c/c9/SlicerTutorialData_Vervet.tar.gz Example Data]
#[http://bsl.ece.vt.edu/download/NHP-EMSTut.zip older Slicer2.x based tutorial]
## [http://www.na-mic.org/Wiki/index.php/Image:EMSegment_Vervet_TrainingTutorial_Slicer2.pdf Vervet segmentation with Slicer2] (extracted from above for convenience)

=== Nonhuman Primate Atlas Development ===
* Vervet Probabalistic Atlas [http://www.nitrc.org/projects/vervet_atlas on NITRC]

Rhesus Probabalistic Atlas - Adult
*[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
*[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

Rhesus Probabalistic Atlas - Juvenile
*[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

Cyno Probabalistic Atlas - Adult
*[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

=== Documentation ===
# [[Atlas-to-subject registration with FSL and Diffeomorphic Demons, for EM segmentation.]]
# [http://wiki.na-mic.org/Wiki/index.php/Vervet_MRI_registration Atlas-to-subject registration with BRAINSFit]
# [[On the performance of Slicer 2 and Slicer3 EM segmentation modules]]
# [[Proposed revised atlas construction workflow]]
# [[Initial atlas construction workflow]] (initial workflow, obsolete)
# [[October_08_2009_Meeting:_VT-NAMIC_Revised_atlas_construction_workflow | Current vervet monkey atlas construction workflow]] (in progress)
# [[NA-MIC WFU VT Collaboration: Segmentation workflow and approaches | Considered segmentation approaches and workflow]] (in progress)
# [[Smoothing multi-label brain segmentations]]

==Publications==
* Fedorov A., Li X., Pohl K.M., Bouix S., Styner M., Addicott M., Wyatt C., Daunais J.B., Wells III W.M., Kikinis R. [http://www.na-mic.org/publications/item/view/2119 Atlas-guided Segmentation of Vervet Monkey Brain MRI.] Open Neuroimag J. 2011 Dec;5:186-97. PMID: 22253661. PMCID: PMC3256578.
* NITRC Vervet Brain Atlas [http://www.nitrc.org/projects/vervet_atlas URL]

==Meetings and Events Specific to this Collaboration==
* [[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
* [[AHM_2008|2008 NA-MIC AHM]]
* [[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week Page]]
* [[2009_Winter_Project_Week_WFU1|2009 NA-MIC Winter Project Week Page]]
* [http://wiki.na-mic.org/Wiki/index.php/Measuring_Alcohol_Stress_Interaction 2009 Summer project week Boston]
* [http://wiki.na-mic.org/Wiki/index.php/Events:VT-NAMIC-NCBC-Collaboration-meeting-2009 2009 October 7-9 VT-NAMIC collaboration meeting]
* [[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|2010 NA-MIC Winter Project Week Page]]

==Resource Links==
* [http://www.slicer.org 3D Slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]
* [http://pin.primate.wisc.edu/factsheets/entry/vervet Primate Info Net: Vervet factsheet]
* Short introduction to the [http://www.youtube.com/watch?v=pSm7BcQHWXk alcohol habits of vervets] :)

2010 University.of.Iowa

2017-07-10T18:27:04Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{| class="wikitable"
| colspan="3"|[[Image:UoI.jpg|center]]
|-
| style="width:25%" |[[Image:NAMIC.jpg‎]]
| style="width:25%" |[[Image:Logo_nac.gif‎]]
|style="width:25%" |[[Image:NCIGTlogo.gif]]
|}

==Training Faculty ==
* [http://www.spl.harvard.edu/~kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Harvard Medical School, Boston, MA
* [http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D.,] Surgical Planning Laboratory, Harvard Medical School, Boston, MA
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA
* Hans Johnson, Ph.D., University of Iowa
* Vince Magnotta, Ph.D., University of Iowa
* Eric Axelson, University of Iowa
* Joy Matsui, University of Iowa

==Logistics==
*Date: Friday April 9 and Saturday April 10, 2010
*Location: University of Iowa, Iowa City
*'''[https://na-mic.org/w/images/0/03/NA-MIC-Flyer-Iowa-2010.pdf Workshop Flyer]'''
* Slicer version: Slicer3.4 release (2009-05-21)
*[https://mri.radiology.uiowa.edu// Additional information]

== Workshop Agenda ==
{| border="1" cellpadding="5" width="1000"
|- style="background:#ebeced; color:#663300; font-size:120%" align="center"
| style="width:10%" | '''Time'''
| style="width:90%" colspan="2"| '''Friday, April 9, 2010'''
|-
| style="background:#efefef; color:#663300"| '''12:00-12:45'''
| style="background:#FBF7BB; color:#522200" colspan="2"|
[[media:Iowa-NA-MIC-2010-04-09.ppt|NA-MIC Overview Lecture]] (Vincent Magnotta)(283 EMRB - Seebohm Conference Room)
|-
| style="background:#efefef; color:#663300"| '''4:00-5:00'''
| style="background:#F5EBD6; color:#522200" colspan="2"|
[[media:Kikinis-NA-MIC-2010-04-09.ppt|NA-MIC Overview for Radiation Oncology Research]] (Ron Kikinis) (01136 - Braley Conference Room)
|-
| style="background:#efefef; color:#663300"| '''5:00-6:00'''
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:3DComputerAssistedBrainMapping_SPujol.pdf‎ |Neurosurgery Department Seminar: 3D Computer-Assisted Brain Mapping]] (Sonia Pujol) (01603 - Neurosurgery)
|-
| style="background:#FFFFFF; height:35px" colspan="3" |
|-style="background:#ebeced; color:#663300; font-size:120%" align="center"
| style="width:10%" | '''Time'''
| style="width:90%" colspan="2"| '''Saturday, April 10, 2010'''
|-
| style="background:#efefef; color:#663300"| '''09:00-9:10'''
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis) (2217 Seamans Center)
|-
| style="background:#efefef; color:#663300"| '''09:10-10:00'''
| style="background:#F5EBD6; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol) (2217 Seamans Center)

|-
| style="background:#efefef; color:#663300"| '''10:00-10:30'''
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:NA-MIC_kit_introduction_SoniaPujol_Iowa2010.pdf‎|Three ways to use the NA-MIC kit]] (Sonia Pujol) (2217 Seamans Center)

|-
| style="background:#efefef; color:#663300"| '''10:30-11:00'''
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break
|-
| style="background:#efefef; color:#663300"| '''11:00-12:30'''
| style="background:#FBF7BB; width:45%; color:#522200"| [[media:Slicer3Course_DataLoadingAndVisualization_Iowa2010_SoniaPujol.pdf‎ |3D Visualization and Diffusion Tensor Imaging ]] - Part 1 <br> (Sonia Pujol/Katie Hayes) (2217 Seamans Center)
| style="background:#FBF7BB; color:#522200"| 3D Visualization and Programming Tutorial - Part 1 <br>(Hans Johnson) (2229 Seamans Center)
|-
| style="background:#efefef; color:#663300"| '''12:30-1:45'''
| style="background:#F5EBD6; color:#522200" colspan="2"| Lunch
|-
| style="background:#efefef; color:#663300"| '''1:45-3:00'''
| style="background:#FBF7BB; color:#522200"| [[media:DiffusionMRITutorial_Iowa2010_SoniaPujol.pdf|Diffusion Tensor Imaging]] ‎ - Part 2 <br>(Sonia Pujol/Katie Hayes) (2217 Seamans Center)
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 2 <br> (Hans Johnson) (2229 Seamans Center)
|-
| style="background:#efefef; color:#663300"| '''3:00-3:15'''
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break
|-
| style="background:#efefef; color:#663300"| '''3:15-4:15'''
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol)<br> (2217 Seamans Center)
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 3 (Hans Johnson)<br> (2229 Seamans Center)
|-
| style="background:#efefef; color:#663300"| '''4:15-5:00'''
| style="background:#F5EBD6; color:#522200" colspan="2"| Concluding Remarks and Feedback
|-
|}

Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

DBP:Harvard:MorphROI

2017-07-10T18:27:04Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

* Amygdala-Hippocampus: (N=16 SZ and N=15 Ctrl)
** Reference: [https://na-mic.org/w/images/6/69/Anderson_2002.pdf Anderson JE, Wible CG, McCarley RW, Jakab M, Kasai K, Shenton ME. An MRI study of temporal lobe abnormalities and negative symptoms in chronic schizophrenia. Schizophr Res. 2002 Dec 1;58(2-3):123-34.]
* Superior Temporal Gyrus: (N=16 SZ; N=17 AFF; N=18 Ctrl)
** Reference: [https://na-mic.org/w/images/f/f2/Hirayasu_1998.pdf Hirayasu Y, Shenton ME, Salisbury DF, Dickey CC, Fischer IA, Mazzoni P, Kisler T, Arakaki H, Kwon JS, Anderson JE, Yurgelun-Todd D, Tohen M, McCarley RW. Lower left temporal lobe MRI volumes in patients with first-episode schizophrenia compared with psychotic patients with first-episode affective disorder and normal subjects. Am J Psychiatry. 1998 Oct;155(10):1384-91.]
* Middle Temporal Gyrus & Inferior Temporal Gyrus: (N=23 SZ; N=28 Ctrl)
** Reference: [https://na-mic.org/w/images/f/f5/Onitsuka_2004.pdf Onitsuka T, Shenton ME, Salisbury DF, Dickey CC, Kasai K, Toner SK, Frumin M, Kikinis R, Jolesz FA, McCarley RW. Middle and inferior temporal gyrus gray matter volume abnormalities in chronic schizophrenia: an MRI study. Am J Psychiatry. 2004 Sep;161(9):1603-11.]
* Caudate Nucleus: (N=15 SPD; N=14 Ctrl)
** Reference: [https://na-mic.org/w/images/2/27/Levitt_2002.pdf Levitt JJ, McCarley RW, Dickey CC, Voglmaier MM, Niznikiewicz MA, Seidman LJ, Hirayasu Y, Ciszewski AA, Kikinis R, Jolesz FA, Shenton ME. MRI study of caudate nucleus volume and its cognitive correlates in neuroleptic-naive patients with schizotypal personality disorder. Am J Psychiatry. 2002 Jul;159(7):1190-7.]
* Insular Cortex & Temporal Pole: (N=27 SZ; N=26 AFF; N=29 Ctrl)
** Reference: [https://na-mic.org/w/images/3/39/Kasai_2003.pdf Kasai K, Shenton ME, Salisbury DF, Onitsuka T, Toner SK, Yurgelun-Todd D, Kikinis R, Jolesz FA, McCarley RW. Differences and similarities in insular and temporal pole MRI gray matter volume abnormalities in first-episode schizophrenia and affective psychosis. Arch Gen Psychiatry. 2003 Nov;60(11):1069-77.]

RSNA2012 Planning

2017-07-10T18:27:04Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

== Process ==

We are following the release schedule documented during [http://www.na-mic.org/Wiki/index.php/Slicer4.2Planning the 4.2 release planning session]. The following tables describe the target behavior for the RSNA 2012 courses and booth.

* Adopt-a-demo program
** For the demos and tutorials listed below, the roles of developer and clinical contact are:
*** '''clinical expert''' who is responsible for the data and content of the tutorial and can answer questions about how the program is meant to work. This person should be providing the data and in some cases provides a step by step tutorial.
*** '''developer / tester'''
**** is the point of contact if anyone finds that the demo in question does not work correctly
**** is responsible for testing that the functionality is working for the demo on all platforms (mac, windows, linux). If you do not have the platform available yourself, you will need to offer to trade some work with another person who has access to the platform. You cannot just ignore testing just because you don't have ready access to all the platforms!
**** needs to get a working familiarity with the demo and investigate any incorrect or unworkable behavior
**** needs to file bug reports and track down appropriate developer resources to get issues resolved (pester your fellow developers as needed so that issues are addressed).
** If there's a tutorial already existing, the developer should be able to go through the testing on all platforms and only contact the tutorial writer with feedback or questions. In the case of demos or atlas datasets, the developer should discuss with the clinical contact about what functionality should be supported and test that this is working as expected on all platforms.
** In all cases the developer should try to provide a test that loads and manipulates the data, using either a python script or Qt testing, to help automate the testing process for future releases.
** Developers should consider following [https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/SelfTestModule these instructions for writing a python self test] so that they can easily and reproducibly confirm that demos are running correctly on all platforms.

== RSNA hands-on courses ==

{| border="1"
|- bgcolor="#abcdef"
!Schedule !! Tutorial slides !! Datasets !! Tools !! Slicer Modules !! Developer/Tester !! Clinical Expert
|-
|| Classroom Course 1 - ICIA32, Nov.27, 12:30-2:00 pm || [http://www.slicer.org/slicerWiki/images/b/b9/3DVisualizationDICOM_RadiologyApplications_SoniaPujol_KittShaffer_RSNA2012.pdf 3D Visualization of DICOM Data for Radiology Applications] || [http://www.na-mic.org/Wiki/index.php/File:RSNA2012_1.zip RSNA2012_Part1] [http://www.na-mic.org/Wiki/index.php/File:RSNA2012_2.zip RSNA2012_Part2] [http://www.na-mic.org/Wiki/index.php/File:RSNA2012_3.zip RSNA2012_Part3]
|| Compare View, Clipping, Save, Restore, Scene Views, Dicom studies sorting, Dicom networking || Data, Volumes, Models, Scene Views + DICOM ( note: the DICOM part will be a new addition to the slides) || Steve || Sonia
|-
|| Classroom Course 2 - ICIA11, Nov.25, 11:00-12:30 pm || [http://www.slicer.org/slicerWiki/images/c/c6/Slicer4QuantitativeImaging.pdf Quantitative Imaging Tutorial] || ICIA 11 datasets: [https://na-mic.org/w/images/7/73/PETCTFusion-Tutorial-Data.zip PETCT data], [http://www.slicer.org/slicerWiki/images/b/b2/ChangeTracker2011.zip Change Tracker Data] || Change Tracker, Compare Views, Volume Rendering, CropVolume, Crosshairs, BRAINSFit || Change Tracker, Volume Rendering, BRAINSFit, CropVolume} || Steve || Sonia
|-
|}

==Quantitative Imaging Reading Room==

Logistics: The exhibit must be fully installed by 5:00 pm on Saturday, November 24. The Lakeside Learning Center exhibit area will open on Saturday, November 24 from 8:00 am until 10:00 pm for installation.

* [[Media:RSNA2012QIRRPoster_3DSlicer-spujol.AF.pptx|Poster PPT]]
* [[Media:RSNA2012QIRRHandout.AF.pptx|Handout PPT]]

Tentative list of demonstrations for the RSNA 2012 Slicer booth. Needs further development and testing
'''Note: RSNA demo machines will need nvidia graphics cards to get GPU Volume Rendering'''
{| border="1"
|- bgcolor="#abcdef"
!# !!DEMO !! Datasets !! Notes !! Tools !! Slicer Modules !! Developer/Tester !! Clinical Expert
|-
||0 ||3D Visualization of DICOM images for Radiology Applications || [http://www.slicer.org/slicerWiki/images/b/b9/3DVisualizationDICOM_RadiologyApplications_SoniaPujol_KittShaffer_RSNA2012.pdf 3D Visualization of DICOM Data for Radiology Applications] || [http://www.na-mic.org/Wiki/index.php/File:RSNA2012_1.zip RSNA2012_Part1] [http://www.na-mic.org/Wiki/index.php/File:RSNA2012_2.zip RSNA2012_Part2] [http://www.na-mic.org/Wiki/index.php/File:RSNA2012_3.zip RSNA2012_Part3]
|| Compare View, Clipping, Save, Restore, Scene Views, Dicom studies sorting, Dicom networking || Data, Volumes, Models, Scene Views || Jim || Sonia
|-
||1 ||Data Loading and Visualization || <strike>[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Slicer3Visualization Data] </strike>[http://www.slicer.org/slicerWiki/images/f/f4/3DVisualizationData.zip 3D Visualization Data] || [https://www.slicer.org/wiki/Documentation/4.1/Training#Slicer4_Data_Loading_and_3D_Visualization ‎ Slicer4Visualization Tutorial]|| Compare View, Clipping, Save, Restore, Scene Views, DICOM studies sorting, DICOM networking (?) || Data, Volumes, Models, Scene Views || Jim || Sonia
|-
||2||MRI-based topographic parcellation of human brain || [[Media:RSNA2010_EMS.zip | EM Segmenter Data]] || registration, segmentation [https://www.slicer.org/wiki/EMSegmenter-Tasks EMSegmenter Tasks] || EM Segmenter || EMSegmenter || Kilian || Ron
|-
||3|| Volume Rendering #1 Head || [[Media:RSNA2010_OsirixManixDataset.zip | Head CT Scan (Osirix Manix Dataset)]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations || Volume Rendering, Annotations, Scene Views || Julien || Ron
|-
||4|| Volume Rendering #2 Abdomen|| [[Media:RSNA2010_OsirixPanoramixDataset.zip | Abdominal CT scan with AAA (Osirix Panoramix Dataset)]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations || Volume Rendering, Annotations, Scene Views || Julien || Ron
|-
||5|| Volume Rendering #3 Thorax|| [[Media:RSNA2010_Lungs_Dataset.zip | Thoracic CT scan]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations || Volume Rendering, Annotations, Scene Views || Julien || Ron
|-
||6|| Traumatic Brain Injury Case Analysis || [[Media:TBI-DemoScene-RSNA2011.zip | TBI Demo Data (UCLA)]] [http://www.nitrc.org/frs/download.php/1766/adult-atlas-abc1.1.zip Atlas data link] || [http://wiki.na-mic.org/Wiki/index.php/File:TBISegmentation_TutorialContestSummer2011.pdf TBI tutorial] || ABC Segmentation, Model Maker, Editor, Annotations || Data, ABC Segmentation, Model Maker, Editor, Annotations, Scene Views || Alex || Jack Van Horn
|-
||7|| Radiotherapy || [http://slicer.kitware.com/midas3/folder/859 SlicerRT ART dose verification data] || [https://www.assembla.com/spaces/slicerrt/wiki/20121127_Slicer_tutorials_at_RSNA_2012 SlicerRT RSNA2012 Tutorial] || SlicerRT, Plastimatch || DICOM, General Registration (BRAINS), Resample Image (BRAINS),<br>SlicerRT: DicomRtImport, Dose Accumulation, Dose Volume Histogram || Csaba || Andras
|-
||8|| White matter exploration for neurosurgical planning || [[media:WhiteMatterExplorationData.zip‎| White Matter Exploration dataset]] || [https://www.slicer.org/wiki/Documentation/4.1/Training#Slicer4_Neurosurgical_Planning_Tutorial Neurosurgical planning Tutorial]] || Diffusion (Estimation, Tractography, Fiducial Seeding), Editor, Model Maker || Data, Volumes, Editor, Fiducials, Diffusion Tensor Estimation, Diffusion Tensor Scalar Measurements, Labelmap Seeding, Tractography Fiducial Seeding, Tractography Display || Demian || Ron
|-
||9|| Longitudinal analysis of meningioma growth|| [https://na-mic.org/w/images/7/73/PETCTFusion-Tutorial-Data.zip PETCT data], [http://www.slicer.org/slicerWiki/images/b/b2/ChangeTracker2011.zip Change Tracker Data] || [http://www.slicer.org/slicerWiki/images/c/c6/Slicer4QuantitativeImaging.pdf Quantitative Imaging Tutorial] || Change Tracker, Compare Views, Volume Rendering, CropVolume, Crosshairs, BRAINSFit || Change Tracker, Volume Rendering, BRAINSFit, CropVolume || Jc || Andrey
|-
||10||Image-guided prostate interventions || [[media:RSNA2011_Prostate.zip | Demo dataset from RSNA'2011 -- crash while switching to a scene view]] see [http://www.na-mic.org/Bug/view.php?id=1523 here.], [[Media:RSNA2012_Prostate.zip | Demo dataset created from scratch in Slicer4 RSNA'2012]] || Pre-op/Intra-op registration; [http://www.na-mic.org/Wiki/index.php/Slicer4:Prostate_mpMRI_review_use_case Use Case Demo] [[media:RSNA2010_Prostate.zip | Prostate Data]] || Linked Viewing || Annotations, Models, Crosshairs, CompareViews || Jim || Andrey
|-
||11|| Brain Atlas || [http://www.na-mic.org/publications/item/view/2037 NAC Multi-modality MRI-based Atlas of the Brain]<br>[http://www.na-mic.org/publications/bitstream/download/5521 Slicer4 version] || Show model hierarchies, visibility, scene views restore|| Linked Viewing || Data, Volumes, Models, Scene Views || Nicole || Marianna
|-
||12|| Head and Neck Atlas || [http://www.na-mic.org/publications/item/view/2271 Head and Neck Atlas]<br>[http://www.spl.harvard.edu/publications/bitstream/download/5527 Slicer4 version] || Show model hierarchies, visibility, scene views restore|| Linked Viewing || Data, Volumes, Models, Scene Views || Nicole || Marianna
|-
||13|| Abdominal Atlas || [http://www.na-mic.org/publications/item/view/1918 Abdominal Atlas]<br>[http://www.na-mic.org/publications/bitstream/download/5522 Slicer4 version]|| Show model hierarchies, visibility, scene views restore|| Linked Viewing || Data, Volumes, Models, Scene Views || Nicole || Marianna
|-
||14|| Knee Atlas|| [http://www.na-mic.org/publications/item/view/1953 Knee Atlas] <br> [http://www.na-mic.org/publications/bitstream/download/5523 Slicer4 version] || Show model hierarchies, visibility, scene views restore || Linked Viewing || Data, Volumes, Models, Scene Views || Nicole || Marianna
|}

== List of Slicer Modules involved in RSNA tutorials & demos==

*Data
*Welcome to Slicer
*Volumes
*Models
*Scene Views
*Annotations
*Volume Rendering
*Editor
*Model Maker
*Diffusion Tensor Estimation
*Diffusion Tensor Scalar Measurements
*Tractography Labelmap Seeding
*Tractography Fiducial Seeding
*Tractography Display
*BRAINSTools
*Change Tracker
*CropVolume
*Extensions:
**ABC
**Plastimatch
**EMSegmenter
**Skull Stripper
** Reporting
** Longitudinal PET CT
*Documentation: We need all [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.2#Core_Modules core modules] reasonably well documented.

AHM2014-SubjectHierarchy

2017-07-10T18:27:04Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

[[AHM_2014#Agenda|Back to AHM_2014 Agenda]]

=Introduction=
* Purpose: Come to an agreement on the architecture and feature set of the new Subject hierarchy module and mechanism
* Time: Tuesday 3:15 - 4:00
* Participants: Csaba Pinter, Andras Lasso, Steve Pieper, JC, Jim Miller, Greg Sharp, Alireza Mehrtash, Nicole, and everybody who is interested

=Agenda=
* Present current state of Subject hierarchy (Csaba) ([https://na-mic.org/w/images/5/5e/SubjectHierarchy_NAMIC2014Jan.pptx slides])
** GUI and features
** Architecture ([https://na-mic.org/w/images/6/6d/Subject_Hierarchy_-_Class_Diagram.png detailed class diagram])
** Design questions, issues, and future work
* Discussion on the features and implementation details
* Come to an agreement
** Features and architecture
** Tentative roadmap

=Discussion=
* See [http://www.na-mic.org/Wiki/index.php/2014_Winter_Project_Week:SubjectHierarchy subject hierarchy project page]

ITK Registration Optimization

2017-07-10T18:27:04Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{|border=1
|This page contains a record of the development of RegisterImages. For user documentation please see [https://www.slicer.org/wiki/Modules:RegisterImages-Documentation-3.4 RegisterImages-Documentation-3.4]
|}

= Slicer3 Module: RegisterImages =

The RegisterImages module is the product of the research discussed below.

== Major Features ==

The major features of the module include:
* Default parameters register many full-head and skull-stripped MRI: rigid, affine, and BSpline
* Offers a complete, pipeline-based registration solution
** Load and apply existing transforms
** Compute rigid, affine, and bspline transforms in sequence with a single command
* Intuitive parameters
** Instead of setting obscure "scales" for parameters, you set global values for "Expected Offset", "Expected Rotation", ... to indicate how much mis-registration is anticipated in the data being registered
* MinimizeMemory option provides a way to compute bspline registrations using a dense set of control points and a large number of samples on "normal" computers (albeit computation time increases)
* SampleFromOverlap option allows images of vastly different sizes to be registered
** Helps to avoid (but does not completely eliminate) the annoying ITK exception, "too many samples falls outside of the image"
* Incorporates testing
** Specify a baseline image, and modules will perform the requested registration, compare its results with the baseline image, and return success/failure
* Based on an extensible and re-usable class structure.

Each of these features is discussed next.

== Head MRI Registration ==

=== Example 1: Problem Cases ===

* Registers images which were not well resolved (or produced seg-faults) using other slicer registration modules:
** https://www.slicer.org/wiki/Slicer3:Registration

==== Difficult affine registration, Same subject, Different protocols: T2 and Fractional Anisotropy ====
{|
|-
| [[Image:RegisterImages-T2-fa-registration-setup-2008-07-30.png|thumb|250px|Setup: T2 (fixed) with FA (moving)]]
| [[Image:RegisterImages-T2-fa-registration-results-2008-07-30.png|thumb|250px|Affine Results: RegisterImages, Default Options (2008-07-30)]]
|-
|}

==== Difficult affine registration, Same subject, Different protocols: T1 and Gradient ====

{|
|-
| [[Image:RegisterImages-Debrecen-affine-setup-2008-07-30.png|thumb|250px|Setup: T1 (fixed) with Gradient (moving)]]
| [[Image:RegisterImages-Debrecen-affine-results-2008-07-30.png|thumb|250px|Affine Results: RegisterImages, Default Options (2008-07-30)]]
|-
|}

=== Example 2: Affine Registration ===

* Task:
** Affine registration of head MRI from two different subjects
* Data:
** Using cases UNC-Healthy-Normal002 (fixed) and UNC-Healthy-Normal004 (moving)
** Data provided by Dr. Bullitt at UNC.
** Data is available from Kitware's MIDAS archive at http://hdl.handle.net/1926/542
** Data can be automatically downloaded into ${RegisterImages_BINARY_DIR}/Testing/Data directory by enabling the CMake variable "BUILD_REGISTER_IMAGES_REAL_WORLD_TESTING"
*** Warning this also enables additional tests that can take 4+ hours to complete.
*** To see the code for automatically downloading from MIDAS (via svn), see Slicer3/Applications/CLI/RegisterImagesModule/Applications/CMakeLists.txt

==== Affine registration of head MRI from two difference subjects ====

{|
|-
| [[Image:RegisterImages-Normal002-004-affine-setup-2008-07-30.png|thumb|250px|Setup: UNC Normal 002 (fixed) with UNC Normal 004 (moving)]]
| [[Image:RegisterImages-Normal002-004-affine-results-2008-07-30.png|thumb|250px|PipelineAffine Results: RegisterImages, Default Options (2008-07-30)]]
|-
|}

==== Affine registration of skull-stripped head MRI from two difference subjects ====

{|
|-
| [[Image:RegisterImages-Normal002-004-stripped-affine-setup-2008-07-30.png|thumb|250px|Setup: Skull Stripped: UNC Normal 002 (fixed) with UNC Normal 004 (moving)]]
| [[Image:RegisterImages-Normal002-004-stripped affine-results-2008-07-30.png|thumb|250px|PipelineAffine Results: Skull Stripped RegisterImages, Default Options (2008-07-30)]]
|-
|}

=== Example 3: BSpline Registration ===

* Task:
** BSpline registration of head MRI from two different subjects
* Data:
** Using cases UNC-Healthy-Normal002 (fixed) and UNC-Healthy-Normal004 (moving)
** Data provided by Dr. Bullitt at UNC.
** Data is available from Kitware's MIDAS archive at http://hdl.handle.net/1926/542
** Data can be automatically downloaded into ${RegisterImages_BINARY_DIR}/Testing/Data directory by enabling the CMake variable "BUILD_REGISTER_IMAGES_REAL_WORLD_TESTING"
*** Warning this also enables additional tests that can take 4+ hours to complete.
*** To see the code for automatically downloading from MIDAS (via svn), see Slicer3/Applications/CLI/RegisterImagesModule/Applications/CMakeLists.txt

==== BSpline, Default Options, Different Subjects, Same Protocol, Head MRI ====
{|
|-
| [[Image:RegisterImages-Normal002-004-bspline-setup-2008-07-30.png|thumb|250px|Setup: UNC Normal 002 (fixed) with UNC Normal 004 (moving)]]
| [[Image:RegisterImages-Normal002-004-bspline-results-2008-07-30.png|thumb|250px|PipelineBSpline Results: RegisterImages, Default Options (2008-07-30)]]
|-
|}

==== BSpline, Dense Control-Point Grid, Different Subjects, Same Protocol, Head MRI ====
{|
|-
| [[Image:RegisterImages-Normal002-004-bspline2-setup-2008-07-30.png|thumb|250px|PipelineBSpline Results: UNC Normal 002 (fixed) with UNC Normal 004 (moving), Default Options]]
| [[Image:RegisterImages-Normal002-004-bspline2-results-2008-07-30.png|thumb|250px|PipelineBSpline Results: RegisterImages, Options: MinimizeMemory and ControlPointSpacing=15 pixels (vs. default ControlPointSpacing=40 pixels) (2008-07-30)]]
|-
|}

==== BSpline, (Default Options vs. Dense Control-Point Grid), Different Subjects, Same Protocol, Skull-Stripped Head MRI ====
{|
|-
| [[Image:RegisterImages-Normal002-004-stripped-bspline-setup-2008-07-30.png|thumb|250px|Setup: Skull Stripped: UNC Normal 002 (fixed) with UNC Normal 004 (moving)]]
| [[Image:RegisterImages-Normal002-004-stripped-bspline-results-2008-07-30.png|thumb|250px|PipelineBSpline Results: RegisterImages, Default Options (2008-07-30)]]
| [[Image:RegisterImages-Normal002-004-stripped bspline-results2-2008-07-30.png|thumb|250px|PipelineBSpline Results: RegisterImages, MinimizeMemeory and ControlPointSpacing=15 pixels (vs. default ControlPointSpacing=40 pixels) (2008-07-30)]]
|-
|}

== Pipeline Registration ==

The module implements a registration pipeline. The steps in that pipeline are as follows:

* Step 1: Loaded transform
** You may load a pre-computed transform to initialize the registration.
** If one is loaded, it is immediately applied (i.e., the moving image is resampled)
* Step 2: Initial registration
** Options are:
*** None (sets the center of rotation to the center of the moving image)
*** Landmark (uses N-pairs of landmarks (passed as vectors) and a least-squared error metric to register the images using a rigid transform
*** Image Centers (shifts the images to align their centers)
*** Centers of Mass (shifts the images to align their centers of mass)
*** Second Moments (shifts and rotates the images to align the 1st and 2nd moments)
* Step 3: Registration
** Options are:
*** None (applies the loaded transforms)
*** Initial
**** computes and applies the initial transform to the loaded registrations)
*** Rigid
**** computes a rigid transform and then applies it to the loaded registrations
*** Affine
**** computes an affine transform and then applies it to the loaded registrations
*** BSpline
**** computes a bspline transform and then applies it to the loaded registrations
*** PipelineRigid
**** computes a rigid transform (initialized using the results from the initial registration) and then applies it to the loaded registrations
*** PipelineAffine
**** computes a rigid transform (initialized using the results from the initial registration), uses those results to initialize and compute an affine transform, and then applies it to the loaded registrations
*** PipelineBSpline
**** computes a rigid transform (initialized using the results from the initial registration), uses those results to initialize and compute an affine transform, and then applies it to the loaded registrations, THEN computes and applies a BSpline transform

== Intuitive Parameters ==

* In rare cases (given unusual acquisition conditions and/or highly inconsistent acquisition protocols) you will need to change the default parameters.
* More often you may wish to tweak parameters to achieve your application-specific speed-vs-accuracy tradeoff

=== IO Tab ===
* Set the fixed and moving images using images in the scene
* Optionally set the ResampleImage to store the output image
** If not set, registration won't conduct the final resampling, saving computation time

=== Registration Parameters Tab ===
* Load Transform
** provide the Loaded Transform for the loaded phase of registration
* Save Transform
** results of the entire registration pipeline will be saved here
* Initialization
** see registration pipeline discussion
* Registration
** see registration pipeline discussion
** For rigid and affine registrations, one-plus-one evoluation optimization is first applied for N iterations, and then FRPR gradient-line-search optimization is applied.
*** For more information, check the code: RegisterImagesModule/itkOptimizedImageToImageRegistrationmethod.h/txx
** For BSpline registration, a hierarchical registration scheme is used. An image pyramid having 3 levels is used to resample the images and the control grids. Heuristics are used to control the various resampling parameters. At each level, registration is conducted using FRPR gradient-line-search optimization.
*** For more information, check the code: RegisterImagesModule/itkBSplineImageToImageRegistrationMethod.h/txx
* Metric
** Use the Mutual Information metric. It is an multithreaded and optimized version of the Mattes MI method.
*** For more information, check the code; Insight/Code/Review/itkOptMattesMutualInformationImageMetric.h/txx
* "Expected" values
** For rigid, affine, and bspline registration, parameter scales (refer to the Insight Software Guide) are represented as hyper-parameters in the RegisterImages module.
*** "Expected Offset" controls the offset scales in rigid and affine registration the deformation vector scale in bspline registration
*** "Expected Rotation" is roughly in terms of radians. It controls the rotation angles in rigid and affine registration
*** "Expected Scale" is for scaling during affine registration
*** "Expected Skew" is for skew for affine registration

=== Advaned Registration Parameters Tab ===
* Verbosity level
** Controls the level of detail in the reports in the log file
* Sample from fixed/moving overlap
** When the fixed image is much larger than the moving image, it is CRITICAL to set this flag and to pick a good initialization method. In that way, only the portion of the fixed image that is initially covered by the moving image will be used during registration. This prevents ITK from throwing an exception (error) stating that too many fixed-image samples miss (map outside of) the moving image.
* Fixed image intensity percentage threshold
** A less robust way to overcome the image overlap issue discussed above, you can specify a threshold as a portion (0 to 1) of the fixed image intensity range that should be used to select fixed image samples for computing the metric. That is, by specifying 0.5, only the pixels in the upper half of the fixed-image's intensity range will be used during random sample selection.
** Remember, it is important to include pixels inside and outside of the object of interest, otherwise the fixed image histogram may be too homogeneous for mis-registrations to be detected.
* Random number seed
** To ensure consistent performance, you can set a seed - repeated runs should produce identical results.
* Number of threads
** Number of multi-core/mult-processor threads to use during metric value computations.
* MimimizeMemory
** Turns off caching of intermediate values during bspline registration
** Provides a way to compute bspline registrations using a dense set of control points and a large number of samples on "normal" computers (albeit computation time increases)
** Rule of thumb, if the BSpline registration crashes - re-run with this option enabled.
* use windowed sinc for final interpolation
** If you have time to kill. Extremely slow and only marginally better than bspline resampling (the default).

=== Registration Testing Parameters ===
* Baseline Image
** Set the image against which the Resampled Image (IO tab) will be compared after registration
* Number of Failed Pixels Tolerance
** Registration returns "failure" if this many pixels are different between the Resampled and Baseline images
* Intensity Tolerance
** Minimum intensity difference between corresponding Resampled and Baseline pixels for those pixels to be counted as failures
* Radius Tolerance
** The program will search this neighborhood size about each Resampled pixel to find the closest matching Baseline pixel. The closest matching pixels are compared using the Intensity Tolerance (above)
* Baseline Difference Image
** Result of subtracting the resampled image from the baseline image
* Baseline Resamples Moving Image
** resampled image, resampled into the space of the baseline image

=== Advanced Initial Registration Parameters ===
* Fixed / Moving Landmarks
** A vector string (comma separated base-3 list) of the indexes of corresponding points in the fixed and moving images
** If supplied, then choose "Landmarks" as the initial registration method (see discussion on registration pipeline)

=== Advanaced Rigid and Affine Parameters ===
* MaxIterations
** Number of iterations for one-plus-one and for FRPR registration
* Sampling Ratio
** Portion of the image pixels to be used when computing the metric

=== Advanced BSpline Parameters ===
* MaxIterations
** Number of iterations for one-plus-one and for FRPR registration
* Sampling Ratio
** Portion of the image pixels to be used when computing the metric
** Do the math...if you have 40 pixels between control points, then there will be 40^3 (64,000) pixels relevant to each control point. That excessive for directing one control point. Keep the sampling small. For 40 pixels between control points, a sampling density of 0.1 provide 6,400 pixels for metric computation at each control point - more than enough.
** When in doubt, turn on MinimizeMemory
* Control point spacing (pixels)
** Don't think about grid size - instead think about the level of detail that needs to be resolved (see discussion on sampling ratio).
** When in doubt, turn on MinimizeMemory

== Incorporates testing ==

* See discussion on the "Registration Testing Parameters" tab.

== Class structure ==

* Try it, you'll like it.
* Follows the coding style of itk
* Limited comments, but meaningful variable names
* No documentation is provided or planned - don't even ask.

= Instructions for Enabling the RegisterImages module =

This module should now be built and distributed by default. No special steps are needed to use this module.

= Background =

== Goals ==

There are two components to this research
# Identify registration algorithms that are suitable for non-rigid registration problems that are endemic to NA-MIC
# Develop implementations of those algorithms that take advantage of multi-core and multi-processor hardware

== Steps involved ==

# Modify ITK's registration framework to support oriented images
# Modify ITK's registration framework to be thread safe
# Develop multi-threaded versions of select registration modules
# Make everything backward compatible with ITK's existing registration methods and framework
# Deliver in ITK
# Develop helper classes and write IJ article

Target date for these deliverables: Jan 1, 2008

== Planned follow-on work ==

Devise a new metric for MI registration
# If we always use every voxel for the metric, then we can cache the weights by the voxel's position wrt the adjacent control points. For example, for Kilian's situation of a control point every 2 voxels, then there really are only a few unique weight sets that are repeated throughout the volume. Luis had already brought up a variation on this idea.
# This method could also be combined with the rule to not evaluate voxels or control points that fall on background voxels. This too has been discussed, but such a rule makes multi-threading tricky in that we don't want to waste threads by allocating them to image regions that contain only background voxels.
# The metric could be closely tied to a multiresolution registration scheme. In fact, the grid and the image resolutions should perhaps be linearly related. That is, we could tie the metric computation to the resolution of the deformation grid by subsampling the image. There are situations where this is not a right thing to do (just because the grid is coarse doesn't mean that a small movement isn't important); HOWEVER, as part of a multiresolution registration strategy, it is perhaps the viable option. This would need to be evaluated on the data.
# Have "don't-care" regions in which bspline control points are processed/don't move, e.g., no need to adjust ones that only contain background

== Status and News ==
Thanks (but not your questions or comments) go to
* Luis Ibanez, Matt Turek, Stephen Aylward
Questions and comments should go to the Slicer Developers' list

== Publications ==

# [http://insight-journal.org/InsightJournalManager/view_reviews.php?pubid=172 Aylward, Stephen; Jomier, Julien; Barre, Sebastien; Davis, Brad; Ibanez, Luis, "Optimizing ITK’s Registration Methods for Multi-processor, Shared-Memory Systems." MICCAI Open Source and Open Data Workshop, 2007] [http://insight-journal.org/InsightJournalManager/download_publication.php?pubid=172&revision=2&name=OptimizingITKRegistrationMethods.pdf&pdf=1 (Download PDF)]
# [[NAC_Grid_Enabled_ITK | BWH Neuroimaging Analysis Center (NAC), 2007-2008: Grid Enabled ITK]]
# IJ article on oriented images and registration in ITK
#* http://www.insight-journal.org/dspace/bitstream/1926/1293/2/Brooks_Arbel_FastOrientedImage_V1.pdf
#* Solution presented by the authors is closely related to the changes made in ITK

== Algorithmic Requirements and Use Cases ==

* Requirements
*# relatively robust, with few parameters to tweak
*# runs on grey scale images
*# has already been published
*# relatively fast (ideally speaking a few minutes for volume to volume).
*# not patented
*# can be implemented in ITK and parallelized.

* Use-cases
*# Intersubject mapping
*#* [[Intersubject|Example data set]] (Kilian)
*# fMRI to hi-res brain morphology mapping
*#* [[FMRI-to-hires|Example data set]] (Steve Pieper)
*# DTI: components of the diffusion tensor
*#* [[DTI-non-rigid|Example data]] (Sylvain)

== Hardware Platform Requirements and Use Cases ==

* Requirements
*# Shared memory
*# Single and multi-core machines
*# Single and multi-processor machines
*# AMD and Intel - Windows, Linux, and SunOS

* Use-cases
*# Intel Core2Duo
*# Intel quad-core Xeon processors, Visual Studio 8, Windows Vista (Kitware: redwall)
*# 6 CPU Sun, Solaris 8 (SPL: vision)
*# 12 CPU Sun, Solaris 8 (SPL: forest and ocean)
*# 16 core Opteron (SPL: john, ringo, paul, george)
*# 16 core, Sun Fire, AMDOpteron (UNC: Styner)

== Historic Results ==

January 5, 2008 - Note: "Opt" results are not using the OptLinearInterpolateImageFunction.

*[https://na-mic.org/w/images/f/fe/MattesGetValue.pdf MattesMI GetValue Results]
*[https://na-mic.org/w/images/1/1b/MattesBSplineGetValue.pdf MattesMI, b-spline interpolation and transform, GetValue Results]
*[https://na-mic.org/w/images/1/16/MeanSquaresGetValue.pdf MeanSquares GetValue Results]
*[http://wiki.na-mic.org/Wiki/images/c/c5/MattesGetValueAndDerivative.pdf MattesMI GetValueAndDerivative Results]
*[http://wiki.na-mic.org/Wiki/images/f/f6/MattesBSplineGetValueAndDerivative.pdf MattesMI, b-spline interpolation and transform, GetValueAndDerivative Results]
*[http://wiki.na-mic.org/Wiki/images/2/2d/MeanSquaresGetValueAndDerivative.pdf MeanSquares GetValueAndDerivative Results]

== Historic Events ==

* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-06-tcon April 6, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-12-tcon April 12, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-18-tcon April 18, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-05-01-tcon May 1, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-06-27-tcon June 27, 2007: NAMIC Programmers' Week]
* [http://wiki.na-mic.org/Wiki/index.php/Registration_Update January, 2008: NAMIC AHM]

= Related Pages =

* [[Non Rigid Registration]]
* [https://www.slicer.org/wiki/Slicer3:Performance_Analysis Slicer3:Performance_Analysis]
* [http://www.na-mic.org/Wiki/index.php/User:Barre/ITK_Registration_Optimization User:Barre/ITK Registration Optimization]
* [[ITK_Registration_Optimization/Testing_And_Backward_Forward_Compatibility | Testing and ITK Backward Forward Compatibility]]

= Notes on Software Profiling Tools =
* [http://www.lw-tech.com/index.php LTProf - simple profilter for Windows - Shareware]
* [http://www.intel.com/cd/software/products/asmo-na/eng/vtune/vlin/239145.htm Intel's VTune for Linux] ($)
* [http://www.cs.uoregon.edu/research/tau/home.php TAU]
* [http://www.cs.brown.edu/research/thmon/thmon.html Threadmon: Thread usage/blockage]
* [http://www.etnus.com/ TotalView] ($)
* [http://perfsuite.ncsa.uiuc.edu/ PerfSuite (POSIX Threads)]
* [http://sam.zoy.org/writings/programming/gprof.html GProf work-around for multi-threaded apps]
* References on multi-threaded profiling and code optimization
** [http://www.mactech.com/articles/mactech/Vol.11/11.04/ExtremeAdvantage/index.html General C++ performance optimization]
** [http://www.cs.princeton.edu/~mji/tmon.pdf Multi-threaded performance measurement (pdf document)]
** [http://en.wikipedia.org/wiki/Performance_analysis Wikipedia - General performance analysis]

RSNA2011 Slicer4

2017-07-10T18:27:03Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

==Slicer4 materials for RSNA 2011 courses==

*Slicer4 software: [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.0.gamma-2011-11-23-win-amd64.exe&checksum=99eda704be622d4189681938f5bf5b4f Slice4-RSNA2011]
*Slicer4 tutorial datasets:
**[[media:3DVisualizationData_Slicer_RSNA2011.tar.gz | 3DVisualization Data]]
**[https://na-mic.org/w/images/3/33/Slicer_data-RSNA2010-CTSA.zip QuantitativeImaging Data]

Projects:RegistrationDocumentation:ReferenceManual

2017-07-10T18:27:03Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

[[Projects:ARRASuplements|Back to ARRA main page]]

[[Projects:RegistrationDocumentation|Back to Registration main page]]
== Main Register Images Parameters ==

*'''Parameter set'': will become "Presets" menu
*IO
**'''Input Fixed Image''':
**'''Input Moving Image''':
**'''Input Mask/ROI''': (optional) provide ROI or labelmap to focus registration only on a particular area of the image. Use the editor to create a labelmap or ROI tool to create an ROI box.
**'''Input Transform''': provide the Loaded Transform for the loaded phase of registration
**'''Output Result Transform''': results of the entire registration pipeline will be saved as Xform node here
**'''Output Resampled Registered Image''': result Xform applied to moving image and resampled, creates a new volume node
*Initialization (only if no input Xform specified above):
**'''None'''
**'''Image Centers''' (shifts the images to align their centers)
**'''Centers of Mass''' (shifts the images to align their centers of mass)
**'''Second Moments''' (shifts and rotates the images to align the 1st and 2nd moments)
*Registration DOF (for details on DOF see xxLinkToBasicsTutorial)
**'''Rigid 6 DOF''':computes a rigid transform with 6DOF: 3 Translations & 3 Rotations
**'''Rigid 7 DOF''':computes a rigid transform + a global scaling factor. Moving image will resize, but aspect ratio stays intact
**'''Similarity 9 DOF''':computes a similarity transform + 3 individual scaling factors. Moving image will resize and aspect ratio will change.
**'''Affine 12 DOF''': computes a full affine transform incl. local scaling and shearing.
**'''BSpline''': -> will become a separate submodule. computes a B-spline transform, which is a non-rigid and nonlinear transform. Image is allowed to deform locally. Also known as "image warping". The amount of regularization, i.e. how much local deformation is allowed is controlled via the grid-spacing.
*Metric
** '''Mutual Information''' metric. It is an multithreaded and optimized version of the Mattes MI method. For more details about how MI works see xxLinkToBasicsTutorial. For developers will find details in the code: Insight/Code/Review/itkOptMattesMutualInformationImageMetric.h/txx
** '''NormCorr''': Normalized Image Correlation. Image cross-correlation as surrogate for similarity. This works well for similar contrast and can give better accuracy than MI, albeit less robust to large misalignment. Current version is not parallelized, i.e. will not take advantage of multiple CPU threads and is therefore much slower than MI.
** '''MeanSqrd''': Mean-square intensity difference. As NormCorr, this works well for similar contrast and can give better accuracy than MI. Depends more on similar contrast than NormCorr.
**'''Cost Function Scaling Factors''': These control on how the optimization landscape is calibrated, i.e. how big translation steps should be relative to rotation etc. These parameters, although complex, are important tools to calibrate a registration to an individual challenge and can greatly improve the result is set correctly.
** '''Expected Offset''' controls the offset scales in rigid and affine registration
** '''Expected Rotation''' is roughly in terms of radians. It controls the rotation angles in rigid and affine registration
** '''Expected Scale''' is for scaling during affine registration
** '''Expected Skew''' is for skew for affine registration
*Advanced Tab
**'''Verbosity Level''': Controls the level of detail in the reports in the log file
**'''Sample from fixed/moving overlap''': When the fixed image is much larger than the moving image, it is CRITICAL to set this flag and to pick a good initialization method. In that way, only the portion of the fixed image that is initially covered by the moving image will be used during registration. This prevents ITK from throwing an exception (error) stating that too many fixed-image samples miss (map outside of) the moving image.
**'''Random Number Seed''': To ensure consistent performance, you can set a seed - repeated runs should produce identical results.
**'''Number of Threads''': Number of multi-core/mult-processor threads to use during metric value computations.
**'''Minimize Memory''': Turns off caching of intermediate values during bspline registration
**''Interpolation'': select interpolation type for resampling result image immediately
**'''Max.iterations''' Number of iterations for one-plus-one and for FRPR registration
**'''Sampling Ratio''' Portion of the image pixels to be used when computing the metric
**'''Apply''' button: this launches the automated registration process. Other functions of Slicer are still accessible while the registration is running. The registration module itself is disabled (appears in gray) and the notice '''Running''' appears at the top.

== Main Algorithm ==
*For rigid and affine registrations, one-plus-one evoluation optimization is first applied for N iterations, and then FRPR gradient-line-search optimization is applied.
*** For more information, check the code: RegisterImagesModule/itkOptimizedImageToImageRegistrationmethod.h/txx
** For BSpline registration, a hierarchical registration scheme is used. An image pyramid having 3 levels is used to resample the images and the control grids. Heuristics are used to control the various resampling parameters. At each level, registration is conducted using FRPR gradient-line-search optimization.
*** For more information, check the code: RegisterImagesModule/itkBSplineImageToImageRegistrationMethod.h/txx

== Register Images Usage ==

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--controlPointSpacing <int>
Number of pixels between control points (default: 40)

--bsplineSamplingRatio <float>
Portion of the image to use in computing the metric during BSpline
registration (default: 0.1)

--bsplineMaxIterations <int>
Maximum number of bspline optimization iterations (default: 20)

--affineSamplingRatio <float>
Portion of the image to use in computing the metric during affine
registration (default: 0.02)

--affineMaxIterations <int>
Maximum number of affine optimization iterations (default: 50)

--rigidSamplingRatio <float>
Portion of the image to use in computing the metric during rigid
registration (default: 0.01)

--rigidMaxIterations <int>
Maximum number of rigid optimization iterations (default: 100)

--movingLandmarks <std::vector<std::vector<float> >> (accepted multiple
times)
Ordered list of landmarks in the moving image

--fixedLandmarks <std::vector<std::vector<float> >> (accepted multiple
times)
Ordered list of landmarks in the fixed image

--baselineResampledMovingImage <std::string>
Result resampling the moving image to the space of the baseline image

--baselineDifferenceImage <std::string>
Result from subtracting the registered moving image from the baseline
image

--baselineRadiusTolerance <int>
Maximum neighborhood that will be searched to find a matching pixel
(default: 0)

--baselineIntensityTolerance <double>
Maximum intensity difference for pixels to be considered matching
(default: 10)

--baselineNumberOfFailedPixelsTolerance <int>
Maximum number of pixels that can differ and the test pass (default:
1000)

--baselineImage <std::string>
Image against which the resampled moving image will be compared

--interpolation <NearestNeighbor|Linear|BSpline>
Method for interpolation within the optimization process (default:
Linear)

--minimizeMemory
Reduce the amount of memory required at the cost of increased
computation time (default: 0)

--numberOfThreads <int>
Number of CPU threads to use (default: 0)

--randomNumberSeed <int>
Seed to generate a consistent random number sequence (default: 0)

--fixedImageMask <std::string>
Image which defines a mask for the fixed image

--sampleFromOverlap
Limit metric evaluation to the fixed image region overlapped by the
moving image (default: 0)

--verbosityLevel <Silent|Standard|Verbose>
Level of detail of reporting progress (default: Standard)

--expectedSkew <float>
Expected misalignment after initialization (default: 0.01)

--expectedScale <float>
Expected misalignment after initialization (default: 0.05)

--expectedRotation <float>
Expected misalignment after initialization (default: 0.1)

--expectedOffset <float>
Expected misalignment after initialization (default: 10)

--metric <MattesMI|NormCorr|MeanSqrd>
Method to quantify image match (default: MattesMI)

--registration <None|Initial|Rigid|Affine|BSpline|PipelineRigid
|PipelineAffine|PipelineBSpline>
Method for the registration process (default: PipelineAffine)

--initialization <None|Landmarks|ImageCenters|CentersOfMass
|SecondMoments>
Method to prime the registration process (default: CentersOfMass)

--saveTransform <std::string>
Save the transform that results from registration

--loadTransform <std::string>
Load a transform that is immediately applied to the moving image

--resampledImage <std::string>
Registration results

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Image which defines the space into which the moving image
is registered

<std::string>
(required) The transform goes from the fixed image's space into the
moving image's space

Description: Provides rigid, affine, and BSpline registration methods
via a simple GUI

Author(s): Stephen R Aylward

== Publications ==
# [http://insight-journal.org/InsightJournalManager/view_reviews.php?pubid=172 Aylward, Stephen; Jomier, Julien; Barre, Sebastien; Davis, Brad; Ibanez, Luis, "Optimizing ITK’s Registration Methods for Multi-processor, Shared-Memory Systems." MICCAI Open Source and Open Data Workshop, 2007] [http://insight-journal.org/InsightJournalManager/download_publication.php?pubid=172&revision=2&name=OptimizingITKRegistrationMethods.pdf&pdf=1 (Download PDF)]
# [[NAC_Grid_Enabled_ITK | BWH Neuroimaging Analysis Center (NAC), 2007-2008: Grid Enabled ITK]]
# IJ article on oriented images and registration in ITK
#* http://www.insight-journal.org/dspace/bitstream/1926/1293/2/Brooks_Arbel_FastOrientedImage_V1.pdf
#* Solution presented by the authors is closely related to the changes made in ITK

== Algorithmic Requirements and Use Cases ==

* Use-cases
*# Intersubject mapping
*#* [[Intersubject|Example data set]] (Kilian)
*# fMRI to hi-res brain morphology mapping
*#* [[FMRI-to-hires|Example data set]] (Steve Pieper)
*# DTI: components of the diffusion tensor
*#* [[DTI-non-rigid|Example data]] (Sylvain)
* Use-cases
*# Intel Core2Duo
*# Intel quad-core Xeon processors, Visual Studio 8, Windows Vista (Kitware: redwall)
*# 6 CPU Sun, Solaris 8 (SPL: vision)
*# 12 CPU Sun, Solaris 8 (SPL: forest and ocean)
*# 16 core Opteron (SPL: john, ringo, paul, george)
*# 16 core, Sun Fire, AMDOpteron (UNC: Styner)

== Historic Results ==

January 5, 2008 - Note: "Opt" results are not using the OptLinearInterpolateImageFunction.

*[https://na-mic.org/w/images/f/fe/MattesGetValue.pdf MattesMI GetValue Results]
*[https://na-mic.org/w/images/1/1b/MattesBSplineGetValue.pdf MattesMI, b-spline interpolation and transform, GetValue Results]
*[https://na-mic.org/w/images/1/16/MeanSquaresGetValue.pdf MeanSquares GetValue Results]
*[http://wiki.na-mic.org/Wiki/images/c/c5/MattesGetValueAndDerivative.pdf MattesMI GetValueAndDerivative Results]
*[http://wiki.na-mic.org/Wiki/images/f/f6/MattesBSplineGetValueAndDerivative.pdf MattesMI, b-spline interpolation and transform, GetValueAndDerivative Results]
*[http://wiki.na-mic.org/Wiki/images/2/2d/MeanSquaresGetValueAndDerivative.pdf MeanSquares GetValueAndDerivative Results]

== Historic Events ==

* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-06-tcon April 6, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-12-tcon April 12, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-18-tcon April 18, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-05-01-tcon May 1, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-06-27-tcon June 27, 2007: NAMIC Programmers' Week]
* [http://wiki.na-mic.org/Wiki/index.php/Registration_Update January, 2008: NAMIC AHM]

= Related Pages =
*built from ITK Registration Documentation
* [[Non Rigid Registration]]
* [https://www.slicer.org/wiki/Slicer3:Performance_Analysis Slicer3:Performance_Analysis]
* [http://www.na-mic.org/Wiki/index.php/User:Barre/ITK_Registration_Optimization User:Barre/ITK Registration Optimization]
* [[ITK_Registration_Optimization/Testing_And_Backward_Forward_Compatibility | Testing and ITK Backward Forward Compatibility]]

= Notes on Software Profiling Tools =
* [http://www.lw-tech.com/index.php LTProf - simple profilter for Windows - Shareware]
* [http://www.intel.com/cd/software/products/asmo-na/eng/vtune/vlin/239145.htm Intel's VTune for Linux] ($)
* [http://www.cs.uoregon.edu/research/tau/home.php TAU]
* [http://www.cs.brown.edu/research/thmon/thmon.html Threadmon: Thread usage/blockage]
* [http://www.etnus.com/ TotalView] ($)
* [http://perfsuite.ncsa.uiuc.edu/ PerfSuite (POSIX Threads)]
* [http://sam.zoy.org/writings/programming/gprof.html GProf work-around for multi-threaded apps]
* References on multi-threaded profiling and code optimization
** [http://www.mactech.com/articles/mactech/Vol.11/11.04/ExtremeAdvantage/index.html General C++ performance optimization]
** [http://www.cs.princeton.edu/~mji/tmon.pdf Multi-threaded performance measurement (pdf document)]
** [http://en.wikipedia.org/wiki/Performance_analysis Wikipedia - General performance analysis]

2015 Winter Project Week COPD Breakout

2017-07-10T18:27:03Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===
[https://na-mic.org/w/images/2/26/BreakoutSession-CIP-COPDIntro.pptx slides]

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[[File:CIPArchitecture.png]]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components [https://na-mic.org/w/images/0/0b/CipTools.pptx slides]
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[https://na-mic.org/w/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [https://na-mic.org/w/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Slicer Module Examples ===
[https://na-mic.org/w/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[https://na-mic.org/w/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2011 Summer Project Week Watersheds

2017-07-10T18:27:03Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:SegmentationEditorITK.gif|Watersheds Segmentation Editor
</gallery>

'''Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer''' ... and general use for segmentation of complex structures!

==Key Investigators==
* University of Utah: Josh Cates, Ross Whitaker

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
The watersheds algorithm produces a hierarchical set of segmented objects. For some applications, an interface exploring this hierarchical set has proven useful for assembling segmentations of complex anatomical structures. The goal of this project is to re-engineer the old ITKApps Watershed Segmentation Editor in Slicer. The resulting tool will allow a user to interactively assemble 3D segmentations of image data using the output of the itk::WatershedImageFilter. During Project Week, we anticipate finalizing the watershed tool design, taking advantage of the available Slicer engineering expertise to resolve any remaining technical challenges.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Work on the Slicer version of the Watershed Segmenter is currently underway. Project week activities include planning for integration into Slicer 4. Some additional Slicer infrastructure will be required to provide the level of interaction needed for this tool.



</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

The design is not completely finalized, but we have made good progress towards that goal. Tentatively, we plan to python wrapping of the Watersheds logic and custom VTK classes, and integration through the new EditorExtension module type. Some experimentation with the new EditorExtensionTemplate will be required in order to finalize our design.

Example: create editor extension with ModuleWizard:

./Scripts/ModuleWizard.py --template ./Extensions/Testing/EditorExtensionTemplate --target ../MyEditorTool MyEditorTool

Makes a new "MyEditorTool" based on the code here: [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/EditorExtensionTemplate/]

Add it to slicer by adding the path to "../MyEditorTool" to the View->Application Settings->Module Settings list.

Extension can also be registered with slicer nightly builds by constructing an s4ext file and giving it to slicer developers [see instructions in tutorial [https://na-mic.org/w/images/2/23/AHM-2011-SlicerExtensions.pdf]
</div>
</div>

<div style="width: 97%; float: left;">

==References==
J. Cates, R. Whitaker, G. Jones, Case Study: An Evaluation of User-Assisted Hierarchical Watershed Segmentation, Medical Image Analysis, V.9, No.6, Dec. 2005


==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline: NO
##Extension -- loadable: YES

DBP:Harvard

2017-07-10T18:27:03Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

Back to [[DBP1:Harvard|Harvard DBP 1]]
__NOTOC__
== IRB Information ==

In order to handle the data,

* You need IRB training (human subjects protection) and we need your proof--most PIs have taken the training and provided copy of the certificate (as a pre-requisite for the grant)--others handling data should do the same.
* Don't give the data to other people. If somebody wants the data, they should go and talk to Sylvain Bouix who will check if the data can be shared.

More guidelines will be discussed during the AHM next week.

Keep in mind that IRB training and certificates are mandatory and access to data is restricted to those with IRB approval.

* Note IRB must be updated annually in some institutions.

== Data access ==

The description of the data can be found [[DataRepository|here]].

* '''2/2005:''' The legacy data has been converted to one single file format, nrrd, which contains information that we think is necessary for handling medical data. We will provide the NAMIC community documentation for the file format at the NAMIC meeting for both the medical and computer oriented public. We have a total of 188 morphological cases and 80 diffusion cases. The cases have a unique BIRN identifier. Information about diagnosis, data parameters and labels associated with Region of Interests (ROI) are on the BIRN site in the following Excel files:
** morph-NAMIC.xls : Gives diagnosis, age, gender as well as the ROIs drawn for each morphological case.
** morph-ROI-description.xls: Gives for each ROI set, the label corresponding to specific structures.
** diffusion-NAMIC.xls: Gives diagnosis, age, gender, ROIs drawn and when existing, the corresonding morphological data ID number.
** diffusion-ROI-description.xls: Gives or each ROI set, the label corresponding to specific structures.

* '''1/2005:''' After discussion with Steve Pieper and Gordon Kindlman we are leaning towards the NIFTI-1 or nrrd format. NIFTI-1 has more info about orientation but is a bit cumbersome for multidimensional data (e.g. tensor). Nrrd lacks information about the world coordinate system. NOTE: orientation information has been added to NRRD, and to the "unu make" command-line tool that is the most convenient way to generate nrrd headers for a given raw datafile, so that now NRRD can losslessly encode all the orientation information found in the in the NIFTI-1 format.

* '''12/2004:''' We are finalizing the collection of complete data sets. Formats vary across different data sets, genesis, signa, dicom, mrml... We need a single file format able that is simple and can handle orientation properly (i.e. not Analyze).

== Ongoing Collaborations ==

{| cellpadding="5"
! width="120"| !! width="300"| Title !! width="200" | Summary !! PIs
|-
| [[Image:Shapeanalysis-UNC.jpg]] ||'''[[DBP:Harvard:Collaboration:UNC|Algorithms: Shape Analysis (PNL-UNC)]]''' || Structural shape analysis of the caudate nucleus and corpus callosum || <i>UNC</i>: Martin Styner, Isabelle Corouge<br><i>PNL</i>: Marek Kubicki, Sylvain Bouix, Marc Neithammer, James Levitt
|-
| [[Image:Dti-UNC.jpg]] || '''[[DBP:Harvard:Collaboration:UNC|Algorithms: Diffusion Tensor Imaging (PNL-UNC)]]''' || Statistical analysis of diffusion measures along white matter fibers of interest || <i>UNC</i>: Isabelle Corouge, Martin Styner<br><i>PNL:</i>Sylvain Bouix, Marc Niethammer, Marek Kubicki, Martha Shenton
|-
| [[Image:Dti-MIT.jpg]] || '''[[DBP:Harvard:Collaboration:MITDTI|Algorithms: Diffusion Tensor Imaging (PNL-MIT)]]''' || Automatic clustering of distinct fiber tracts, and diffusion measures along tracts of interest || <i>MIT</i>: Lauren O'Donnell, CF Westing, Raul San Jose<br><i>PNL:</i> Marek Kubicki, Sylvain Bouix, Marc Niethammer, Mark Dreusicke
|-
| [[Image:Seg-MIT.jpg]] || '''[[DBP:Harvard:Collaboration:MIT|Algorithms: Anatomical Segmentation (PNL-MIT)]]''' || Brain tissue classification and parcellation of structures || <i>MIT</i>: Kilian Pohl, Sandy Wells, Eric Grimson<br><i>PNL</i>: Sylvain Bouix, Motoaki Nakamura, Min-Seong Koo, Martha Shenton
|-
| [[Image:Striatum-GAT.jpg]] || '''[[DBP:Harvard:Collaboration:GTech|Algorithms: Rule-based Segmentation (PNL-GaTech)]]''' || Automatic segmentation of the striatum || <i>GaTech</i>: Ramsey Al-Hakim, Delphine Nain, Allen Tannenbaum<br><i>PNL:</i> Sylvain Bouix, James Levitt, Marc Niethammer, Martha Shenton
|-
| || '''[[DBP:Harvard:Collaboration:Utah|Algorithms: Tensor Based Statistics (PNL-Utah)]]'''
|-
| || '''[[DBP:Harvard:Collaboration:Slicer|Engineering: Slicer Improvement and Testing]]'''
|-
| || '''[[DBP:Harvard:Collaboration:Training|Training: Training Material and Expert Users Feedback]]'''
|-
| || '''[[DBP:Harvard:Collaboration:Toronto|Biology: Genetics and Imaging (Toronto)]]'''
|}

== Meeting Reports ==

* '''[[DBP:Harvard:Software:Minutes|Weekly DTI Meeting Minutes/Agenda]]'''

* '''[[Collaboration:UNC-Utah-PNL_2006ProjectWk|June 28, 2006: Meeting with Utah and UNC at the PNL during 2006 NA-MIC Project Week]]'''
* '''[[Collaboration:UNC-PNL|October 7, 2005, UNC visit at the Psychiatry NeuroImaging Laboratory]]'''
** Discuss two collaboration projects: Shape Analysis of Caudate Nucleus and Fiber Based Diffusion Analysis.
* '''[[Engineering:Core_3_Programming_Week#1_Feedback|9/2005. DBP and Engineering Feedback Session]]'''
** Suggested implementation of tests for consistency of results (segmentation, registration, etc..) as the software evolves
** Gave some feedback on the slicer usage to other DBPs
* '''[[Dissemination:Workshop_May_26-27_2005|5/2005 User training Seminar at Dartmouth]]'''
** Gave some presentations on useage of slicer by the lab
** Hands on help during the training sessions
* '''3/2005 Visit from Ross Whitaker and Tom Fletcher from UofU.'''
** Presentation of non linear statistics for tensors by Tom Fletcher.
** Possible collaboration on comparing new and old anisotropy measures in the context of Schizophrenia.
* '''2/2005 Utah AHM.'''
** prepared and presented the data.
** participated in the DTI engineering workshop.
* '''12/2004 Software development meeting.'''
** Tina Kapur & Steve Pieper: Intro on the NAMIC project.
** Presentations of existing software from the different institutes:
*** UNC, Martin Styner: Presentation of existing ITK tools created at UNC. Some interesting software for DTI processing.
*** MIT, Lauren O'Donnell: Presentation of MIT algorithms. Polina Golland's shape analysis methods (classifier based on DT and statistical classifier). Kilian Pohl's Atlas Based EM segmentation which we are already using.
*** Gtech, Delphine Nain: Presentation of GTech tools. Surface Evolution segmentation tool, Fast marching implementation in Slicer. Anisotropic image smoothing already in slicer. Future will be shape analysis (wavelets), stochastic curve evolution.
*** UCLA: presentation of LONI, a pipeline building tool. Release date for beta testing is 5/2005.
*** MGH, Dave Tuch: Presentation of the tools for Diffusion Imaging at MGH. Two major contributions: Q-ball, a high angular resolution imaging process; Sub parcellation of the thalamus based on DTI images.
*** SPL: Presentation of the slicer by Steve Pieper and CF Westin. The DTI module is offering a number of very interesting properties. The schiz group is alpha testing it.
** Presentations on Software Development within the NAMIC framework:
*** Luis Ibanez: Talk on Good Software Development Practices.
*** Insight Toolkit (ITK) tutorial by Luis Ibanez. Highly templated modular library with many implemented image processing algorithms.
*** Raul Estepar: How to integrate ITK classes in VTK.
*** Steve Pieper: How to build and write code for the slicer.
* '''11/2004 Introduced project to the Schizophrenia lab personnel'''
** RAs will be involved in collecting data and update site on patient recruitment
** Sylvain Bouix will be the point person for Core 3.1 @ Harvard
* '''10/2004 Kickoff meeting'''
** [[https://na-mic.org/w/images/7/76/2004-09-25-RK-NAMIC.ppt NA-MIC Introductory Slides]].
** [[Kickoff:Core3.1breakout-GG_Specific_aims_of_3.1_core]].

2009 Winter Project Week Interactive 3D Widgets In Slicer3

2017-07-10T18:27:03Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:widgets_storyboard_slicer3.png|thumb|320px|Concept screenshot of widgets in slicer3]]
|}

__NOTOC__

===Key Investigators===
* Kitware: Karthik Krishnan, Will Schroeder
* BWH: Nicole Aucoin

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
Integrate existing 3D widgets (and develop new widgets) from VTK into Slicer. Over the last two years VTK has included several new widgets, which can potentially benefit Slicer3.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
A brief overview of the widgets in VTK can be found here [https://na-mic.org/w/images/b/bb/VTKWidgets2.ppt]. Relevant widgets for Slicer include:
* Measurement widgets
** Distance widget (2D and 3D)
** Angle widget (2D and 3D)
** BiDimensional widget (2D)
** Seed/Fiducial widget
* Segmentation widgets
** Livewire widget (2D)
* ROI widgets
** Contour widget
** Box widget
* Image Manipulation widgets
** Affine widget
* Registration widgets
** Checkerboard widget
* Annotation widgets
** Leader widget
** Balloon widget
* Add interaction cues
** Some widgets (e.g., implicit plane widget) should modify the cursor, or change appearance, when the mouse is moved over interactive handles.

The plan is to include a subset of these widgets in Slicer3, specifically the 4 measurement widgets and the livewire widget.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

* Write a 3D representation for the Distance widget. --- Done
* Write a 3D representaiton for the angle widget. --- Done
* Rewrite the existing fiducial widget and replace it with vtkSeedWidget
** This involves generalizing vtkHandleWidget to support arbitrary polygonal shapes since Slicer3 has several geometrical representations for seeds (2D: dash, cross, thickcross, triangle, square, circle, diamond, arrow, arrow), (3D: Sphere, Diamond)
** Generalized representation written (vtkPolygonalHandleRepresentation3D). --- Done
* Livewire widget --- Exists

</div>

<br style="clear: both;" />

</div>

AHM 2010 Tutorial Contest - CoronaryArteriesCenterlinesVMTK

2017-07-10T18:27:03Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

== Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools ==
<gallery>
File:VMTKCenterlines Tutorial first slide.png|
Image:Vmtkcloseupvoronoicenterlinewithreference.png|Lumen Segmentation, Voronoi diagram and centerline of a coronary artery.
Image:Vmtkafterevolutionanim.gif|An over-layed label map showing the segmentation in 2D.
</gallery>

=== Objective ===
Guiding you step by step through the process of centerline extraction of Coronary Arteries in a cardiac blood-pool MRI using VMTK based Tools.

=== Downloads ===
# [https://na-mic.org/w/images/4/40/TutorialVMTKCoronariesCenterlinesMRI_Winter2010AHM.pdf Tutorial Slides]
# [https://na-mic.org/w/images/a/aa/TutorialVMTKCoronariesCenterlinesMRI_Data_Winter2010AHM.zip Tutorial Data]

Summer2013 Training Tutorials Update

2017-07-10T18:27:02Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

Approach:
#Step 1 is update the tutorials to a recent version of Slicer: Slicer4.2.2013-06-24 (r22121)
#Step 2 is to report any bugs to the Mantis Bug tracker
#Step 3 is to implement self-tests for the tutorials.

*Completed
**[[Media:3DDataLoadingandVisualization_06-21-2013.pdf|3D Data Loading and Visualization]]
**[[Media:3D_DICOM_07-25-2013.pdf‎|3D DICOM Tutorial]]
**[[Media:Slicer4minute_07-18-2013.pdf|Slicer4Minute Tutorial]]
**[[Media:SlicerWelcome_Tutorial_07-19-2013.pdf|SlicerWelcome Tutorial]]
**[[Media:WhiteMatterExplorationTutorial_08-29-2013.pdf|WhiteMatterExplorationNeurosurgicalPlanning Tutorial]]

*In progress
**Tokyo tutorial: [https://na-mic.org/w/images/9/9f/3DVisualizationDICOM_RadiologyApplications_SoniaPujol_JRC2013.pdf |Dicom tutorial Tokyo 2013]
**[[Media:DiffusionMRIanalysis_Tutorial_08-05-2013.pdf|Diffusion Tensor Imaging Tutorial]]

* Datasets:
**[[Media:3DVisualizationData.zip|3D Data Loading and Visualization Dataset]]
**[[media:3Dvisualization_DICOM_Data-RSNA2012-Part1.zip|3D Visualization DICOM-RSNA Dataset]]
**[[Media:Slicer4minute.zip|Slicer4Minute Dataset]]
**[[Media:WhiteMatterExplorationData.zip|WhiteMatterExplorationNeurosurgicalPlanning Dataset]]
**[[media:Dcmtk-db.zip|DCMTK Database Folder Dataset (Tokyo)]]
**[[Media:DiffusionMRI_tutorialData.zip|Diffusion MRI Analysis Dataset]]

*Weekly Update of Work Accomplished
**August 1-7: Parth and Matt worked on the Diffusion MRI Analysis tutorial. We were only able to finish 75% of the tutorial because we ran into a memory issue when trying to conduct glyphs and tractography. This issue has been reported to the bug tractor and the issue is currently being solved. As of now, the tutorial still remains incomplete until the new nightly 32 bit installer is updated.
**August 12-16: During this week, Parth updated the issues with the current updated tutorials on the wiki page that Chrystel and Yuzheng had reported to [https://www.slicer.org/wiki/Documentation/Labs/TutorialTesting/4.3-Release]. Parth created mini clips of fMRI images using a screen recording application named Jing. He inserted text in the mini video clips and edited the video using a video editing software named Camtasia.
**August 19-23: Parth is working on surveys created by Sonia Pujol and running tests to see how accurate they are working. Also, Parth and Matt are editing the images in the survey by applying text with the team numbers using a software named GIMP. Parth updated the 101 wiki page with the 2013 Summer Contest Tutorials.
**August 26-30: During this week, Parth and Matt edited more images for the surveys using GIMP. Also, they took new screenshots for the Neurosurgical Planning Tutorial since the GUI has changed for the newly updated Slicer. The latest version of the Neurosurgical Planning Tutorial is posted above in "completed" tutorials. Parth and Matt will finish working on the Diffusion MRI Analysis tutorial.

Dec-2009-SlicerAIMBrainstorming

2017-07-10T18:27:02Z

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

== Current Status of Annotation and MarkUp Modules ==
* Summary of [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] that currently exists in annotation tools of large software vendors (created by Kilian after RSNA visit)
* Suggested design of [[Media:AMI-GUI-Design.ppt | GUI ]] and [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] structure
* [[ Projects:ARRA:SlicerAM | Progress report ]]

== Logistics ==
*Confirmed date: Wednesday and Thursday, '''December 16 (1-5pm) and 17 (9am-1pm), 2009'''
*Location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room
*Tcon Number: (218) 862-1115 Conference ID 348265#

== Goals ==
The purpose of this meeting is to coordinate the efforts of the [[Projects:ARRA:SlicerAM|Markup and Annotation project]] with the development of the fiducial, measurement model, ROI, and LabelDiameterEstimation. Important questions to consider at the meeting are
* What are similarities and differences between the modules ?
* How should we proceed with the development of the three modules ? Should they be totally separate, share a basic framework, or be combined to one ?
* What should be the overall design of the GUI for the three modules?
* What functionality do we need ? What are specific user scenarios we need to address ?
* What Qt functionality do we need in Slicer ?
* Which interaction are inherently 3D and which are best performed on slice views? How to reconcile these in the most logical and productive way.

== Schedule ==
* Wednesday - Dec 16th
** 1:00 Intro: What is the vision of the AIM project (Kilian)
*** A simple user interface such as ClearCanvas
*** A [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] structure that consolidates several existing structures. Furthermore, the structure should be flexible enough to extend to new functionality and work flows
** 1:15 Demo's
*** Measurement and Fiducial (Nicole) [[Media:Annotation_Brainstorming_Mini_Retreat.ppt‎ | PPT]]
*** ROI and LabelDiameterEstimation (Andriy, Alex)
*** MarkUp and Annotation (Kilian)
** 2:15 Annotation and markup widgets in VTK (Karthik)
*** Currently available Annotation and Markup widgets in VTK [http://wiki.na-mic.org/Wiki/images/1/11/VTK-AnnotationAndMarkupWidgets.pdf link].
*** VTK's 3D Widgets in general [https://na-mic.org/w/images/b/bb/VTKWidgets2.ppt link]
*** VTK widget gallery [http://www.vtk.org/Wiki/VTK_Widget_Examples link]
*** Tcon: 1 800 704 9804, code: 718324
*** [http://connect.acrobat.com/KitwareDemo Presentation] via Adobe Connection
** 2:35 Current State of Qt in Slicer [http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt presentation]. Julien Finet and Jean-Christophe Fillion-Robin.
*** Tcon: 1 800 704 9804, code: 718324
*** [http://connect.acrobat.com/KitwareDemo Presentation] via Adobe Connection
** 2:55 Break
** 3:15 Discussion Session:Integrate Modules Into One Coherent User Experience
*** Design overall architecture of the three module - possible [[http://wiki.na-mic.org/Wiki/images/d/d5/AMI_MRMLMarkUpNode.ppt MRML ]] structure
*** Create a feature list based on [[ Projects:ARRA:SlicerAM_RSNA09Report | functionality ]] of annotation capabilities of major vendors
*** Create a description of user-experience and target look & feel (current [[Media:AMI-GUI-Design.ppt | design ]])
** 5:00 Happy hour
* Thursday - Dec 17th
** 9:00 Programming
** 12:00 Final Wrap Up over Lunch
** 1:00 Fly home

== Attendance ==
Open to all self-declared Slicer developers:
#Kilian Pohl
#Steve Pieper (by phone on Wednesday afternoon only)
#Nicole Aucoin
#Andriy Fedorov (Wed only)
#Ron Kikinis (Wed only)
#Wendy Plesniak
#Alex Yarmarkovich (probably Wed)
#Julien Finet
#Karthik Krishnan
#Michael Halle

== References ==

* [http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelDiameterEstimation-Documentation-3.5 Slicer LabelDiameterEstimation extension documentation]
* [http://wiki.slicer.org/slicerWiki/index.php/Modules:ExractSubvolumeROI-Documentation-3.5 Slicer ExtractSubvolumeROI module documentation]