https://www.na-mic.org/w/api.php?action=feedcontributions&user=Andy&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T11:29:08ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=User:Andy&diff=14031User:Andy2007-08-01T16:05:53Z<p>Andy: </p>
<hr />
<div>{|<br />
|- valign="top"<br />
|<br />
[[Image:AndyCedilnik.jpg|AndyCedilnik.jpg]]<br />
|<br />
'''Andy Cedilnik'''<br /><br />
<br />
Senior Systems Software Engineer,<br />Tivo Inc.<br />
|}<br />
<br />
<br /> Look at [http://www.cmake.org/Wiki/User_talk:Andy my talk page].<br />
<br />
== Dart 2 Submissions ==<br />
<br />
To submit to dart2:<br />
<br />
SET (NIGHTLY_START_TIME "21:00:00 EDT")<br />
SET (DROP_METHOD "xmlrpc")<br />
SET (DROP_SITE "http://www.na-mic.org:8081/")<br />
SET (DROP_LOCATION "Insight")<br />
SET (COMPRESS_SUBMISSION ON)<br />
<br />
<br />[[User:Andy#Dart_2_Submissions|User:Andy#Dart_2_Submissions]]<br />
<br />
=== Dart 2 - Ajax suggestions ===<br />
<br />
* Ajax patterns: http://www.ajaxpatterns.org/<br />
* Ajax Blog: http://www.ajaxian.com/<br />
* Ajax Library from Yahoo http://developer.yahoo.net/yui/<br />
* Ajax Patterns from Yahoo http://developer.yahoo.net/ypatterns/<br />
* Google Ajax http://code.google.com/webtoolkit/<br />
<br />
== Subversion Issues ==<br />
<br />
* [[Subversion_Input_Filters|Subversion Input Filters]]<br />
* Add information about ASCII on Windows<br />
<br />
== Math Test ==<br />
<br />
<math>ff_{22}=\sum_{n=0}^\infty \part{Z}\frac{x^n}{n!}\int_{x_0}^{x_n}\cos{\theta/2}</math></div>Andyhttps://www.na-mic.org/w/index.php?title=File:DSC00838.JPG&diff=9131File:DSC00838.JPG2007-04-15T20:14:18Z<p>Andy: </p>
<hr />
<div></div>Andyhttps://www.na-mic.org/w/index.php?title=Slicer:User_Workshop_Jan26&diff=8966Slicer:User Workshop Jan262007-04-10T16:46:05Z<p>Andy: Reverted edits by Sd4Uxp (Talk); changed back to last version by Andy</p>
<hr />
<div>'''Using 3D Slicer for Medical Image Analysis & Visualization'''<br />
<br />
----<br />
<br />
== Logistics ==<br />
<br />
January 26, 2005<br />
<br />
8am to 3.45pm<br />
<br />
1249 Boylston St. Boston, Room 245, 2nd Fl. conference room (SPL) [http://splweb.bwh.harvard.edu:8000/pages/directions/1249Boylston/Boylston-facility.html Directions]<br />
<br />
(Lunch and refreshments provided)<br />
<br />
== Registration ==<br />
<br />
* Registration is required, deadline is January 21st.*<br />
** *Fee is $50 for all registrants.*<br />
<br />
<br /> To register visit: www.hcnr.med.harvard.edu/courses.php [http://www.hcnr.med.harvard.edu/courses.php [1]]<br />
<br />
<br /><br />
<br />
== Overview: ==<br />
<br />
This workshop offers day-long instruction on using 3D Slicer software, hands-on overview of its basic use, and demonstrations of advanced features. Participants will become familiar with the 3D Slicer's extensive functionality, and should depart with the ability to apply its suite of tools in their own work.<br />
<br />
* Background<br />
<br />
3D Slicer is a freely-available and open source package for medical imaging analysis; its development began at the MIT Artificial Intelligence Laboratory and the Surgical Planning Laboratory at Brigham and Women's Hospital. 3D Slicer (or simply "Slicer") uniquely integrates several facets of image-guided medicine into a single environment. It provides capabilities for automatic registration (aligning data sets), semi-automatic segmentation (extracting structures such as vessels and tumors from the data), generation of 3D surface models, 3D visualization, and quantitative analysis (measuring distances, angles, surface areas, and volumes) of various medical scans. Slicer is available for download both in source code format for developers who wish to add custom features, and in pre-compiled binaries for Linux, Windows, and Sun Solaris platforms (for users familiar with a point-and-click menu environment). Slicer has a broad base of users and developers (with over 4000 downloads worldwide as of early 2004) and is actively used as a research tool in diagnostic and interventional clinical settings worldwide.<br />
<br />
Participants should be comfortable with the use of GUI-based software tools, familiar with medical imaging applications, and have an interest in applying image analysis or visualization in their work.<br />
<br />
== Schedule ==<br />
<br />
8:00 - 9:00 Verify Slicer Installations, Coffee<br />
<br />
9:00 - 9:30 Introduction (Sandy Wells)<br />
<br />
9:30 - 10:30 Slicer Basics - Loading Data, Viewing, UI Overview (Steve Pieper)<br />
<br />
10:30 - 10:45 Break<br />
<br />
10:45 - 12:00 Manual and Semi-Automatic Segmentation (Steve Pieper)<br />
<br />
12:00 - 1:00 Lunch<br />
<br />
1:00 - 1:35 DTI Processing (Sandy Wells and Steve Pieper)<br />
<br />
1:35 - 2:10 Statistical Segmentation (Sandy Wells and Steve Pieper)<br />
<br />
2:10 - 2:25 Break<br />
<br />
2:25 - 3:00 Registration (Sandy Wells and Steve Pieper)<br />
<br />
3:00 - 3:45 fMRI Processing (Sandy Wells and Wendy Plesniak)<br />
<br />
<br /><br />
<br />
== Computer Requirements ==<br />
<br />
Participants must bring their own laptop, configured as noted below, and must have Slicer preinstalled. The simplest installation involves downloading precompiled binaries appropriate for your platform. To get the software, visit: www.slicer.org http://www.slicer.org<br />
<br />
* speed: at least 500 MHz<br />
* memory: at least 500 MB<br />
* graphics: ATI, nVIDIA, or other 3D acceleration hardware<br />
* OpenGL (typically pre-installed with system)<br />
* platform: Windows or Red Hat Linux 7.3<br />
* Disk Space: 11.5 MB for installer, which expands to 45 MB<br />
* + 37 MB for tutorial data set<br />
<br />
<br /><br />
<br />
== Last-minute Updates ==<br />
<br />
For participants bringing a Windows laptop, please download an updated Slicer2.4 binary from: https://share.spl.harvard.edu/share/birn/public/software/slicer2.4/slicer2.4-win32-2005-01-24.zip<br />
<br />
In addition to the standard tutorial dataset you've already downloaded, please also download and unzip the following two additional tutorial datasets containing structural and functional MRI volumes (together, they will require about 200MB): ftp://ftp.fil.ion.ucl.ac.uk/spm/data/MoAEpilot/MoAEpilot.tgz ftp://ftp.fil.ion.ucl.ac.uk/spm/data/MoAEpilot/MoAEpilot_snrf.tgz<br />
<br />
* Additional data for registration examples is available here: [[Media:Mrt-images.zip| MRT Data]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Main_Page&diff=8148Main Page2007-03-08T19:36:25Z<p>Andy: Reverted edits by Fggfgfgffg (Talk); changed back to last version by Andy</p>
<hr />
<div>{{Editing Guide}}<br />
== '''Welcome to the NA-MIC Wiki!''' ==<br />
<br />
[[Image:NIH_Logo.png|[[Image:NIH_Logo.png|Image:NIH_Logo.png]]]][[Image:Dhhs_logo.png|[[Image:Dhhs_logo.png|Image:Dhhs_logo.png]]]]<br />
<br />
''Welcome!'' This system is meant to encourage quick and efficient communication among the participating investigators and the interested users. If you are interested in the BIG picture or need an introduction to our project please go to our main web page [http://www.na-mic.org/ NA-MIC]. To get an idea of the ongoing activities in this project, follow the links in the Navigation box on the left side of this page: Cores and Projects contains information about the activities in the individual NA-MIC cores as well as cross-NCBC activities, the Events pages contains information about upcoming and past NA-MIC events including teleconferences, and the Resources pages contain information about NA-MIC software.<br />
<br />
=== [[Events|Events]] ===<br />
<br />
A list of all our past and upcoming events.<br />
<br />
=== [[NA-MIC_Collaborations|NA-MIC Collaborations]] ===<br />
<br />
This is a list of our internal and external collaborative projects.<br />
<br />
=== [[SoftwareInventory|NA-MIC kit]] ===<br />
<br />
The NA-MIC Kit consists of all software that is being made available under the NA-MIC project, including [[Slicer3|Slicer3]].<br />
<br />
[http://lwn.net/Articles/188693/ '''Why the KDE project switched to CMake''']. One of the largest FOSS efforts adopts a component of the NA-MIC kit for the next major release.<br />
<br />
=== [[Engineering:Programming_Events|Results from Programming Events]] ===<br />
<br />
These are the results from our programming events held in 2005, 2006, and 2007.<br />
<br />
<br /><br />
<br />
----<br />
<br />
<br /><br />
<br />
=== Pages for Affiliated Research Teams and Organizations ===<br />
<br />
==== [[NIH-Page|NIH Page]] ====<br />
<br />
* This page contains useful information provided by our NIH officers.<br />
<br />
==== [[Mbirn:Main_Page|Morphometry BIRN Page (to Wiki pages)]] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Morphometry Biomedical Informatics Research Network (to web pages)] Project, a close NA-MIC collaboration.<br />
<br />
==== [[FBIRN:Main_Page|Function BIRN Page (to Wiki pages)]] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Function Biomedical Informatics Research Network (to web pages)] Project, a close NA-MIC collaboration.<br />
<br />
==== [http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/WebHome Mouse BIRN Wiki] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Mouse Biomedical Informatics Research Network (to web pages)] Project, a BIRN testbed examining mouse models of neurodegenerative disease.<br />
<br />
==== [[NAC:Main_Page|Neuroimage Analysis Center (to Wiki pages)]] ====<br />
<br />
* This page contains information about the Neuroimage Analysis Center (NAC) Project.<br />
<br />
==== [[NCIGT:Main_Page|NCIGT - National Center for Image-Guided Therapy]] ====<br />
<br />
* This page contains information about the [http://www.ncigt.org National Center for Image-Guided Therapy] Project, a close NA-MIC collaboration.<br />
* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT This page] contains information about '''Slicer for IGT''' co-sponsored by NCIGT and NA-MIC.<br />
<br />
==== [[CIMIT:Main_Page|CIMIT (to Wiki pages)]] ====<br />
<br />
* This page contains information about CIMIT.</div>Andyhttps://www.na-mic.org/w/index.php?title=User:Andy&diff=8140User:Andy2007-03-07T16:35:36Z<p>Andy: /* Test of Bogus links */</p>
<hr />
<div>{|<br />
|- valign="top"<br />
|<br />
[[Image:AndyCedilnik.jpg|AndyCedilnik.jpg]]<br />
|<br />
'''Andy Cedilnik'''<br /><br />
<br />
Senior Software Engineer,<br /> Kitware Inc.<br />http://www.kitware.com/profile/team/cedilnik.html<br />
|}<br />
<br />
<br /> Look at [http://www.cmake.org/Wiki/User_talk:Andy my talk page].<br />
<br />
== Dart 2 Submissions ==<br />
<br />
To submit to dart2:<br />
<br />
SET (NIGHTLY_START_TIME "21:00:00 EDT")<br />
SET (DROP_METHOD "xmlrpc")<br />
SET (DROP_SITE "http://www.na-mic.org:8081/")<br />
SET (DROP_LOCATION "Insight")<br />
SET (COMPRESS_SUBMISSION ON)<br />
<br />
<br />[[User:Andy#Dart_2_Submissions|User:Andy#Dart_2_Submissions]]<br />
<br />
=== Dart 2 - Ajax suggestions ===<br />
<br />
* Ajax patterns: http://www.ajaxpatterns.org/<br />
* Ajax Blog: http://www.ajaxian.com/<br />
* Ajax Library from Yahoo http://developer.yahoo.net/yui/<br />
* Ajax Patterns from Yahoo http://developer.yahoo.net/ypatterns/<br />
* Google Ajax http://code.google.com/webtoolkit/<br />
<br />
== Subversion Issues ==<br />
<br />
* [[Subversion_Input_Filters|Subversion Input Filters]]<br />
* Add information about ASCII on Windows<br />
<br />
== Math Test ==<br />
<br />
<math>ff_{22}=\sum_{n=0}^\infty \part{Z}\frac{x^n}{n!}\int_{x_0}^{x_n}\cos{\theta/2}</math><br />
<br />
== Template Test ==<br />
<br />
This is a test template.<br />
<br />
== Graph Test ==<br />
<br />
=== Dependency Graph ===<br />
<br />
[[Image:0c186a896319620a6ac74ade6b72f603.png]]<br />
<br />
== Test of Bogus links ==<br />
<br />
www.cmake.orG<br />
<br />
http://www.na-mic.org<br />
<br />
http://www.cmake.org<br />
<br />
http://www.kitware.com<br />
<br />
http://www.volview.com<br />
<br />
http://www.csail.mit.edu<br />
<br />
http://x0.org<br />
<br />
https://kitware.com<br />
<br />
http://legoandy.com<br />
<br />
These links should work<br />
<br />
www.kitware.com</div>Andyhttps://www.na-mic.org/w/index.php?title=User:Andy&diff=8139User:Andy2007-03-07T16:33:38Z<p>Andy: /* Test of Bogus links */</p>
<hr />
<div>{|<br />
|- valign="top"<br />
|<br />
[[Image:AndyCedilnik.jpg|AndyCedilnik.jpg]]<br />
|<br />
'''Andy Cedilnik'''<br /><br />
<br />
Senior Software Engineer,<br /> Kitware Inc.<br />http://www.kitware.com/profile/team/cedilnik.html<br />
|}<br />
<br />
<br /> Look at [http://www.cmake.org/Wiki/User_talk:Andy my talk page].<br />
<br />
== Dart 2 Submissions ==<br />
<br />
To submit to dart2:<br />
<br />
SET (NIGHTLY_START_TIME "21:00:00 EDT")<br />
SET (DROP_METHOD "xmlrpc")<br />
SET (DROP_SITE "http://www.na-mic.org:8081/")<br />
SET (DROP_LOCATION "Insight")<br />
SET (COMPRESS_SUBMISSION ON)<br />
<br />
<br />[[User:Andy#Dart_2_Submissions|User:Andy#Dart_2_Submissions]]<br />
<br />
=== Dart 2 - Ajax suggestions ===<br />
<br />
* Ajax patterns: http://www.ajaxpatterns.org/<br />
* Ajax Blog: http://www.ajaxian.com/<br />
* Ajax Library from Yahoo http://developer.yahoo.net/yui/<br />
* Ajax Patterns from Yahoo http://developer.yahoo.net/ypatterns/<br />
* Google Ajax http://code.google.com/webtoolkit/<br />
<br />
== Subversion Issues ==<br />
<br />
* [[Subversion_Input_Filters|Subversion Input Filters]]<br />
* Add information about ASCII on Windows<br />
<br />
== Math Test ==<br />
<br />
<math>ff_{22}=\sum_{n=0}^\infty \part{Z}\frac{x^n}{n!}\int_{x_0}^{x_n}\cos{\theta/2}</math><br />
<br />
== Template Test ==<br />
<br />
This is a test template.<br />
<br />
== Graph Test ==<br />
<br />
=== Dependency Graph ===<br />
<br />
[[Image:0c186a896319620a6ac74ade6b72f603.png]]<br />
<br />
== Test of Bogus links ==<br />
<br />
http://www.na-mic.org<br />
<br />
http://www.cmake.org<br />
<br />
http://www.kitware.com<br />
<br />
http://www.volview.com<br />
<br />
http://www.csail.mit.edu<br />
<br />
http://x0.org<br />
<br />
https://kitware.com<br />
<br />
http://legoandy.com<br />
<br />
These links should work<br />
<br />
www.kitware.com</div>Andyhttps://www.na-mic.org/w/index.php?title=Main_Page&diff=8136Main Page2007-03-07T16:29:03Z<p>Andy: Reverted edits by Fgfggfgf (Talk); changed back to last version by Andy</p>
<hr />
<div>{{Editing Guide}}<br />
== '''Welcome to the NA-MIC Wiki!''' ==<br />
<br />
[[Image:NIH_Logo.png|[[Image:NIH_Logo.png|Image:NIH_Logo.png]]]][[Image:Dhhs_logo.png|[[Image:Dhhs_logo.png|Image:Dhhs_logo.png]]]]<br />
<br />
''Welcome!'' This system is meant to encourage quick and efficient communication among the participating investigators and the interested users. If you are interested in the BIG picture or need an introduction to our project please go to our main web page [http://www.na-mic.org/ NA-MIC]. To get an idea of the ongoing activities in this project, follow the links in the Navigation box on the left side of this page: Cores and Projects contains information about the activities in the individual NA-MIC cores as well as cross-NCBC activities, the Events pages contains information about upcoming and past NA-MIC events including teleconferences, and the Resources pages contain information about NA-MIC software.<br />
<br />
=== [[Events|Events]] ===<br />
<br />
A list of all our past and upcoming events.<br />
<br />
=== [[NA-MIC_Collaborations|NA-MIC Collaborations]] ===<br />
<br />
This is a list of our internal and external collaborative projects.<br />
<br />
=== [[SoftwareInventory|NA-MIC kit]] ===<br />
<br />
The NA-MIC Kit consists of all software that is being made available under the NA-MIC project, including [[Slicer3|Slicer3]].<br />
<br />
[http://lwn.net/Articles/188693/ '''Why the KDE project switched to CMake''']. One of the largest FOSS efforts adopts a component of the NA-MIC kit for the next major release.<br />
<br />
=== [[Engineering:Programming_Events|Results from Programming Events]] ===<br />
<br />
These are the results from our programming events held in 2005, 2006, and 2007.<br />
<br />
<br /><br />
<br />
----<br />
<br />
<br /><br />
<br />
=== Pages for Affiliated Research Teams and Organizations ===<br />
<br />
==== [[NIH-Page|NIH Page]] ====<br />
<br />
* This page contains useful information provided by our NIH officers.<br />
<br />
==== [[Mbirn:Main_Page|Morphometry BIRN Page (to Wiki pages)]] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Morphometry Biomedical Informatics Research Network (to web pages)] Project, a close NA-MIC collaboration.<br />
<br />
==== [[FBIRN:Main_Page|Function BIRN Page (to Wiki pages)]] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Function Biomedical Informatics Research Network (to web pages)] Project, a close NA-MIC collaboration.<br />
<br />
==== [http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/WebHome Mouse BIRN Wiki] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Mouse Biomedical Informatics Research Network (to web pages)] Project, a BIRN testbed examining mouse models of neurodegenerative disease.<br />
<br />
==== [[NAC:Main_Page|Neuroimage Analysis Center (to Wiki pages)]] ====<br />
<br />
* This page contains information about the Neuroimage Analysis Center (NAC) Project.<br />
<br />
==== [[NCIGT:Main_Page|NCIGT - National Center for Image-Guided Therapy]] ====<br />
<br />
* This page contains information about the [http://www.ncigt.org National Center for Image-Guided Therapy] Project, a close NA-MIC collaboration.<br />
* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT This page] contains information about '''Slicer for IGT''' co-sponsored by NCIGT and NA-MIC.<br />
<br />
==== [[CIMIT:Main_Page|CIMIT (to Wiki pages)]] ====<br />
<br />
* This page contains information about CIMIT.</div>Andyhttps://www.na-mic.org/w/index.php?title=Main_Page&diff=8122Main Page2007-03-06T21:17:57Z<p>Andy: Reverted edits by Fggfgff (Talk); changed back to last version by Millerjv</p>
<hr />
<div>{{Editing Guide}}<br />
== '''Welcome to the NA-MIC Wiki!''' ==<br />
<br />
[[Image:NIH_Logo.png|[[Image:NIH_Logo.png|Image:NIH_Logo.png]]]][[Image:Dhhs_logo.png|[[Image:Dhhs_logo.png|Image:Dhhs_logo.png]]]]<br />
<br />
''Welcome!'' This system is meant to encourage quick and efficient communication among the participating investigators and the interested users. If you are interested in the BIG picture or need an introduction to our project please go to our main web page [http://www.na-mic.org/ NA-MIC]. To get an idea of the ongoing activities in this project, follow the links in the Navigation box on the left side of this page: Cores and Projects contains information about the activities in the individual NA-MIC cores as well as cross-NCBC activities, the Events pages contains information about upcoming and past NA-MIC events including teleconferences, and the Resources pages contain information about NA-MIC software.<br />
<br />
=== [[Events|Events]] ===<br />
<br />
A list of all our past and upcoming events.<br />
<br />
=== [[NA-MIC_Collaborations|NA-MIC Collaborations]] ===<br />
<br />
This is a list of our internal and external collaborative projects.<br />
<br />
=== [[SoftwareInventory|NA-MIC kit]] ===<br />
<br />
The NA-MIC Kit consists of all software that is being made available under the NA-MIC project, including [[Slicer3|Slicer3]].<br />
<br />
[http://lwn.net/Articles/188693/ '''Why the KDE project switched to CMake''']. One of the largest FOSS efforts adopts a component of the NA-MIC kit for the next major release.<br />
<br />
=== [[Engineering:Programming_Events|Results from Programming Events]] ===<br />
<br />
These are the results from our programming events held in 2005, 2006, and 2007.<br />
<br />
<br /><br />
<br />
----<br />
<br />
<br /><br />
<br />
=== Pages for Affiliated Research Teams and Organizations ===<br />
<br />
==== [[NIH-Page|NIH Page]] ====<br />
<br />
* This page contains useful information provided by our NIH officers.<br />
<br />
==== [[Mbirn:Main_Page|Morphometry BIRN Page (to Wiki pages)]] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Morphometry Biomedical Informatics Research Network (to web pages)] Project, a close NA-MIC collaboration.<br />
<br />
==== [[FBIRN:Main_Page|Function BIRN Page (to Wiki pages)]] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Function Biomedical Informatics Research Network (to web pages)] Project, a close NA-MIC collaboration.<br />
<br />
==== [http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/WebHome Mouse BIRN Wiki] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Mouse Biomedical Informatics Research Network (to web pages)] Project, a BIRN testbed examining mouse models of neurodegenerative disease.<br />
<br />
==== [[NAC:Main_Page|Neuroimage Analysis Center (to Wiki pages)]] ====<br />
<br />
* This page contains information about the Neuroimage Analysis Center (NAC) Project.<br />
<br />
==== [[NCIGT:Main_Page|NCIGT - National Center for Image-Guided Therapy]] ====<br />
<br />
* This page contains information about the [http://www.ncigt.org National Center for Image-Guided Therapy] Project, a close NA-MIC collaboration.<br />
* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT This page] contains information about '''Slicer for IGT''' co-sponsored by NCIGT and NA-MIC.<br />
<br />
==== [[CIMIT:Main_Page|CIMIT (to Wiki pages)]] ====<br />
<br />
* This page contains information about CIMIT.</div>Andyhttps://www.na-mic.org/w/index.php?title=Main_Page&diff=7896Main Page2007-02-15T14:09:17Z<p>Andy: </p>
<hr />
<div>{{Editing Guide}}<br />
== '''Welcome to the NA-MIC Wiki!''' ==<br />
<br />
[[Image:NIH_Logo.png|[[Image:NIH_Logo.png|Image:NIH_Logo.png]]]][[Image:Dhhs_logo.png|[[Image:Dhhs_logo.png|Image:Dhhs_logo.png]]]]<br />
<br />
''Welcome!'' This system is meant to encourage quick and efficient communication among the participating investigators and the interested users. If you are interested in the BIG picture or need an introduction to our project please go to our main web page [http://www.na-mic.org/ NA-MIC]. To get an idea of the ongoing activities in this project, follow the links in the Navigation box on the left side of this page: Cores and Projects contains information about the activities in the individual NA-MIC cores as well as cross-NCBC activities, the Events pages contains information about upcoming and past NA-MIC events including teleconferences, and the Resources pages contain information about NA-MIC software.<br />
<br />
=== [[Events|Events]] ===<br />
<br />
A list of all our past and upcoming events.<br />
<br />
=== [[NA-MIC_Collaborations|NA-MIC Collaborations]] ===<br />
<br />
This is a list of our internal and external collaborative projects.<br />
<br />
=== [[SoftwareInventory|NA-MIC kit]] ===<br />
<br />
The NA-MIC Kit consists of all software that is being made available under the NA-MIC project, including [[Slicer3|Slicer3]].<br />
<br />
[http://lwn.net/Articles/188693/ '''Why the KDE project switched to CMake''']. One of the largest FOSS efforts adopts a component of the NA-MIC kit for the next major release.<br />
<br />
=== [[Engineering:Programming_Events|Results from Programming Events]] ===<br />
<br />
These are the results from our programming events held in 2005 and 2006 so far.<br />
<br />
<br /><br />
<br />
----<br />
<br />
<br /><br />
<br />
=== Pages for Affiliated Research Teams and Organizations ===<br />
<br />
==== [[NIH-Page|NIH Page]] ====<br />
<br />
* This page contains useful information provided by our NIH officers.<br />
<br />
==== [[Mbirn:Main_Page|Morphometry BIRN Page (to Wiki pages)]] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Morphometry Biomedical Informatics Research Network (to web pages)] Project, a close NA-MIC collaboration.<br />
<br />
==== [[FBIRN:Main_Page|Function BIRN Page (to Wiki pages)]] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Function Biomedical Informatics Research Network (to web pages)] Project, a close NA-MIC collaboration.<br />
<br />
==== [http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/WebHome Mouse BIRN Wiki] ====<br />
<br />
* This page contains information about the [http://www.nbirn.net Mouse Biomedical Informatics Research Network (to web pages)] Project, a BIRN testbed examining mouse models of neurodegenerative disease.<br />
<br />
==== [[NAC:Main_Page|Neuroimage Analysis Center (to Wiki pages)]] ====<br />
<br />
* This page contains information about the Neuroimage Analysis Center (NAC) Project.<br />
<br />
==== [[NCIGT:Main_Page|NCIGT - National Center for Image-Guided Therapy]] ====<br />
<br />
* This page contains information about the [http://www.ncigt.org National Center for Image-Guided Therapy] Project, a close NA-MIC collaboration.<br />
* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT This page] contains information about '''Slicer for IGT''' co-sponsored by NCIGT and NA-MIC.<br />
<br />
==== [[CIMIT:Main_Page|CIMIT (to Wiki pages)]] ====<br />
<br />
* This page contains information about CIMIT.</div>Andyhttps://www.na-mic.org/w/index.php?title=Template:Editing_Guide&diff=7895Template:Editing Guide2007-02-15T14:08:29Z<p>Andy: </p>
<hr />
<div>{| class="toccolours" align="right"<br />
! | Editing Guide<br />
|-<br />
|<br />
* [[Editing_Guide:Getting_Started|Getting Started]]<br />
* [[Editing_Guide:Edit_Existing_Page|Edit Existing Page]]<br />
* [[Editing_Guide:Text_Formatting|Text Formatting]]<br />
* [[Editing_Guide:TOCs_and_Headers|TOCs and Headers]]<br />
* [[Editing_Guide:Links|Links]]<br />
* [[Editing_Guide:Add_New_Page|Add New Page/Link]]<br />
* [[Editing_Guide:Uploading_Documents_and_Images|Uploading Documents and<br />
Images]]<br />
|}</div>Andyhttps://www.na-mic.org/w/index.php?title=Special:Badtitle/NS100:Gallery&diff=7797Special:Badtitle/NS100:Gallery2007-02-07T18:45:10Z<p>Andy: </p>
<hr />
<div>{{Projects/NAMICWeb}}<br />
=='''Image Gallery'''==<br />
<br />
[[Image:park.png|thumb|500px|left|Upper left panel displays fiber tractography combined with cortical thickness map obtained with Free Surfer. Upper right panel demonstrates a sagittal cross-sectional view of brain parenchyma segmented into white and gray matter combined with fiber tractography map. Lower left figure shows a coronal cross-sectional view of automatic parcellation of white matter overplayed with the gray matter surface. Lower right figure shows the parcellation of gray matter surface and corresponding white matter fibers.]]<br />
<br />
<br clear="all" /><br />
<br />
<br />
[[Image:gerig.png|thumb|500px|left| Visualization of variation in ventricle volume for pairs of subjects (MZ – monozygotic twins, DS – monozygotic twins discordant for schizophrenia, DZ – dizygotic twins, NR – nonrelated pairs). The distances are color-coded to show absolute differences between 2 and 8mm. The figures illustrate decreasing shape similarity MZ = DS < DZ < NR. Healthy MZ are not significantly different from MZ discordant for schizophrenia (DS).]]<br />
<br />
<br clear="all" /><br />
<br />
<br />
[[Image:mgh.png|thumb|500px|left| DTI fractional anisotropy (FA) map on computationally inflated cortical surface. The cortical surface FA map indicates the microstructural integrity of the white matter 2mm subcortical to the white matter-gray matter interface.]]<br />
<br />
<br clear="all" /><br />
<br />
[[Image:mit.png|thumb|500px|left| Principal deformation for the right hippocampus for normal controls (top) and schizophrenia patients (bottom). Four views (front, lateral, back, medial) of each shape are shown. The color indicates the direction and the magnitude of the deformation, changing from blue (inwards) to green (no deformation) to red (outwards).]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Special:Badtitle/NS100:Gallery&diff=7796Special:Badtitle/NS100:Gallery2007-02-07T18:26:57Z<p>Andy: </p>
<hr />
<div>{{Projects/NAMICWeb}}<br />
=='''Image Gallery'''==<br />
<br />
[[Image:park.png|thumb|400px|left|Upper left panel displays fiber tractography combined with cortical thickness map obtained with Free Surfer. Upper right panel demonstrates a sagittal cross-sectional view of brain parenchyma segmented into white and gray matter combined with fiber tractography map. Lower left figure shows a coronal cross-sectional view of automatic parcellation of white matter overplayed with the gray matter surface. Lower right figure shows the parcellation of gray matter surface and corresponding white matter fibers.]]<br />
<br />
<br clear="all" /><br />
<br />
<br />
[[Image:gerig.png|thumb|400px|left| Visualization of variation in ventricle volume for pairs of subjects (MZ – monozygotic twins, DS – monozygotic twins discordant for schizophrenia, DZ – dizygotic twins, NR – nonrelated pairs). The distances are color-coded to show absolute differences between 2 and 8mm. The figures illustrate decreasing shape similarity MZ = DS < DZ < NR. Healthy MZ are not significantly different from MZ discordant for schizophrenia (DS).]]<br />
<br />
<br clear="all" /><br />
<br />
<br />
[[Image:mgh.png|thumb|400px|left| DTI fractional anisotropy (FA) map on computationally inflated cortical surface. The cortical surface FA map indicates the microstructural integrity of the white matter 2mm subcortical to the white matter-gray matter interface.]]<br />
<br />
<br clear="all" /><br />
<br />
[[Image:mit.png|thumb|400px|left| Principal deformation for the right hippocampus for normal controls (top) and schizophrenia patients (bottom). Four views (front, lateral, back, medial) of each shape are shown. The color indicates the direction and the magnitude of the deformation, changing from blue (inwards) to green (no deformation) to red (outwards).]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Projects/NAMICWeb&diff=7541Projects/NAMICWeb2007-01-31T14:54:36Z<p>Andy: Redirecting to Projects/NAMICWeb:Main Page</p>
<hr />
<div>#REDIRECT [[Projects/NAMICWeb:Main Page]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Projects/NAMICWeb&diff=7442Projects/NAMICWeb2007-01-30T20:07:33Z<p>Andy: </p>
<hr />
<div></div>Andyhttps://www.na-mic.org/w/index.php?title=Special:Badtitle/NS100:Main_Page&diff=7441Special:Badtitle/NS100:Main Page2007-01-30T20:07:25Z<p>Andy: </p>
<hr />
<div>The National Alliance for Medical Imaging Computing (NA-MIC) is a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who develop computational tools for the analysis and visualization of medical image data. The purpose of the center is to provide the infrastructure and environment for the development of computational algorithms and open source technologies, and then oversee the training and dissemination of these tools to the medical research community. This world-class software and development environment serves as a foundation for accelerating the development and deployment of computational tools that are readily accessible to the medical research community. The team combines cutting-edge computer vision research (to create medical imaging analysis algorithms) with state of the art software engineering techniques (based on "extreme" programming techniques in a distributed, open-source environment) to enable computational examination of both basic neurosience and neurological disorders. In developing this infrastructure resource, the team will significantly expand upon proven open systems technology and platforms.<br />
<br />
The driving biological projects will come initially from the study of schizophrenia, but the methods will be applicable to many other diseases. The computational tools and open systems technologies and platforms developed by NA-MIC will initially be used to study anatomical structures and connectivity patterns in the brain, derangements of which have long been thought to play a role in the etiology of schizophrenia. The overall analysis will occur at a range of scales, and will occur across a range of modalities including diffusion MRI, quantitative EGG, and metabolic and receptor PET, but potentially including microscopic, genomic, and other image data. It will apply to image data from individual patients,and to studies executed across large poplulations. The data will be taken from subjects across a wide range of time scales and ultimately apply to a broad range of diseases in a broad range of organs.<br />
<br />
<center>Supported by the National Institutes of Health, Roadmap Initiative for Bioinformatics and Computational Biology.<br />
For more information, see http://www.bisti.nih.gov/ncbc<br />
<br />
Day-to-day organization of NA-MIC is done using http://wiki.na-mic.org.<br />
<br />
Information about collaborating with NA-MIC is available at this information page on our wiki.</center></div>Andyhttps://www.na-mic.org/w/index.php?title=Projects/NAMICWeb&diff=7440Projects/NAMICWeb2007-01-30T20:07:00Z<p>Andy: </p>
<hr />
<div>The National Alliance for Medical Imaging Computing (NA-MIC) is a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who develop computational tools for the analysis and visualization of medical image data. The purpose of the center is to provide the infrastructure and environment for the development of computational algorithms and open source technologies, and then oversee the training and dissemination of these tools to the medical research community. This world-class software and development environment serves as a foundation for accelerating the development and deployment of computational tools that are readily accessible to the medical research community. The team combines cutting-edge computer vision research (to create medical imaging analysis algorithms) with state of the art software engineering techniques (based on "extreme" programming techniques in a distributed, open-source environment) to enable computational examination of both basic neurosience and neurological disorders. In developing this infrastructure resource, the team will significantly expand upon proven open systems technology and platforms.<br />
<br />
The driving biological projects will come initially from the study of schizophrenia, but the methods will be applicable to many other diseases. The computational tools and open systems technologies and platforms developed by NA-MIC will initially be used to study anatomical structures and connectivity patterns in the brain, derangements of which have long been thought to play a role in the etiology of schizophrenia. The overall analysis will occur at a range of scales, and will occur across a range of modalities including diffusion MRI, quantitative EGG, and metabolic and receptor PET, but potentially including microscopic, genomic, and other image data. It will apply to image data from individual patients,and to studies executed across large poplulations. The data will be taken from subjects across a wide range of time scales and ultimately apply to a broad range of diseases in a broad range of organs.<br />
<br />
<center>Supported by the National Institutes of Health, Roadmap Initiative for Bioinformatics and Computational Biology.<br />
For more information, see http://www.bisti.nih.gov/ncbc<br />
<br />
Day-to-day organization of NA-MIC is done using http://wiki.na-mic.org.<br />
<br />
Information about collaborating with NA-MIC is available at this information page on our wiki.</center></div>Andyhttps://www.na-mic.org/w/index.php?title=User:Andy&diff=7073User:Andy2007-01-20T15:24:13Z<p>Andy: /* Math Test */</p>
<hr />
<div>{|<br />
|- valign="top"<br />
|<br />
[[Image:AndyCedilnik.jpg|AndyCedilnik.jpg]]<br />
|<br />
'''Andy Cedilnik'''<br /><br />
<br />
Senior Software Engineer,<br /> Kitware Inc.<br />http://www.kitware.com/profile/team/cedilnik.html<br />
|}<br />
<br />
<br /> Look at [http://www.cmake.org/Wiki/User_talk:Andy my talk page].<br />
<br />
== Dart 2 Submissions ==<br />
<br />
To submit to dart2:<br />
<br />
SET (NIGHTLY_START_TIME "21:00:00 EDT")<br />
SET (DROP_METHOD "xmlrpc")<br />
SET (DROP_SITE "http://www.na-mic.org:8081/")<br />
SET (DROP_LOCATION "Insight")<br />
SET (COMPRESS_SUBMISSION ON)<br />
<br />
<br />[[User:Andy#Dart_2_Submissions|User:Andy#Dart_2_Submissions]]<br />
<br />
=== Dart 2 - Ajax suggestions ===<br />
<br />
* Ajax patterns: http://www.ajaxpatterns.org/<br />
* Ajax Blog: http://www.ajaxian.com/<br />
* Ajax Library from Yahoo http://developer.yahoo.net/yui/<br />
* Ajax Patterns from Yahoo http://developer.yahoo.net/ypatterns/<br />
* Google Ajax http://code.google.com/webtoolkit/<br />
<br />
== Subversion Issues ==<br />
<br />
* [[Subversion_Input_Filters|Subversion Input Filters]]<br />
* Add information about ASCII on Windows<br />
<br />
== Math Test ==<br />
<br />
<math>ff_{22}=\sum_{n=0}^\infty \part{Z}\frac{x^n}{n!}\int_{x_0}^{x_n}\cos{\theta/2}</math><br />
<br />
== Template Test ==<br />
<br />
This is a test template.<br />
<br />
== Graph Test ==<br />
<br />
=== Dependency Graph ===<br />
<br />
[[Image:0c186a896319620a6ac74ade6b72f603.png]]<br />
<br />
== Test of Bogus links ==<br />
<br />
http://www.na-mic.org<br />
<br />
http://www.cmake.org<br />
<br />
http://www.kitware.com<br />
<br />
http://www.volview.com<br />
<br />
http://www.csail.mit.edu<br />
<br />
http://x0.org<br />
<br />
https://kitware.com<br />
<br />
http://legoandy.com<br />
<br />
These links should work</div>Andyhttps://www.na-mic.org/w/index.php?title=Slicer3:Contributing_codes_to_Slicer3&diff=7071Slicer3:Contributing codes to Slicer32007-01-20T15:10:33Z<p>Andy: /* How to obtain Slicer 3 codes from SVN */</p>
<hr />
<div>=Objective=<br />
The goal of this page is to give quick instruction to download Slicer3 from Subversion Control (SVN) server, and contribute codes by committing them back to SVN.<br />
<br />
<br />
== How to obtain Slicer 3 codes from SVN ==<br />
<br />
The Slicer3 svn repository sits in a server at Brigham and Women's Hospital in Boston. You can checkout codes by:<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
<br />
'''You don't need to obtain an account discussed below''' if you don't commit codes back to the sever, but we enthusiastically invite you to do so.<br />
<br />
== How to commit codes ==<br />
<br />
First, fill the form at https://www.kitware.com/Admin/SendPassword.cgi and under Comment type "Request password for NA-MIC Sandbox". '''It says NA-MIC Sandbox since Slicer 3 is part of NA-MIC activity.''' Once you have access to write to SVN, you can work with repository using the following commands:<br />
<br />
To update repository:<br />
<br />
svn update<br />
<br />
To check current state of your edits:<br />
<br />
svn status<br />
<br />
To check the current state compared to the repository:<br />
<br />
svn -u status<br />
<br />
To add new file:<br />
<br />
svn add filename<br />
<br />
followed by (very important):<br />
<br />
svn commit -m"ENH: Adding a new file" filename<br />
<br />
To remove file:<br />
<br />
svn remove filename<br />
<br />
To rename file:<br />
<br />
svn move oldname newname<br />
<br />
If the update results in conflict, fix the file first before commiting it.<br />
<br />
Once you have fixed the file:<br />
<br />
svn resolved <filename><br />
<br />
==GUI tools for eash SVN handling==<br />
It is handy to use GUI tool for SVN. I particulary like a cross-platform GUI tool called [http://rapidsvn.tigris.org/ RapidSVN].</div>Andyhttps://www.na-mic.org/w/index.php?title=Engineering:TCON_05_05_2005&diff=6751Engineering:TCON 05 05 20052007-01-13T14:15:50Z<p>Andy: /* Xiaodong's ITK examples */</p>
<hr />
<div>== Agenda: ==<br />
<br />
* Discussion of Programming Week infrastructure projects. (Steve, Mike)<br />
* itk::SymmetricSecondRankTensor, itk::DiffusionTensor3D. (Luis)<br />
* Dynamic loading of file formats in ITK ([http://www.itk.org/Wiki/Plugin_IO_mechanisms ITK IO Plugins]). (Jim)<br />
* ITK LabelStatisticsImageFilter (now with histograms), LabelMomentsImageFilter (under development). (Jim)<br />
<br />
<br /><br />
<br />
== Attendees: ==<br />
<br />
Rick Avila, Andy Cedilnik, Karthik Krishnan, Luis Ibanez, Tina Kapur, Jim Miller, Ron Kikinis, Steve Pieper, Michael Pan, Jagadeeswaran Rajendiran, Xiaodong tao<br />
<br />
== Meeting Notes: ==<br />
<br />
=== SUN grid for Programmer's Week = ===<br />
<br />
Steve has put in a request to SUN to provide a set of loaner machines (3 dual core, quad processor, 32GB RAM) for the upcoming programmer's week.<br />
<br />
=== Slicer ===<br />
<br />
Steve is looking at using the KW Widgets for the next version of slicer. These widgets provide a cross platform C++ abstraction for widgets in a VTK-like API. Currently the KW Widgets require the CVS version of VTK.<br />
<br />
=== Tensor Images related code from Jeffrey Duda ===<br />
<br />
* http://www.seas.upenn.edu/~jtduda/<br />
* http://www.seas.upenn.edu/~jtduda/vector.html<br />
* http://www.seas.upenn.edu/~jtduda/tensor.html<br />
<br />
The new SymmetricSecondRankTensor class in ITK was largely based on Jeffrey's class, although his page points out that his class was also inspired from<br />
<br />
http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:ITK-DiffusionTensorPixelType:Header<br />
<br />
=== NRRD Header ===<br />
<br />
Suggestions from discussions among Guido Gerig, Dave Tuch, Gordon Kindlmann and others [[NAMIC_Wiki:DTI:Tensor_format|NAMIC_Wiki:DTI:Tensor_format]].<br />
<br />
=== DTI in slicer ===<br />
<br />
VTK class to estimate tensors: [http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/slicer2/Modules/vtkDTMRI/cxx/vtkImageDiffusionTensor.cxx?annotate=1.7&cvsroot=slicer http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/slicer2/Modules/vtkDTMRI/cxx/vtkImageDiffusionTensor.cxx?annotate=1.7&cvsroot=slicer]<br />
<br />
Code that uses slicer's vtkAG class to register tensor values: [http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/slicer2/Modules/vtkDTMRI/tcl/DTMRITensorRegistration.tcl?annotate=1.4&cvsroot=slicer http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/slicer2/Modules/vtkDTMRI/tcl/DTMRITensorRegistration.tcl?annotate=1.4&cvsroot=slicer]<br />
<br />
=== Xiaodong's ITK examples ===<br />
<br />
Xiaodong has written some tensor reconstruction and analysis code using ITK. This code is currently in the sandbox [http://www.na-mic.org/websvn/listing.php?repname=NAMICSandBox&path=%2FNrrdDWITensorReconstruction%2F&rev=0&sc=0 http://www.na-mic.org/websvn/listing.php?repname=NAMICSandBox&path=%2FNrrdDWITensorReconstruction%2F&rev=0&sc=0] This code needs to be packaged into the appropriate ITK filters and examples and use the new ITK tensor classes.<br />
<br />
<br /> The following images show the fractional anisotropy colored by the components of the first principle direction, with red being x-component, green being y-component, and blue being z-component. The lines on the zoom-in view show the projections of the first principle direction (unit vectors) onto the plane. The line and the little brain on top shows the rough location of this axial slice.<br />
<br />
'''Correction'''<nowiki>: The vector field orientations in this image seem incorrect. Please check the orientations.<br />
</nowiki><br />
<br />
[[Image:DTI.png|thumb|right|350px|Fractional Anisotropy of an axial slice of a brain]]<br />
<br />
The vectors shown above have wrong x-components. The reason was that the x component in the gradient directions is flipped. The following is an image showing the FA as well as the principal vectors computed using the CORRECTED gradient direction.<br />
<br />
[[Image:Xiaodong-flip-x.png|thumb|right|350px|DTI example with corrected X gradient component]]<br />
<br />
=== Tensor registration ===<br />
<br />
With tensor support coming into ITK, the topic of tensor registration arose. For ITK to support tensor registration, we need to add an interpolator for tensor images and a metric from comparing two tensors. For comparing two tensors, Jim suggested using<br />
<br />
<span class="texhtml">''t''''r''''a''''c''''e''(''A''<sup> - 1</sup>''B'')</span><br />
<br />
This is simple but not intuitively pleasing because for the scalar case, this becomes a/b instead of a-b which is normally used for comparing scalars. Paulo Mendonca at GE Research suggested using the Frobenius norm of A-B. This translates nicely back to the scalar metric. You can also justify the Frobenius norm if the desired metric is that the difference between the quadratic forms of two tensor be small everywhere<br />
<br />
[[Image:10824166b57b30e7c417386f7da67f34.png|\int (x'Ax - x'Bx)^2 dx = \int (x'(A-B)x)^2 dx]]</div>Andyhttps://www.na-mic.org/w/index.php?title=AHM_2006:ProjectsJointRegistrationSegmentation&diff=6750AHM 2006:ProjectsJointRegistrationSegmentation2007-01-13T14:15:14Z<p>Andy: </p>
<hr />
<div>= Define Joint Registration and Segmentation Framework =<br />
<br />
We are interested in extending the ITK registration framework with our joint atlas registration and MR segmentation algorithm. Our work is described in detail in the progress report [[Progress_Report:Shape_Based_Segmentation_And_Registration|Shape based Segmentation and Registration]]. We have implemented the algorithm in VTK and are planning to release it into the 3D Slicer 2.6.<br />
<br />
[[Image:2006_Programming-JointRegistrationSegmentation.ppt|Image:2006 Programming-JointRegistrationSegmentation.ppt]]<br />
<br />
== Status ==<br />
<br />
* Initial code is in the NAMIC Sandbox under directory /JointRegistrationSegmentation that implements the registration part<br />
** http://www.na-mic.org/svn/NAMICSandBox/JointRegistrationSegmentation/<br />
** Using the customized Metric that Kilian developed http://www.na-mic.org/svn/NAMICSandBox/JointRegistrationSegmentation/itkKullbackLeiblerDivergenceImageToImageMetric.h<br />
<br />
* Possiblity of taking advantage of the BayesianSegmentationModule in order to implement the Expectation Maximization<br />
** http://www.na-mic.org/svn/NAMICSandBox/BayesianSegmentationModule/<br />
<br />
== Pending Tasks ==<br />
<br />
* Update the RecursiveGaussianImageFilter to work on VectorImages<br />
** http://www.itk.org/Insight/Doxygen/html/classitk_1_1GradientRecursiveGaussianImageFilter.html<br />
<br />
* Create a connection between the output of the MRIBiasFieldCorrectionImageFilter and the itkBayesianClassifierInitializationImageFilter in order to recompute the new weight from the corrected intensity values of the input MRI image, and the new GaussianDensity functions<br />
** http://www.itk.org/Insight/Doxygen/html/classitk_1_1MRIBiasFieldCorrectionFilter.html</div>Andyhttps://www.na-mic.org/w/index.php?title=Slicer3:Build_Instructions&diff=6749Slicer3:Build Instructions2007-01-13T14:14:37Z<p>Andy: /* Links */</p>
<hr />
<div>= All-in-one Script to checkout and build Slicer3 =<br />
<br />
There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. Just do the following two commands (see [[Slicer3:Build_Instructions#getbuildtest_on_windows|for windows users]] below):<br />
<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
<br /> Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.<br />
<br />
To run on unix:<br />
<br />
./Slicer3-build/bin/Slicer3<br />
<br />
To run on Windows:<br />
<br />
./Slicer3-build/bin/RelWithDebInfo/Slicer3.exe<br />
<br />
Note: the whole build environment takes about 1.5G of disk space.<br />
<br />
== Testing ==<br />
<br />
Note also that getbuildtest will do an Experimental submission to the [http://www.na-mic.org:8081/Slicer3/Dashboard/ Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with<br />
<br />
getbuildtest.tcl -t ""<br />
<br />
Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).<br />
<br />
== What does getbuildtest.tcl do? ==<br />
<br />
This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.<br />
<br />
Specifically, getbuildtest does the following steps:<br />
<br />
* Refreshes Slicer3 svn<br />
* Runs Scripts/genlib.tcl which does the following for each of the support libraries<br />
** does a cvs/svn checkout/update<br />
** runs cmake with the correct settings for use with Slicer3<br />
** runs make (or developer studio) to build the libraries<br />
* Runs cmake on Slicer3<br />
* Builds Slicer3<br />
* Runs ctest on Slicer3<br />
* (optionally) Runs CPack on Slicer3<br />
<br />
== Usage ==<br />
<br />
Usage:<br />
<br />
usage: getbuildtest [options] [target]<br />
[target] is determined automatically if not specified<br />
[options] is one of the following:<br />
--help : prints this message and exits<br />
--clean : delete lib and build directories first<br />
-t --test-type : CTest test target<br />
--release : compile with optimization flags<br />
--update : does a cvs/svn update on each lib<br />
--pack : builds a distribution package (cpack)<br />
<br />
== Errors from getbuildtest ==<br />
<br />
You will need to have your firewall configured to allow access to na-mic.org for cvs access through port 2401. Also you need 8081 for submitting to the dashboard.<br />
<br />
Other errors might mean you don't have all the build tools (see next section).<br />
<br />
== Updating Your getbuildtest Build ==<br />
<br />
There are a few options:<br />
<br />
* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)<br />
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).<br />
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.<br />
<br />
The following command for unix machines will update, build, and launch the latest Slicer3:<br />
<br />
svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)<br />
<br />
<br /><br />
<br />
== getbuildtest on windows ==<br />
<br />
While still experimental, the script should also work on a properly configured windows environment. Current requirements are:<br />
<br />
* Developer studio 8 Visual C++ Express which is free from Microsoft - be sure to install the Platform SDK and follow the ridiculous manual steps to set up the paths [[Slicer3:Build_Instructions#Information_on_Free_Microsoft_C.2B.2B_Compiler_on_Windows|see below]].<br />
** Other releases of visual studio also work (7 and 7.1)<br />
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically<br />
* [http://www.cygwin.com Cygwin] with the following packages<br />
** tcltk<br />
** svn<br />
** cvs<br />
** unzip<br />
** curl<br />
* With Developers Studio and cygwin installed, you only need to do the svn checkout and getbuildtest script to get a fully working Slicer3 plus all the tools you need to develop new code.<br />
<br />
== configuration options ==<br />
<br />
The file Slicer3/slicer_variables.tcl includes configuration options for which support libraries to use. You may want to change thes for testing or to get access to new functionality. <br />
<br />
set ::SLICER_TAG "http://www.na-mic.org/svn/Slicer3/trunk"<br />
set ::CMAKE_TAG "CMake-2-4-2"<br />
set ::TEEM_TAG "Teem-1-9-0-patches"<br />
set ::KWWidgets_TAG "HEAD"<br />
set ::VTK_TAG "VTK-5-0"<br />
set ::ITK_TAG ITK-3-0<br />
set ::TCL_TAG "core-8-4-6"<br />
set ::TK_TAG "core-8-4-6"<br />
set ::ITCL_TAG "itcl-3-2-1"<br />
set ::IWIDGETS_TAG "iwidgets-4-0-1"<br />
set ::BLT_TAG "blt24z"<br />
set ::SANDBOX_TAG "http://svn.na-mic.org/svn/NAMICSandBox/branches/Slicer-2-6"<br />
<br />
For example, you may want a build against the ITK cvs head. Change the flag value and then run <br />
<br />
getbuildtest.tcl --update <br />
<br />
which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use --clean.<br />
<br />
Another useful option is to change your build type to include support debugging.<br />
<br />
set ::VTK_BUILD_TYPE "RelWithDebInfo"<br />
<br />
options are Debug, Release, or RelWithDebInfo. RelWithDebInfo is a compromise between speed and debuggability. If you are tracking down a tough C++ bug you will get better information in Debug mode. After changing this flag, you should run<br />
<br />
getbuildtest.tcl --clean<br />
<br />
to create a completely new build.<br />
<br />
= Manual checkout/build of Slicer3 and support libraries: =<br />
<br />
== Prerequisite software ==<br />
<br />
You need to get and build the following packages if you aren't using the getbuildtest script:<br />
<br />
# [http://www.cmake.org CMake (2.4.1 or later)]<br />
# [http://www.tcl.tk Tcl/Tk (8.4 or later)]<br />
# [http://sourceforge.net/projects/incrtcl/ incrTcl (3.2.1)]<br />
# [http://www.vtk.org VTK 5.0]<br />
# [http://www.itk.org ITK 2.8]<br />
# [http://www.kwwidgets.org KWWidgets CVS head]<br />
<br />
== Build Steps ==<br />
<br />
Steps:<br />
<br />
$ svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
$ cvs -d :pserver:anoncvs@www.vtk.org:/cvsroot/VTK co VTK<br />
$ cvs -d :pserver:anoncvs@www.itk.org:/cvsroot/Insight co Insight<br />
$ cvs -d :pserver:anoncvs@www.kwwidgets.org:/cvsroot/KWWidgets co KWWidgets<br />
<br />
You may choose to take VTK5 instead of VTK CVS<br />
<br />
=== Configure and build ITK ===<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
=== Configure and build VTK ===<br />
<br />
* All systems:<br />
** BUILD_SHARED_LIBS ON<br />
** CMAKE_SKIP_RPATH ON<br />
** VTK_WRAP_TCL ON<br />
** VTK_DEBUG_LEAKS ON<br />
<br />
<br /><br />
<br />
* MacOSX specific (Make sure to install [http://www.apple.com/downloads/macosx/apple/x11formacosx.html X11]):<br />
** VTK_USE_CARBON OFF<br />
** VTK_USE_X ON<br />
<br />
<br /><br />
<br />
* Note, those options '''should not''' appear, since they disapear since VTK5:<br />
** VTK_USE_HYBRID ON<br />
** VTK_USE_PATENTED ON<br />
<br />
* Make sure that the TCL and TK path are set properly<br />
** TCL_* and TK_*<br />
<br />
=== Configure and build KWWidgets ===<br />
<br />
* You need to specify where your VTK build tree is.<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
== Build and Run Slicer3 ==<br />
<br />
=== Manually ===<br />
<br />
# Check out and build slicer3 (e.g. on linux)<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
mkdir Slicer3-build<br />
cd Slicer3-build<br />
ccmake ../Slicer3<br />
make<br />
<br />
Again make sure to turn:<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
<br /> Start slicer with the Slicer3Launcher executable in your bin directory.<br />
<br />
= Links =<br />
<br />
* http://www.na-mic.org/Wiki/index.php/Slicer3<br />
* http://www.na-mic.org/websvn/listing.php?repname=Slicer3<br />
<br />
== Information on Free Microsoft C++ Compiler on Windows ==<br />
<br />
Be sure to follow '''all''' the steps on Microsoft link. Yes it means you need to download the compiler '''and''' sdk.<br />
<br />
* http://msdn.microsoft.com/vstudio/express/visualc/usingpsdk/</div>Andyhttps://www.na-mic.org/w/index.php?title=Slicer3:Build_Instructions&diff=6748Slicer3:Build Instructions2007-01-13T14:14:25Z<p>Andy: /* Manually */</p>
<hr />
<div>= All-in-one Script to checkout and build Slicer3 =<br />
<br />
There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. Just do the following two commands (see [[Slicer3:Build_Instructions#getbuildtest_on_windows|for windows users]] below):<br />
<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
<br /> Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.<br />
<br />
To run on unix:<br />
<br />
./Slicer3-build/bin/Slicer3<br />
<br />
To run on Windows:<br />
<br />
./Slicer3-build/bin/RelWithDebInfo/Slicer3.exe<br />
<br />
Note: the whole build environment takes about 1.5G of disk space.<br />
<br />
== Testing ==<br />
<br />
Note also that getbuildtest will do an Experimental submission to the [http://www.na-mic.org:8081/Slicer3/Dashboard/ Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with<br />
<br />
getbuildtest.tcl -t ""<br />
<br />
Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).<br />
<br />
== What does getbuildtest.tcl do? ==<br />
<br />
This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.<br />
<br />
Specifically, getbuildtest does the following steps:<br />
<br />
* Refreshes Slicer3 svn<br />
* Runs Scripts/genlib.tcl which does the following for each of the support libraries<br />
** does a cvs/svn checkout/update<br />
** runs cmake with the correct settings for use with Slicer3<br />
** runs make (or developer studio) to build the libraries<br />
* Runs cmake on Slicer3<br />
* Builds Slicer3<br />
* Runs ctest on Slicer3<br />
* (optionally) Runs CPack on Slicer3<br />
<br />
== Usage ==<br />
<br />
Usage:<br />
<br />
usage: getbuildtest [options] [target]<br />
[target] is determined automatically if not specified<br />
[options] is one of the following:<br />
--help : prints this message and exits<br />
--clean : delete lib and build directories first<br />
-t --test-type : CTest test target<br />
--release : compile with optimization flags<br />
--update : does a cvs/svn update on each lib<br />
--pack : builds a distribution package (cpack)<br />
<br />
== Errors from getbuildtest ==<br />
<br />
You will need to have your firewall configured to allow access to na-mic.org for cvs access through port 2401. Also you need 8081 for submitting to the dashboard.<br />
<br />
Other errors might mean you don't have all the build tools (see next section).<br />
<br />
== Updating Your getbuildtest Build ==<br />
<br />
There are a few options:<br />
<br />
* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)<br />
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).<br />
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.<br />
<br />
The following command for unix machines will update, build, and launch the latest Slicer3:<br />
<br />
svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)<br />
<br />
<br /><br />
<br />
== getbuildtest on windows ==<br />
<br />
While still experimental, the script should also work on a properly configured windows environment. Current requirements are:<br />
<br />
* Developer studio 8 Visual C++ Express which is free from Microsoft - be sure to install the Platform SDK and follow the ridiculous manual steps to set up the paths [[Slicer3:Build_Instructions#Information_on_Free_Microsoft_C.2B.2B_Compiler_on_Windows|see below]].<br />
** Other releases of visual studio also work (7 and 7.1)<br />
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically<br />
* [http://www.cygwin.com Cygwin] with the following packages<br />
** tcltk<br />
** svn<br />
** cvs<br />
** unzip<br />
** curl<br />
* With Developers Studio and cygwin installed, you only need to do the svn checkout and getbuildtest script to get a fully working Slicer3 plus all the tools you need to develop new code.<br />
<br />
== configuration options ==<br />
<br />
The file Slicer3/slicer_variables.tcl includes configuration options for which support libraries to use. You may want to change thes for testing or to get access to new functionality. <br />
<br />
set ::SLICER_TAG "http://www.na-mic.org/svn/Slicer3/trunk"<br />
set ::CMAKE_TAG "CMake-2-4-2"<br />
set ::TEEM_TAG "Teem-1-9-0-patches"<br />
set ::KWWidgets_TAG "HEAD"<br />
set ::VTK_TAG "VTK-5-0"<br />
set ::ITK_TAG ITK-3-0<br />
set ::TCL_TAG "core-8-4-6"<br />
set ::TK_TAG "core-8-4-6"<br />
set ::ITCL_TAG "itcl-3-2-1"<br />
set ::IWIDGETS_TAG "iwidgets-4-0-1"<br />
set ::BLT_TAG "blt24z"<br />
set ::SANDBOX_TAG "http://svn.na-mic.org/svn/NAMICSandBox/branches/Slicer-2-6"<br />
<br />
For example, you may want a build against the ITK cvs head. Change the flag value and then run <br />
<br />
getbuildtest.tcl --update <br />
<br />
which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use --clean.<br />
<br />
Another useful option is to change your build type to include support debugging.<br />
<br />
set ::VTK_BUILD_TYPE "RelWithDebInfo"<br />
<br />
options are Debug, Release, or RelWithDebInfo. RelWithDebInfo is a compromise between speed and debuggability. If you are tracking down a tough C++ bug you will get better information in Debug mode. After changing this flag, you should run<br />
<br />
getbuildtest.tcl --clean<br />
<br />
to create a completely new build.<br />
<br />
= Manual checkout/build of Slicer3 and support libraries: =<br />
<br />
== Prerequisite software ==<br />
<br />
You need to get and build the following packages if you aren't using the getbuildtest script:<br />
<br />
# [http://www.cmake.org CMake (2.4.1 or later)]<br />
# [http://www.tcl.tk Tcl/Tk (8.4 or later)]<br />
# [http://sourceforge.net/projects/incrtcl/ incrTcl (3.2.1)]<br />
# [http://www.vtk.org VTK 5.0]<br />
# [http://www.itk.org ITK 2.8]<br />
# [http://www.kwwidgets.org KWWidgets CVS head]<br />
<br />
== Build Steps ==<br />
<br />
Steps:<br />
<br />
$ svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
$ cvs -d :pserver:anoncvs@www.vtk.org:/cvsroot/VTK co VTK<br />
$ cvs -d :pserver:anoncvs@www.itk.org:/cvsroot/Insight co Insight<br />
$ cvs -d :pserver:anoncvs@www.kwwidgets.org:/cvsroot/KWWidgets co KWWidgets<br />
<br />
You may choose to take VTK5 instead of VTK CVS<br />
<br />
=== Configure and build ITK ===<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
=== Configure and build VTK ===<br />
<br />
* All systems:<br />
** BUILD_SHARED_LIBS ON<br />
** CMAKE_SKIP_RPATH ON<br />
** VTK_WRAP_TCL ON<br />
** VTK_DEBUG_LEAKS ON<br />
<br />
<br /><br />
<br />
* MacOSX specific (Make sure to install [http://www.apple.com/downloads/macosx/apple/x11formacosx.html X11]):<br />
** VTK_USE_CARBON OFF<br />
** VTK_USE_X ON<br />
<br />
<br /><br />
<br />
* Note, those options '''should not''' appear, since they disapear since VTK5:<br />
** VTK_USE_HYBRID ON<br />
** VTK_USE_PATENTED ON<br />
<br />
* Make sure that the TCL and TK path are set properly<br />
** TCL_* and TK_*<br />
<br />
=== Configure and build KWWidgets ===<br />
<br />
* You need to specify where your VTK build tree is.<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
== Build and Run Slicer3 ==<br />
<br />
=== Manually ===<br />
<br />
# Check out and build slicer3 (e.g. on linux)<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
mkdir Slicer3-build<br />
cd Slicer3-build<br />
ccmake ../Slicer3<br />
make<br />
<br />
Again make sure to turn:<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
<br /> Start slicer with the Slicer3Launcher executable in your bin directory.<br />
<br />
= Links =<br />
<br />
* http://www.na-mic.org/Wiki/index.php/Slicer3<br />
* http://www.na-mic.org:8000/websvn/listing.php?repname=Slicer3<br />
<br />
== Information on Free Microsoft C++ Compiler on Windows ==<br />
<br />
Be sure to follow '''all''' the steps on Microsoft link. Yes it means you need to download the compiler '''and''' sdk.<br />
<br />
* http://msdn.microsoft.com/vstudio/express/visualc/usingpsdk/</div>Andyhttps://www.na-mic.org/w/index.php?title=Slicer3:Build_Instructions&diff=6747Slicer3:Build Instructions2007-01-13T14:14:09Z<p>Andy: /* Build Steps */</p>
<hr />
<div>= All-in-one Script to checkout and build Slicer3 =<br />
<br />
There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. Just do the following two commands (see [[Slicer3:Build_Instructions#getbuildtest_on_windows|for windows users]] below):<br />
<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
<br /> Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.<br />
<br />
To run on unix:<br />
<br />
./Slicer3-build/bin/Slicer3<br />
<br />
To run on Windows:<br />
<br />
./Slicer3-build/bin/RelWithDebInfo/Slicer3.exe<br />
<br />
Note: the whole build environment takes about 1.5G of disk space.<br />
<br />
== Testing ==<br />
<br />
Note also that getbuildtest will do an Experimental submission to the [http://www.na-mic.org:8081/Slicer3/Dashboard/ Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with<br />
<br />
getbuildtest.tcl -t ""<br />
<br />
Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).<br />
<br />
== What does getbuildtest.tcl do? ==<br />
<br />
This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.<br />
<br />
Specifically, getbuildtest does the following steps:<br />
<br />
* Refreshes Slicer3 svn<br />
* Runs Scripts/genlib.tcl which does the following for each of the support libraries<br />
** does a cvs/svn checkout/update<br />
** runs cmake with the correct settings for use with Slicer3<br />
** runs make (or developer studio) to build the libraries<br />
* Runs cmake on Slicer3<br />
* Builds Slicer3<br />
* Runs ctest on Slicer3<br />
* (optionally) Runs CPack on Slicer3<br />
<br />
== Usage ==<br />
<br />
Usage:<br />
<br />
usage: getbuildtest [options] [target]<br />
[target] is determined automatically if not specified<br />
[options] is one of the following:<br />
--help : prints this message and exits<br />
--clean : delete lib and build directories first<br />
-t --test-type : CTest test target<br />
--release : compile with optimization flags<br />
--update : does a cvs/svn update on each lib<br />
--pack : builds a distribution package (cpack)<br />
<br />
== Errors from getbuildtest ==<br />
<br />
You will need to have your firewall configured to allow access to na-mic.org for cvs access through port 2401. Also you need 8081 for submitting to the dashboard.<br />
<br />
Other errors might mean you don't have all the build tools (see next section).<br />
<br />
== Updating Your getbuildtest Build ==<br />
<br />
There are a few options:<br />
<br />
* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)<br />
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).<br />
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.<br />
<br />
The following command for unix machines will update, build, and launch the latest Slicer3:<br />
<br />
svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)<br />
<br />
<br /><br />
<br />
== getbuildtest on windows ==<br />
<br />
While still experimental, the script should also work on a properly configured windows environment. Current requirements are:<br />
<br />
* Developer studio 8 Visual C++ Express which is free from Microsoft - be sure to install the Platform SDK and follow the ridiculous manual steps to set up the paths [[Slicer3:Build_Instructions#Information_on_Free_Microsoft_C.2B.2B_Compiler_on_Windows|see below]].<br />
** Other releases of visual studio also work (7 and 7.1)<br />
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically<br />
* [http://www.cygwin.com Cygwin] with the following packages<br />
** tcltk<br />
** svn<br />
** cvs<br />
** unzip<br />
** curl<br />
* With Developers Studio and cygwin installed, you only need to do the svn checkout and getbuildtest script to get a fully working Slicer3 plus all the tools you need to develop new code.<br />
<br />
== configuration options ==<br />
<br />
The file Slicer3/slicer_variables.tcl includes configuration options for which support libraries to use. You may want to change thes for testing or to get access to new functionality. <br />
<br />
set ::SLICER_TAG "http://www.na-mic.org/svn/Slicer3/trunk"<br />
set ::CMAKE_TAG "CMake-2-4-2"<br />
set ::TEEM_TAG "Teem-1-9-0-patches"<br />
set ::KWWidgets_TAG "HEAD"<br />
set ::VTK_TAG "VTK-5-0"<br />
set ::ITK_TAG ITK-3-0<br />
set ::TCL_TAG "core-8-4-6"<br />
set ::TK_TAG "core-8-4-6"<br />
set ::ITCL_TAG "itcl-3-2-1"<br />
set ::IWIDGETS_TAG "iwidgets-4-0-1"<br />
set ::BLT_TAG "blt24z"<br />
set ::SANDBOX_TAG "http://svn.na-mic.org/svn/NAMICSandBox/branches/Slicer-2-6"<br />
<br />
For example, you may want a build against the ITK cvs head. Change the flag value and then run <br />
<br />
getbuildtest.tcl --update <br />
<br />
which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use --clean.<br />
<br />
Another useful option is to change your build type to include support debugging.<br />
<br />
set ::VTK_BUILD_TYPE "RelWithDebInfo"<br />
<br />
options are Debug, Release, or RelWithDebInfo. RelWithDebInfo is a compromise between speed and debuggability. If you are tracking down a tough C++ bug you will get better information in Debug mode. After changing this flag, you should run<br />
<br />
getbuildtest.tcl --clean<br />
<br />
to create a completely new build.<br />
<br />
= Manual checkout/build of Slicer3 and support libraries: =<br />
<br />
== Prerequisite software ==<br />
<br />
You need to get and build the following packages if you aren't using the getbuildtest script:<br />
<br />
# [http://www.cmake.org CMake (2.4.1 or later)]<br />
# [http://www.tcl.tk Tcl/Tk (8.4 or later)]<br />
# [http://sourceforge.net/projects/incrtcl/ incrTcl (3.2.1)]<br />
# [http://www.vtk.org VTK 5.0]<br />
# [http://www.itk.org ITK 2.8]<br />
# [http://www.kwwidgets.org KWWidgets CVS head]<br />
<br />
== Build Steps ==<br />
<br />
Steps:<br />
<br />
$ svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
$ cvs -d :pserver:anoncvs@www.vtk.org:/cvsroot/VTK co VTK<br />
$ cvs -d :pserver:anoncvs@www.itk.org:/cvsroot/Insight co Insight<br />
$ cvs -d :pserver:anoncvs@www.kwwidgets.org:/cvsroot/KWWidgets co KWWidgets<br />
<br />
You may choose to take VTK5 instead of VTK CVS<br />
<br />
=== Configure and build ITK ===<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
=== Configure and build VTK ===<br />
<br />
* All systems:<br />
** BUILD_SHARED_LIBS ON<br />
** CMAKE_SKIP_RPATH ON<br />
** VTK_WRAP_TCL ON<br />
** VTK_DEBUG_LEAKS ON<br />
<br />
<br /><br />
<br />
* MacOSX specific (Make sure to install [http://www.apple.com/downloads/macosx/apple/x11formacosx.html X11]):<br />
** VTK_USE_CARBON OFF<br />
** VTK_USE_X ON<br />
<br />
<br /><br />
<br />
* Note, those options '''should not''' appear, since they disapear since VTK5:<br />
** VTK_USE_HYBRID ON<br />
** VTK_USE_PATENTED ON<br />
<br />
* Make sure that the TCL and TK path are set properly<br />
** TCL_* and TK_*<br />
<br />
=== Configure and build KWWidgets ===<br />
<br />
* You need to specify where your VTK build tree is.<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
== Build and Run Slicer3 ==<br />
<br />
=== Manually ===<br />
<br />
# Check out and build slicer3 (e.g. on linux)<br />
<br />
svn co http://www.na-mic.org:8000/svn/Slicer3/trunk Slicer3<br />
mkdir Slicer3-build<br />
cd Slicer3-build<br />
ccmake ../Slicer3<br />
make<br />
<br />
Again make sure to turn:<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
<br /> Start slicer with the Slicer3Launcher executable in your bin directory.<br />
<br />
= Links =<br />
<br />
* http://www.na-mic.org/Wiki/index.php/Slicer3<br />
* http://www.na-mic.org:8000/websvn/listing.php?repname=Slicer3<br />
<br />
== Information on Free Microsoft C++ Compiler on Windows ==<br />
<br />
Be sure to follow '''all''' the steps on Microsoft link. Yes it means you need to download the compiler '''and''' sdk.<br />
<br />
* http://msdn.microsoft.com/vstudio/express/visualc/usingpsdk/</div>Andyhttps://www.na-mic.org/w/index.php?title=Slicer3:Build_Instructions&diff=6746Slicer3:Build Instructions2007-01-13T14:13:54Z<p>Andy: /* Errors from getbuildtest */</p>
<hr />
<div>= All-in-one Script to checkout and build Slicer3 =<br />
<br />
There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. Just do the following two commands (see [[Slicer3:Build_Instructions#getbuildtest_on_windows|for windows users]] below):<br />
<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
<br />
./Slicer3/Scripts/getbuildtest.tcl<br />
<br />
<br /> Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.<br />
<br />
To run on unix:<br />
<br />
./Slicer3-build/bin/Slicer3<br />
<br />
To run on Windows:<br />
<br />
./Slicer3-build/bin/RelWithDebInfo/Slicer3.exe<br />
<br />
Note: the whole build environment takes about 1.5G of disk space.<br />
<br />
== Testing ==<br />
<br />
Note also that getbuildtest will do an Experimental submission to the [http://www.na-mic.org:8081/Slicer3/Dashboard/ Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with<br />
<br />
getbuildtest.tcl -t ""<br />
<br />
Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).<br />
<br />
== What does getbuildtest.tcl do? ==<br />
<br />
This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.<br />
<br />
Specifically, getbuildtest does the following steps:<br />
<br />
* Refreshes Slicer3 svn<br />
* Runs Scripts/genlib.tcl which does the following for each of the support libraries<br />
** does a cvs/svn checkout/update<br />
** runs cmake with the correct settings for use with Slicer3<br />
** runs make (or developer studio) to build the libraries<br />
* Runs cmake on Slicer3<br />
* Builds Slicer3<br />
* Runs ctest on Slicer3<br />
* (optionally) Runs CPack on Slicer3<br />
<br />
== Usage ==<br />
<br />
Usage:<br />
<br />
usage: getbuildtest [options] [target]<br />
[target] is determined automatically if not specified<br />
[options] is one of the following:<br />
--help : prints this message and exits<br />
--clean : delete lib and build directories first<br />
-t --test-type : CTest test target<br />
--release : compile with optimization flags<br />
--update : does a cvs/svn update on each lib<br />
--pack : builds a distribution package (cpack)<br />
<br />
== Errors from getbuildtest ==<br />
<br />
You will need to have your firewall configured to allow access to na-mic.org for cvs access through port 2401. Also you need 8081 for submitting to the dashboard.<br />
<br />
Other errors might mean you don't have all the build tools (see next section).<br />
<br />
== Updating Your getbuildtest Build ==<br />
<br />
There are a few options:<br />
<br />
* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)<br />
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).<br />
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.<br />
<br />
The following command for unix machines will update, build, and launch the latest Slicer3:<br />
<br />
svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)<br />
<br />
<br /><br />
<br />
== getbuildtest on windows ==<br />
<br />
While still experimental, the script should also work on a properly configured windows environment. Current requirements are:<br />
<br />
* Developer studio 8 Visual C++ Express which is free from Microsoft - be sure to install the Platform SDK and follow the ridiculous manual steps to set up the paths [[Slicer3:Build_Instructions#Information_on_Free_Microsoft_C.2B.2B_Compiler_on_Windows|see below]].<br />
** Other releases of visual studio also work (7 and 7.1)<br />
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically<br />
* [http://www.cygwin.com Cygwin] with the following packages<br />
** tcltk<br />
** svn<br />
** cvs<br />
** unzip<br />
** curl<br />
* With Developers Studio and cygwin installed, you only need to do the svn checkout and getbuildtest script to get a fully working Slicer3 plus all the tools you need to develop new code.<br />
<br />
== configuration options ==<br />
<br />
The file Slicer3/slicer_variables.tcl includes configuration options for which support libraries to use. You may want to change thes for testing or to get access to new functionality. <br />
<br />
set ::SLICER_TAG "http://www.na-mic.org/svn/Slicer3/trunk"<br />
set ::CMAKE_TAG "CMake-2-4-2"<br />
set ::TEEM_TAG "Teem-1-9-0-patches"<br />
set ::KWWidgets_TAG "HEAD"<br />
set ::VTK_TAG "VTK-5-0"<br />
set ::ITK_TAG ITK-3-0<br />
set ::TCL_TAG "core-8-4-6"<br />
set ::TK_TAG "core-8-4-6"<br />
set ::ITCL_TAG "itcl-3-2-1"<br />
set ::IWIDGETS_TAG "iwidgets-4-0-1"<br />
set ::BLT_TAG "blt24z"<br />
set ::SANDBOX_TAG "http://svn.na-mic.org/svn/NAMICSandBox/branches/Slicer-2-6"<br />
<br />
For example, you may want a build against the ITK cvs head. Change the flag value and then run <br />
<br />
getbuildtest.tcl --update <br />
<br />
which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use --clean.<br />
<br />
Another useful option is to change your build type to include support debugging.<br />
<br />
set ::VTK_BUILD_TYPE "RelWithDebInfo"<br />
<br />
options are Debug, Release, or RelWithDebInfo. RelWithDebInfo is a compromise between speed and debuggability. If you are tracking down a tough C++ bug you will get better information in Debug mode. After changing this flag, you should run<br />
<br />
getbuildtest.tcl --clean<br />
<br />
to create a completely new build.<br />
<br />
= Manual checkout/build of Slicer3 and support libraries: =<br />
<br />
== Prerequisite software ==<br />
<br />
You need to get and build the following packages if you aren't using the getbuildtest script:<br />
<br />
# [http://www.cmake.org CMake (2.4.1 or later)]<br />
# [http://www.tcl.tk Tcl/Tk (8.4 or later)]<br />
# [http://sourceforge.net/projects/incrtcl/ incrTcl (3.2.1)]<br />
# [http://www.vtk.org VTK 5.0]<br />
# [http://www.itk.org ITK 2.8]<br />
# [http://www.kwwidgets.org KWWidgets CVS head]<br />
<br />
== Build Steps ==<br />
<br />
Steps:<br />
<br />
$ svn co http://www.na-mic.org:8000/svn/Slicer3/trunk Slicer3<br />
$ cvs -d :pserver:anoncvs@www.vtk.org:/cvsroot/VTK co VTK<br />
$ cvs -d :pserver:anoncvs@www.itk.org:/cvsroot/Insight co Insight<br />
$ cvs -d :pserver:anoncvs@www.kwwidgets.org:/cvsroot/KWWidgets co KWWidgets<br />
<br />
You may choose to take VTK5 instead of VTK CVS<br />
<br />
=== Configure and build ITK ===<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
=== Configure and build VTK ===<br />
<br />
* All systems:<br />
** BUILD_SHARED_LIBS ON<br />
** CMAKE_SKIP_RPATH ON<br />
** VTK_WRAP_TCL ON<br />
** VTK_DEBUG_LEAKS ON<br />
<br />
<br /><br />
<br />
* MacOSX specific (Make sure to install [http://www.apple.com/downloads/macosx/apple/x11formacosx.html X11]):<br />
** VTK_USE_CARBON OFF<br />
** VTK_USE_X ON<br />
<br />
<br /><br />
<br />
* Note, those options '''should not''' appear, since they disapear since VTK5:<br />
** VTK_USE_HYBRID ON<br />
** VTK_USE_PATENTED ON<br />
<br />
* Make sure that the TCL and TK path are set properly<br />
** TCL_* and TK_*<br />
<br />
=== Configure and build KWWidgets ===<br />
<br />
* You need to specify where your VTK build tree is.<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
== Build and Run Slicer3 ==<br />
<br />
=== Manually ===<br />
<br />
# Check out and build slicer3 (e.g. on linux)<br />
<br />
svn co http://www.na-mic.org:8000/svn/Slicer3/trunk Slicer3<br />
mkdir Slicer3-build<br />
cd Slicer3-build<br />
ccmake ../Slicer3<br />
make<br />
<br />
Again make sure to turn:<br />
<br />
* BUILD_SHARED_LIBS ON<br />
* CMAKE_SKIP_RPATH ON<br />
<br />
<br /> Start slicer with the Slicer3Launcher executable in your bin directory.<br />
<br />
= Links =<br />
<br />
* http://www.na-mic.org/Wiki/index.php/Slicer3<br />
* http://www.na-mic.org:8000/websvn/listing.php?repname=Slicer3<br />
<br />
== Information on Free Microsoft C++ Compiler on Windows ==<br />
<br />
Be sure to follow '''all''' the steps on Microsoft link. Yes it means you need to download the compiler '''and''' sdk.<br />
<br />
* http://msdn.microsoft.com/vstudio/express/visualc/usingpsdk/</div>Andyhttps://www.na-mic.org/w/index.php?title=Dart2Summary&diff=6676Dart2Summary2007-01-12T17:56:21Z<p>Andy: /* Source code */</p>
<hr />
<div>== Description ==<br />
<br />
DART2 is a ground up re-write of the [[DartSummary|DART]] server. Some very different design critera are being used for DART2, some of which are described in this [http://svn.na-mic.org:8000/svn/Dart/trunk/Dart.pdf document]. DART2 is currently being designed and implemented as part of NAMIC's Core 2 Engineering activities. A [[Media:Dart2.ppt|progress report]] was given at the 2006 NAMIC All Hands Meeting in Salt Lake City.<br />
<br />
== Documentation, Resources & Plans ==<br />
<br />
This page serves as the main Dart home page. Most questions can be answered in the [http://svn.na-mic.org:8000/svn/Dart/trunk/Documentation/Manual/Dart.pdf Dart manual], if not, please see the [http://public.kitware.com/mailman/listinfo/dart Dart mailing list].<br />
<br />
Currently, Dart is being used for the [http://dart.na-mic.org/Slicer3/Dashboard Slicer3 dashboard]. Over the upcoming months, Dart will be adapted and "hardened" for the enterprise environment. This mainly consists of using MySQL rather than Derby. MySQL is highly scalable with mature management tools, mitigating a point of failure for Dart (though Derby performs wonderfully for most applications).<br />
<br />
== Releases ==<br />
<br />
Release 1.0.7 (June 20, 2006)<br />
<br />
[[Media:Dart1.0.7.zip| Dart1.0.7.zip]] or [[Media:Dart1.0.7.tar.gz| Dart1.0.7.tar.gz]]<br />
<br />
===== For JDK 1.4 =====<br />
<br />
[[Media:Dart1.0.7-jdk1.4.zip| Dart1.0.7-jdk1.4.zip]] or [[Media:Dart1.0.7-jdk1.4.tar.gz| Dart1.0.7-jdk1.4.tar.gz]]<br />
<br />
This release fixes several resource exhaustion bugs, and includes an (untested) HTTP PUT method for submission. Please download and update any existing Dart servers.<br />
<br />
[[Dart2:PreviousReleases |Previous Releases]]<br />
<br />
== Source code ==<br />
The Source code for Dart2 is current under the Subversion revision control system ([http://subversion.tigris.org/ homepage]), and may be [http://www.na-mic.org/websvn/ browsed] or checked out:<br />
<br />
svn co http://svn.na-mic.org/svn/Dart/trunk Dart<br />
<br />
== Status ==<br />
<br />
The current plan is that DART2 will be written in the single language Java. Besides its simplicity and portability, Java provides many different packages dedicated to particular programming tasks. Some of the packages used in DART2 are described here including accompaning descriptions and licenses.<br />
<br />
{|<br />
! Package Name<br />
! Description<br />
! License<br />
|-<br />
|<br />
[http://www.opensymphony.com/quartz/ Quartz]<br />
| Enterprise scheduler, has features similar to cron<br />
| BSD-like<br />
|-<br />
|<br />
[http://ws.apache.org/xmlrpc/ Apache XML-RPC]<br />
| XMLRPC implementation, integrates with servlet engines<br />
| Apache<br />
|-<br />
|<br />
[http://jakarta.apache.org/commons/digester/ Digester]<br />
| Part of the Apache Jakarta Commons project. Converts XML to Java objects<br />
| Apache<br />
|-<br />
|<br />
[http://jakarta.apache.org/commons/cli/ Command Line Interface]<br />
| Command line processing<br />
| Apache<br />
|-<br />
|<br />
[http://www.freemarker.org FreeMarker]<br />
| Template engine, provides HTML generation from Java objects<br />
| BSD-like<br />
|-<br />
|<br />
[http://jaxor.sourceforge.net/ Jaxor]<br />
| Object-Relational bridge. Generates objects that are dynamically mapped to RDBMS<br />
| BSD<br />
|-<br />
|<br />
[http://logging.apache.org/log4j/docs/ log4j]<br />
| Very flexible logging system<br />
| Apache<br />
|-<br />
|<br />
[http://incubator.apache.org/derby/ Derby]<br />
| Embedded RDBMS donated to Apache by IBM. Formely known as Cloudscape<br />
| Apache<br />
|-<br />
|<br />
[http://www.junit.org/index.htm JUnit]<br />
| Excellent unit testing framework. All Dart2 Server tests use JUnit<br />
| Common Public License<br />
|-<br />
|<br />
[http://jakarta.apache.org/commons/dbcp/ DB Connection Pooling]<br />
| DB Connection pooling library, helps manage server resources.<br />
| Apache<br />
|-<br />
|<br />
[http://jakarta.apache.org/commons/sandbox/vfs/index.html Virtual File System]<br />
| Manipulate files in the file system, JAR files, FTP, etc... uniformly and transparently.<br />
| Apache<br />
|-<br />
|<br />
[http://jetty.mortbay.org/jetty/index.html Jetty]<br />
| An embeddable servlet and web server engine<br />
| Apache<br />
|-<br />
|<br />
[http://ant.apache.org/ Ant]<br />
| Where would we be without Ant? Ant is a Java version of Make.<br />
| Apache<br />
|-<br />
|<br />
[http://www.jfree.org/jfreechart/index.php JFreeChart]<br />
| Charting tools accessible via a servlet<br />
| GNU Lesser General Public License<br />
|}<br />
<br />
[[Image:Dart2-Architecture.png|thumb|left|802px|Dart 2 architecture]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Dart2Summary&diff=6675Dart2Summary2007-01-12T17:56:11Z<p>Andy: /* Source code */</p>
<hr />
<div>== Description ==<br />
<br />
DART2 is a ground up re-write of the [[DartSummary|DART]] server. Some very different design critera are being used for DART2, some of which are described in this [http://svn.na-mic.org:8000/svn/Dart/trunk/Dart.pdf document]. DART2 is currently being designed and implemented as part of NAMIC's Core 2 Engineering activities. A [[Media:Dart2.ppt|progress report]] was given at the 2006 NAMIC All Hands Meeting in Salt Lake City.<br />
<br />
== Documentation, Resources & Plans ==<br />
<br />
This page serves as the main Dart home page. Most questions can be answered in the [http://svn.na-mic.org:8000/svn/Dart/trunk/Documentation/Manual/Dart.pdf Dart manual], if not, please see the [http://public.kitware.com/mailman/listinfo/dart Dart mailing list].<br />
<br />
Currently, Dart is being used for the [http://dart.na-mic.org/Slicer3/Dashboard Slicer3 dashboard]. Over the upcoming months, Dart will be adapted and "hardened" for the enterprise environment. This mainly consists of using MySQL rather than Derby. MySQL is highly scalable with mature management tools, mitigating a point of failure for Dart (though Derby performs wonderfully for most applications).<br />
<br />
== Releases ==<br />
<br />
Release 1.0.7 (June 20, 2006)<br />
<br />
[[Media:Dart1.0.7.zip| Dart1.0.7.zip]] or [[Media:Dart1.0.7.tar.gz| Dart1.0.7.tar.gz]]<br />
<br />
===== For JDK 1.4 =====<br />
<br />
[[Media:Dart1.0.7-jdk1.4.zip| Dart1.0.7-jdk1.4.zip]] or [[Media:Dart1.0.7-jdk1.4.tar.gz| Dart1.0.7-jdk1.4.tar.gz]]<br />
<br />
This release fixes several resource exhaustion bugs, and includes an (untested) HTTP PUT method for submission. Please download and update any existing Dart servers.<br />
<br />
[[Dart2:PreviousReleases |Previous Releases]]<br />
<br />
== Source code ==<br />
The Source code for Dart2 is current under the Subversion revision control system ([http://subversion.tigris.org/ homepage]), and may be [http://www.na-mic.org:8000/websvn/ browsed] or checked out:<br />
<br />
svn co http://svn.na-mic.org/svn/Dart/trunk Dart<br />
<br />
== Status ==<br />
<br />
The current plan is that DART2 will be written in the single language Java. Besides its simplicity and portability, Java provides many different packages dedicated to particular programming tasks. Some of the packages used in DART2 are described here including accompaning descriptions and licenses.<br />
<br />
{|<br />
! Package Name<br />
! Description<br />
! License<br />
|-<br />
|<br />
[http://www.opensymphony.com/quartz/ Quartz]<br />
| Enterprise scheduler, has features similar to cron<br />
| BSD-like<br />
|-<br />
|<br />
[http://ws.apache.org/xmlrpc/ Apache XML-RPC]<br />
| XMLRPC implementation, integrates with servlet engines<br />
| Apache<br />
|-<br />
|<br />
[http://jakarta.apache.org/commons/digester/ Digester]<br />
| Part of the Apache Jakarta Commons project. Converts XML to Java objects<br />
| Apache<br />
|-<br />
|<br />
[http://jakarta.apache.org/commons/cli/ Command Line Interface]<br />
| Command line processing<br />
| Apache<br />
|-<br />
|<br />
[http://www.freemarker.org FreeMarker]<br />
| Template engine, provides HTML generation from Java objects<br />
| BSD-like<br />
|-<br />
|<br />
[http://jaxor.sourceforge.net/ Jaxor]<br />
| Object-Relational bridge. Generates objects that are dynamically mapped to RDBMS<br />
| BSD<br />
|-<br />
|<br />
[http://logging.apache.org/log4j/docs/ log4j]<br />
| Very flexible logging system<br />
| Apache<br />
|-<br />
|<br />
[http://incubator.apache.org/derby/ Derby]<br />
| Embedded RDBMS donated to Apache by IBM. Formely known as Cloudscape<br />
| Apache<br />
|-<br />
|<br />
[http://www.junit.org/index.htm JUnit]<br />
| Excellent unit testing framework. All Dart2 Server tests use JUnit<br />
| Common Public License<br />
|-<br />
|<br />
[http://jakarta.apache.org/commons/dbcp/ DB Connection Pooling]<br />
| DB Connection pooling library, helps manage server resources.<br />
| Apache<br />
|-<br />
|<br />
[http://jakarta.apache.org/commons/sandbox/vfs/index.html Virtual File System]<br />
| Manipulate files in the file system, JAR files, FTP, etc... uniformly and transparently.<br />
| Apache<br />
|-<br />
|<br />
[http://jetty.mortbay.org/jetty/index.html Jetty]<br />
| An embeddable servlet and web server engine<br />
| Apache<br />
|-<br />
|<br />
[http://ant.apache.org/ Ant]<br />
| Where would we be without Ant? Ant is a Java version of Make.<br />
| Apache<br />
|-<br />
|<br />
[http://www.jfree.org/jfreechart/index.php JFreeChart]<br />
| Charting tools accessible via a servlet<br />
| GNU Lesser General Public License<br />
|}<br />
<br />
[[Image:Dart2-Architecture.png|thumb|left|802px|Dart 2 architecture]]</div>Andyhttps://www.na-mic.org/w/index.php?title=File:NA-MIC_EAB_01_11_07_uci_2007.ppt&diff=6670File:NA-MIC EAB 01 11 07 uci 2007.ppt2007-01-12T14:53:13Z<p>Andy: </p>
<hr />
<div></div>Andyhttps://www.na-mic.org/w/index.php?title=EAB_Meeting_AHM2007&diff=6669EAB Meeting AHM20072007-01-12T14:52:23Z<p>Andy: </p>
<hr />
<div> Back to [[AHM_2007]]<br />
<br />
Information about NA-MIC EAB is available [[EAB|here]].<br />
<br />
*Confirmed EAB Attendees:<br />
**Chris Johnson (Chair)<br />
**Sanjoy Mitter<br />
**Sandy Napel<br />
**Godfrey Pearlson<br />
**Carlo Pierpaoli<br />
**Fred Prior<br />
**Michael Ackerman (ex officio)<br />
<br />
Schedule for the EAB Meeting at AHM 2007:<br />
<br />
* 8-10am: <br />
** 5-min each Site PI Presentations to the EAB: <br />
** What did you do for NA-MIC and/or what did NA-MIC do for you<br />
** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation<br />
*** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[Media:NAMIC_2007_EAB_UTAH.ppt|slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf|slides]])<br />
*** Core 2: GE GRC ([[slides]]), Kitware ([[media:AHM-SLC-Jan2007-EAB-KitwareCore2.ppt|slides]]), UCLA ([[Media:NamicEAB_LONI_2007.ppt|slides]]), UCSD ([[media:NA-MIC_EAB_UCSD_2007v2.ppt|Slides]]), Isomics ([[media:EAB Isomics-2007.ppt | slides]])<br />
*** Core 3: Harvard ([[Media:NA-MIC_EAB_01_13_shenton_2007.ppt|slides]]), Dartmouth ([[Media:NA-MIC_EAB_01_11_Saykin_2007.ppt|slides]]), UCI and U Toronto ([[Media:NA-MIC_EAB_01_11_07_uci_2007.ppt|slides]])<br />
*** Cores 4-6: Service ([[media:AHM-SLC-Jan2007-EAB-KitwareCore4.ppt|slides]]), Dissemination ([[slides]]), Training ([[media:AHM_2007_EABmeeting_Training_SPujol.ppt|slides]])<br />
* 10-10:30am: Coffee break<br />
* 10:30am-11am: Discussion of Site PIs with EAB<br />
* 11am-12pm: Closed session of the EAB<br />
* 12pm adjourn<br />
<br />
<br />
Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]</div>Andyhttps://www.na-mic.org/w/index.php?title=File:2007_AHM_Programming_Half_Week_PackagingAndDeployment.ppt&diff=6435File:2007 AHM Programming Half Week PackagingAndDeployment.ppt2007-01-10T15:50:01Z<p>Andy: </p>
<hr />
<div></div>Andyhttps://www.na-mic.org/w/index.php?title=2007_Project_Half_Week&diff=64342007 Project Half Week2007-01-10T15:49:44Z<p>Andy: /* NA-MIC Kit */</p>
<hr />
<div>Back to [[AHM_2007|AHM_2007]]<br />
<br />
== Results ==<br />
Results of this event will be summarized here after it is completed.<br />
<br />
==Please note==<br />
* Everyone should '''bring a laptop'''. We will have three or four projectors.<br />
* About half the time will be spent working on projects and the other half in project related discussions.<br />
<br />
== Projects ==<br />
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page. <br />
<br />
===Structural Analysis===<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]<br />
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]<br />
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] <br />
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]] <br />
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]<br />
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)<br />
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]<br />
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]<br />
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]<br />
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]<br />
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.ppt| 4-block PPT Jan 2007]]<br />
<br />
===Diffusion Image Analysis===<br />
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]<br />
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]<br />
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]<br />
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]<br />
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]<br />
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]<br />
#ITK Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)<br />
<br />
===NA-MIC Kit===<br />
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]<br />
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4-block ppt]]<br />
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)<br />
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]<br />
##See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]<br />
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)<br />
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]<br />
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]<br />
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]<br />
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]<br />
##[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying'''<br />
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]<br />
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]<br />
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]<br />
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]] <br />
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')<br />
#Malab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]<br />
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2, [[Media:2007_Programming_Half_Week_HierModel.ppt| 4-block PPT Jan 2007]]<br />
<br />
===External Collaborations===<br />
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]<br />
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]<br />
#Radiology Workstation Module for Slicer3 (Pat, Steve)<br />
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] <br />
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]] <br />
##Voxel meshing as an execuation module in Slicer3 [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)<br />
##Mesh Quality Visualization Development [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)<br />
##Bounding Box Projection Meshing [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)<br />
##Tetrahedral Mesh Generation Tools in VTK [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)<br />
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]<br />
<br />
== Logistics ==<br />
<br />
'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)<br />
<br />
'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].<br />
<br />
== Background and Preparation ==<br />
<br />
We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.<br />
<br />
=== Goals ===<br />
<br />
The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.<br />
<br />
* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.<br />
* The event is open to people outside NA-MIC, subject to availability.<br />
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br />
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br />
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.<br />
* This is not an introduction to the components of the NA-MIC Kit.<br />
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.<br />
<br />
=== Preparation for the workshop ===<br />
<br />
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]<br />
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]<br />
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)<br />
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]<br />
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)<br />
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]<br />
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
== A History in Wiki Links ==<br />
<br />
A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].</div>Andyhttps://www.na-mic.org/w/index.php?title=Svn&diff=6053Svn2007-01-08T19:43:11Z<p>Andy: /* Example Repositories */</p>
<hr />
<div>== Description ==<br />
<br />
The goal of the Subversion project is to build a version control system that is a compelling replacement for CVS in the open source community. The software is released under an Apache/BSD-style open source license.<br />
<br />
== Documentation ==<br />
<br />
* http://subversion.tigris.org/<br />
* [[Subversion_Input_Filters|Subversion_Input_Filters]] for commit checks.<br />
<br />
=== Create Repository ===<br />
<br />
This is tested on Debian GNU/Linux and it may or may not work on other operating systems.<br />
<br />
sudo svnadmin create /directory/to/the/project/<br />
sudo chown -R www-data:www-data /directory/to/the/project/<br />
sudo vim /etc/apache2/mods-enabled/dav_svn.conf<br />
<br />
add:<br />
<br />
<br />
<Location /svn/ProjectPath><br />
DAV svn<br />
SVNPath /directory/to/the/project<br />
AuthType Basic<br />
AuthName "Subversion Repository"<br />
AuthUserFile /project/passwords/file.passwords<br />
<br />
<LimitExcept GET PROPFIND OPTIONS REPORT><br />
Require valid-user<br />
</LimitExcept><br />
</Location><br />
<br />
== Example Repositories ==<br />
<br />
http://www.na-mic.org/websvn/</div>Andyhttps://www.na-mic.org/w/index.php?title=Slicer3:Developers&diff=6052Slicer3:Developers2007-01-08T19:42:21Z<p>Andy: /* Slicer 3 Quick links */</p>
<hr />
<div>{| class="toccolours" style="margin-right: 25px" align="right"<br />
! bgcolor="#ccccff" align="center" | Slicer3<br />
|-<br />
|<br />
[[Slicer3|Home]]<br />
|-<br />
|<br />
[[Slicer3:About|About]]<br />
|-<br />
|<br />
[[Slicer3:FAQ|FAQ]]<br />
|-<br />
|<br />
[[Slicer3:Status|Status]]<br />
|-<br />
|<br />
[[Slicer3:Downloads|Downloads]]<br />
|-<br />
|<br />
[[Slicer3:Documentation|Documentation]]<br />
|-<br />
|<br />
[[Slicer3:Community_Support|Community Support]]<br />
|-<br />
| '''Developers'''<br />
|-<br />
|<br />
[[Slicer3:Acknowledgements|Acknowledgements]]<br />
|-<br />
|<br />
[[Slicer3:Links|Links]]<br />
|}<br />
<br />
== Slicer 3 Overview ==<br />
[[Image:Slicer3LogoHorizontalBeta.png]]<br />
<br />
* For more details on the slicer architecture see: [http://www.na-mic.org/Wiki/images/e/e3/Slicer_3-alpha-2006-04-03.ppt Architecture Slides].<br />
* Highlights of the new architecture<br />
<br />
{|<br />
|[[Image:Slicer3-Architecture.jpg|thumb|200px]]<br />
|[[Image:Slicer3-Architecture-MRML.jpg|thumb|200px]]<br />
|[[Image:Slicer3-Architecture-Layers.jpg|200px|thumb]]<br />
|[[Image:ExecutionModelPlugins.png|200px|thumb]]<br />
|}<br />
<br />
* GUI anatomy<br />
<br />
== Information for Developers ==<br />
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers. The content is currently being developed for the January AHM.<br />
<br />
* Introduction to Slicer3 (Steve)<br />
** [[Slicer3:Build_Instructions | Getting the software and troubleshooting]]<br />
** [[Slicer3:Status_Summary | Status overview]] and Demo<br />
** Overall Architecture and Coding Conventions<br />
** [[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]<br />
* Two module types (Command line and Interactive)<br />
** [[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] (Jim and Bill - already on wiki)<br />
**[[Slicer3:UIEngineering#How_to_draft_a_Slicer_module_.28MyModule.29_GUI_class | How to add an interactive module]] (wjp)<br />
* MRML (Alex)<br />
** [[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]] (Alex)<br />
** [[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]] (Alex)<br />
** [[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]] (Alex)<br />
* GUI<br />
** Keeping the GUI stateless (wjp)<br />
** [[Slicer3:EventBindings | Adding keyboard shortcuts]] (wjp)<br />
** [[Slicer3:Interface_Design#General_Principles | GUI style guidelines for consistent look & feel]] (wjp)<br />
** [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]] (Jim)<br />
* Engineering<br />
** Tips for avoiding memory leaks<br />
*** Current Practice (Steve)<br />
*** [[Slicer3:Memory Management | Suggested change to SmartPointers]] (Jim)<br />
** Generating tests (Bill)<br />
* Where to go for help (Steve)<br />
* Status Review and Plan (Steve)<br />
<br />
== Slicer 3 Projects ==<br />
<br />
Updated November 2006 to reflect activities in preparation for January 2007 AHM. Projects should correspond to the outstanding issues listed on the '''[[Slicer3:Status_Summary|Status Summary]]'''. Please refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.<br />
<br />
''If your name is in bold, you are responsible for that aspect of the project''<br />
<br />
* '''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)<br />
* '''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)<br />
* '''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)<br />
* '''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan)<br />
** See [[Slicer3:EventBindings|Slicer3:EventBindings]].<br />
* '''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)<br />
** [[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]<br />
** [[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''<br />
** [[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''<br />
** [[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''<br />
** [[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''<br />
** [[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''<br />
* '''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)<br />
* '''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')<br />
* '''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)<br />
* '''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')<br />
<br />
== Slicer 3 Quick links ==<br />
<br />
The Slicer3 svn repository:<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
<br />
([[Engineering:SandBox|Instructions for NA-MIC svn]]).<br />
<br />
[[Slicer3:Build_Instructions|Slicer3 build instructions]] can be found on the wiki.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Doxygen documentation for Slicer3].<br />
<br />
A [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.<br />
<br />
Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].<br />
<br />
[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard]<br />
<br />
[http://www.na-mic.org/Bug/index.php Slicer Bug Tracker] (offline right now)<br />
<br />
Discussion of slicer3 takes place on the slicer-devel@bwh.harvard.edu list. To join developer's mailing list, send a request to: [mailto:slicer-devel-request@lists.bwh.harvard.edu slicer-devel-request@lists.bwh.harvard.edu] with the keyword ''subscribe'' as the subject.<br />
<br />
== Design Information ==<br />
<br />
May 23, 2006: [[Algorithms:Core1Visit_May06|Algorithm Core workshop.]]<br />
<br />
<br /> April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.<br />
<br />
<br /><br />
<br />
= Events =<br />
<br />
== Upcoming ==<br />
<br />
=== Slicer3.0 Beta ===<br />
<br />
* Official release at [[AHM_2007 | AHM January 2007]]<br />
<br />
=== Migration Tutorials (from Slicer 2.x to 3.0) by March 2007 ===<br />
<br />
* First set of Migration tutorials by Jan 1, 2007<br />
* Second set of Migration tutorials by Feb 1, 2007<br />
* Complete by March 2007<br />
<br />
== Past ==<br />
<br />
=== April 3, 2006 ===<br />
<br />
There was a [[Slicer3:_Alpha1_Meeting|Slicer3 Alpha1 Design Review]] meeting.<br />
<br />
'''[[Slicer3:Alpha|Definition of Alpha Milestone]]'''<br />
<br />
=== Slicer3 Alpha2/Beta1 by End of July 2006 ===<br />
<br />
* Initial Testing with Core 3 participation<br />
* Base functionality in place, but still subject to API changes and other improvements.<br />
* Packaged versions not yet available, but testers are able to easily build their own versions.<br />
<br />
=== Implementation of Slicer3 Alpha1 by end of March 2006 ===</div>Andyhttps://www.na-mic.org/w/index.php?title=Salt_Lake_AHM:AHM_Main_Page&diff=5967Salt Lake AHM:AHM Main Page2007-01-07T18:33:17Z<p>Andy: Redirecting to AHM 2005:Main</p>
<hr />
<div>#REDIRECT [[AHM_2005:Main]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Goals_for_Data_Management_%26_Workflow_Milestones&diff=5966Goals for Data Management & Workflow Milestones2007-01-07T18:30:36Z<p>Andy: Redirecting to Mbirn: Goals for Data Management and Workflow Milestones</p>
<hr />
<div>#REDIRECT [[Mbirn: Goals for Data Management and Workflow Milestones]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Mbirn:_Goals_for_Data_Management_%26amp;_Workflow_Milestones&diff=5965Mbirn: Goals for Data Management & Workflow Milestones2007-01-07T18:30:15Z<p>Andy: Redirecting to Mbirn: Goals for Data Management and Workflow Milestones</p>
<hr />
<div>#REDIRECT [[Mbirn: Goals for Data Management and Workflow Milestones]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Mbirn:_Goals_for_Data_Management_and_Workflow_Milestones&diff=5964Mbirn: Goals for Data Management and Workflow Milestones2007-01-07T18:29:59Z<p>Andy: </p>
<hr />
<div>== From: Morphometry BIRN Annual Meeting, Miami, Mar 2-4, 2005 ==<br />
<br />
'''Participants'''<br />
<br />
N. Aucoin, J. Sacks, D.Kennedy, H. Schmidt, M. Mendis, S.Murphy, A.Toga, C. Fennema-Notestine, K.Crawford, R. Nor, D. Marcus, R. Buckner, J. Grethe, D. Keator, M. Miller, T.Brown<br />
<br />
----<br />
<br />
'''Agenda and Goals'''<br />
<br />
* [[Data_Provenance:Goals|Goals and Milestones For Data Provenance]]<br />
* [[Goals_for_Data_Management_%26_Workflow_Milestone|Goals for Data Management]]<br />
* [[Goals_for_Workflow|Goals for Workflow]]<br />
<br />
----<br />
<br />
* [[Media:Comp_Inf_Mar05_milestones.ppt| Powerpoint of Data Management Goals]]<br />
<br />
----</div>Andyhttps://www.na-mic.org/w/index.php?title=FBIRN:NeuroinfMonPM&diff=5961FBIRN:NeuroinfMonPM2007-01-07T18:11:29Z<p>Andy: </p>
<hr />
<div>Back to [[FBIRN:retreat2006|FBIRN March 2006 AHM]]</div>Andyhttps://www.na-mic.org/w/index.php?title=User:Jfallon&diff=5957User:Jfallon2007-01-07T18:02:39Z<p>Andy: </p>
<hr />
<div>Attached is a montage of the meeting of Core 1 (Georgia Tech Tannenbaum lab) and Core 3 (UC Irvine Fallon Potkin Kuester) this past long weekend (Thurs-Sun) as per Salt Lake City NAMIC meeting directive to "...put Fallon's brain into Tannenbaum's computer..." ie Neuroanatomical structures with many shape types and levels of difficulty into mathematical shape algorithms.<br />
<br />
<br /> Very successful meeting.<br />
<br />
[[Image:Fallon_Tannenbaum_Kuester_labs_LR.jpg|600px]]<br />
<br />
Top left- Allen Tannenbaum, John Melonak, Jim Fallon, Ramsey Al-Hakim (Fallon house) Top right- Fallon (Fallon house) Middle left- Tannenbaum, Fallon Middle right-Zhiyu He, Falko Kuester, Ramsey Al-Hakim, John Melonak, Jim Fallon, Martina Panzenboeck (Kuester UCI Visualization Lab) Lower left- John Melonak, Zhiyu He, Ramsey Al-Hakim (Kuester UCI Visualization Lab) Lower right- Allen Tannenbaum, Steven Potkin, Ramsey Al-Hakim, Thang Nguyen (Fallon house)<br />
<br />
Not shown- Fri mtg at UC Irvine BIRN/NAMIC lab/conf room</div>Andyhttps://www.na-mic.org/w/index.php?title=MorphBIRN_02.03.2005&diff=5956MorphBIRN 02.03.20052007-01-07T17:55:52Z<p>Andy: Redirecting to Mbirn: MorphBIRN 02.03.2005</p>
<hr />
<div>#REDIRECT [[Mbirn: MorphBIRN 02.03.2005]]</div>Andyhttps://www.na-mic.org/w/index.php?title=BIRN_Portal/SRB&diff=5955BIRN Portal/SRB2007-01-07T17:55:12Z<p>Andy: Redirecting to Mbirn: BIRN Portal/SRB</p>
<hr />
<div>#REDIRECT [[Mbirn: BIRN Portal/SRB]]</div>Andyhttps://www.na-mic.org/w/index.php?title=BIRN_Rocks_Releases&diff=5954BIRN Rocks Releases2007-01-07T17:44:39Z<p>Andy: Redirecting to Mbirn: BIRN Rocks Releases</p>
<hr />
<div>#REDIRECT [[Mbirn: BIRN Rocks Releases]]</div>Andyhttps://www.na-mic.org/w/index.php?title=AHM_2005:Main&diff=5953AHM 2005:Main2007-01-07T17:41:08Z<p>Andy: </p>
<hr />
<div>'''Venue'''<br />
<br />
* Hotel Monaco ( http://www.monaco-saltlakecity.com/index.html )<br />
* Local contact: Raelynn Potts (rpotts at sci.utah.edu), SCI Institute, 50 S. Central Campus Dr., Room 3490 MEB, Salt Lake City, UT 84112,Phone: 801-585-5983,Fax: (801) 585-6513<br />
* [[AHM_2005:logistics|Logistics]]<br />
* [[AHM_2005:AHM_Attendee_List|List of Attendees]]<br />
* [[AHM_2005:Discussion_of_Agenda|Discussion Topics]]<br />
* [[AHM_2005:Feedback|Attendee Feedback]]<br />
* External Links to Photos from the meeting : [http://sylvain.homelinux.org/~sylvain/gallery/album50 Sylvain's Photos from Day -1] [http://web.media.mit.edu/~halazar/pics/slc_02_2005 Photos from Day 0] [http://web.media.mit.edu/~halazar/pics/slc_02_2005_d1 Photos from Day 1] [http://www.cs.unc.edu/~styner/pics/SLC04 Martin's Photos & Movies]<br />
<br />
'''Schedule'''<br />
<br />
'''Day 0 (Sunday, Feb 20, 2005): DTI Workshop'''<br />
<br />
* 9:00-9:15am Breakfast and Introduction (Kapur)<br />
* 9:15am-10:15am Q/A session to address ITK/Slicer questions of core 1 researchers/engineers and to demo any NAMIC algorithms developed so far<br />
* [[AHM_2005:DTI_Workshop|Agenda for DTI Workshop]], 10:15am-5pm<br />
** Workgroup to discuss engineering infrastructure to support DTI processing and DTI representation in ITK, VTK, and Slicer.<br />
<br />
[http://web.media.mit.edu/~halazar/pics/slc_02_2005 Photos from Day 0]<br />
<br />
'''Day 1 (Monday, Feb 21, 2005): Progress Reports'''<br />
<br />
* 08:30—09:00 am Breakfast<br />
* 09:00—09:15 am Introduction (Kikinis, [[Media:Intro-Feb-20-2005.ppt|Ron's Intro]])<br />
* 09:15—09:45 am Update: Core 3.1 DBP ([[Media:Core_3.1_new.ppt|Kubickis]] & [[Media:Core_3.1-2_Saykin-rev.ppt|Saykins talk]] )<br />
* 09:45—10:15 am Update: Core 3.2 DBP ([[Media:NAMIC_Core_3.2_2.20.05.ppt|Potkin & Kennedy talk ]])<br />
* 10:15—10:45 am Update: Core 1 (Grimson, [[Media:Core1_AHM_02_19_05.ppt|Core 1 Overview]])<br />
* 10:45—11:00 am Update: Core 2 (Lorensen, [[Media:Core2Progress.ppt|Core 2 Overview]])<br />
* 11:00—11:20 am Break<br />
* 11:20—11:30 am Update: Core 4 (Schroeder, [[Media:Core4Progress-AHM-SLC-Feb05.ppt|Core 4 Progress]])<br />
* 11:30—11:40 am Update: Core 5 (Gollub, [[Media:Core5_AHM.ppt|Training Update]])<br />
* 11:40—11:50 am Update: Core 6 (Pieper [[Media:NAMIC-Dissemination-2005-02-21.ppt| Dissemination Update]])<br />
* 11:50—12:00 am Update: Core 7 (Manandhar [[Media:ManagementUpdate.ppt| ManagementUpdate ]])<br />
<br />
'''Working Meetings'''<br />
<br />
* 12-1:30pm "What Core 3 wants from Cores 1&2" (Facilitator: Ron Kikinis)<br />
** [[DataRepository|Data downloading]] (Tina Kapur)<br />
** Core 3.1 ([[Media:HarvardWishList.ppt|Kubicki]], [[Media:Saykin-Core_3.1-2_What_we_Need.ppt|Saykin]])<br />
** Core 3.2 (Jim Fallon & Jim Kennedy [[Media:NAMIC_Fallon_final_edit.ppt| Powerpoint]])<br />
* 1:30-3:50pm Engineering Topics (Facilitator: Bill Lorensen)<br />
** [[Media:SoftwareEngineeringOverview.ppt|Software Engineering Process]] (Bill Lorensen)<br />
** [[Media:Dart2.ppt|Software Quality, Past, Present, Future]] (Dan Blezek)<br />
** [[Media:NA-MIC-dataflow-02-2005.ppt|Dataflow Discussion]]<nowiki>: why, where, and how NAMIC would use data flow architecture (Guido Gerig) </nowiki><br />
** [http://www.loni.ucla.edu/twiki/pub/Pipeline/PresentationSlides/pipeline.050221.ppt LONI pipeline presentation] (Michael Pan)<br />
** [[Media:ImageCoordinateSystem.ppt|Image Coordinate System]] (Bill Lorensen)<br />
** [[Media:NA-MICahm_UCSDengCore2.ppt|Infrastructure and Grid Computing]] (Jeff Grethe)<br />
* 3:50-4pm Break<br />
* 4-5:30pm (Facilitator: Eric Grimson)<br />
** [[Media:Publications_guidelines.ppt|Publications presentation]], [[Media:NAMIC_Publications_Guidelines.pdf|Draft of Proposed Publications Guidelines]]<br />
** [[Media:IP_Issues.ppt|IP issues]], [[Media:License-namic.ppt|Software License Issues]]<br />
** [[Media:NA-MIC-DataSharing.ppt|Data Sharing]]<br />
* 5:30-6pm: Roadmap Update, General discussion (Stephen Wong, Ron Kikinis)<br />
<br />
[http://web.media.mit.edu/~halazar/pics/slc_02_2005 Photos from Day 0] [http://web.media.mit.edu/~halazar/pics/slc_02_2005_d1 Photos from Day 1]<br />
<br />
'''Day 2 (Tuesday, Feb 22, 2005): Working Meetings and Plans for the Future'''<br />
<br />
* 8-9am: [[Media:FMRI-sw-NA-MIC-02-04-distribute.ppt]] (Sandy Wells)<br />
* 9-10am: [[Media:ShapeAnalysisDiscussion-1.ppt|Challenges of Shape Analysis]],[http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:ShapeAnalysis:AHHFeb05SLC_Minutes<br />
<br />
Minutes of the discussion] (Polina Golland, Martin Styner)<br />
<br />
* 10-10:15am Break<br />
* 10:15-11am: [[Media:Namic_levelsets.tannenbaum.ppt|Level-set segmentation]]<nowiki>: what it is/not good for (Allen Tannebaum) </nowiki><br />
* 11am-12:00 (Kikinis)<br />
** Potential use of an electronic journal (Luis Ibanez [[Media:InsightOpenScience.ppt|NIH Open Access Policy and the Insight Journal]])<br />
* 12-12:30pm Lunch<br />
* 12:30—2:00pm Breakout Core sessions for future planning and working lunch<br />
** Core 1: DTI versus fMRI versus morphometry (Grimson)<br />
** Core 2: Sandboxes (Lorensen)<br />
** Core 3: Prospective Data Acquisitions (Kubicki, Saykin, Kennedy, Potkin)<br />
* 2:00—3:00 pm Breakout session summaries(each 10 minutes presentation and 10 minutes discussion)<br />
* 03pm Conclusion<br />
* 03pm— Informal subgroup meetings and discussions<br />
<br />
[http://www.cs.unc.edu/~styner/pics/SLC04 Martin's Photo collection (including 2 movies in the Sushi restaurant...)]</div>Andyhttps://www.na-mic.org/w/index.php?title=2007_Project_Half_Week&diff=59522007 Project Half Week2007-01-07T17:39:57Z<p>Andy: /* NA-MIC Kit */</p>
<hr />
<div>Back to [[AHM_2007|AHM_2007]]<br />
<br />
== Results ==<br />
Results of this event will be summarized here after it is completed.<br />
<br />
==Please note==<br />
* Everyone should '''bring a laptop'''. We will have three or four projectors.<br />
* About half the time will be spent working on projects and the other half in project related discussions.<br />
<br />
== Projects ==<br />
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page. <br />
<br />
===Structural Analysis===<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]<br />
# Scripts to run and visualize [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]<br />
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] <br />
#SVM Shape Analysis (Brad, Polina, Martin)<br />
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration (Stephen, Jim, Ross)]] [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]<br />
## Driving problem: Congealing with B-spline (Lilla, Stephen)<br />
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)<br />
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]<br />
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]<br />
<br />
===Diffusion Image Analysis===<br />
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]<br />
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]<br />
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]<br />
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]<br />
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]<br />
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]<br />
#ITK Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)<br />
<br />
===NA-MIC Kit===<br />
#Slicer3 Infrastructure Projects<br />
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)<br />
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)<br />
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)<br />
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]<br />
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]<br />
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)<br />
###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]<br />
###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]<br />
###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''<br />
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''<br />
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''<br />
###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''<br />
###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''<br />
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)<br />
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]<br />
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')<br />
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)<br />
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')<br />
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[Image:2007_Project_Half_Week_GridExecution.ppt]]<br />
#Tractography in Slicer3 (Lauren, Raul)<br />
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.<br />
<br />
===External Collaborations===<br />
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT 2007]]<br />
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]<br />
#Radiology Workstation Module for Slicer3 (Pat, Steve)<br />
#vmtk module for Slicer [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 2007 Project Half Week vmtkSlicerModule.ppt]] (Luca Antiga, Jim Miller)<br />
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]] <br />
##Voxel meshing as an execuation module in Slicer3 [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)<br />
##Mesh Quality Visualization Development [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)<br />
##Bounding Box Projection Meshing [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)<br />
##Tetrahedral Mesh Generation Tools in VTK [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)<br />
#Nonhuman Primate slicer Module (Alcohol Exposure)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT]] (Kilian Pohl, Chris Wyatt)<br />
<br />
----<br />
This following is a list of projects carried out at the last project week (summer 2006). For new attendees, these projects can be used as templates. For attendees involved in the last project week, please move projects from the list below to the list above if you intend to continue these projects. And please do add a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT for 2007]].<br />
<br />
=== 2006 Structural Analysis ===<br />
<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Xavier Le Faucheur, GT, Delphine Nain, GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez, Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/ShapeStatisticsWithPermTestCorrectionAndFDR|ITK statistical analysis using non-parametric permutation analysis and false discovery rate]] (Martin Styner, UNC): [[Media:2006_06_PW_StatAnal.ppt| 4 block PPT 2006 ]]<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/Correspondence|Local curvature based correspondence in ITK]] (Ipek Oguz, Martin Styner, UNC): [[Media:2006_MIT_Project_Week_LocalCurvatureBasedCorrespondence.ppt| 4 block PPT 2006]]<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/FemaleSPDCaudates|Shape analysis of female SPD dataset]] (Jim Levitt, PNL, Marc Niethammer, PNL, Sylvain Bouix, PNL, Martin Styner, UNC): [[Media:2006_06_PW_female_SPD.ppt| 4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Structural/Mesh/Mesh_Untangling|Mesh Untangling]] (Gheorghe Postelnicu, MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_Mesh_Untangling.ppt|4 block PPT 2006]]<br />
# [[NA-MIC/Projects/Structural/Registration/Histology_MR_Registration|MR Histology Registration]] (Gheorghe Postelnicu MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_MGH_Histology_MR_Registration.ppt|4 block PPT 2006]]<br />
<br />
=== 2006 Diffusion Image Analysis ===<br />
<br />
# [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|ITK DTI Image Processing Modules]] (Casey Goodlett UNC, Tom Fletcher Utah, Bill Lorensen GE, John Melonakos GT/GE): [[Media:2006_Summer_Project_Week_DTI_Processing.ppt|4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fiber_Tools_Slicer_Integration|Fiber Tools / Slicer 3 Integration]] (Casey Goodlett UNC, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_FiberTracking_Slicer_Integration.ppt|4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Stochastic_Fiber_Tracing_Applications|Stochastic Fiber Tracing Applications]] (C-F Westin, Marek Kubicki, Raul San-Jose, AW de Vries, All LMI):[[Media:2006_Summer_Project_Week_stochastictracking.ppt| 4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Slicer_Fiber_Anatomical_Labeling|Slicer Fiber (Model) Labeling Interface]] (Lauren O'Donnell MIT, Marek Kubicki BWH) :[[Media:2006_Summer_Project_Week_ModelLabel.ppt| 4-block PPT 2006]]<br />
<br />
=== 2006 FMRI Image Analysis ===<br />
<br />
# [[NA-MIC/Projects/Structural/Conformal_Flattening_in_ITK|Conformal Flattening in ITK]](Yi Gao GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware, Marc Niethammer BWH): [[Media:2006_Summer_Project_Week_ConformalFlattening.ppt| 4-block PPT 2006]]<br />
# [[NA-MIC/Projects/fMRI_Analysis/Spatial_Regularization_for_fMRI_Detection|Spatial Regularization in fMRI Analysis]](Wanmei Ou, Polina Golland, Sandy Wells, and Carsten) [[Media:2006_Summer_Project_Week_fMRIMRF.ppt| 4-block PPT 2006]]<br />
<br />
=== 2006 NA-MIC Kit ===<br />
<br />
# [[2006_Project_Week_MIT_SlicerUI|Slicer3 Interface]] (Wendy Plesniak, Sebastien Barre, Steve Pieper, Mathieu Malaterre, Randy Gollub, Michael Halle), [[Media:2006_Summer_Project_Week_Slicer3UI.ppt|4-block PPT 2006]]<br />
# [[2006_Project_Week_MIT_Migrating_Slicer2.x_Modules_to_Slicer3|Migrating Slicer2.x Modules to Slicer3]] (Nicole Aucoin, Mathieu Malaterre, Katie Hayes, Bill Lorensen): [[Media:2006_Summer_Project_Week_Migrating_Slicer2x_Modules_to_Slicer3.ppt|4-block PPT 2006]]<br />
# [[2006_Project_Week_Kitware_Slicer3_Packaging|Slicer3 Packaging]] (Andy Cedilnik, Steve Pieper) [[Media:2006_Summer_Project_Week_Slicer3_Packaging.ppt|4-block PPT 2006]]<br />
# [[2006_Project_Week_MIT_Grid_Integration|Slicer3 Grid Integration]] (Jeff Grethe, Brendan Faherty, Steve Pieper, Katie Hayes), [[Media:2006_Summer_Project_Week_Grid_Interface_for_Slicer3.ppt|4-block PPT 2006]]<br />
# [[2006_Project_Week_MIT_LONIPipelineIntegration|Slicer3 Pipeline Integration ]] (Jagadeeswaran Rajendiran, Martin Styner, Steve Pieper), [[Media:2006_Summer_Project_Week_Jagadeeswaran_June30.ppt|4 block PPT 2006]]<br />
# [[2006_Project_MGH_File_Format_Converter|2006 Project MGH File Format Converter]](Gheorghe Postelnicu, Bill Lorensen) [[Media:2006_Summer_Project_MIT_MGH_IO.ppt|4-block PPT 2006]]<br />
# Volumetric Meshing (Kiran Shivanna, Vincent Magnotta, Nicole Grosland):[[Media:2006_Summer_Project_Week_Volumetric_Meshing.ppt|4-block PPT 2006]]<br />
# Dicom Query/Retrieve (Eduardo Suárez, Rafael Nebot, Steve Pieper, Jim Miller):[[Media:2006_Summer_Project_Week_Slicer_Query_Retrieve.ppt|4-block PPT 2006]]<br />
# A Translation Station for Imaging (Pat Mongkolwat, Alex Kogan, Tom Lechner, Steve Pieper, Wendy Plesniak):[[Media:2006_Project_Week_MIT_IntegrateSlicerWith_A_PACS_Workstation.ppt|4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Slicer3_for_IGT/Converting_vtkFMRIEngine_and_vtkMRAblation_to_Slicer3_modules|Converting vtkFMRIEngine and vtkMRAblation to Slicer3 modules]] (Noby Hata, Haiying Liu, Steve Pieper, Jim Miller): [[Media:2006_Summer_Project_Week_Slicer3_IGT.ppt| 4-block ppt 2006]]<br />
<br />
=== 2006 NA-MIC Kit Support for Non-Medical Data ===<br />
<br />
# ITK IO support for reading astronomy data and coordinates from FITS files (Douglas Alan IIC, Michael Halle BWH/IIC, Luis Ibanez Kitware)[[Media:2006_Summer_Project_Week_Astronomy_FITS_Reader_Prelim_Results.ppt| 4-block PPT 2006]]<br />
<br />
== Logistics ==<br />
<br />
'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)<br />
<br />
'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].<br />
<br />
== Background and Preparation ==<br />
<br />
We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.<br />
<br />
=== Goals ===<br />
<br />
The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.<br />
<br />
* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.<br />
* The event is open to people outside NA-MIC, subject to availability.<br />
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br />
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br />
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.<br />
* This is not an introduction to the components of the NA-MIC Kit.<br />
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.<br />
<br />
=== Preparation for the workshop ===<br />
<br />
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]<br />
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]<br />
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)<br />
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]<br />
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)<br />
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]<br />
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
== A History in Wiki Links ==<br />
<br />
A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].</div>Andyhttps://www.na-mic.org/w/index.php?title=2007_Project_Half_Week&diff=59502007 Project Half Week2007-01-07T17:39:32Z<p>Andy: /* NA-MIC Kit */</p>
<hr />
<div>Back to [[AHM_2007|AHM_2007]]<br />
<br />
== Results ==<br />
Results of this event will be summarized here after it is completed.<br />
<br />
==Please note==<br />
* Everyone should '''bring a laptop'''. We will have three or four projectors.<br />
* About half the time will be spent working on projects and the other half in project related discussions.<br />
<br />
== Projects ==<br />
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page. <br />
<br />
===Structural Analysis===<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]<br />
# Scripts to run and visualize [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]<br />
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] <br />
#SVM Shape Analysis (Brad, Polina, Martin)<br />
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration (Stephen, Jim, Ross)]] [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]<br />
## Driving problem: Congealing with B-spline (Lilla, Stephen)<br />
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)<br />
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]<br />
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]<br />
<br />
===Diffusion Image Analysis===<br />
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]<br />
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]<br />
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]<br />
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]<br />
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]<br />
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]<br />
#ITK Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)<br />
<br />
===NA-MIC Kit===<br />
#Slicer3 Infrastructure Projects<br />
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)<br />
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)<br />
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)<br />
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]<br />
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]<br />
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)<br />
###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]<br />
###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]<br />
###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''<br />
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''<br />
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''<br />
###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''<br />
###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''<br />
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)<br />
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]<br />
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')<br />
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)<br />
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')<br />
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[Media:2007_Project_Half_Week_GridExecution.ppt]]<br />
#Tractography in Slicer3 (Lauren, Raul)<br />
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.<br />
<br />
===External Collaborations===<br />
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT 2007]]<br />
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]<br />
#Radiology Workstation Module for Slicer3 (Pat, Steve)<br />
#vmtk module for Slicer [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 2007 Project Half Week vmtkSlicerModule.ppt]] (Luca Antiga, Jim Miller)<br />
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]] <br />
##Voxel meshing as an execuation module in Slicer3 [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)<br />
##Mesh Quality Visualization Development [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)<br />
##Bounding Box Projection Meshing [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)<br />
##Tetrahedral Mesh Generation Tools in VTK [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)<br />
#Nonhuman Primate slicer Module (Alcohol Exposure)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT]] (Kilian Pohl, Chris Wyatt)<br />
<br />
----<br />
This following is a list of projects carried out at the last project week (summer 2006). For new attendees, these projects can be used as templates. For attendees involved in the last project week, please move projects from the list below to the list above if you intend to continue these projects. And please do add a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT for 2007]].<br />
<br />
=== 2006 Structural Analysis ===<br />
<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Xavier Le Faucheur, GT, Delphine Nain, GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez, Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/ShapeStatisticsWithPermTestCorrectionAndFDR|ITK statistical analysis using non-parametric permutation analysis and false discovery rate]] (Martin Styner, UNC): [[Media:2006_06_PW_StatAnal.ppt| 4 block PPT 2006 ]]<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/Correspondence|Local curvature based correspondence in ITK]] (Ipek Oguz, Martin Styner, UNC): [[Media:2006_MIT_Project_Week_LocalCurvatureBasedCorrespondence.ppt| 4 block PPT 2006]]<br />
# [[NA-MIC/Projects/Structural/Shape_Analysis/FemaleSPDCaudates|Shape analysis of female SPD dataset]] (Jim Levitt, PNL, Marc Niethammer, PNL, Sylvain Bouix, PNL, Martin Styner, UNC): [[Media:2006_06_PW_female_SPD.ppt| 4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Structural/Mesh/Mesh_Untangling|Mesh Untangling]] (Gheorghe Postelnicu, MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_Mesh_Untangling.ppt|4 block PPT 2006]]<br />
# [[NA-MIC/Projects/Structural/Registration/Histology_MR_Registration|MR Histology Registration]] (Gheorghe Postelnicu MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_MGH_Histology_MR_Registration.ppt|4 block PPT 2006]]<br />
<br />
=== 2006 Diffusion Image Analysis ===<br />
<br />
# [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|ITK DTI Image Processing Modules]] (Casey Goodlett UNC, Tom Fletcher Utah, Bill Lorensen GE, John Melonakos GT/GE): [[Media:2006_Summer_Project_Week_DTI_Processing.ppt|4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fiber_Tools_Slicer_Integration|Fiber Tools / Slicer 3 Integration]] (Casey Goodlett UNC, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_FiberTracking_Slicer_Integration.ppt|4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Stochastic_Fiber_Tracing_Applications|Stochastic Fiber Tracing Applications]] (C-F Westin, Marek Kubicki, Raul San-Jose, AW de Vries, All LMI):[[Media:2006_Summer_Project_Week_stochastictracking.ppt| 4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Slicer_Fiber_Anatomical_Labeling|Slicer Fiber (Model) Labeling Interface]] (Lauren O'Donnell MIT, Marek Kubicki BWH) :[[Media:2006_Summer_Project_Week_ModelLabel.ppt| 4-block PPT 2006]]<br />
<br />
=== 2006 FMRI Image Analysis ===<br />
<br />
# [[NA-MIC/Projects/Structural/Conformal_Flattening_in_ITK|Conformal Flattening in ITK]](Yi Gao GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware, Marc Niethammer BWH): [[Media:2006_Summer_Project_Week_ConformalFlattening.ppt| 4-block PPT 2006]]<br />
# [[NA-MIC/Projects/fMRI_Analysis/Spatial_Regularization_for_fMRI_Detection|Spatial Regularization in fMRI Analysis]](Wanmei Ou, Polina Golland, Sandy Wells, and Carsten) [[Media:2006_Summer_Project_Week_fMRIMRF.ppt| 4-block PPT 2006]]<br />
<br />
=== 2006 NA-MIC Kit ===<br />
<br />
# [[2006_Project_Week_MIT_SlicerUI|Slicer3 Interface]] (Wendy Plesniak, Sebastien Barre, Steve Pieper, Mathieu Malaterre, Randy Gollub, Michael Halle), [[Media:2006_Summer_Project_Week_Slicer3UI.ppt|4-block PPT 2006]]<br />
# [[2006_Project_Week_MIT_Migrating_Slicer2.x_Modules_to_Slicer3|Migrating Slicer2.x Modules to Slicer3]] (Nicole Aucoin, Mathieu Malaterre, Katie Hayes, Bill Lorensen): [[Media:2006_Summer_Project_Week_Migrating_Slicer2x_Modules_to_Slicer3.ppt|4-block PPT 2006]]<br />
# [[2006_Project_Week_Kitware_Slicer3_Packaging|Slicer3 Packaging]] (Andy Cedilnik, Steve Pieper) [[Media:2006_Summer_Project_Week_Slicer3_Packaging.ppt|4-block PPT 2006]]<br />
# [[2006_Project_Week_MIT_Grid_Integration|Slicer3 Grid Integration]] (Jeff Grethe, Brendan Faherty, Steve Pieper, Katie Hayes), [[Media:2006_Summer_Project_Week_Grid_Interface_for_Slicer3.ppt|4-block PPT 2006]]<br />
# [[2006_Project_Week_MIT_LONIPipelineIntegration|Slicer3 Pipeline Integration ]] (Jagadeeswaran Rajendiran, Martin Styner, Steve Pieper), [[Media:2006_Summer_Project_Week_Jagadeeswaran_June30.ppt|4 block PPT 2006]]<br />
# [[2006_Project_MGH_File_Format_Converter|2006 Project MGH File Format Converter]](Gheorghe Postelnicu, Bill Lorensen) [[Media:2006_Summer_Project_MIT_MGH_IO.ppt|4-block PPT 2006]]<br />
# Volumetric Meshing (Kiran Shivanna, Vincent Magnotta, Nicole Grosland):[[Media:2006_Summer_Project_Week_Volumetric_Meshing.ppt|4-block PPT 2006]]<br />
# Dicom Query/Retrieve (Eduardo Suárez, Rafael Nebot, Steve Pieper, Jim Miller):[[Media:2006_Summer_Project_Week_Slicer_Query_Retrieve.ppt|4-block PPT 2006]]<br />
# A Translation Station for Imaging (Pat Mongkolwat, Alex Kogan, Tom Lechner, Steve Pieper, Wendy Plesniak):[[Media:2006_Project_Week_MIT_IntegrateSlicerWith_A_PACS_Workstation.ppt|4-block PPT 2006]]<br />
# [[NA-MIC/Projects/Slicer3_for_IGT/Converting_vtkFMRIEngine_and_vtkMRAblation_to_Slicer3_modules|Converting vtkFMRIEngine and vtkMRAblation to Slicer3 modules]] (Noby Hata, Haiying Liu, Steve Pieper, Jim Miller): [[Media:2006_Summer_Project_Week_Slicer3_IGT.ppt| 4-block ppt 2006]]<br />
<br />
=== 2006 NA-MIC Kit Support for Non-Medical Data ===<br />
<br />
# ITK IO support for reading astronomy data and coordinates from FITS files (Douglas Alan IIC, Michael Halle BWH/IIC, Luis Ibanez Kitware)[[Media:2006_Summer_Project_Week_Astronomy_FITS_Reader_Prelim_Results.ppt| 4-block PPT 2006]]<br />
<br />
== Logistics ==<br />
<br />
'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)<br />
<br />
'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].<br />
<br />
== Background and Preparation ==<br />
<br />
We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.<br />
<br />
=== Goals ===<br />
<br />
The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.<br />
<br />
* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.<br />
* The event is open to people outside NA-MIC, subject to availability.<br />
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.<br />
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.<br />
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.<br />
* This is not an introduction to the components of the NA-MIC Kit.<br />
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.<br />
<br />
=== Preparation for the workshop ===<br />
<br />
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]<br />
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]<br />
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)<br />
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]<br />
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)<br />
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]<br />
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
== A History in Wiki Links ==<br />
<br />
A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].</div>Andyhttps://www.na-mic.org/w/index.php?title=IGT:2005_Nov_16_IGT_Consortium_Kickoff&diff=5949IGT:2005 Nov 16 IGT Consortium Kickoff2007-01-07T17:38:13Z<p>Andy: /* Place/Time */</p>
<hr />
<div>= Meeting Agenda =<br />
<br />
== 1. Introduction of Projects (getting to know each other) '''10:15-2:00''' ==<br />
<br />
Each party presents Example Applications, Design, Requirements, Codying Style, Dashboard, Choice of linked tool, License, Support, etc<br />
<br />
Each party is expected to upload PPT files (and/or their handouts in PDF) after the workshop.<br />
<br />
* IGSTK (Kevin Cleary)'''(10:15-11:00)'''<br />
** [[Image:IGT-Meeting-Nov16-IGSTK-Architecture-Overview.ppt|Image:IGT-Meeting-Nov16-IGSTK-Architecture-Overview.ppt]]<br />
** [[Image:IGT-Meeting-Nov16-IGSTK-StateMachine.ppt|Image:IGT-Meeting-Nov16-IGSTK-StateMachine.ppt]]<br />
* [[Image:CADDLab-IGS.ppt|Image:CADDLab-IGS.ppt]] (Julien Jomier & Stephen Aylward) '''(11:00-11:45)'''<br />
* CISST-MRC (Peter Kazanzides)'''(11:45-12:30)'''<br />
** [[Image:CISST-Software.ppt|Image:CISST-Software.ppt]]<br />
<br />
* LUNCH (from Brown Sugar Cafe Thai Food) Please look at the lunch menu for the Fenway location and be ready to place your order by 10:30)<br />
<br />
* Slicer-Navigator: incl. History of IGT at BWH, Current State of MRT research, Dr. Jolesz's priority cases in AMIGO<br />
<br />
(Randy Ellis)'''(1:00-1:30)'''<br />
<br />
* GE Relationship (Tina K) '''(1:45-2:15)'''<br />
<br />
- equipment shipments/installation - perspectives on the software infrastructure<br />
<br />
== 2. Discussion (Clarifying the difference/overlap) '''2:00-3:00''' ==<br />
<br />
Chair: Randy Ellis<br />
<br />
Participants go through various aspects of IGT software and find difference/similarity in their approach.<br />
<br />
The chair of the session has summarized the discussion (below).<br />
<br />
* License<br />
* Dashboard<br />
* Linked library (numeric library, interface tool kit)<br />
* Thread-safety<br />
* Communication with external programs<br />
<br />
- Integration of new trackers/instruments/<br />
<br />
* Architecture<br />
<br />
- State machines - Integration of various toolkits<br />
<br />
* IRB<br />
* Requirements for FDA Platform (i.e. nav system)<br />
<br />
== 3. Collaboration (Finding the complimentary/collaborating relathionship)'''3:00-3:30''' ==<br />
<br />
Open discussion<br />
<br />
== 4. Action Plan (what do we do next?)'''3:30-4:00''' ==<br />
<br />
* Workshop in March, 2006 (Ron to work with Kevin Cleary on 2-page proposal with the group)<br />
<br />
= Logistics =<br />
<br />
=== Place/Time ===<br />
<br />
10:00am - 4:00pm<br />
<br />
at SPL,1249 Boylston Street, Boston MA<br />
<br />
Direction -> http://splweb.bwh.harvard.edu:8000/pages/directions/1249Boylston/Boylston-facility.html<br />
<br />
=== Lunch ===<br />
<br />
Look at menu (Thai food link above on this page). Place order by 10:30.<br />
<br />
=== T-CON Instruction ===<br />
<br />
Dial 1-218-936-1100 and enter the Conference ID 43123 followed by # key. If conference is not in session, system will put you on hold until the moderator arrives. During the Conference<br />
<br />
* 3 - increase volume on the line<br />
* 6 - mute individual line<br />
* 7 - un-mute individual line<br />
* 9 - decrease volume on the line<br />
<br />
= Attendees (please add your name, available time, method of attendance) =<br />
<br />
* Nobuhiko Hata (BWH), not available to attend, in flight from Tokyo to LAX<br />
* Tina Kapur (NAMIC, BWH IGT), available at 1249<br />
* Steve Pieper, at 1249<br />
* Julien Jomier (CADDLab), at 1249<br />
* Stephen Aylward (CADDLab), TCon only<br />
* Kevin Cleary (Georgetown), tcon, not available 11 am to 1 pm<br />
* Peter Kazanzides (JHU, ERC-CISST), attend<br />
* Patrick Cheng (Georgetown), attend<br />
* Ron Kikinis<br />
* Luis Ibanez (Kitware), attend at 1249<br />
* Will Schroeder (Kitware), attend at 1249<br />
* Rick Avila (Kitware), attend at 1249<br />
* Bill Lorensen<br />
* Ferenc Jolesz<br />
* Mike Halle<br />
* Jim Miller<br />
* Xiaodong Tao<br />
* Sandy Wells<br />
<br />
= Summary Meeting Notes =<br />
<br />
* License details:<br />
** General agreement that BSD-style license are preferred<br />
** GPL-LGPL details were rehashed -- a continuing discussion...<br />
* Dashboard: Most eagerly await DASH2, all agreed that dashboards<br />
<br />
are an important part of software QA (during both development and maintenance phases of software development)<br />
<br />
* Libraries: general agreement on sharing of VTK/ITK, we noted<br />
** JHU vector/matrix classes have efficiency advantages<br />
** JHU robotics interfaces are best available<br />
** Overlap of JHU and Kitware NETLIB wrappers/translations<br />
** Significant divergence of tracker libraries: JHU has CISST classes, IGTSK has other classes, BWH is inclined to use OpenTracker libraries (an inevitable consequence of independent needs of a critical software resource)<br />
* Thread safety raised two matters:<br />
** Legacy code is being ported as resources permit (Kitware is tasked by Terry Yu of NLM to decontaminate NETLIB)<br />
** All are aware of thread safety in development of new code, with proviso that this needs sophisticated developers<br />
* Communication with external programs raised lively debated:<br />
** The Slicer Navigation system must communicate with Slicer 3.x processes that run "hard, non-realtime" computations that support interventional applications<br />
** Numerous publish-subscribe mechanisms were mentioned, the chair (REE) saw no consensus on solutions within this evolving space<br />
** Much discussion of CORBA, which is clearly necessary for interaction with GE software (especially navigation)<br />
* Architecture was a subliminal topic of the day:<br />
** No explicit discussion<br />
** Consensus was for layers: build on ITK/VTK, have toolkits such as IGSTK provide software base, and then applications (i.e., interventional procedures) in distinct "silos" that solve specific clinical problems<br />
** State machines were identified as a particularly apt abstraction of task-based descriptions of interventional procedures<br />
* IRB (Institutional Review Board)<br />
** Identified as the target audience of the quality-assurance process of sn interventional software/system<br />
** We noted the complex relationship of the IRB, patients consenting to an investigational treatment, and the discretion of physicians who may treat patients using their clinical judgment based on the totality of information available at the time of treatment<br />
* FDA (Fooda nd Drug Agency): consensus was that we are following good manufacturing processes in our development and testing phases; discussion on processes for elucidating software design processes and bug issues (reportin, correcting, disseminating fixes, interim warnings, etc.) raised topics for future discussion</div>Andyhttps://www.na-mic.org/w/index.php?title=Data_Provenance:Documentation:Output:Examples&diff=5944Data Provenance:Documentation:Output:Examples2007-01-07T17:32:54Z<p>Andy: Redirecting to Mbirn: Data Provenance:Documentation:Output:Examples</p>
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<div>#REDIRECT [[Mbirn: Data Provenance:Documentation:Output:Examples]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Slicer3:Contributing_codes_to_Slicer3&diff=5942Slicer3:Contributing codes to Slicer32007-01-07T17:30:23Z<p>Andy: /* GUI tools for eash SVN handling */</p>
<hr />
<div>=Objective=<br />
The goal of this page is to give quick instruction to download Slicer3 from Subversion Control (SVN) server, and contribute codes by committing them back to SVN.<br />
<br />
<br />
== How to obtain Slicer 3 codes from SVN ==<br />
<br />
The Slicer3 svn repository sits in a server at Brigham and Women's Hospital in Boston. You can checkout codes by:<br />
<br />
svn co http://www.na-mic.org:8000/svn/Slicer3/trunk Slicer3<br />
<br />
'''You don't need to obtain an account discussed below''' if you don't commit codes back to the sever, but we enthusiastically invite you to do so.<br />
<br />
== How to commit codes ==<br />
<br />
First, fill the form at https://www.kitware.com/Admin/SendPassword.cgi and under Comment type "Request password for NA-MIC Sandbox". '''It says NA-MIC Sandbox since Slicer 3 is part of NA-MIC activity.''' Once you have access to write to SVN, you can work with repository using the following commands:<br />
<br />
To update repository:<br />
<br />
svn update<br />
<br />
To check current state of your edits:<br />
<br />
svn status<br />
<br />
To check the current state compared to the repository:<br />
<br />
svn -u status<br />
<br />
To add new file:<br />
<br />
svn add filename<br />
<br />
followed by (very important):<br />
<br />
svn commit -m"ENH: Adding a new file" filename<br />
<br />
To remove file:<br />
<br />
svn remove filename<br />
<br />
To rename file:<br />
<br />
svn move oldname newname<br />
<br />
If the update results in conflict, fix the file first before commiting it.<br />
<br />
Once you have fixed the file:<br />
<br />
svn resolved <filename><br />
<br />
==GUI tools for eash SVN handling==<br />
It is handy to use GUI tool for SVN. I particulary like a cross-platform GUI tool called [http://rapidsvn.tigris.org/ RapidSVN].</div>Andyhttps://www.na-mic.org/w/index.php?title=Upload/Download_to_SRB_and_HID&diff=5933Upload/Download to SRB and HID2007-01-07T17:20:28Z<p>Andy: Redirecting to Mbirn: Upload/Download to SRB and HID</p>
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<div>#REDIRECT [[Mbirn: Upload/Download to SRB and HID]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Data_Provenance:Documentation:XSD&diff=5930Data Provenance:Documentation:XSD2007-01-07T17:12:23Z<p>Andy: Redirecting to Mbirn: Data Provenance:Documentation:XSD</p>
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<div>#REDIRECT [[Mbirn: Data Provenance:Documentation:XSD]]</div>Andyhttps://www.na-mic.org/w/index.php?title=Software_Correction_Tools&diff=5928Software Correction Tools2007-01-07T17:08:10Z<p>Andy: Redirecting to Mbirn: Software Correction Tools</p>
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<div>#REDIRECT [[Mbirn: Software Correction Tools]]</div>Andy