https://www.slicer.org/w/api.php?action=feedcontributions&user=Zack&feedformat=atomSlicer Wiki - User contributions [en]2024-03-29T05:34:39ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=User:Zack&diff=17152User:Zack2010-07-09T17:19:33Z<p>Zack: </p>
<hr />
<div><flash>file=example.swf|quality=best</flash><br />
<br />
<br />
<br />
<math><br />
\operatorname{erfc}(x) =<br />
\frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2}\,dt =<br />
\frac{e^{-x^2}}{x\sqrt{\pi}}\sum_{n=0}^\infty (-1)^n \frac{(2n)!}{n!(2x)^{2n}}<br />
</math><br />
<br />
<br />
<graphviz border='frame' format='svg'><br />
digraph G {Hello->World!}<br />
</graphviz></div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Downloads/&diff=17065Special:Badtitle/NS100:Downloads/2010-06-23T13:55:41Z<p>Zack: Redirected page to Special:SlicerDownloads</p>
<hr />
<div>#REDIRECT [[Special:SlicerDownloads]]</div>Zackhttps://www.slicer.org/w/index.php?title=User:Zack&diff=13417User:Zack2010-04-12T17:39:22Z<p>Zack: </p>
<hr />
<div><flash>file=example.swf|quality=best</flash><br />
<br />
<br />
<br />
<math><br />
\operatorname{erfc}(x) =<br />
\frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2}\,dt =<br />
\frac{e^{-x^2}}{x\sqrt{\pi}}\sum_{n=0}^\infty (-1)^n \frac{(2n)!}{n!(2x)^{2n}}<br />
</math></div>Zackhttps://www.slicer.org/w/index.php?title=User_talk:JChris.FillionR&diff=11508User talk:JChris.FillionR2009-12-01T18:08:47Z<p>Zack: Welcome!</p>
<hr />
<div>'''Welcome to ''SlicerWiki''!'''<br />
We hope you will contribute much and well. <br />
You will probably want to read the [[Help:Contents|help pages]].<br />
Again, welcome and have fun! [[User:Zack|Zack]] 18:08, 1 December 2009 (UTC)</div>Zackhttps://www.slicer.org/w/index.php?title=User_talk:Smorgan&diff=11125User talk:Smorgan2009-11-02T14:42:48Z<p>Zack: Welcome!</p>
<hr />
<div>'''Welcome to ''SlicerWiki''!'''<br />
We hope you will contribute much and well. <br />
You will probably want to read the [[Help:Contents|help pages]].<br />
Again, welcome and have fun! [[User:Zack|Zack]] 14:42, 2 November 2009 (UTC)</div>Zackhttps://www.slicer.org/w/index.php?title=User_talk:Lasso&diff=11124User talk:Lasso2009-11-02T14:42:37Z<p>Zack: Welcome!</p>
<hr />
<div>'''Welcome to ''SlicerWiki''!'''<br />
We hope you will contribute much and well. <br />
You will probably want to read the [[Help:Contents|help pages]].<br />
Again, welcome and have fun! [[User:Zack|Zack]] 14:42, 2 November 2009 (UTC)</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Downloads&diff=8666Special:Badtitle/NS100:Downloads2009-03-19T20:55:33Z<p>Zack: Redirecting to Special:SlicerDownloads</p>
<hr />
<div>#REDIRECT [[Special:SlicerDownloads]]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Downloads&diff=8665Special:Badtitle/NS100:Downloads2009-03-19T20:53:22Z<p>Zack: Redirecting to Special:SlicerDownlaods</p>
<hr />
<div>#REDIRECT [[Special:SlicerDownlaods]]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:OldDownloads&diff=8662Special:Badtitle/NS100:OldDownloads2009-03-19T19:39:03Z<p>Zack: Projects/slicerWeb:Downloads moved to Projects/slicerWeb:OldDownloads: make room for new download script</p>
<hr />
<div>__NOTOC__<br />
= Slicer Downloads =<br />
<br />
This is the download page for compiled versions of the 3D Slicer software. <br />
<br />
== License Agreement ==<br />
Please fill out the '''[http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl Slicer License Form]''' before downloading any binary releases of Slicer.<br />
<br />
== Downloads ==<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
'''Hardware/OS requirement''': <br />
* Either Windows XP or more recent, Linux (x86 or x86_64), Mac OS X (ppc or Intel), min 2 GB of RAM and a dedicated graphic accelerator with at least 128 MB of on-board graphic memory. Shared memory graphics will result in slow render speeds. <br />
* '''Mac''': On Mac OS X you will need to install X11 from the CD. As an alternative, we had good experience with [http://xquartz.macosforge.org/trac/wiki xquartz].<br />
* '''Linux''': Type glxgears in a shell to check if the graphics acceleration is working properly.<br />
<br />
=== Recommended Stable Slicer Releases ===<br />
'''[http://www.slicer.org/DownloadSlicer.php/Release Stable Release Download]''': Pre-compiled stable Slicer Releases for Linux, Windows, Mac and Solaris (this is where you find '''Slicer 3.2''' pre-compiled versions for supported platforms).<br />
<br />
=== Bleeding Edge Slicer Releases ===<br />
*''[http://www.slicer.org/DownloadSlicer.php/Snapshots Snapshots]'': Custom built Slicer binaries, in various states of completion<br />
*''[http://www.slicer.org/DownloadSlicer.php/Nightly Nightly]'': This page contains a week's worth of nightly builds<br />
<br />
| style="background: #e5e5e5" colspan="2" align="center"| <b><font color=#666699>Slicer Download Statistics</font></b><br><br />
([[Projects/slicerWeb:Downloads#Download_Statistics|live version at the bottom of this page]])<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerStats-02-2009.png|center|300px]] <br />
|}<br />
<br />
== Training ==<br />
Training materials on how to use 3D Slicer.<br />
*[http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training '''Slicer 3''']<br />
*[http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 '''Slicer 2''']<br />
<br />
== Other Resources ==<br />
*'''[http://www.na-mic.org/Bug/login_page.php Mantis Tracker]''': Report bugs and make feature requests here.<br />
*'''[http://public.kitware.com/dashboard.php?name=slicer3 Slicer Dashboard]''': Information about the nightly builds.<br />
*'''[[Projects/slicerWeb:SourceCode|Source Code]]''': This page points to the source code repositories.<br />
*'''[http://slicer.org/pages/Mailinglist Slicer mailing lists]''': This page contains points to the Slicer user and developers mailing lists.<br />
<br />
== Download Statistics ==<br />
* See [http://slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 '''here'''] for 3D Slicer download statistics.<br />
== Directory Listing View of Downloads ==<br />
http://slicer.org/download_files/</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Download_Stats_Methodology&diff=6801Special:Badtitle/NS100:Download Stats Methodology2008-12-11T15:53:55Z<p>Zack: </p>
<hr />
<div>Whenever someone downloads a file from [[Special:Slicer Downloads|Slicer Downloads]], we record the following information in a MySQL database:<br />
<br />
*The name of the file that's being requested<br />
*The current time<br />
*The IP address of the person who's downloading this file<br />
*The approximate latitude and longitude that corresponds with this IP address<br />
<br />
Only one download is recorded for a particular file from a particular IP address during a two hour period.<br />
<br />
Currently a new download is recorded as soon as the user clicks on a link. At some point in the future I will try to change this behavior so that we don't record information about cancelled/incomplete downloads.<br />
<br />
We have some preventative measures in place to prevent spiders from artificially inflating our download statistics. Our robots.txt file for slicer.org looks like this:<br />
User-agent: *<br />
Crawl-delay: 10<br />
Disallow: /Downloads/Release<br />
Disallow: /Downloads/Data<br />
Disallow: /Downloads/External<br />
Disallow: /Downloads/Nightly<br />
Disallow: /Downloads/Patches<br />
Disallow: /Downloads/Snapshots<br />
Disallow: /source<br />
<br />
[[Special:Download_Stats|Back to download stats]].</div>Zackhttps://www.slicer.org/w/index.php?title=User:Spujol&diff=3057User:Spujol2008-04-02T17:17:06Z<p>Zack: </p>
<hr />
<div>==Join the 3DSlicer Community ==<br />
[[Image:3DSlicerCommunity.PNG|thumb|right|250 px]]<br />
<br />
Slicer is an open-source delivery platform for scientific breakthroughs in image analysis, that is being used in more than 15 countries.<br />
<br />
The Slicer community gathers users and developers interested in the latest technical updates of the platform and Slicer-related events worldwide.<br />
<br />
To create your Slicer Community account, please complete the following form: [http://www.slicer.org/cgi-bin/License/SlicerCommunityForm.pl SlicerCommunityForm]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:SlicerCommunity&diff=3056Special:Badtitle/NS100:SlicerCommunity2008-04-02T17:12:06Z<p>Zack: </p>
<hr />
<div>==Join the 3DSlicer Community ==<br />
[[Image:3DSlicerCommunity.PNG|thumb|right|250 px]]<br />
<br />
Slicer is an open-source delivery platform for scientific breakthroughs in image analysis, that is being used in more than 15 countries.<br />
<br />
The Slicer community gathers users and developers interested in the latest technical updates of the platform and Slicer-related events worldwide.<br />
<br />
To create your Slicer Community account, please complete the following form: [http://www.slicer.org/cgi-bin/License/SlicerCommunityForm.pl SlicerCommunityForm]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Acknowledgments&diff=3049Special:Badtitle/NS100:Acknowledgments2008-03-28T15:27:56Z<p>Zack: </p>
<hr />
<div>__NOTOC__<br />
=Acknowledgments=<br />
<br />
== Major Sponsors and Contributors==<br />
<br />
{| class="wikitable2" <br />
|[[Image:NIH.gif|116px]]<br/> [http://www.nih.gov National Institutes of Health]<br />
|[[Image:logo-NCRR.png|100px]]<br/> [http://www.ncrr.nih.gov National Center for Research Resources]<br />
|[[Image:logo-NIbib.gif|88px]]<br/> [http://www.nibib.nih.gov National Institute of Biomedical Imaging and Bioengineering]<br />
|[[Image:logo-nci.gif|120px]]<br/> [http://www.cancer.gov/ National Cancer Institute]<br />
|[[Image:TATRC.jpg|150px]]<br/> [http://www.tatrc.org/ Telemedicine & Advanced Technology Research Center of the US Army]<br />
|- <br />
|[[Image:logo-nac2.jpg|44px]]<br/> [http://nac.spl.harvard.edu/ Neuroimaging Analysis Center]<br />
|[[Image:logo-namic.jpg|88px]]<br/> [http://www.na-mic.org/ National Alliance for Medical Image Computing]<br />
|[[Image:logo-ncigt.jpg|120px]]<br/> [http://www.ncigt.org National Center for Image Guided Therapy] <br />
|[[Image:logo-BIRN.jpg|160px]]<br/> [http://www.nbirn.net Biomedical Informatics Research Network]<br />
|[[Image:logo-cimit.jpg|150px]]<br/> [http://www.cimit.org Center for Integration of Medicine and Innovative Technology]<br />
|- <br />
|[[Image:logo-NEWSPL.jpg|115px]]<br/>[http://www.spl.harvard.edu Surgical Planning Laboratory] <br />
|[[Image:logo-CSAILNEW.jpg|100px]]<br/> [http://www.csail.mit.edu Massachusetts Institute of Technology] <br />
|[[Image:logo-cisst.gif|150px]]<br/> [http://cisstweb.cs.jhu.edu Johns Hopkins University CISST] <br />
|[[Image:logo-gatech.gif|150px]]<br/> [http://www.gatech.edu/ Georgia Institute of Technology] <br />
|[[Image:logo-HCNR2.gif|87px]]<br/> [http://www.neurodiscovery.harvard.edu Harvard NeuroDiscovery Center] <br />
|- <br />
|[[Image:logo-NMR2.gif|100px]]<br/> [http://www.nmr.mgh.harvard.edu The Martinos Center<br>Massachusetts General Hospital] <br />
|[[Image:logo-kitwarenew.gif|160px]]<br/> [http://www.kitware.com Kitware, Inc.]<br />
|[[Image:logo-geresearch.gif|160px]]<br/> [http://www.ge.com/research/ GE Global Research]<br />
|[[Image:logo-isomics.png|150px]]<br/> [http://www.isomics.com Isomics, Inc.] <br />
|[[Image:logo_pnl2.png|90px]]<br/> [http://pnl.bwh.harvard.edu Psychiatric Neuroimaging Laboratory]<br />
|}<br />
<br />
==Slicer3: Individual/Group Contributors==<br />
<br />
{|style="font-size:80%;"<br />
|style="border-bottom:3px solid #669;" | <font color="#669"> Contribution<br />
|style="border-bottom:3px solid #669;"| <font color="#669"> Developer(s)<br />
|-<br />
| Overall concept<br />
| Steve Pieper, Ron Kikinis, Jim Miller, Michael Halle, Bill Lorensen, Will Schroeder<br />
|-<br />
| Major designer and implementer<br />
| Steve Pieper<br />
|- <br />
| MRML, Viewer, and many other things<br />
| Alex Yarmarkovich<br />
|- <br />
| GUI<br />
| Wendy Plesniak, Sebastien Barre, Yumin Yuan<br />
|- <br />
| Command Line Modules<br />
| Jim Miller, Dan Blezek, Bill Lorensen, Luis Ibanez<br />
|- <br />
| Colors, Fiducials, FreeSurfer, QDEC<br />
| Nicole Aucoin<br />
|- <br />
| Testing, Release Engineering<br />
| Katie Hayes, Andy Cedilnik, Bill Hoffman<br />
|- <br />
| Diffusion Support<br />
| Raul San Jose Estepar, Lauren O'Donnell<br />
|- <br />
| BatchMake Integration<br />
| Stephen Aylward, Julien Jomier<br />
|- <br />
| Image Guided Therapy<br />
| Noby Hata, Sandy Wells, Haiying Liu <br />
|-<br />
| Volume Rendering<br />
| Andreas Freudling, Lisa Avila, Sebastien Barre<br />
|}<br />
<br />
==Slicer2: Individual/Group Contributors==<br />
<br />
===The main individual contributors to this joint effort are listed below.===<br />
<br />
{|style="font-size:80%;"<br />
|style="border-bottom:3px solid #669;" | <font color="#669"> Contribution<br />
|style="border-bottom:3px solid #669;"| <font color="#669"> Developer(s)<br />
|-<br />
| Overall concept<br />
| Ron Kikinis, Ferenc Jolesz, Eric Grimson, William Wells III, Michael Halle<br />
|-<br />
| Major designer and implementer<br />
| Dave Gering (1997-1999), Lauren O'Donnell (1999-), Steve Pieper (2001-)<br />
|-<br />
| Prototype<br />
| Noby Hata (1997), Ron Kikinis<br />
|-<br />
| OpenMR interface<br />
| Arya Nabavi (1998-1999), Ferenc Jolesz<br />
|-<br />
|Image Guided Therapy <br />
|Noby Hata, Sandy Wells, Haiying Liu<br />
|-<br />
| Measurement tools<br />
| William Lorensen (GE), Peter Everett (SPL), Krishna Yeshwant (SPL)<br />
|-<br />
| Robot simulation tools<br />
| Noby Hata, Oliver Schorr<br />
|-<br />
| 3D connectivity algorithm<br />
| Andre Robatino<br />
|-<br />
| MI registration<br />
| William Wells III<br />
|-<br />
| Virtual endoscopy tool<br />
| Delphine Nain (MIT AI lab)<br />
|-<br />
| DICOM functionality, robot control, volume rendering<br />
| Attila Tanacs (Johns Hopkins University)<br />
|-<br />
| Cryotherapy planning<br />
| Torsten Butz (EPFL)<br />
|-<br />
| Architecture<br />
| Michael Halle (SPL)<br />
|-<br />
| EMSegmenter<br />
| Kilian Pohl (MIT AI lab)<br />
|-<br />
| Tetramesh, volumeMath, developer.tcl<br />
| Samson Timoner (MIT AI lab)<br />
|-<br />
| Print header<br />
| Mark Anderson (SPL)<br />
|-<br />
| Training and Download requests<br />
| Marianna Jakab (SPL)<br />
|-<br />
| Model Hierarchies<br />
| Arne Hans (SPL)<br />
|-<br />
| Application development<br />
| Steven Haker (SPL)<br />
|-<br />
| Craniofacial<br />
| Krishna Yeshwant (SPL)<br />
|-<br />
| FreeSurfer Volume Readers<br />
| Kevin Teich (MGH), Nicole Aucoin (BWH)<br />
|-<br />
| Nightly Builds, Testing, QA<br />
| Kathryn Hayes (BWH)<br />
|-<br />
| Training Materials<br />
| Sonia Pujol (BWH)<br />
|-<br />
| Feedback/Recommendations on Tool Development<br />
| Martha Shenton and Members of the Psychiatric Neuroimaging Laboratory<br />
|}<br />
<br />
===We are sincerely thankful for the grants and fellowships supporting this project, and we wish to acknowledge them here.===<br />
<br />
{| style="font-size:80%;"<br />
|style="border-bottom:3px solid #669;" | <font color="#669"> Individual<br />
|style="border-bottom:3px solid #669;" | <font color="#669"> Support<br />
|-<br />
|David Gering<br />
|GE Medical Systems<br />
|-<br />
|Lauren O'Donnell<br />
|National Science Foundation Graduate Research Fellowship<br />
|-<br />
|Ron Kikinis<br />
|NIH grants P41 RR13218, P01 CA67165, and R01 RR11747; ERC 9731748<br />
|-<br />
|Ferenc Jolesz<br />
|NIH grants P41 RR13218 and P01 CA67165 <br />
|-<br />
|William Wells III<br />
|Whitaker Foundation Biomedical Engineering Research Grant<br />
|-<br />
|W. Eric L. Grimson<br />
|NSF grant IIS-9610249, ERC 9731748<br />
|-<br />
|Attila Tanacs<br />
|ERC 9731748<br />
|-<br />
|Kevin Teich<br />
|NIH-NCRR grant 3 P41 RR14075-03S1<br />
|}<br />
<br />
==Slicer Programming==<br />
<br />
Slicer is built on an open source software infrastructure based on the [http://www.na-mic.org/Wiki/index.php/NA-MIC-Kit NA-MIC Kit] and consisting of the following elements:<br />
<br />
'''Toolkits'''<br />
* [http://www.vtk.org The Visualization Toolkit] <br />
* [http://www.itk.org The Insight Toolkit]<br />
* [http://www.kwwidgets.org KWWidgets]<br />
* [http://teem.sf.net Teem]<br />
<br />
'''Software Tools to Support Software Engineering Methodology'''<br />
* [http://www.cmake.org CMake]<br />
* [http://www.tcl.tk/ Tcl/Tk]<br />
* [http://public.kitware.com/Dart/HTML/Index.shtml Dart ]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Download_Stats_Methodology&diff=3048Special:Badtitle/NS100:Download Stats Methodology2008-03-27T14:12:52Z<p>Zack: </p>
<hr />
<div>Whenever someone downloads a file from [[Special:Slicer Downloads|Slicer Downloads]], we record the following information in a MySQL database:<br />
<br />
*The name of the file that's being requested<br />
*The current time<br />
*The IP address of the person who's downloading this file<br />
*The approximate latitude and longitude that corresponds with this IP address<br />
<br />
Currently a new download is recorded as soon as the user clicks on a link. At some point in the future I will try to change this behavior so that we don't record information about cancelled/incomplete downloads.<br />
<br />
We have some preventative measures in place to prevent spiders from artificially inflating our download statistics. Our robots.txt file for slicer.org looks like this:<br />
User-agent: *<br />
Crawl-delay: 10<br />
Disallow: /Downloads/Release<br />
Disallow: /Downloads/Data<br />
Disallow: /Downloads/External<br />
Disallow: /Downloads/Nightly<br />
Disallow: /Downloads/Patches<br />
Disallow: /Downloads/Snapshots<br />
Disallow: /source<br />
<br />
[[Special:Download_Stats|Back to download stats]].</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Download_Stats_Methodology&diff=3047Special:Badtitle/NS100:Download Stats Methodology2008-03-27T14:11:32Z<p>Zack: </p>
<hr />
<div>Whenever someone downloads a file from [[Special:Slicer Downloads|Slicer Downloads]], we record the following information in a MySQL database:<br />
<br />
*The name of the file that's being requested<br />
*The current time<br />
*The IP address of the person who's downloading this file<br />
*The approximate latitude and longitude that corresponds with this IP address<br />
<br />
Currently a new download is recorded as soon as the user clicks on a link. At some point in the future I will try to change this behavior so that we don't record information about cancelled/incomplete downloads.<br />
<br />
We have some preventative measures in place to prevent spiders from artificially inflating our download statistics. Our robots.txt file for slicer.org looks like this:<br />
User-agent: *<br />
Crawl-delay: 10<br />
Disallow: /Downloads/Release<br />
Disallow: /Downloads/Data<br />
Disallow: /Downloads/External<br />
Disallow: /Downloads/Nightly<br />
Disallow: /Downloads/Patches<br />
Disallow: /Downloads/Snapshots<br />
Disallow: /source</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Contact&diff=2952Special:Badtitle/NS100:Contact2008-02-13T18:51:42Z<p>Zack: </p>
<hr />
<div>=Contact=<br />
<br />
Steve Pieper, Slicer's principal architect, can be reached via this e-mail: [mailto:pieper@bwh.harvard.edu pieper at bwh.harvard.edu].</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Contact&diff=2946Special:Badtitle/NS100:Contact2008-02-12T20:46:34Z<p>Zack: testing w2w</p>
<hr />
<div>=Contact=<br />
<br />
Steve Pieper, Slicer's principal architect, can be reached via this e-mail: [mailto:pieper@bwh.harvard.edu pieper at bwh.harvard.edu]</div>Zackhttps://www.slicer.org/w/index.php?title=User:Zack&diff=2940User:Zack2008-02-12T16:17:19Z<p>Zack: </p>
<hr />
<div><flash>file=example.swf|quality=best</flash></div>Zackhttps://www.slicer.org/w/index.php?title=File:Example.swf&diff=2939File:Example.swf2008-02-12T16:16:39Z<p>Zack: testing flash extension</p>
<hr />
<div>testing flash extension</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:UserOrientation&diff=2877Special:Badtitle/NS100:UserOrientation2008-01-03T19:34:14Z<p>Zack: </p>
<hr />
<div>__NOTOC__<br />
=Slicer User Orientation=<br />
<br />
Slicer is an open-source software application for computer scientists and clinical researchers. <br />
<br />
The platform provides functionalities for segmentation, registration and three-dimensional visualization of multimodal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging and image-guided therapy. Standard image file formats are supported, and the application integrates interface capabilities to biomedical research software.<br />
<br />
Slicer is available for Linux, Mac, Windows and Unix.<br />
<br />
[[Image:Tharin_Neurosurgery.jpg|thumb|right|250 px|A coronal brain slice with super-imposed diffusion tensor tractography to show alteration in the arrangement of the tracts around a tumor. See [[Special:PubDB_View?dspaceid=327| Tharin et al Neurosurgery 2007]] for more info.]]<br />
<br />
==Slicer Versions==<br />
Slicer is freely available after completion of the [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl Slicer license form]. All versions of the software are accessible through the [[Projects/slicerWeb:Downloads| Slicer Downloads home page ]].<br />
<br />
The [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 101] provides a series of courses on different image analysis functionalities of Slicer.<br />
<br><br><br />
{| class="wikitable" <br />
|<br />
|'''Slicer 2.7 '''<br />
|'''Slicer 3 '''<br />
|-<br />
|'''Download'''<br />
|[[Projects/slicerWeb:Downloads| Downloads home page]]<br />
|-<br />
|'''Tutorials'''<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 101]<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Documentation Slicer3 Documentation ]<br />
|-<br />
|}<br />
<br><br />
==Support==<br />
<br />
Feature requests and bug reports can be posted on the [http://www.na-mic.org/Bug/main_page.php Slicer bug tracker] page.<br />
<br />
Please contact the [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Slicer Users mailing list] for questions related to the software, archives of slicer-users and subscription management tools.</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Slicer_3.0_User_Information&diff=2876Special:Badtitle/NS100:Slicer 3.0 User Information2008-01-03T19:30:37Z<p>Zack: </p>
<hr />
<div>==Slicer 3.0: Getting Started==<br />
<br />
Slicer 3 is the latest version of 3D Slicer. It reflects a dedication to the Slicer software platform with an intention to make the software both easier to use for researchers and to extend for programmers. More specifically, Slicer 3 has:<br />
<br />
* features of Slicer 2.x that are needed by the user community, such as its comprehensive visualization ability, various modules for segmentation, registration, DTI analysis, volume measurements,<br />
* added functionality desired by the computer science community, such as the ease of adding new modules, interfacing existing to non-slicer software modules, scaling to grid architectures and an automated graphical user-interface testing, and<br />
* new features requested by the user community, such as undo-redo facility, improved 3D rendered images.<br />
<br />
There are a couple different ways to obtain Slicer3 to run on your own computer. You can either:<br />
<br />
* build Slicer 3 yourself from an SVN checkout, or<br />
* download a precompiled Slicer3 installer for your platform, or<br />
<br />
== Building Slicer ==<br />
<br />
To build Slicer 3 yourself from an SVN checkout, refer to the [[build instructions]].<br />
<br />
Windows<br />
*Distributed versions are built with Microsoft Visual Studio .NET in release mode (Note that there may be some problems compiling with .NET 2003.)<br />
<br />
Linux<br />
*For building, g++ version 3.4.3 on RedHat Enterprise Linux 4 is used.<br />
<br />
Mac OSX<br />
*For building, gcc version 4.0.1 is used.<br />
<br />
== Downloading ==<br />
<br />
Deciding to download? Access Slicer 3.0 [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Downloads downloads here]<br />
<br />
===Obtaining a Precompiled Binary=== <br />
<br />
Compiled '''Slicer3 executables''' are [http://www.na-mic.org/Slicer/Download/Snapshots/ '''available here''']. From the Snapshots directory, select your architecture. <br />
<br />
The current supported architectures are:<br />
<br />
* darwin-x86: Mac OSX - Darwin x86 Intel<br />
* darwin-ppc: Mac OSX - Darwin Power PC<br />
* linux-x86: Linux-x86 - Linux 32-bit<br />
* linux-x86_64: Linux-x86_64 - Linux 64-bit<br />
* win32: Windows<br />
<br />
The Snapshots directory contains both Slicer2 and Slicer3 binaries. For the latest build, select the filename that begins with "Slicer3" and has the most recent date. For the beta binary released prior to the January 2007 All Hands Meeting, choose the file with "PreAHM" in the filename. These are all beta builds, so you might find some bugs. If you do, or are having trouble installing Slicer3, please email slicer-users@bwh.harvard.edu so we can continue to improve Slicer3. <br />
<br />
With many modules on Slicer already developed, much of Slicer documentation is modules specific. Consult [http://www.na-mic.org/Wiki/index.php/Slicer3:Module_Documentation module documentation] to aid you in using Slicer.<br />
<br />
==Installing on Different Operating Systems==<br />
<br />
===Installing on Mac OSX===<br />
<br />
The latest Mac OSX builds are either tar.gz files or .sh files. To install Slicer3, open up an X11 terminal window and copy the binary to the location where you want to install. Change the filename in the examples below to reflect the binary you downloaded. <br />
<br />
=====Unpacking .tar.gz Files=====<br />
<br />
To unzip and untar the .tar.gz binary, type:<br />
<br />
gunzip ./Slicer3-3.0.2007-01-10-Darwin-x86.tar.gz<br />
tar -xvf ./Slicer3-3.0.2007-01-10-Darwin-x86.tar<br />
<br />
=====Unpacking .sh Files=====<br />
<br />
To unpack the .sh binary, type:<br />
<br />
./Slicer3-3.0.2007-01-10-Darwin-x86.sh<br />
<br />
You will be prompted to accept the license agreement, and asked where you want to install it. Respond "Y" to both questions.<br />
<br />
=====Running Slicer3=====<br />
<br />
To run Slicer3, cd into the Slicer3-3.0.2007-xx-xx/bin directory and type:<br />
<br />
./Slicer3<br />
<br />
===Installing on Linux===<br />
<br />
After downloading the file, move it to where you would like to install Slicer3, and then execute the .sh binary. To do this, simply do the following (replace the filename with the one you downloaded):<br />
<br />
./Slicer3-3.0.2007-01-08-Linux-x86_64.sh<br />
<br />
If the file doesn't execute, make sure that you have execute permission set. To add execute permission, type:<br />
<br />
chmod a+x ./Slicer3-3.0.2007-01-08-Linux-x86_64.sh<br />
<br />
Some shells have problems executing the script. If so, you might need to specify which shell you want to execute the script, e.g.:<br />
<br />
/bin/sh ./Slicer3-3.0.2007-01-08-Linux-x86_64.sh<br />
<br />
To run Slicer3, cd into the Slicer3-3.0.2007-xx-xx/bin directory and type:<br />
<br />
./Slicer3<br />
<br />
===Installing on Windows===<br />
<br />
After downloading the file, simply double-click on it to start the installation process. To uninstall Slicer3, double-click the Uninstall icon in the Slicer3 directory. To run Slicer, go to Start -> Programs -> Slicer3-3.0.2007.xx-xx -> Slicer<br />
<br />
== Known Issues: Base Operations ==<br />
<br />
All Platforms:<br />
* Slicer 3's interface is optimized for screen resolutions equal to or higher than 1280x1024. While it is usable below that resolution, using the GUI may become less efficient.<br />
* In Slicer 3, fonts currently do not resize, making the text hard to read on extremely large monitors with very high resolutions.<br />
<br />
Linux: <br />
* csh must be installed (It's not on Ubuntu by default).<br />
* The sh shell on some systems is incompatible with the installer (it will work, but with warnings)<br />
<br />
== Known Issues: Modules ==<br />
<br />
As a research platform, Slicer includes several modules that are not yet fully implemented and yet available because developers felt they were far enough along in functionality to provide utility. As such, you may find that some operations do not behave as expected, particularly at the intersection point with other Slicer functions. To help us improve these modules, please let us know about these issues by filing appropriate bug reports.<br />
<br />
==== Reporting Bugs ====<br />
Please go to http://www.na-mic.org/Bug/ and report bugs for Slicer version 3.<br />
<br />
==== Finding Help ====<br />
For help, consult the [[Projects/slicerWeb:Mailinglist| mailing lists]].</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:Introduction&diff=2875Special:Badtitle/NS100:Introduction2008-01-03T19:28:00Z<p>Zack: </p>
<hr />
<div>=Introduction=<br />
<br />
Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os x. <br />
<br />
Slicer's capabilities include:<br />
<br />
* interactive visualization of images, <br />
* manual editing, <br />
* fusion and co-registering of data, <br />
* automatic segmentation,<br />
* analysis of diffuse tensor imaging data, and<br />
* visualization of tracking information for image-guided procedures.<br />
<br />
<br />
Slicer started as a masters thesis project between the Surgical Planning Laboratory at the Brigham and Women's Hospital and the MIT Artificial Intelligence Laboratory in 1998. Today, Slicer2 has been downloaded many thousand times. A variety of [http://wiki.na-mic.org/Wiki/index.php/Slicer:Feedback publications] were enabled by the Slicer software. A new, completely rearchitected version of Slicer was developed and has been released in 2007. <br />
<br />
This massive effort has been enabled by the participation of several large scale NIH funded efforts, including the [http://www.na-mic.org NA-MIC], [http://nac.spl.harvard.edu/ NAC], [http://www.nbirn.net BIRN], [http://www.cimit.org CIMIT] and [http://www.ncigt.org NCIGT] communities. The funding support comes from several federal funding sources including [http://www.ncrr.nih.gov NCRR], [http://www.nibib.nih.gov NIBIB], [http://nihroadmap.nih.gov NIH Roadmap], [http://www.cancer.gov NCI], [http://www.nsf.gov NSF] and the [http://www.defenselink.mil/ DOD] as well as others.<br />
<br />
Portal pages on this website have been designed for [[Projects/slicerWeb:UserOrientation |end users]] or [[Projects/slicerWeb:DeveloperOrientation| developers]]. Some of the core functionality that enables the applications listed above include the capability to save and restore scenes using a format called MRML, a plug-in archtecture to interface to external programs including ITK, a sophisticated statistical classification environment based on the EM algorithm, capabilities for rigid and non-rigid data fusion and registration, and processing of DTI MRI data.<br />
<br />
Slicer executables and [[Projects/slicerWeb:SourceCode| source code]] are available under a BSD-style, free open source [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl licensing agreement] under which there are no reciprocity requirements, no '''restrictions''' on use, and no guarantees of performance. Slicer leverages a variety of toolkits and software methodologies that have been labeled the NA-MIC kit. Please click [http://wiki.na-mic.org/Wiki/index.php/NA-MIC-Kit here] to read more about the NA-MIC kit. <br />
<br />
===Slicer and Image-Guided Therapy===<br />
<br />
[[Image:Fedorov-Supercomputing2006-fig3.png|thumb|right|400 px|Overlaying MRI Images To Guide Decision-making When Resecting Tumor. See [[Special:PubDB_View?dspaceid=44| Chrisochoides et al ICHPC 2006]] for more info.]]<br />
<br />
With IRB clinical protocols appropriately created and managed, Slicer has been used in clinical research. In image-guided therapy research, Slicer is frequently used to construct and visualize collections of MRI data that are available pre- and intraoperatively to allow for the acquiring of spatial coordinates for instrument tracking. In fact, Slicer has already played such a pivotal role in image-guided therapy, it could be thought of as growing up alongside that field.<br />
<br />
In addition to producing 3D models from conventional MRI images, Slicer has also been used to present information derived from fMRI (using MRI to assess blood flow in the brain related to neural or spinal cord activity), DTI (using MRI to measure the restricted diffusion of water in imaged tissue), and electrocardiography. For example, Slicer's DTI package allows the conversion and analysis of DTI images. The results of such analysis can be integrated with the results from analysis of morphologic MRI, MR angiograms and fMRI.</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:ImageArchive&diff=2874Special:Badtitle/NS100:ImageArchive2008-01-03T19:26:44Z<p>Zack: </p>
<hr />
<div>__NOTOC__<br />
=Image Archive=<br />
<br><br />
<br />
===November 2007===<br />
<br />
[[Image:Akselrod-Ballin-MICCAI2006-fig2.png|left|thumb|490px|'''Atlas guided identification of brain structures by combining 3D segmentation and SVM classification:''' The upper row presents classification results projected on a 2D T1 slice. The lower row demonstrates a 3D view of the results. [[Special:PubDB_Finishsubmission?dspaceid=622| Read more here]]]]<br />
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br />
<br />
<br />
===August 2007===<br />
<br />
[[Image:Brem-AcadRadiol2007-fig1.png|left|thumb|490px|'''Screen shots of the segmentation software, the 3D Slicer:''' Sagittal slice of the knee with segmented<br />
femur and tibial cartilage (a). 3D models of the femur and tibial<br />
cartilage (b). Zoom view of the segmented region, (femur cartilage is pink, the tibia cartilage is orange). The zoom view offers the possibility of precise, pixel by pixel segmentation. [[Special:PubDB_Finishsubmission?dspaceid=78| Read more here]]]]<br />
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br />
<br />
===July 2007===<br />
<br />
[[Image:OShea-IJMRCAS2006-fig6.png|left|thumb|490px|'''Patient with Mixed Oligoastrocytoma:''' The fMRI activation (blue) displayed from the active left-hand motor task. Because the local maximum was several millimetres below the cortical surface, the model of the cortical surface was rendered to be transparent, revealing the lesion (pink mass). The positive ECS sites are depicted in red, negative ECS sites in green and electrodes in yellow. [[Special:PubDB_Finishsubmission?dspaceid=355| Read more here]]]]<br />
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br />
===June 2007===<br />
<br />
[[Image:image_focal.png|left|thumb|490px|'''Patient with Ganglioglioma:''' Three-dimensional visualization is helpful for navigation during neurosurgical procedures. This image was generated in Slicer3 by postprocessing and combining information from several MR acquisitions. The brain tumor is colored green, the vessels are red, the ventricles are blue. White matter tracts are colored in yellow. A 3D model of the brain provides anatomical context. [[Special:PubDB_Finishsubmission?dspaceid=96| Read more here]]]]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:DeveloperOrientation&diff=2873Special:Badtitle/NS100:DeveloperOrientation2008-01-03T19:25:18Z<p>Zack: </p>
<hr />
<div>=Slicer Developer Orientation=<br />
<br />
Welcome Slicer Developers. You are creating Slicer's future. After all, Slicer is an open source package suited for easy modular expansion by developers with ideas for Slicer designs and applications. This page acts as a portal to acquaint you with the basics of Slicer development and route you through the table below to an interactive Wiki exclusive to Slicer development that represents a vast community of individuals. The following table contains links to useful resources within the Slicer Wiki:<br />
<br />
<br><br />
Before getting started, please look at the [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl '''Slicer license'''].<br />
<br><br><br />
<br />
{| class="wikitable" align="left"<br />
|<br />
|'''Slicer 2.6 (Release)'''<br />
|'''Slicer 3 (Beta)'''<br />
|-<br />
|Slicer Developer Documentation<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started Slicer 2 Getting Started]<br />
|[http://www.na-mic.org/Wiki/index.php/Slicer3:Module_Documentation Module Documentation] and [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Slicer 3 Documentation in Development]<br />
|-<br />
|Build Instructions<br />
|[http://www.na-mic.org/Wiki/index.php/Slicer:Slicer_2.6_Building Slicer 2.6 Build Instructions] and [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Transition_of_Slicer2.x_Modules#List_of_Modules Transitioning Slicer 2 to Slicer 3]<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Build_Instructions Slicer 3 Build Instructions] and [[Projects/slicerWeb:Building a Slicer 3 Module GUI| Building a Slicer 3 Module GUI]]<br />
|-<br />
|Coding Considerations<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 101 Tutorial]<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Style Slicer 3 Coding Style] and [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Interface_Design Slicer 3 Interface Design] <br />
|-<br />
|VC for Browsing Repository<br />
|[http://www.na-mic.org/ViewVC/index.cgi/ View VC]<br />
|[http://www.na-mic.org/ViewVC/index.cgi/ View VC]<br />
|-<br />
|Slicer svn Repository and SVN Instructions<br />
|[http://www.na-mic.org/Wiki/index.php/Slicer#Accessing_Source_Code Accessing Source Code]<br />
|[http://www.na-mic.org/svn/Slicer3/trunk/Slicer svn Repository] and [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox Instructions for svn]<br />
|-<br />
|Dashboard and Visual Blog<br />
||[http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 101 Tutorial]<br />
|[http://www.na-mic.org/Dart/Slicer3/Dashboard/ Slicer 3 Dashboard] and [http://wiki.na-mic.org/Wiki/index.php/Slicer3:VisualBlog Visual Blog] <br />
|-<br />
|Status Report<br />
||[http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 101 Tutorial]<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Status_Summary Status Reports]<br />
|-<br />
|Bug Tracker<br />
||[http://na-mic.org/Mantis/login_page.php?return=%2FMantis%2Fmain_page.php Slicer 2 Bug Tracker]<br />
|[http://na-mic.org/Mantis/login_page.php?return=%2FMantis%2Fmain_page.php Slicer 3 Bug Tracker]<br />
|-<br />
|Developer Discussion<br />
||[mailto:slicer-devel@massmail.spl.harvard.edu Developer's Mailing List]<br />
|[mailto:slicer-devel@massmail.spl.harvard.edu Developer's Mailing List]<br />
|- <br />
|Module Execution Documentation<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Documentation Execution Model]<br />
|[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Documentation Execution Model] and [[Projects/slicerWeb:Adapting_Slicer_to_Large-Scale_Experiments| Adapting Slicer to Large Scale Experiments]]<br />
|- <br />
|}<br />
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br />
<br />
===Slicer Development Basics===<br />
<br><br />
[[Image:Kubicki_2007_J Psychiatr Res.jpg|thumb|right|350px|Example of fiber tracking. See [[Special:PubDB_View?dspaceid=99| Kubicki et al J Psychiatr Res 2007]] for more info.]]<br />
<br />
Slicer is based on Vtk, a graphical library that provides a high-level interface to OpenGL and a pipeline mechanism to connect graphical filters. The library is implemented in C++ but provides a Tcl wrapper to instantiate and execute its methods. Tcl/Tk comprises the rest of 3D Slicer user interface and event handling.<br />
<br />
Slicer software supports automatic testing and employs an extreme programming approach with nightly builds natively on multiple platforms. Recent accomplishments include added capability for plugging in external modules using XML-based command line interface.<br />
<br />
Slicer 3 is the latest version of Slicer that has integrated within it features to make adding to Slicer easier than before. If you are new to Slicer, viewing slides on its [[Media: 2007_Slicer Architecture slides.ppt |architecture]] will familiarize you with its framework.</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:OldDownloads&diff=2825Special:Badtitle/NS100:OldDownloads2007-10-18T15:38:06Z<p>Zack: </p>
<hr />
<div>= Introduction =<br />
<br />
This is the download page for compiled versions of the 3D Slicer software. If you are looking for the source code, please [[Projects/slicerWeb:SourceCode|click here]].<br />
<br />
= License Agreement =<br />
<br />
Please fill out the '''[http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl Slicer License Form]''' before downloading any binary releases of Slicer.<br />
<br />
= Downloads =<br />
<br />
== Stable releases and support packages ==<br />
<br />
*'''[[Special:Slicer_Downloads/Release|Release]]: stable Slicer Releases'''<br />
*[[Special:Slicer_Downloads/Data|Data]]: sample data sets, see information below about how to use Slicer<br />
*[[Special:Slicer_Downloads/External|External]]: external support packages (ie precompiled win32 binaries, patches for mac tcl)<br />
*[[Special:Slicer_Downloads/Patches|Patches]]: things missing from some binary packages<br />
<br />
== Bleeding edge stuff ==<br />
*'''[[Special:Slicer_Downloads/Snapshots|Snapshots]]: custom built binaries, in various states of completion<br />
*[[Special:Slicer_Downloads/Nightly|Nightly]]: nightly builds<br />
<br />
= For more information =<br />
== Release Notes ==<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer3:Slicer3_Alpha_Release_Notes Slicer 3 Alpha]<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Release_Notes Slicer 2.6]<br />
* [http://na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Release_Notes Slicer 2.5]<br />
* [http://na-mic.org/Wiki/index.php/Slicer:Slicer2.4_Release_Notes Slicer 2.4]<br />
<br />
== Training ==<br />
<br />
For training on how to use Slicer, please see the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 User Training 101] page.<br />
For more information, please see the following links:<br />
<br />
* Main Slicer website: [http://www.slicer.org http://www.slicer.org]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:OldDownloads&diff=2824Special:Badtitle/NS100:OldDownloads2007-10-18T15:37:16Z<p>Zack: </p>
<hr />
<div>== Introduction == <br />
<br />
This is the download page for compiled versions of the 3D Slicer software. If you are looking for the source code, please [[Projects/slicerWeb:SourceCode|click here]].<br />
<br />
= License Agreement =<br />
<br />
Please fill out the '''[http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl Slicer License Form]''' before downloading any binary releases of Slicer.<br />
<br />
= Downloads =<br />
<br />
== Stable releases and support packages ==<br />
<br />
*'''[[Special:Slicer_Downloads/Release|Release]]: stable Slicer Releases'''<br />
*[[Special:Slicer_Downloads/Data|Data]]: sample data sets, see information below about how to use Slicer<br />
*[[Special:Slicer_Downloads/External|External]]: external support packages (ie precompiled win32 binaries, patches for mac tcl)<br />
*[[Special:Slicer_Downloads/Patches|Patches]]: things missing from some binary packages<br />
<br />
== Bleeding edge stuff ==<br />
*'''[[Special:Slicer_Downloads/Snapshots|Snapshots]]: custom built binaries, in various states of completion<br />
*[[Special:Slicer_Downloads/Nightly|Nightly]]: nightly builds<br />
<br />
= For more information =<br />
== Release Notes ==<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer3:Slicer3_Alpha_Release_Notes Slicer 3 Alpha]<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Release_Notes Slicer 2.6]<br />
* [http://na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Release_Notes Slicer 2.5]<br />
* [http://na-mic.org/Wiki/index.php/Slicer:Slicer2.4_Release_Notes Slicer 2.4]<br />
<br />
== Training ==<br />
<br />
For training on how to use Slicer, please see the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 User Training 101] page.<br />
For more information, please see the following links:<br />
<br />
* Main Slicer website: [http://www.slicer.org http://www.slicer.org]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:OldDownloads&diff=2823Special:Badtitle/NS100:OldDownloads2007-10-18T15:35:03Z<p>Zack: </p>
<hr />
<div>== Introduction == <br />
<br />
This is the download page for compiled versions of the 3D Slicer software. If you are looking for the source code, please [[Projects/slicerWeb:SourceCode|click here]].<br />
<br />
== License Agreement ==<br />
<br />
Please fill out the '''[http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl Slicer License Form]''' before downloading any binary releases of Slicer.<br />
<br />
== Downloads ==<br />
<br />
=== Stable releases and support packages ===<br />
<br />
*'''[[Downloads/Release|Release]]: stable Slicer Releases'''<br />
*[[Downloads/Data|Data]]: sample data sets, see information below about how to use Slicer<br />
*[[Downloads/External|External]]: external support packages (ie precompiled win32 binaries, patches for mac tcl)<br />
*[[Downloads/Patches|Patches]]: things missing from some binary packages<br />
<br />
=== Bleeding edge stuff ===<br />
*'''[[Downloads/Snapshots|Snapshots]]: custom built binaries, in various states of completion<br />
*[[Downloads/Nightly|Nightly]]: nightly builds<br />
<br />
== For more information ==<br />
=== Release Notes ===<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer3:Slicer3_Alpha_Release_Notes Slicer 3 Alpha]<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Release_Notes Slicer 2.6]<br />
* [http://na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Release_Notes Slicer 2.5]<br />
* [http://na-mic.org/Wiki/index.php/Slicer:Slicer2.4_Release_Notes Slicer 2.4]<br />
<br />
=== Training ===<br />
<br />
For training on how to use Slicer, please see the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 User Training 101] page.<br />
For more information, please see the following links:<br />
<br />
* Main Slicer website: [http://www.slicer.org http://www.slicer.org]</div>Zackhttps://www.slicer.org/w/index.php?title=Special:Badtitle/NS100:OldDownloads&diff=2822Special:Badtitle/NS100:OldDownloads2007-10-18T15:30:23Z<p>Zack: </p>
<hr />
<div>== Introduction == <br />
<br />
This is the download page for compiled versions of the 3D Slicer software. If you are looking for the source code, please [[Projects/slicerWeb:SourceCode|click here]].<br />
<br />
== License Agreement ==<br />
<br />
Please fill out the '''[http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl Slicer License Form]''' before downloading any binary releases of Slicer.<br />
<br />
== Downloads ==<br />
<br />
=== Stable releases and support packages ===<br />
<br />
*'''[[Projects/slicerWeb:Downloads/Release|Release]]: stable Slicer Releases'''<br />
*[[Projects/slicerWeb:Downloads/Data|Data]]: sample data sets, see information below about how to use Slicer<br />
*[[Projects/slicerWeb:Downloads/External|External]]: external support packages (ie precompiled win32 binaries, patches for mac tcl)<br />
*[[Projects/slicerWeb:Downloads/Patches|Patches]]: things missing from some binary packages<br />
<br />
=== Bleeding edge stuff ===<br />
*'''[[Projects/slicerWeb:Downloads/Snapshots|Snapshots]]: custom built binaries, in various states of completion<br />
*[[Projects/slicerWeb:Downloads/Nightly|Nightly]]: nightly builds<br />
<br />
== For more information ==<br />
=== Release Notes ===<br />
<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer3:Slicer3_Alpha_Release_Notes Slicer 3 Alpha]<br />
* [http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Release_Notes Slicer 2.6]<br />
* [http://na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Release_Notes Slicer 2.5]<br />
* [http://na-mic.org/Wiki/index.php/Slicer:Slicer2.4_Release_Notes Slicer 2.4]<br />
<br />
=== Training ===<br />
<br />
For training on how to use Slicer, please see the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 User Training 101] page.<br />
For more information, please see the following links:<br />
<br />
* Main Slicer website: [http://www.slicer.org http://www.slicer.org]</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer3:Web_Presence&diff=3459Slicer3:Web Presence2007-10-02T13:38:59Z<p>Zack: /* Counting Downloads */</p>
<hr />
<div>== Overview ==<br />
<br />
Infrastructure work to support a uniform Slicer web presence. <br />
Work building on [http://www.na-mic.org/Wiki/index.php/AHM_2006:ProjectsSlicer3WebPresence AHM 2006 Project Slicer3 Web Presence]<br />
<br />
Requirements:<br />
* counting number of downloads of Slicer binaries<br />
* record user information as they agree to abide by the Slicer license agreement<br />
* integrated download page that will provide links to binary Slicer packages, for nightly builds, developer snapshots, and official releases<br />
<br />
== Counting Downloads ==<br />
<br />
We need the ability to report number of unique Slicer binaries downloaded per month and per grant year, per release version, as well as aggregate numbers. <br />
Needed for grant reporting. The old method involved examining the flat files written as output from the Slicer license agreement web form and counting numbers of discrete entries by hand. <br />
<br />
Current page: http://websrv.bwh.harvard.edu/usage/na-mic-usage/ <br />
<br />
Do we need to parse the apache download logs directly or use multiple configuration files for [http://www.mrunix.net/webalizer/ Webalizer]?<br />
<br />
Inspiration page: [https://simtk.org/project/stats/?group_id=91 SimTK download statistics] and [https://simtk.org/project/stats/usagemap.php?group_id=91 SimTK geography of use].<br />
<br />
Publications data base download page implemented at http://www.na-mic.org/Special:Publications with admin interface to see the [http://www.na-mic.org/Special:PubDB_Stats Download statistics].<br />
<br />
From Ron 12 Sept 2007:<br />
Don't over report! (missing 1% is okay)<br />
No duplicate downloads.<br />
Disclose the method by which we are counting (report to NIH).<br />
<br />
'''Update''': I have modified the download scripts to start counting downloads. The results are stored in a MySQL database on na-mic1. Here is how I'm going to proceed from this point:<br />
#I'm will create a new page that displays how many times Slicer3 has been downloaded within a given period of time.<br />
#I will improve the appearance of the downloads section per Ron's request<br />
#Work on generating a nightly package of Slicer3 using CPack<br />
<br />
[[User:Zack|Zack]] 09:38, 2 October 2007 (EDT)<br />
<br />
== License Agreement ==<br />
<br />
We need to record some basic information from users so we have a record of their agreeing to the Slicer license agreement. Needed for grant reporting in conjunction with download counting.<br />
<br />
Current page: [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl]<br />
<br />
The original license form was written as an HTML form that submitted data to a perl script that would verify the form entries and then write the user information to a series of flat files, one per month. <br />
<br />
The move to use Wiki2Web for the Slicer web pages complicates the issue, as the form has to be translated into a MediaWiki page that will translate to the final web page and still work. From Nicole 3 Aug 2007:<br />
<br />
Marianna and I were working on the Slicer License form this afternoon, trying to get it working within the wiki to web framework, and <br />
we've hit a major roadblock.<br />
Mediawiki isn't rendering the html form tag, it's printing it out as text.<br />
From looking at<br />
http://meta.wikimedia.org/wiki/Help:Inputbox<br />
it seems like we could install an extension to get certain pre-defined input boxes, but<br />
a) we can't get the example to work (following the installation instructions)<br />
b) once we get the example to work, a new extension will have to be written in PHP to support the license form.<br />
<br />
== Download Page ==<br />
<br />
Current page: [http://www.na-mic.org/Slicer/Download/ http://www.na-mic.org/Slicer/Download/]<br />
<br />
Needs to be integrated into the Wiki2Web framework in such a way that supports automatic uploads from nightly builds, developer snapshot uploads, as well as automatic downloads of Windows prebuilt binary sub-packages during the building of Slicer.<br />
<br />
From Andy 4 Jun 2007:<br />
You could also create a MediaWiki extension for downloading files.<br />
Then you can use W2W to write text around the page, but use the extension to give you the list of files.<br />
<br />
From Ron 12 Sept 2007:<br />
Try progressive drop down menus, that will navigate you to the proper slicer version that you wish <br />
(ie latest release for your platform, or a release from a specific date)<br />
Goal: www.slicer.org/Download, click through the license, then see the drop down menus<br />
Major requirement: has to be '''very''' easy to use, no barriers for first time users.<br />
Needs to have same look and feel as the rest of the slicer.org pages<br />
<br />
== Team Members ==<br />
<br />
* Nicole Aucoin<br />
* Zack Galbreath<br />
* SPL system administrators</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer3:WebPresence:ContentIndex&diff=3457Slicer3:WebPresence:ContentIndex2007-01-08T13:58:50Z<p>Zack: Update from Wiki</p>
<hr />
<div>Historically, documentation for Slicer has been collected on [http://www.slicer.org slicer.org], but with the rise of the NA-MIC consortium, the [http://www.na-mic.org/Wiki Wiki] has been the preferred location to create and update documentation. This page will attempt to catalogue all the current content so that it can be collected and moved or archived in the new scheme.<br />
<br />
= Slicer.org =<br />
<br />
* [http://www.slicer.org Slicer.org]<br />
* [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl License form]<br />
<br />
= MIT =<br />
<br />
The slicer@ai.mit.edu email account that is used as a general contact point forwards emails to a list of people.<br />
<br />
= NA-MIC Servers =<br />
<br />
* [https://www.na-mic.org/Admin/SendPassword.cgi CVS write access request]<br />
* Nightly documentation: [http://www.na-mic.org/Slicer/Doc/tcl/index.html tcl] [http://www.na-mic.org/Slicer/Doc/vtk/html/index.html Base] [http://www.na-mic.org/Slicer/Doc/vtk/Modules/index.html Modules]<br />
<br />
== Wiki ==<br />
<br />
* [http://www.na-mic.org/Wiki/index.php?title=Special%3AAllpages&from=Slicer&namespace=0 Search results for all pages starting at "Slicer"]<br />
<br />
== Bug Tracker ==<br />
<br />
* [http://www.na-mic.org/Bug/index.php Bug tracker]<br />
<br />
== Downloads ==<br />
<br />
* Binary downloads: [http://www.na-mic.org/Slicer/Download/ na-mic.org/Slicer/Download]<br />
* Download statistics: [[https://www.na-mic.org/Stats/ Statistics]]<br />
<br />
= Sourceforge =<br />
<br />
The Sourceforge site is used as a portal, no code is hosted in it's repository.<br />
<br />
* [http://sourceforge.net/projects/slicer Slicer sourceforge project]<br />
** [http://slicer.sourceforge.net/ Home page]<br />
** [https://sourceforge.net/forum/?group_id=29131 Forum] - '''deleted''' email sent to person who posted a question in 2006<br />
** [https://sourceforge.net/tracker/?group_id=29131&atid=395336 Bugs] - migrated into the [http://www.na-mic.org/Bug/index.php Bug tracker on na-mic.org]<br />
** [https://sourceforge.net/tracker/?group_id=29131&atid=395339 Feature Requests]<br />
** [http://sourceforge.net/docman/?group_id=29131 Slicer Developer meeting notes] 2001/11/01-2004/10/26, with presentation power points<br />
<br />
= SPL =<br />
<br />
The Surgical Planning Lab at BWH hosts the current slicer.org web site, via host mapping and redirect. It also hosts the following exclusive content:<br />
<br />
* The CVS server and the [http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/slicer2/?cvsroot=slicer#dirlist CVS Web interface]<br />
* Papers?</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer:DICOM_PATCH&diff=4053Slicer:DICOM PATCH2007-01-07T17:33:18Z<p>Zack: Redirecting to Slicer:DICOM PATCH for Slicer 2.5</p>
<hr />
<div>#REDIRECT [[Slicer:DICOM PATCH for Slicer 2.5]]</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer:Simbio_Editing_Modifications&diff=4125Slicer:Simbio Editing Modifications2007-01-07T17:01:39Z<p>Zack: Redirecting to Slicer:Simbios Editing Modifications</p>
<hr />
<div>#REDIRECT [[Slicer:Simbios Editing Modifications]]</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer:Slicer2.6Ubuntu&diff=4143Slicer:Slicer2.6Ubuntu2007-01-05T18:36:46Z<p>Zack: Update from Wiki</p>
<hr />
<div>== '''Slicer''' 2.6 on Ubuntu ==<br />
<br />
=== Notes for installing '''Slicer''' 2.6 on Ubuntu: ===<br />
<br />
* '''Slicer''' requires csh, which isn't installed by default on some Ubuntu distributions. It can be found in Synaptic (Berkeley version).<br />
<br />
=== If you are having problems with OpenGL: ===<br />
<br />
To verify your OpenGL installation is working, run the command<br />
<br />
glxgears<br />
<br />
'''To install an NVIDIA graphics driver that supports OpenGL:'''<br />
<br />
sudo apt-get install nvidia-glx nvidia-kernel-common<br />
sudo nvidia-glx-config enable<br />
<br />
Edit the /etc/X11/xorg.conf file to change 'nv' to 'nvidia' in this section:<br />
<br />
Section "Device"<br />
Identifier "NVIDIA Corporation NV41 [Quadro FX 3450/4000 SDI]"<br />
Driver "nvidia"<br />
BusID "PCI:5:0:0"<br />
EndSection<br />
<br />
'''To install an ATI graphics driver that supports OpenGL:'''<br />
<br />
sudo apt-get update<br />
sudo apt-get install linux-restricted-modules-$(uname -r)<br />
sudo apt-get install xorg-driver-fglrx<br />
sudo depmod -a<br />
sudo aticonfig --initial<br />
sudo aticonfig --overlay-type=Xv</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer:Developer_Meetings:20060829&diff=4087Slicer:Developer Meetings:200608292007-01-05T18:36:31Z<p>Zack: Update from Wiki</p>
<hr />
<div>== '''Slicer''' Developers Meeting ==<br />
<br />
August 29, 2006, 2-3pm, at 1249 Boylston St., second floor demo room.<br />
<br />
'''Topic:''' MRT '''Slicer''', '''Slicer''' 3, '''Slicer''' 2.6<br />
<br />
'''Present:''' Steve Pieper, Katie Hayes, Nicole Aucoin, Haiying Liu<br />
<br />
* In mid September there will be an executive meeting for BIRN to prepare for the October all hands meeting<br />
* MRT '''Slicer'''<br />
** '''Slicer''' 1.6 has been officially retired, they've used '''Slicer''' 2.6 for 50+ cases in the Open MR, mostly laser ablation.<br />
* '''Slicer''' 3<br />
** NAMIC '''Slicer''' 3 meeting will be here Sept 11 & 12<br />
** Fiducials<br />
*** Alex will do the display portion<br />
*** Nicole will add in a method on the fiducial list class to add a fiducial with non default values<br />
** FreeSurfer models<br />
*** get the models with scalar overlays into '''Slicer''' 3 before the BIRN AHM in October<br />
*** Nicole will talk to Alex about the integration with the current model reading capabilities, probably won't go to an archetype reader, too complex<br />
*** Steve will link it in with the query atlas, and the faster cell picker and overlay value browswer<br />
*** colour code the file types when browsing for them? There will be a KW File Browswer improvement soon<br />
*** Alex will add in a model directory reading option so can read in a series of models<br />
** Reading in xml files from the commmand line? It should be an option in the ARGS macro, in Slicer3.cxx need to use it and pass it to the scene reader (std::str vector holds the unparsed arguments, when pass in a tcl script using -f they'd get passed to that script, but not defined yet what happens if no script is there)<br />
* '''Slicer''' 2.6 trouble shooting<br />
** Trying to get a linux 32 bit machine set up to debug a user's problem with the vtkFreeSurferReaders module<br />
** In 32 bit CVS head, when reading in mgz files, there are rows of voxels that are repeated, not present in the 2.6 official release<br />
** problem with zlib versus vtk_zlib? shouldn't be an issue as it's only a change when the vtk version changes to 4.6 and above</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer:license-2005-12-20&diff=4185Slicer:license-2005-12-202007-01-05T18:34:29Z<p>Zack: Update from Wiki</p>
<hr />
<div>3D '''Slicer''' Contribution and Software License Agreement ("Agreement") Version 1.0 (December 20, 2005)<br />
<br />
This Agreement covers contributions to and downloads from the 3D '''Slicer''' project ("'''Slicer'''") maintained by The Brigham and Women's Hospital, Inc. ("Brigham"). Part A of this Agreement applies to contributions of software and/or data to '''Slicer''' (including making revisions of or additions to code and/or data already in '''Slicer'''). Part B of this Agreement applies to downloads of software and/or data from '''Slicer'''. Part C of this Agreement applies to all transactions with '''Slicer'''. If you distribute Software (as defined below) downloaded from '''Slicer''', all of the paragraphs of Part B of this Agreement must be included with and apply to such Software.<br />
<br />
Your contribution of software and/or data to '''Slicer''' (including prior to the date of the first publication of this Agreement, each a "Contribution") and/or downloading, copying, modifying, displaying, distributing or use of any software and/or data from '''Slicer''' (collectively, the "Software") constitutes acceptance of all of the terms and conditions of this Agreement. If you do not agree to such terms and conditions, you have no right to contribute your Contribution, or to download, copy, modify, display, distribute or use the Software.<br />
<br />
PART A. CONTRIBUTION AGREEMENT - License to Brigham with Right to Sublicense ("Contribution Agreement").<br />
<br />
1. As used in this Contribution Agreement, "you" means the individual contributing the Contribution to '''Slicer''' and the institution or entity which employs or is otherwise affiliated with such individual in connection with such Contribution.<br />
<br />
2. This Contribution Agreement applies to all Contributions made to '''Slicer''', including without limitation Contributions made prior to the date of first publication of this Agreement. If at any time you make a Contribution to '''Slicer''', you represent that (i) you are legally authorized and entitled to make such Contribution and to grant all licenses granted in this Contribution Agreement with respect to such Contribution; (ii) if your Contribution includes any patient data, all such data is de-identified in accordance with U.S. confidentiality and security laws and requirements, including but not limited to the Health Insurance Portability and Accountability Act (HIPAA) and its regulations, and your disclosure of such data for the purposes contemplated by this Agreement is properly authorized and in compliance with all applicable laws and regulations; and (iii) you have preserved in the Contribution all applicable attributions, copyright notices and licenses for any third party software or data included in the Contribution.<br />
<br />
3. Except for the licenses granted in this Agreement, you reserve all right, title and interest in your Contribution.<br />
<br />
4. You hereby grant to Brigham, with the right to sublicense, a perpetual, worldwide, non-exclusive, no charge, royalty-free, irrevocable license to use, reproduce, make derivative works of, display and distribute the Contribution. If your Contribution is protected by patent, you hereby grant to Brigham, with the right to sublicense, a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable license under your interest in patent rights covering the Contribution, to make, have made, use, sell and otherwise transfer your Contribution, alone or in combination with any other code.<br />
<br />
5. You acknowledge and agree that Brigham may incorporate your Contribution into '''Slicer''' and may make '''Slicer''' available to members of the public on an open source basis under terms substantially in accordance with the Software License set forth in Part B of this Agreement. You further acknowledge and agree that Brigham shall have no liability arising in connection with claims resulting from your breach of any of the terms of this Agreement.<br />
<br />
6. YOU WARRANT THAT TO THE BEST OF YOUR KNOWLEDGE YOUR CONTRIBUTION DOES NOT CONTAIN ANY CODE THAT REQURES OR PRESCRIBES AN "OPEN SOURCE LICENSE" FOR DERIVATIVE WORKS (by way of non-limiting example, the GNU General Public License or other so-called "reciprocal" license that requires any derived work to be licensed under the GNU General Public License or other "open source license").<br />
<br />
PART B. DOWNLOADING AGREEMENT - License from Brigham with Right to Sublicense ("Software License").<br />
<br />
1. As used in this Software License, "you" means the individual downloading and/or using, reproducing, modifying, displaying and/or distributing the Software and the institution or entity which employs or is otherwise affiliated with such individual in connection therewith. The Brigham and Women’s Hospital, Inc. ("Brigham") hereby grants you, with right to sublicense, with respect to Brigham's rights in the software, and data, if any, which is the subject of this Software License (collectively, the "Software"), a royalty-free, non-exclusive license to use, reproduce, make derivative works of, display and distribute the Software, provided that:<br />
<br />
(a) you accept and adhere to all of the terms and conditions of this Software License;<br />
<br />
(b) in connection with any copy of or sublicense of all or any portion of the Software, all of the terms and conditions in this Software License shall appear in and shall apply to such copy and such sublicense, including without limitation all source and executable forms and on any user documentation, prefaced with the following words: "All or portions of this licensed product (such portions are the "Software") have been obtained under license from The Brigham and Women's Hospital, Inc. and are subject to the following terms and conditions:"<br />
<br />
(c) you preserve and maintain all applicable attributions, copyright notices and licenses included in or applicable to the Software;<br />
<br />
(d) modified versions of the Software must be clearly identified and marked as such, and must not be misrepresented as being the original Software; and<br />
<br />
(e) you consider making, but are under no obligation to make, the source code of any of your modifications to the Software freely available to others on an open source basis.<br />
<br />
2. The license granted in this Software License includes without limitation the right to (i) incorporate the Software into proprietary programs (subject to any restrictions applicable to such programs), (ii) add your own copyright statement to your modifications of the Software, and (iii) provide additional or different license terms and conditions in your sublicenses of modifications of the Software; provided that in each case your use, reproduction or distribution of such modifications otherwise complies with the conditions stated in this Software License.<br />
<br />
3. This Software License does not grant any rights with respect to third party software, except those rights that Brigham has been authorized by a third party to grant to you, and accordingly you are solely responsible for (i) obtaining any permissions from third parties that you need to use, reproduce, make derivative works of, display and distribute the Software, and (ii) informing your sublicensees, including without limitation your end-users, of their obligations to secure any such required permissions.<br />
<br />
4. The Software has been designed for research purposes only and has not been reviewed or approved by the Food and Drug Administration or by any other agency. YOU ACKNOWLEDGE AND AGREE THAT CLINICAL APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. Any commercialization of the Software is at the sole risk of the party or parties engaged in such commercialization. You further agree to use, reproduce, make derivative works of, display and distribute the Software in compliance with all applicable governmental laws, regulations and orders, including without limitation those relating to export and import control.<br />
<br />
5. The Software is provided "AS IS" and neither Brigham nor any contributor to the software (each a "Contributor") shall have any obligation to provide maintenance, support, updates, enhancements or modifications thereto. BRIGHAM AND ALL CONTRIBUTORS SPECIFICALLY DISCLAIM ALL EXPRESS AND IMPLIED WARRANTIES OF ANY KIND INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL BRIGHAM OR ANY CONTRIBUTOR BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, EXEMPLARY OR CONSEQUENTIAL DAMAGES HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY ARISING IN ANY WAY RELATED TO THE SOFTWARE, EVEN IF BRIGHAM OR ANY CONTRIBUTOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. TO THE MAXIMUM EXTENT NOT PROHIBITED BY LAW OR REGULATION, YOU FURTHER ASSUME ALL LIABILITY FOR YOUR USE, REPRODUCTION, MAKING OF DERIVATIVE WORKS, DISPLAY, LICENSE OR DISTRIBUTION OF THE SOFTWARE AND AGREE TO INDEMNIFY AND HOLD HARMLESS BRIGHAM AND ALL CONTRIBUTORS FROM AND AGAINST ANY AND ALL CLAIMS, SUITS, ACTIONS, DEMANDS AND JUDGMENTS ARISING THEREFROM.<br />
<br />
6. None of the names, logos or trademarks of Brigham or any of Brigham's affiliates or any of the Contributors, or any funding agency, may be used to endorse or promote products produced in whole or in part by operation of the Software or derived from or based on the Software without specific prior written permission from the applicable party.<br />
<br />
7. Any use, reproduction or distribution of the Software which is not in accordance with this Software License shall automatically revoke all rights granted to you under this Software License and render Paragraphs 1 and 2 of this Software License null and void.<br />
<br />
8. This Software License does not grant any rights in or to any intellectual property owned by Brigham or any Contributor except those rights expressly granted hereunder.<br />
<br />
PART C. MISCELLANEOUS<br />
<br />
This Agreement shall be governed by and construed in accordance with the laws of The Commonwealth of Massachusetts without regard to principles of conflicts of law. This Agreement shall supercede and replace any license terms that you may have agreed to previously with respect to '''Slicer'''.</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer:Bugs&diff=4049Slicer:Bugs2007-01-02T14:58:32Z<p>Zack: </p>
<hr />
<div>To enter a bug for Slicer, you need to create an account on our bug tracker. Go to http://www.na-mic.org/Bug/ , then click on "Create a new account" at the top of the page. Enter your email address and name, and your temporary password will be sent to your email address. Go back to http://www.na-mic.org/Bug/ and enter your email address and password. Now you will be allowed to add and edit bugs.<br />
<br />
<br />
<br />
To add a bug, click on "Add a new bug". Choose "Slicer" as the project. Use the Version drop down menu to choose the Slicer version you are reporting the bug for. Include a brief summary in the Summary box, such as "Segfault on OSX when adding new model". If the problem is in a module, try to put the module name in the Summary. In the description area, include as much detail as you can, including what you were doing at the time, if this has worked in the past but is now broken, error messages, any debugging you have tried, links to screenshots, etc.<br />
<br />
<br />
<br />
The Severity and Priority fields are somewhat arbitrary and redundant at this point. Use your best judgement, and these can always been changed later. Fill out the Component, Module, and OS information. If there is additional information about those fields that aren't covered by the drop down menu, put them in the description. Click Submit when you have filled out this information.<br />
<br />
<br />
<br />
Go back to http://www.na-mic.org/Bug/ . The bug you just submitted should be listed under "Five most recently submitted bugs" Click on your bug to edit it further.<br />
<br />
<br />
<br />
You can add additional comments in the "Additional Comments, module author, etc" field, and put your email address in the CC: field to be notified when the bug changes. You can also adjust priorities here as you see fit.<br />
<br />
<br />
<br />
If you want versions, module names, names of developers, etc. to be added, contact Andy Cedilnik at andy.cedilnik@kitware.com and ask him to add new fields to the bug tracker.<br />
<br />
<br />
<br />
When a bug is fixed, go to the [http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/slicer2/ Slicer Viewcvs], find the file that you edited and submitted to cvs to fix the bug, and click on the file name. You will see something like this:<br />
<br />
<br />
<br />
Revision 1.36.2.6 / (as text) / (view) - annotate - [select for diffs] , Fri May 13 20:18:41 2005 UTC (7 weeks, 4 days ago) by hayes<br />
Branch: release-2-5-patches<br />
CVS Tags: release-2-5-dev-patches, release-2-5-dev<br />
Changes since 1.36.2.5: +1 -1 lines<br />
Diff to previous 1.36.2.5 to a branchpoint 1.36<br />
<br />
<br />
<br />
Right click on the Diff (in this case, Diff to previous 1.36.2.5), and select Copy Link Location. Paste this link into the Link to Diff of Fix field on the bug page.<br />
<br />
<br />
<br />
When you resolve a bug, set Status to Closed, and Resolution to fixed.<br />
<br />
<br />
<br />
'''When you edit a bug, make sure to click Submit in the lower right hand corner, or your changes will not be saved!'''</div>Zackhttps://www.slicer.org/w/index.php?title=Slicer3:Execution_Model_Discussion&diff=3840Slicer3:Execution Model Discussion2006-12-27T20:26:09Z<p>Zack: </p>
<hr />
<div>=== Introduction ===<br />
<br />
This page contains the initial proposal and subsequent '''discussion''' regarding the [[Slicer3:Execution_Model|'''Slicer3'''<nowiki>:Execution_Model</nowiki>]].<br />
<br />
=== Initial Standard ===<br />
<br />
This sample describes the initial standard. The current best implementation is to write your XML algorithm description by hand, then have your executable respond to the --xml flag by producing the XML description to standard output.<br />
<br />
Some notes about the sample below.<br />
<br />
# The <category> tag corresponds to where the executable should show up in a menu on the calling Application<br />
# <parameters> tags are grouped together by name in the GUI, in the example "Registration Parameters" and "IO"<br />
# The currently described parameters are<br />
## <integer> for simple integers<br />
## <double> for floating point numbers<br />
## <string> for string arguments<br />
## <boolean> for boolean switches<br />
## <image> for images. The current standard is 3d images, but may be agumented in the future<br />
## <file> for files.<br />
## <directory> for directories.<br />
## <integer-vector> for a comma separated list of integers<br />
## <float-vector> for a comma separated list of floats<br />
## <double-vector> for a comma separated list of doubles<br />
# Most parameters share some common attributes<br />
## <flag> the short flag for this parameter, ''i.e.'' <flag>f</flag><br />
## <longflag> the long flag for this parameter, ''i.e.'' <longflag>foo</longflag><br />
## <label> the text to display next to the parameter<br />
## <default> default value<br />
## <description> a useful description of the parameter, suitable for tool tips, ''etc...''<br />
## <constraints> currently <minimum>, <maximum>, and <step> for <integer> and <double><br />
# For positional arguments, an index is required, in this case Fixed and Moving images are indices 0 and 1<br />
# For images and files, there is a <channel> tag. <channel>input</channel> indicates that this file is read by the executable, <channel>output</channel> indicates the executale writes the image<br />
<br />
==== To Do ====<br />
<br />
* Add radiobutton like choices<br />
* Add image format discription, ''i.e.'' does this algorithm handle 2D images, need DICOM files, ''etc...''<br />
* Establish convention for progress indications<br />
* XSD<br />
<br />
<br /><br />
<br />
==== This is the example from the NAMIC Sandbox. ====<br />
<br />
<br />
{practical:CommandLineAPI-Linux}1356:./CLRegistration --xml<br />
<?xml version="1.0" encoding="utf-8"?><br />
<executable><br />
<category>registration</category><br />
<title>NAMIC sample registration</title><br />
<description>Registers two images together using a rigid transform and MI</description><br />
<version>1.0</version><br />
<documentationurl></documentationurl><br />
<license></license><br />
<contributor>Daniel Blezek</contributor><br />
<br />
<parameters><br />
<label>Registration Parameters</label><br />
<description>Parameters used for registration</description><br />
<integer><br />
<flag>b</flag><br />
<longflag>histogrambins</longflag><br />
<description>Number of histogram bins to use for Mattes Mutual Information</description><br />
<label>Histogram Bins</label><br />
<default>30</default><br />
<constraints><br />
<minimum>1</minimum><br />
<maximum>500</maximum><br />
<step>5</step><br />
</constraints><br />
</integer><br />
<br />
<integer><br />
<flag>s</flag><br />
<longflag>spatialsamples</longflag><br />
<description>Number of spatial samples to use in estimating Mattes Mutual Information</description><br />
<label>Spatial Samples</label><br />
<default>10000</default><br />
<constraints><br />
<minimum>1000</minimum><br />
<maximum>50000</maximum><br />
<step>1000</step><br />
</constraints><br />
</integer><br />
<br />
<string><br />
<flag>i</flag><br />
<longflag>iterations</longflag><br />
<description>Comma separated list of iterations must have the same number of elements as learning rate</description><br />
<label>Iterations</label><br />
<default>200,100</default><br />
</string><br />
<br />
<string><br />
<flag>l</flag><br />
<longflag>learningrate</longflag><br />
<description>Comma separated list of learning rates must have the same number of elements as iterations</description><br />
<label>Learning Rates</label><br />
<default>0.05,0.005</default><br />
</string><br />
<br />
<double><br />
<longflag>translationscale</longflag><br />
<flag>t</flag><br />
<description>Relative scale of translations to rotations, i.e. a value of 100 means 10mm = 1 degree</description><br />
<label>Translation scaling</label><br />
<default>100.0</default><br />
<constraints><br />
<minimum>10.0</minimum><br />
<maximum>500.0</maximum><br />
<step>50.0</step><br />
</constraints><br />
</double><br />
</parameters><br />
<br />
<parameters><br />
<label>IO</label><br />
<description>Input/output parameters</description><br />
<image><br />
<name>Fixed</name><br />
<label>Fixed Image</label><br />
<channel>input</channel><br />
<index>0</index><br />
<description>Fixed image to register to</description><br />
</image><br />
<image><br />
<name>Moving</name><br />
<label>Moving Image</label><br />
<channel>input</channel><br />
<index>1</index><br />
<description>Moving image</description><br />
</image><br />
<image><br />
<name>Output</name><br />
<label>Output Volume</label><br />
<channel>output</channel><br />
<index>2</index><br />
<description>Resampled Moving Image</description><br />
</image><br />
</parameters><br />
<br />
</executable><br />
<br />
<br />
<br />
==== Sample screenshots ====<br />
<br />
{|<br />
|- valign="top"<br />
!<br />
[[Image:NAMICSampleRegistrationMenu.png|thumb|right|180px|Sample GUI generated from XML above]]<br />
|}<br />
<br />
==== Open questions ====<br />
<br />
# What classes of algorithms should '''Slicer3''' be aware of?<br />
## Registration, classification, segmentation, filtering?<br />
# How should '''Slicer3''' communicate with the executables?<br />
## Special FileIO objects (for ITK) has been suggested.<br />
## MMapped files for efficient IO.<br />
## Shared memory.<br />
## Standard files.<br />
# Does '''Slicer3''' need to communicate with the executing process?<br />
## For status, "Cancel" operations, ''etc''...<br />
<br />
=== Proposal ===<br />
<br />
If we adopt a standard XML description of the parameters to the algorithm, any application should be able to parse the XML and construct a GUI suitable for interaction with the software.<br />
<br />
Below are potential ideas for an XML file format:<br />
<br />
==== Initial JSON output from sample registration package ====<br />
<br />
<br />
/* JSON version 1.0 */<br />
{<br />
"class" : "registration",<br />
"name" : "CLRegistration",<br />
"info" : "Register two volumes",<br />
"executable" : "CLRegistration",<br />
"requiredparameters": {<br />
"fixed" : {<br />
"type" : "file",<br />
"index" : "0",<br />
"channel" : "input",<br />
/* what about image dimension: 2, 3, ... */<br />
},<br />
"moving" : {<br />
},<br />
"output" : {<br />
}<br />
"parameters" : {<br />
"histogrambins" : {<br />
"flag" : "b",<br />
"name" : "histogrambins",<br />
"displayname" : "Number of histogram bins",<br />
"description" : "Number of histogram bins",<br />
"type" : "integer",<br />
"guihints" : "slider",<br />
"range" : "[5-200]",<br />
"default" : "100"<br />
},<br />
"randomseed" : {<br />
"flag" : "d",<br />
"name" : "randomseed",<br />
},<br />
"gradtolerance" : {<br />
"flag" : "g",<br />
"name" : "gradtolerance",<br />
},<br />
"iterations" : {<br />
"flag" : "i",<br />
"name" : "iterations",<br />
},<br />
"learningrate" : {<br />
"flag" : "l",<br />
"name" : "learningrate",<br />
},<br />
"spatialsamples" : {<br />
"flag" : "s",<br />
"name" : "spatialsamples",<br />
},<br />
"translationscale" : {<br />
"flag" : "t",<br />
"name" : "translationscale",<br />
},<br />
"noinitializetransform" : {<br />
"flag" : "u",<br />
"name" : "noinitializetransform",<br />
},<br />
"help" : {<br />
"flag" : "h",<br />
"name" : "help",<br />
},<br />
"json" : {<br />
"flag" : "j",<br />
"name" : "json",<br />
},<br />
}<br />
}<br />
<br />
XML Version of the same description<br />
<br />
<sl<br />
class = "registration"<br />
name = "CLRegistration"<br />
info = "Register two volumes"<br />
executable = "CLRegistration"><br />
<requiredparameters><br />
<requirement name="fixed"><br />
type = "file"<br />
index = "0"<br />
channel = "input"<br />
<!-- what about image dimension: 2 3 ... --><br />
</requirement><br />
<requirement name="moving" /><br />
<requirement name="output" /><br />
</requiredparameters><br />
<parameters><br />
<parameter name="histogrambins"<br />
flag = "b"<br />
name = "histogrambins"<br />
displayname = "Number of histogram bins"<br />
description = "Number of histogram bins"<br />
type = "integer"<br />
guihints = "slider"<br />
range = "[5-200]"<br />
default = "100"<br />
/><br />
<parameter name="randomseed"<br />
flag = "d"<br />
name = "randomseed"<br />
/><br />
<parameter name="gradtolerance"<br />
flag = "g"<br />
name = "gradtolerance"<br />
/><br />
<parameter name="iterations"<br />
flag = "i"<br />
name = "iterations"<br />
/><br />
<parameter name="learningrate"<br />
flag = "l"<br />
name = "learningrate"<br />
/><br />
<parameter name="spatialsamples"<br />
flag = "s"<br />
name = "spatialsamples"<br />
/><br />
<parameter name="translationscale"<br />
flag = "t"<br />
name = "translationscale"<br />
/><br />
<parameter name="noinitializetransform"<br />
flag = "u"<br />
name = "noinitializetransform"<br />
/><br />
<parameter name="help"<br />
flag = "h"<br />
name = "help"<br />
/><br />
<parameter name="json"<br />
flag = "j"<br />
name = "json"<br />
/><br />
</parameters><br />
</sl><br />
<br />
==== Data-centric proposal ====<br />
<br />
<br />
<?xml version="1.0" encoding="utf-8"?><br />
<executable class="registration"><br />
<Name>CLRegistration</name><br />
<Description>Registers two images, writes the resampled moving image</description><br />
<Parameters><br />
<Parameter required="false" flag="t" name="threshold"><br />
<Description>Threshold</Description><br />
<Type>integer</Type><br />
<Constraints><br />
<Range minimum="0" maximum="100"/><br />
</Constraints><br />
</Parameter><br />
<Parameter required="true"><br />
</Parameter><br />
</Parameters><br />
</executable><br />
<br />
<br />
==== GUI-centric proposal ====<br />
<br />
<br />
<?xml version="1.0" encoding="utf-8"?><br />
<executable class="register"><br />
<name>Register3d</name><br />
<version>1.0</version><br />
<description>This registers and resamples two images</description><br />
<br />
<parameters><br />
<!-- a switch is a boolean flag, likely a checkbox.<br />
on the command line, name is the long version, flag is the<br />
one character version of the argument<br />
--><br />
<switch name="interpolate" flag="i" default="true" required="false"><br />
<description></description><br />
</switch><br />
<br />
<!-- a value takes a single argument, may be required to be present<br />
and has a type. In this case, the "metric" value is constrained to be<br />
one of the listed options below. This should be represented by a<br />
group of radio buttons or drop down menu.<br />
--><br />
<value name="metric" flag="m" default="mattes" required="false" type="string"><br />
<description></description><br />
<constraints><br />
<list><br />
<constraint>mattes</constraint><br />
<constraint>mi</constraint><br />
<constraint>normalizedcorrelation</constraint><br />
</list><br />
</constraints><br />
</value><br />
<br />
<!-- an integer value with a range --><br />
<value name="threshold" flag="t" type="integer"><br />
<constraints><br />
<range minimum="0" maximum="100"/><br />
<increment>.1</increment><br />
</constraints><br />
</value><br />
<br />
<!-- a value argument that allow several instances of the argument to be specified.<br />
The values are appended to each other and returned in a vector.<br />
In the GUI, this could be a list of numbers in a string, or a<br />
dynamic list constructed by the user.<br />
--><br />
<value name="iterations" flag="e" type="iteration" allowrepeats="true"><br />
<constraints><br />
<range minimum="1"/><br />
</constraints><br />
</value><br />
<br />
<!-- xor specifies that only one of it's contained parameters<br />
be specified. In this case, we want a file or url, but not<br />
both --><br />
<xor><br />
<value name="file" flag="f" type="filename"/><br />
<value name="url" flag="u"/><br />
</xor><br />
<br />
<!-- unlabeledvalue do not have a flag associated with them, and are positional.<br />
In this case, we are looking for 3 filenames.<br />
--><br />
<unlabeledvalue name="fixedimage" position="0" type="filename"/><br />
<unlabeledvalue name="movingimage" position="1" type="filename"/><br />
<unlabeledvalue name="outputimage" position="2" type="filename"/><br />
</parameters><br />
</executable><br />
<br />
==== JSON description ====<br />
<br />
<br />
/* JSON version 1.0<br />
January 11, 2005 */<br />
{<br />
"class" : "registration",<br />
"name" : "CLRegistration",<br />
"info" : "Registers two images, writes the resampled moving image",<br />
"executable" : "CLRegistration",<br />
"parameters" :<br />
"threshold" : {<br />
"info" : "threshold"<br />
"flag" : "t",<br />
"required" : "true",<br />
"type" : "integer",<br />
"default" : "50",<br />
"contraints" : {<br />
"range" : {<br />
"minimum" : "0",<br />
"maximum" : "100" } },<br />
"guihints" : {<br />
"control" : "slider",<br />
"group" : "preprocessing" } },<br />
"xsigma" : {<br />
"info" : "X Direction in sigma",<br />
"flag" : "x",<br />
"required" : "false",<br />
"type" : "float",<br />
"default" : "1.0",<br />
"contraints" : {<br />
"range" : {<br />
"minimum" : "0",<br />
"maximum" : "5.0" } },<br />
"guihints" : {<br />
"control" : "slider",<br />
"group" : "preprocessing" } },<br />
"fixedfile" : {<br />
"info" : "Fixed Image",<br />
"order" : "0",<br />
"required" : "true",<br />
"type" : "file",<br />
"contraints" : {<br />
"filetypes" : [<br />
"ITK",<br />
"Slicerd",<br />
"MRML" ] },<br />
"guihints" : {<br />
"control" : "fileselection",<br />
"group" : "io" } },<br />
<br />
}<br />
<br />
=== Related Work ===<br />
<br />
==== MetaCommand ====<br />
<br />
Julien Jomier and Stephen Aylward have added support for command line parsing to itk with the MetaCommand class (Utilities/MetaIO/metaCommand.{h,cxx}). It supports a -xml flag to output args in an xml syntax.<br />
<br />
==== Qt Designer XML Format ====<br />
<br />
Qt has an xml syntax for representing their GUI layouts. It's unclear if this tool could be used to design layouts used by other GUI packages.<br />
<br />
==== ParaView Server ====<br />
<br />
ParaView has a syntax to extend the GUI described [http://www.paraview.org/Wiki/ParaView:Extend on their wiki here].<br />
<br />
==== LONI Pipeline ====<br />
<br />
Parameters to executables are described in an XML file as part of the process of wrapping them for the pipeline. These XML descriptions are quite similar to the example given above. Some example pipelines are available at the [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/PipelineModules Pipeline Wiki]. A working draft of the language description is found also on the [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/DeveloperDocumentation Wiki].<br />
<br />
==== JSON ====<br />
<br />
Mike Halle suggested looking a JSON to describe the command line arguments to the parser, then to fill in the values from the command line. With this description, a GUI could build an interface for your code and/or communicate with your executable using JSON. Requires a standard set of elements.<br />
<br />
[http://www.json.org/ JSON (JavaScript Object Notation)] is a lightweight data-interchange format. It is easy for humans to read and write. It is easy for machines to parse and generate. It is based on a subset of the JavaScript Programming Language, Standard ECMA-262 3rd Edition - December 1999. JSON is a text format that is completely language independent but uses conventions that are familiar to programmers of the C-family of languages, including C, C++, C#, Java, JavaScript, Perl, Python, and many others. These properties make JSON an ideal data-interchange language.</pre><br />
<br />
==== DICOM Working Group 23 ====<br />
<br />
Dave Channin suggests this group be aware of the efforts of [http://medical.nema.org/DICOM/minutes/WG-23/ DICOM Working Group 23] along these lines. Although termed ''application hosting'' the work group is defining a DICOM standard mechanism by which a workstation can ''invoke'' an algorithm, send it (DICOM) data and receive from it (DICOM) results (as well as statuses, etc.) Although still in draft form they are thinking about using web services and in particular, [http://www.globus.org/ogsa/ OGSA (Open Grid Services Architecture)]. This has the interesting repercussion of allowing invoked algorihtms to be run locally or over the grid. This effort may be of interest to this group along two lines: 1) IMNSHO, Slicer should support the DICOM WG23 plug so as to be able to invoke compliant algorithms, and 2) Algorithm developers need to decide whether to add their specific functionality to ''base Slicer'' or as a DICOM WG23. In th elatter case it would then be possible to run these (presumably VTK and iTK based) algorithms not only on Slicer but on other (potentially commercial workstations) that support DICOM WG23. (I hope this is the right group to consider this).</div>Zack