https://www.slicer.org/w/api.php?action=feedcontributions&user=Sylvainjaume&feedformat=atomSlicer Wiki - User contributions [en]2024-03-29T04:50:56ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=17009Modules:SpineSegmentation-Documentation-3.62010-06-16T13:37:22Z<p>Sylvainjaume: add link to HBM 2010 poster</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|After 3 minutes, the segmentation results appear: a label map (blue) and a 3D model (3D view).]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
{|<br />
|[[Image:MIT_NAMIC_Logo.png|thumb|200px|MIT & NA-MIC]]<br />
|}<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module builds on Pattern Recognition theory to provide for a fully automated segmentation. The module first defines a shape model of the spinal cord modeling both the inner volume and the outer volume. Then the segmentation algorithm uses this model to explored the image space and find the best match given the field on intensities in the image. The advantage of this method relies on its unsupervised property: no need for any parameter setting or any initialization.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|600px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|600px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|600px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|600px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|600px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|600px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|600px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|600px|7. review result]]<br />
|}<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|600px|8. save results]]<br />
|}<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|600px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input:''' select the input image<br />
** '''Image output:''' create Slicer node for output image<br />
** '''Model output:''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default:''' reset input and output nodes to blank values<br />
** '''Cancel:''' cancel the execution of the algorithm<br />
** '''Apply:''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Module source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Doxygen generated documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html Slicer Doxygen]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
[http://people.csail.mit.edu/sylvain/Sylvain_Jaume_HBM_poster_2010.pdf Stochastic Neurography], S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Announcments-3.6-Team&diff=16659Announcments-3.6-Team2010-06-08T16:52:42Z<p>Sylvainjaume: </p>
<hr />
<div>Back to the [[Announcements:Slicer3.6|Slicer 3.6 announcement]]<br />
<br />
Development of Slicer 3.6 has been supported through volunteer work and through a number of funding mechanisms and sources. Please see the [http://www.slicer.org/pages/Acknowledgments Slicer Acknowledgements] page.<br />
<br />
Major contributors for the Slicer 3.6 release include (in alphabetic order):<br />
* [http://www.orobix.com/luca Luca Antiga]: Python integration, CLI<br />
* [http://www.spl.harvard.edu/pages/People/nicole Nicole Aucoin]: Software development, Fiducials, Informatics<br />
* [http://kitware.com/company/team/aylward.html Stephen Aylward]: Registration, ITK<br />
* [http://www.kitware.com/company/team/barre.html Sébastien Barré]: GUI, KWWidgets<br />
* [http://www.niral.unc.edu/people Francois Budin]: Resampling of scalar images and DTI<br />
* Andriy Fedorov: ChangeTracker, FastMarching Segmentation, CropVolume, LabelDiameterEstimation, N4ITK Bias field correction, debugging<br />
* [http://www.kitware.com/company/team/fillion.html Jean-Christophe Fillion-Robin]: CTK, Qt<br />
* [http://kitware.com/company/team/finet.html Julien Finet]: Volume rendering, CTK<br />
* [http://kitware.com/company/team/galbreath.html Zack Galbreath]: CDash, Wiki, Sys Admin<br />
* [http://www.kitware.com/company/team/goodlett.html Casey Goodlett]: Registration<br />
* [http://www.spl.harvard.edu/~hayes Kathryn Hayes]: Release engineering, software development, quality assurance<br />
* [http://www.kitware.com/company/team/hoffman.html Bill Hoffman]: CMake, CTest, CPack, Software Process<br />
* [http://kitware.com/company/team/ibanez.html Luis Ibanez]: Registration, Segmentation, ITK, Software Process (Testing)<br />
* [http://people.csail.mit.edu/sylvain Sylvain Jaume]: SpineSegmentation, MRIBiasFieldCorrection, EMSegment<br />
* [http://www.uiowa.edu Hans Johnson]: BRAINSFit, BRAINSDemonWarp, BRAINSResample, BRAINSROIAuto<br />
* [http://kitware.com/company/team/jomier.html Julien Jomier]: MIDAS, CDash<br />
* [http://www.spl.harvard.edu/~kikinis Ron Kikinis]: Principal Investigator, busboy<br />
* [http://www.kitware.com/company/team/krishnan.html Karthik Krishnan]: 3D Widgets.<br />
* [http://isp.ncifcrf.gov/abcc Yanling Liu]: Volume rendering.<br />
* Mahnaz Maddah: EM Clustering of tractography<br />
* [http://www.uiowa.edu Vincent Magnotta]: IA_FEM Mesh<br />
* [http://wiki.na-mic.org/Wiki/index.php/User:Millerjv Jim Miller]: CLI, Registration, Lightbox, Compare View, Crosshairs<br />
* [http://kitware.com/company/team/partyka.html Dave Partyka]: Cross-platform build and installation, CDash<br />
* [http://www.spl.harvard.edu/~pieper Steve Pieper]: Chief architect, editor<br />
* [http://www.spl.harvard.edu/pages/People/wjp Wendy Plesniak]: GUI, Informatics<br />
* [http://www.csail.mit.edu/~pohl Kilian Pohl]: EMSegmenter<br />
* [http://lmi.bwh.harvard.edu/~spujol/ Sonia Pujol]: Workshops, Tutorials, Testing<br />
* [http://kitware.com/company/team/schroeder.html Will Schroeder]: VTK, 3D widgets<br />
* Xiaodong Tao: Diffusion DICOM, Skull stripping, HAMMER, MS Lesion<br />
* [http://www.niral.unc.edu/people Clement Vachet]: ARCTIC cortical thickness, Shape Analysis module<br />
* [http://pnl.bwh.harvard.edu/people/profiles/wassermann.html Demian Wassermann]: Diffusion MRI modules, documentation.<br />
* [http://lmi.bwh.harvard.edu/~westin Carl-Fredrik Westin]: Diffusion MRI overview<br />
* Andrew Wiles: IGT tool selector, collect patient fiducials<br />
* [http://www.spl.harvard.edu/~alexy Alex Yarmarkovich]: MRML, DTI modules, software development</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15886Modules:SpineSegmentation-Documentation-3.62010-05-14T17:20:03Z<p>Sylvainjaume: /* Source code & documentation */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|After 3 minutes, the segmentation results appear: a label map (blue) and a 3D model (3D view).]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
{|<br />
|[[Image:MIT_NAMIC_Logo.png|thumb|200px|MIT & NA-MIC]]<br />
|}<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module builds on Pattern Recognition theory to provide for a fully automated segmentation. The module first defines a shape model of the spinal cord modeling both the inner volume and the outer volume. Then the segmentation algorithm uses this model to explored the image space and find the best match given the field on intensities in the image. The advantage of this method relies on its unsupervised property: no need for any parameter setting or any initialization.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|600px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|600px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|600px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|600px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|600px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|600px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|600px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|600px|7. review result]]<br />
|}<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|600px|8. save results]]<br />
|}<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|600px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input:''' select the input image<br />
** '''Image output:''' create Slicer node for output image<br />
** '''Model output:''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default:''' reset input and output nodes to blank values<br />
** '''Cancel:''' cancel the execution of the algorithm<br />
** '''Apply:''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Module source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Doxygen generated documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html Slicer Doxygen]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Documentation/3.6&diff=15884Documentation/3.62010-05-14T17:18:24Z<p>Sylvainjaume: /* Slicer Extensions */ remove 'no documentation' icon</p>
<hr />
<div>=Documentation Draft notes=<br />
Key for flagged modules below:<br />
<br />
[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation<br />
<br />
[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:<br />
* for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.<br />
* for interactive modules, see other modules in Base/GUI for an example.<br />
<br />
[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation<br />
<br />
=Introduction=<br />
<br />
3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications. <br />
<br />
3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.<br />
<br />
The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized colormaps). To the best of our knowledge, no individual segmentation tool provides such powerful visualization capabilities for the user as 3D Slicer. (These paragraphs were provided by A. Fedorov and C. Lisle)<br />
<br />
The 3.6 release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Announcements:Slicer3.6 |3.6 Announcement page]] for a list of those changes. The community contributing to Slicer 3.6 is and the following [[Announcments-3.6-Team|acknowledged here]]. <br />
<br />
*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.<br />
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].<br />
*For sample data see [[SampleData|here]]<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak) <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak) <br />
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br />
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)<br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)<br />
<br />
=Modules=<br />
<br />
==Core==<br />
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)<br />
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich) <br />
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) <br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)<br />
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller) <br />
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)<br />
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper) <br />
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich) <br />
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin) <br />
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)<br />
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)<br />
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich) <br />
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)<br />
<br />
==Wizards==<br />
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)<br />
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)<br />
<br />
==Informatics Modules==<br />
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) <br />
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)<br />
<br />
==Registration==<br />
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.<br />
*Fast Registration<br />
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)<br />
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller) <br />
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller) <br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen) <br />
*Robust Registration<br />
**[[Modules:RegisterImages-Documentation-3.6|Expert Automated Registration]]: automated registration (rigid to affine to nonrigid) with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)<br />
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)<br />
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).<br />
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).<br />
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).<br />
*Brain Only Registration<br />
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)<br />
*Non-Raster-Image Data Registration<br />
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)<br />
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)<br />
<br />
==Segmentation==<br />
*[[Modules:SegmentationOverview3.6|Overview]]<br />
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl) <br />
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl) <br />
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl) <br />
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)<br />
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)<br />
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).<br />
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).<br />
<br />
==Quantification==<br />
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)<br />
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)<br />
<br />
==Diffusion MRI==<br />
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]<br />
* DWI filtering<br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) <br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br />
* Diffusion tensor utilities<br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar) <br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) <br />
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)<br />
* Tractography<br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar) <br />
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper) <br />
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich) <br />
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo) <br />
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)<br />
<br />
==IGT==<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)<br />
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)<br />
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)<br />
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)<br />
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)<br />
<br />
==Time Series==<br />
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)<br />
<br />
==Filtering==<br />
*[[Registration:Resampling|'''Overview of Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)<br />
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK<br />
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)<br />
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)<br />
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)<br />
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich) <br />
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)<br />
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)<br />
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)<br />
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)<br />
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen) <br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan) <br />
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan) <br />
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin) <br />
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image<br />
**[[Image:WeakDoc.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan) <br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)<br />
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)<br />
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao) <br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller) <br />
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)<br />
<br />
==Surface Models==<br />
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin) <br />
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev) <br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) <br />
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich) <br />
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)<br />
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)<br />
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) <br />
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)<br />
<br />
==Converters==<br />
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)<br />
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao) <br />
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)<br />
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao) <br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)<br />
<br />
==Endoscopy==<br />
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)<br />
<br />
==Slicer Extensions==<br />
<br />
[[Documentation-3.6:ExtensionStatus|Extension Status]]<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.<br />
*'''While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.'''<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.<br />
* The version that is available through the extension manager is chosen by the developer of that extension<br />
<br />
'''Available Extensions'''<br />
<br />
* Segmentation<br />
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. <br />
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .<br />
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). <br />
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com). <br />
* Registration<br />
**Robust<br />
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) . <br />
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com). <br />
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu). <br />
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).<br />
* Wizards<br />
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) . <br />
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
* Tractography<br />
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).<br />
* DWI<br />
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .<br />
* Time Series<br />
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
* Quantification<br />
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)<br />
<br />
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins<br />
<br />
:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models<br />
<br />
:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface<br />
<br />
:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution<br />
<br />
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures<br />
<br />
'''Installation Instructions'''<br />
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)<br />
[[image:Slicertoolbar.png|Extensions Wizard]]<br />
<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
<br />
'''Info for Developers'''<br />
<br />
*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.<br />
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.<br />
<br />
*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]<br />
<br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper<br />
<br />
=Other information=<br />
<br />
'''Developer Tools'''<br />
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)<br />
*Note: most developer tools are not documented for end users, but contain comments in the source code<br />
<br />
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)<br />
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)<br />
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)<br />
<br />
<br />
'''Non-SPL Supported Compatibility Packages'''<br />
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''<br />
<br />
<br />
'''QA Table'''<br />
<br />
[[Slicer-3.6-QA|Slicer 3.6 QA table]]<br />
<br />
'''Modules'''<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]] <br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
'''Requirements for Modules'''<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.<br />
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. <br />
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)<br />
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.<br />
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15878Modules:SpineSegmentation-Documentation-3.62010-05-14T06:37:46Z<p>Sylvainjaume: /* Quick Tour of Features and Use */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|After 3 minutes, the segmentation results appear: a label map (blue) and a 3D model (3D view).]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
{|<br />
|[[Image:MIT_NAMIC_Logo.png|thumb|200px|MIT & NA-MIC]]<br />
|}<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module builds on Pattern Recognition theory to provide for a fully automated segmentation. The module first defines a shape model of the spinal cord modeling both the inner volume and the outer volume. Then the segmentation algorithm uses this model to explored the image space and find the best match given the field on intensities in the image. The advantage of this method relies on its unsupervised property: no need for any parameter setting or any initialization.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|600px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|600px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|600px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|600px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|600px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|600px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|600px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|600px|7. review result]]<br />
|}<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|600px|8. save results]]<br />
|}<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|600px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input:''' select the input image<br />
** '''Image output:''' create Slicer node for output image<br />
** '''Model output:''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default:''' reset input and output nodes to blank values<br />
** '''Cancel:''' cancel the execution of the algorithm<br />
** '''Apply:''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation08.png&diff=15877File:SpineSegmentation Slicer3.6 documentation08.png2010-05-14T06:36:39Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation08.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation07.png&diff=15876File:SpineSegmentation Slicer3.6 documentation07.png2010-05-14T06:36:02Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation07.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation06.png&diff=15875File:SpineSegmentation Slicer3.6 documentation06.png2010-05-14T06:35:32Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation06.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation05.png&diff=15874File:SpineSegmentation Slicer3.6 documentation05.png2010-05-14T06:34:55Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation05.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation04.png&diff=15873File:SpineSegmentation Slicer3.6 documentation04.png2010-05-14T06:34:27Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation04.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation03.png&diff=15872File:SpineSegmentation Slicer3.6 documentation03.png2010-05-14T06:33:57Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation03.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation02.png&diff=15871File:SpineSegmentation Slicer3.6 documentation02.png2010-05-14T06:33:22Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation02.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation01.png&diff=15870File:SpineSegmentation Slicer3.6 documentation01.png2010-05-14T06:32:57Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation01.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation00.png&diff=15869File:SpineSegmentation Slicer3.6 documentation00.png2010-05-14T06:32:17Z<p>Sylvainjaume: uploaded a new version of "File:SpineSegmentation Slicer3.6 documentation00.png":&#32;add annotations</p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15868Modules:SpineSegmentation-Documentation-3.62010-05-14T06:31:24Z<p>Sylvainjaume: /* Module Description */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|After 3 minutes, the segmentation results appear: a label map (blue) and a 3D model (3D view).]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
{|<br />
|[[Image:MIT_NAMIC_Logo.png|thumb|200px|MIT & NA-MIC]]<br />
|}<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module builds on Pattern Recognition theory to provide for a fully automated segmentation. The module first defines a shape model of the spinal cord modeling both the inner volume and the outer volume. Then the segmentation algorithm uses this model to explored the image space and find the best match given the field on intensities in the image. The advantage of this method relies on its unsupervised property: no need for any parameter setting or any initialization.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|600px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|600px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|600px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|600px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|600px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|600px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|600px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|600px|7. review result]]<br />
|}<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|600px|8. save results]]<br />
|}<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|600px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15867Modules:SpineSegmentation-Documentation-3.62010-05-14T05:54:13Z<p>Sylvainjaume: /* Tutorial */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|After 3 minutes, the segmentation results appear: a label map (blue) and a 3D model (3D view).]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
{|<br />
|[[Image:MIT_NAMIC_Logo.png|thumb|200px|MIT & NA-MIC]]<br />
|}<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|600px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|600px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|600px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|600px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|600px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|600px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|600px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|600px|7. review result]]<br />
|}<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|600px|8. save results]]<br />
|}<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|600px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15866Modules:SpineSegmentation-Documentation-3.62010-05-14T05:51:28Z<p>Sylvainjaume: /* Authors, Collaborators & Contact */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|After 3 minutes, the segmentation results appear: a label map (blue) and a 3D model (3D view).]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
{|<br />
|[[Image:MIT_NAMIC_Logo.png|thumb|200px|MIT & NA-MIC]]<br />
|}<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|400px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation09.png&diff=15865File:SpineSegmentation Slicer3.6 documentation09.png2010-05-14T05:47:54Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation08.png&diff=15864File:SpineSegmentation Slicer3.6 documentation08.png2010-05-14T05:47:34Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation07.png&diff=15863File:SpineSegmentation Slicer3.6 documentation07.png2010-05-14T05:47:15Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation06.png&diff=15862File:SpineSegmentation Slicer3.6 documentation06.png2010-05-14T05:46:57Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation05.png&diff=15861File:SpineSegmentation Slicer3.6 documentation05.png2010-05-14T05:46:40Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation04.png&diff=15860File:SpineSegmentation Slicer3.6 documentation04.png2010-05-14T05:46:19Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation03.png&diff=15859File:SpineSegmentation Slicer3.6 documentation03.png2010-05-14T05:46:00Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation02.png&diff=15858File:SpineSegmentation Slicer3.6 documentation02.png2010-05-14T05:45:39Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation01.png&diff=15857File:SpineSegmentation Slicer3.6 documentation01.png2010-05-14T05:45:12Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=File:SpineSegmentation_Slicer3.6_documentation00.png&diff=15856File:SpineSegmentation Slicer3.6 documentation00.png2010-05-14T05:44:48Z<p>Sylvainjaume: </p>
<hr />
<div></div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15855Modules:SpineSegmentation-Documentation-3.62010-05-14T05:44:14Z<p>Sylvainjaume: /* Module Name */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|After 3 minutes, the segmentation results appear: a label map (blue) and a 3D model (3D view).]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|400px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15854Modules:SpineSegmentation-Documentation-3.62010-05-14T05:42:07Z<p>Sylvainjaume: /* Module Name */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|400px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15853Modules:SpineSegmentation-Documentation-3.62010-05-14T04:40:31Z<p>Sylvainjaume: /* Tutorial */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 0/9. Download Sample Data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|400px|0. download sample data]]<br />
|}<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
* Step 1/9. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15852Modules:SpineSegmentation-Documentation-3.62010-05-14T04:38:06Z<p>Sylvainjaume: /* Tutorial */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Step 0. Download Sample Data<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
* Step 1. Load the sample data<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load sample data]]<br />
|}<br />
<br />
* Step 2/9. Select the SpineSegmentation module.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
* Step 3/9. Select the input image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
* Step 4/9. Create a Slicer node for the output image.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
* Step 5/9. Create a Slicer node for the output model.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9. Apply the segmentation algorithm.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9. Review segmentation result.<br />
{|<br />
|<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9. Save result image and model.<br />
{|<br />
|<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9. Find contact information for help and paper reference.<br />
{|<br />
|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15851Modules:SpineSegmentation-Documentation-3.62010-05-14T04:35:00Z<p>Sylvainjaume: /* Notes from the Developer(s) */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Reports of new use cases are welcome (email: sylvain at csail.mit.edu). If time permits, we will tune the algorithm for your data sets.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15850Modules:SpineSegmentation-Documentation-3.62010-05-14T04:32:49Z<p>Sylvainjaume: /* Tests */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
Tests are automatically generated using CTest to verify that the module is working on all platforms supported by Slicer.<br />
<br />
* SpineSegmentation's [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
* Slicer's [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15849Modules:SpineSegmentation-Documentation-3.62010-05-14T04:30:18Z<p>Sylvainjaume: /* Dependencies */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Linking to Slicer 3.6 is sufficient. This module requires the typical packages bundled with Slicer.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* Automated testing using CTest [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15848Modules:SpineSegmentation-Documentation-3.62010-05-14T04:28:37Z<p>Sylvainjaume: /* Known bugs */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* Automated testing using CTest [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
<br />
===Known bugs===<br />
<br />
No bugs have been found yet. If you find a bug, please first email the Slicer mailing list to verify that this is a bug due to SpineSegmentation. Once you have received an answer, follow the link below to add a bug report:<br />
<br />
* [http://www.na-mic.org/Bug/view.php? Slicer bug tracker]<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15847Modules:SpineSegmentation-Documentation-3.62010-05-14T04:18:51Z<p>Sylvainjaume: /* Source code & documentation */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* Automated testing using CTest [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code (revision 151):<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15846Modules:SpineSegmentation-Documentation-3.62010-05-14T04:17:00Z<p>Sylvainjaume: /* Tests */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* Automated testing using CTest [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/CMakeLists.txt?annotate=151&root=sylvainproject CMakeLists.txt]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code:<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?root=sylvainproject&view=markup SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?root=sylvainproject&view=markup SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15845Modules:SpineSegmentation-Documentation-3.62010-05-14T04:13:23Z<p>Sylvainjaume: /* Source code & documentation */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
SpineSegmentation's source code:<br />
<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?root=sylvainproject&view=markup SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?root=sylvainproject&view=markup SpineSegmentation.xml]<br />
<br />
Slicer's Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15844Modules:SpineSegmentation-Documentation-3.62010-05-14T04:11:14Z<p>Sylvainjaume: /* Source code & documentation */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the SpineSegmentation's source code:<br />
<br />
Source code:<br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?root=sylvainproject&view=markup SpineSegmentation.cxx] <br />
*[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?root=sylvainproject&view=markup SpineSegmentation.xml]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15843Modules:SpineSegmentation-Documentation-3.62010-05-14T04:07:25Z<p>Sylvainjaume: /* References */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15842Modules:SpineSegmentation-Documentation-3.62010-05-14T04:06:52Z<p>Sylvainjaume: /* Acknowledgment */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15841Modules:SpineSegmentation-Documentation-3.62010-05-14T04:05:54Z<p>Sylvainjaume: /* Module Name */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|The documentation link and reference can be found in the Help and Acknowledgement tabs.]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15840Modules:SpineSegmentation-Documentation-3.62010-05-14T03:56:49Z<p>Sylvainjaume: /* Authors, Collaborators & Contact */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|Load volume into Slicer3.6 and select the SpineSegmentation module]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|300px|Select input and output nodes and click Apply]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15839Modules:SpineSegmentation-Documentation-3.62010-05-14T03:54:02Z<p>Sylvainjaume: /* Authors, Collaborators & Contact */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|Load volume into Slicer3.6 and select the SpineSegmentation module]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|300px|Select input and output nodes and click Apply]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT CSAIL<br />
* Contact: Sylvain Jaume, sylvain at csail.mit.edu<br />
<br />
{|<br />
|[[Image:MIT_NAMIC_Logo.png|thumb|300px|MIT NAMIC]]<br />
|}<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15838Modules:SpineSegmentation-Documentation-3.62010-05-14T03:49:35Z<p>Sylvainjaume: /* Tutorial */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|Load volume into Slicer3.6 and select the SpineSegmentation module]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|300px|Select input and output nodes and click Apply]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT & logo, if desired<br />
* Contact: Sylvain Jaume, sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
Step 1.<br />
{|<br />
|<br />
Load the sample data<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
Step 2/9.<br />
{|<br />
|<br />
Select the SpineSegmentation module.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
Step 3/9.<br />
{|<br />
|<br />
Select the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
Step 4/9.<br />
{|<br />
|<br />
Create a Slicer node for the output image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
Step 5/9.<br />
{|<br />
|<br />
Create a Slicer node for the output model<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
* Step 6/9.<br />
{|<br />
|<br />
Apply the segmentation algorithm<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
* Step 7/9.<br />
{|<br />
|<br />
Review segmentation result.<br />
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
* Step 8/9.<br />
{|<br />
|<br />
Save result image and model.<br />
The output image and the 3D model can be saved using the Slicer user interface.<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
* Step 9/9.<br />
{|<br />
|<br />
Find contact information for help and paper reference<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
<br />
===Quick Tour of Features and Use===<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15837Modules:SpineSegmentation-Documentation-3.62010-05-14T03:37:34Z<p>Sylvainjaume: /* Tutorial */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|Load volume into Slicer3.6 and select the SpineSegmentation module]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|300px|Select input and output nodes and click Apply]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT & logo, if desired<br />
* Contact: Sylvain Jaume, sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
* Sample Data Set<br />
The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
{|<br />
|<br />
Step 1. Load the sample data<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 2/9. Select the SpineSegmentation module<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 3/9. Select the input image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 4/9. Create a Slicer node for the output image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 5/9. Create a Slicer node for the output model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 6/9. Apply the segmentation algorithm<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 7/9. Review segmentation result<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 8/9. Save result image and model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 9/9. Find contact information for help and paper reference<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15836Modules:SpineSegmentation-Documentation-3.62010-05-14T03:32:44Z<p>Sylvainjaume: /* Tutorial */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|Load volume into Slicer3.6 and select the SpineSegmentation module]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|300px|Select input and output nodes and click Apply]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT & logo, if desired<br />
* Contact: Sylvain Jaume, sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
Links to sample data to use with the module tutorial:<br />
<br />
* Download sample data set<br />
Go to http://nitrc.org and create a username. Copy MRI_Spine.mhd and MRI_Spine.zraw from the link below to your local directory.<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
{|<br />
|<br />
Step 1. Load the sample data<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 2/9. Select the SpineSegmentation module<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 3/9. Select the input image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 4/9. Create a Slicer node for the output image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 5/9. Create a Slicer node for the output model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 6/9. Apply the segmentation algorithm<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 7/9. Review segmentation result<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 8/9. Save result image and model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 9/9. Find contact information for help and paper reference<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15835Modules:SpineSegmentation-Documentation-3.62010-05-14T03:30:36Z<p>Sylvainjaume: /* Quick Tour of Features and Use */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|Load volume into Slicer3.6 and select the SpineSegmentation module]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|300px|Select input and output nodes and click Apply]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT & logo, if desired<br />
* Contact: Sylvain Jaume, sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
Links to sample data to use with the module tutorial:<br />
<br />
* Tutorial: see section below<br />
** Data Set<br />
To download the sample data, you need to go to http://nitrc.org and create a username. <br />
The data are located at<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
{|<br />
|<br />
Step 1. Load the sample data<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 2/9. Select the SpineSegmentation module<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 3/9. Select the input image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 4/9. Create a Slicer node for the output image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 5/9. Create a Slicer node for the output model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 6/9. Apply the segmentation algorithm<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 7/9. Review segmentation result<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 8/9. Save result image and model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 9/9. Find contact information for help and paper reference<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15834Modules:SpineSegmentation-Documentation-3.62010-05-14T03:24:43Z<p>Sylvainjaume: /* Use Cases, Examples */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|Load volume into Slicer3.6 and select the SpineSegmentation module]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|300px|Select input and output nodes and click Apply]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT & logo, if desired<br />
* Contact: Sylvain Jaume, sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for this use case:<br />
<br />
* Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.<br />
<br />
Examples of the module in use:<br />
<br />
* Image-guided surgery for the treatment of disk herniation<br />
<br />
===Tutorial===<br />
<br />
Links to sample data to use with the module tutorial:<br />
<br />
* Tutorial: see section below<br />
** Data Set<br />
To download the sample data, you need to go to http://nitrc.org and create a username. <br />
The data are located at<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
{|<br />
|<br />
Step 1. Load the sample data<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 2/9. Select the SpineSegmentation module<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 3/9. Select the input image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 4/9. Create a Slicer node for the output image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 5/9. Create a Slicer node for the output model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 6/9. Apply the segmentation algorithm<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 7/9. Review segmentation result<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 8/9. Save result image and model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 9/9. Find contact information for help and paper reference<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaumehttps://www.slicer.org/w/index.php?title=Modules:SpineSegmentation-Documentation-3.6&diff=15833Modules:SpineSegmentation-Documentation-3.62010-05-14T03:15:49Z<p>Sylvainjaume: /* Tutorial and Usage */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Module Name===<br />
SpineSegmentation module for Slicer 3.6<br />
<br />
{|<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|Load volume into Slicer3.6 and select the SpineSegmentation module]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|300px|Select input and output nodes and click Apply]]<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Sylvain Jaume: MIT & logo, if desired<br />
* Contact: Sylvain Jaume, sylvain at csail.mit.edu<br />
<br />
===Module Description===<br />
Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.<br />
<br />
== Usage ==<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for these use cases:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
Examples of the module in use:<br />
<br />
* Example 1<br />
* Example 2<br />
<br />
===Tutorial===<br />
<br />
Links to sample data to use with the module tutorial:<br />
<br />
* Tutorial: see section below<br />
** Data Set<br />
To download the sample data, you need to go to http://nitrc.org and create a username. <br />
The data are located at<br />
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
Below are the step-by-step instructions to load, process and save some sample data (see link above).<br />
<br />
{|<br />
|<br />
Step 1. Load the sample data<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 2/9. Select the SpineSegmentation module<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 3/9. Select the input image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 4/9. Create a Slicer node for the output image<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 5/9. Create a Slicer node for the output model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 6/9. Apply the segmentation algorithm<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 7/9. Review segmentation result<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 8/9. Save result image and model<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]<br />
|}<br />
<br />
{|<br />
|<br />
Step 9/9. Find contact information for help and paper reference<br />
* '''Input panel:'''<br />
** '''Image input''' select the input image<br />
** '''Image output''' create Slicer node for output image<br />
** '''Model output''' create Slicer node for output model<br />
* '''Command panel:'''<br />
** '''Default''' reset input and output nodes to blank values<br />
** '''Cancel''' cancel the execution of the algorithm<br />
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)<br />
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]<br />
|}<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
Algorithms used, library classes depended upon, use cases, etc.<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br />
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Sylvainjaume