https://public.kitware.com/Wiki/api.php?action=feedcontributions&user=Guillaume.sala&feedformat=atomKitwarePublic - User contributions [en]2024-03-28T17:37:43ZUser contributionsMediaWiki 1.38.6https://public.kitware.com/Wiki/index.php?title=PET-CT/Installation/Main&diff=52986PET-CT/Installation/Main2013-06-18T18:22:28Z<p>Guillaume.sala: </p>
<hr />
<div>== System requirements ==<br />
SlicerPET requires 1GB of RAM minimum, with more highly recommended. Common data sets may require 4GB or more RAM for processing. A fast graphics card or GPU that supports OpenGL is also recommended.<br />
SlicerPET runs on Microsoft Windows 7 and a variety of Linux distributions.<br />
<br />
== Pre-compiled binaries ==<br />
<br />
* Download packages on [http://packages.kitware.com/packages/application/view?applicationId=19 packages.kitware.com]<br />
* Install SlicerPET<br />
** Execute SlicerPET-xxx.exe on Windows<br />
** Untar SlicerPET-xxx.tar.gz on Linux<br />
<br />
== Installing from source ==<br />
<br />
# To get access to the SlicerPET repository:<br />
#: *Fill the form for [https://www.kitware.com/Admin/SendPassword.cgi SlicerPET access]<br />
#: *Email Andinet Enquobahrie for more information (See [http://public.kitware.com/Wiki/PET-CT/Team Contact])<br />
# Retrieve source:<br />
#: <pre> git clone git@www.kitware.com:SlicerPET.git </pre><br />
# Configure with [http://www.cmake.org CMake] >= 2.8.10 and comply with the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Developers/Build_Instructions/Prerequisites Slicer prerequisites]<br />
#: If you build your own CMake, please do so with SSH(curl) support. It would fail downloading external library Eigen otherwise.<br />
# Build SlicerPET<br />
# The executable <code>SlicerPET</code> is found in <code>SlicerPET-build/Slicer-build</code></div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Installation/Main&diff=52985PET-CT/Installation/Main2013-06-18T18:20:26Z<p>Guillaume.sala: </p>
<hr />
<div>== System requirements ==<br />
SlicerPET requires 1GB of RAM minimum, with more highly recommended. Common data sets may require 4GB or more RAM for processing. A fast graphics card or GPU that supports OpenGL is also recommended.<br />
SlicerPET runs on Microsoft Windows 7 and a variety of Linux distributions.<br />
<br />
== Pre-compiled binaries ==<br />
<br />
* Download packages on [http://packages.kitware.com/packages/application/view?applicationId=19 packages.kitware.com]<br />
* Install SlicerPET<br />
** Execute SlicerPET-xxx.exe on Windows<br />
** Untar SlicerPET-xxx.tar.gz on Linux<br />
<br />
== Installing from source ==<br />
<br />
# To get access to the SlicerPET repository:<br />
#: *Email Andinet Enquobahrie (See [http://public.kitware.com/Wiki/PET-CT/Team Contact])<br />
#: *Fill the form for [https://www.kitware.com/Admin/SendPassword.cgi SlicerPET access]<br />
# Retrieve source:<br />
#: <pre> git clone git@www.kitware.com:SlicerPET.git </pre><br />
# Configure with [http://www.cmake.org CMake] >= 2.8.10 and comply with the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Developers/Build_Instructions/Prerequisites Slicer prerequisites]<br />
#: If you build your own CMake, please do so with SSH(curl) support. It would fail downloading external library Eigen otherwise.<br />
# Build SlicerPET<br />
# The executable <code>SlicerPET</code> is found in <code>SlicerPET-build/Slicer-build</code></div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Installation/Main&diff=52984PET-CT/Installation/Main2013-06-18T18:17:10Z<p>Guillaume.sala: </p>
<hr />
<div>== System requirements ==<br />
SlicerPET requires 1GB of RAM minimum, with more highly recommended. Common data sets may require 4GB or more RAM for processing. A fast graphics card or GPU that supports OpenGL is also recommended.<br />
SlicerPET runs on Microsoft Windows 7 and a variety of Linux distributions.<br />
<br />
== Pre-compiled binaries ==<br />
<br />
* Download packages on [http://packages.kitware.com/packages/application/view?applicationId=19 packages.kitware.com]<br />
* Install SlicerPET<br />
** Execute SlicerPET-xxx.exe on Windows<br />
** Untar SlicerPET-xxx.tar.gz on Linux<br />
<br />
== Installing from source ==<br />
<br />
# To get access to the SlicerPET repository:<br />
#: *Email Andinet Enquobahrie (See [http://public.kitware.com/Wiki/PET-CT/Team Contact])<br />
#: *Fill the form for [https://www.kitware.com/Admin/SendPassword.cgi SlicerPET access]<br />
# Retrieve source:<br />
#: <pre> git clone git@www.kitware.com:SlicerPET.git </pre><br />
# Configure with [http://www.cmake.org CMake] >= 2.8.10 and comply with the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/Build_Instructions/Prerequisites Slicer prerequisites]<br />
#: If you build your own CMake, please do so with SSH(curl) support. It would fail downloading external library Eigen otherwise.<br />
# Build SlicerPET<br />
# The executable <code>SlicerPET</code> is found in <code>SlicerPET-build/Slicer-build</code></div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Installation/Main&diff=52972PET-CT/Installation/Main2013-06-17T20:50:58Z<p>Guillaume.sala: </p>
<hr />
<div>== System requirements ==<br />
SlicerPET requires 1GB of RAM minimum, with more highly recommended. Common data sets may require 4GB or more RAM for processing. A fast graphics card or GPU that supports OpenGL is also recommended.<br />
SlicerPET runs on Microsoft Windows 7 and a variety of Linux distributions.<br />
<br />
== Pre-compiled binaries ==<br />
<br />
* Download packages on [http://packages.kitware.com/packages/application/view?applicationId=19 packages.kitware.com]<br />
* Install SlicerPET<br />
** Execute SlicerPET-xxx.exe on Windows<br />
** Untar SlicerPET-xxx.tar.gz on Linux</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:Upload-SlicerPET-to-packages-kitware-com.cmake&diff=52957File:Upload-SlicerPET-to-packages-kitware-com.cmake2013-06-12T15:47:05Z<p>Guillaume.sala: uploaded a new version of &quot;File:Upload-SlicerPET-to-packages-kitware-com.cmake&quot;</p>
<hr />
<div>Use this script to upload SlicerPET packages to packages.kitware.com</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Team/Main&diff=52956PET-CT/Team/Main2013-06-12T14:45:08Z<p>Guillaume.sala: </p>
<hr />
<div>= Team =<br />
<br />
* Kitware Inc.<br />
** Andinet Enquobahrie (andinet.enquobahrie@kitware.com)<br />
** Danielle Pace (danielle.pace@kitware.com)<br />
** Guillaume Sala (guillaume.sala@kitware.com)<br />
<br />
* Children's National Medical Center<br />
** Kevin Cleary (KCleary@childrensnational.org)<br />
** Rahul Khare (RKhare@childrensnational.org)<br />
<br />
* Georgetown University<br />
** Fil Banovac (Banovac@isis.georgetown.edu)<br />
** Giuseppe Esposito (EXG11@gunet.georgetown.edu)</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/About/Main&diff=52955PET-CT/About/Main2013-06-12T14:43:46Z<p>Guillaume.sala: </p>
<hr />
<div>= License =<br />
<br />
The application and the modules developed in this project are distributed under the [http://www.apache.org/licenses/LICENSE-2.0 Apache 2.0 license]. You are free to use, modify, and redistribute SlicerPET for non-commercial and commercial uses.<br />
<br />
= Acknowledgement =<br />
<br />
This project received support from NCI/NIH grants 2R42CA153488-02A1 and R41CA153488-01.<br />
<br />
PET-CT guidance needle biopsy application is built upon and contributes back to a variety of open-source efforts, including the following:<br />
<br />
{| border="0" cellpadding="20" align="center"<br />
| align="center" | [[image:NeuralNav-SlicerLogo.jpg|100px]] [http://www.slicer.org <br> Slicer]<br />
| align="center" | <ImageLink>http://www.itk.org/Wiki/images/8/81/ITK-PNG.png|http://www.itk.org</ImageLink><br> [http://www.itk.org <br> ITK]<br />
| align="center" | <ImageLink>http://public.kitware.com/Wiki/images/a/ac/Logo_optionVF-downsized.png|http://www.igstk.org</ImageLink><br> [http://www.igstk.org <br> IGSTK]<br />
| align="center" | <ImageLink>http://public.kitware.com/Wiki/images/a/ac/Plus.png|http://https://www.assembla.com/spaces/plus/wiki</ImageLink><br> [https://www.assembla.com/spaces/plus/wiki <br> PLUS]<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development/Main&diff=52954PET-CT/Development/Main2013-06-12T14:38:06Z<p>Guillaume.sala: /* Video Tools */</p>
<hr />
<div>==External Projects==<br />
The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes <br />
# PlusLib<br />
##SVN_REPOSITORY: "https://subversion.assembla.com/svn/plus/branches/Plus-1.8/PlusLib"<br />
##SVN_REVISION: "-r "2670"<br />
# PathPlanner <br />
##GIT_REPOSITORY: "[https://github.com/andinet/PathPlanner https://github.com/andinet/PathPlanner]"<br />
##GIT_TAG: "2d2ed19b89d477a8540ac4dd76468e4911c3f7de"<br />
# VisualLine<br />
##GIT_REPOSITORY "[https://github.com/andinet/VisuaLine https://github.com/andinet/VisuaLine]"<br />
##GIT_TAG "75b442fe6d81b230620e9c689766571dfc37e5c8"<br />
#VolumeResliceDrive<br />
##GIT_REPOSITORY "[https://github.com/andinet/VolumeResliceDriver https://github.com/andinet/VolumeResliceDriver]"<br />
##GIT_TAG "6f5b0e868f6f0a37404ee5cf09757de1ab7b43d4"<br />
<br />
==Upload packages==<br />
How to upload packages to [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]:<br />
* Create an account and join the PET-CT community<br />
* Download the following script : [http://public.kitware.com/Wiki/File:Upload-SlicerPET-to-packages-kitware-com.cmake Upload-SlicerPET-to-packages-kitware-com.cmake]<br />
** Change the MIDAS_USER and enter you MIDAS_API_KEY that you can generate in your packages.kitware.com profile.<br />
** Modify the following lines if you are uploading windows or linux executables to the appropriate values:<br />
file(GLOB packages "SlicerPET-*.exe")<br />
...<br />
PACKAGE_TYPE "NSIS installer"<br />
* Run the command line "cmake -P Upload-SlicerPET-to-packages-kitware-com.cmake"<br />
<br />
==Video Tools==<br />
To produce the videos showing how the different modules work [http://public.kitware.com/Wiki/PET-CT/Images#Videos], we used the following tools:<br />
* On Windows:<br />
** We used [http://camstudio.org/ CamStudio], a tool that allows to record all screen and audio activity on the computer. To improve the quality of the videos, we boosted the video option of the tool to the maximum (Quality 100% and 1000 frame per second).<br />
** We used VLC to record the streaming video from a camera device.<br />
* On Mac:<br />
** We used iMovie for post-production, editing and voice-over</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development/Main&diff=52953PET-CT/Development/Main2013-06-12T13:41:37Z<p>Guillaume.sala: </p>
<hr />
<div>==External Projects==<br />
The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes <br />
# PlusLib<br />
##SVN_REPOSITORY: "https://subversion.assembla.com/svn/plus/branches/Plus-1.8/PlusLib"<br />
##SVN_REVISION: "-r "2670"<br />
# PathPlanner <br />
##GIT_REPOSITORY: "[https://github.com/andinet/PathPlanner https://github.com/andinet/PathPlanner]"<br />
##GIT_TAG: "2d2ed19b89d477a8540ac4dd76468e4911c3f7de"<br />
# VisualLine<br />
##GIT_REPOSITORY "[https://github.com/andinet/VisuaLine https://github.com/andinet/VisuaLine]"<br />
##GIT_TAG "75b442fe6d81b230620e9c689766571dfc37e5c8"<br />
#VolumeResliceDrive<br />
##GIT_REPOSITORY "[https://github.com/andinet/VolumeResliceDriver https://github.com/andinet/VolumeResliceDriver]"<br />
##GIT_TAG "6f5b0e868f6f0a37404ee5cf09757de1ab7b43d4"<br />
<br />
==Upload packages==<br />
How to upload packages to [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]:<br />
* Create an account and join the PET-CT community<br />
* Download the following script : [http://public.kitware.com/Wiki/File:Upload-SlicerPET-to-packages-kitware-com.cmake Upload-SlicerPET-to-packages-kitware-com.cmake]<br />
** Change the MIDAS_USER and enter you MIDAS_API_KEY that you can generate in your packages.kitware.com profile.<br />
** Modify the following lines if you are uploading windows or linux executables to the appropriate values:<br />
file(GLOB packages "SlicerPET-*.exe")<br />
...<br />
PACKAGE_TYPE "NSIS installer"<br />
* Run the command line "cmake -P Upload-SlicerPET-to-packages-kitware-com.cmake"<br />
<br />
==Video Tools==<br />
To produce the videos showing how the different modules work, we used the following tools:<br />
* On Windows:<br />
** We used [http://camstudio.org/ CamStudio], a tool that allows to record all screen and audio activity on the computer. To improve the quality of the videos, we boosted the video option of the tool to the maximum (Quality 100% and 1000 frame per second).<br />
** We used VLC to record the streaming video from a camera device.<br />
* On Mac:<br />
** We used iMovie for post-production, editing and voice-over</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Data&diff=52952PET-CT/Data2013-06-12T13:37:19Z<p>Guillaume.sala: </p>
<hr />
<div>{| border="1" cellpadding="10" cellspacing="0"<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
{{:PET-CT/Panel}}<br />
| align="left" width="800px" | <br />
{{:PET-CT/Data/Main}}<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Data/Main&diff=52951PET-CT/Data/Main2013-06-12T13:36:37Z<p>Guillaume.sala: Created page with "= Publications = # Enquobahrie A., Cheng P., Wilson E., Esposito G., Kinahan P., Banovac F., Korn R., Cleary K., '''PET/CT image fusion and electromagnetic tracking for image-gui..."</p>
<hr />
<div>= Publications =<br />
# Enquobahrie A., Cheng P., Wilson E., Esposito G., Kinahan P., Banovac F., Korn R., Cleary K., '''PET/CT image fusion and electromagnetic tracking for image-guided needle biopsy using open source software: Initial phantom results''', Computer Assisted Radiology and Surgery (CARS), 25th International Congress and Exhibition, 2011<br />
# Khare R., Sala G., Kinahan P., Esposito G., Banovac F., Cleary K., Enquobahrie A., '''Experimental Evaluation of a Deformable Registration Algorithm for Motion Correction in PET-CT Guided Biopsy''' (Submitted), IEEE Nuclear Science Symposium and Medical Imaging Conference, 2013</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/About&diff=52950PET-CT/About2013-06-12T13:35:41Z<p>Guillaume.sala: </p>
<hr />
<div>{| border="1" cellpadding="10" cellspacing="0"<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
{{:PET-CT/Panel}}<br />
| align="left" width="800px" | <br />
{{:PET-CT/About/Main}}<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/About/Main&diff=52949PET-CT/About/Main2013-06-12T13:34:55Z<p>Guillaume.sala: Created page with "= License = The application and the modules developed in this project are distributed under the [http://www.apache.org/licenses/LICENSE-2.0 Apache 2.0 license]. You are free to ..."</p>
<hr />
<div>= License =<br />
<br />
The application and the modules developed in this project are distributed under the [http://www.apache.org/licenses/LICENSE-2.0 Apache 2.0 license]. You are free to use, modify, and redistribute Bender for non-commercial and commercial uses.<br />
<br />
= Acknowledgement =<br />
<br />
This project received support from NCI/NIH grants 2R42CA153488-02A1 and R41CA153488-01.<br />
<br />
PET-CT guidance needle biopsy application is built upon and contributes back to a variety of open-source efforts, including the following:<br />
<br />
{| border="0" cellpadding="20" align="center"<br />
| align="center" | [[image:NeuralNav-SlicerLogo.jpg|100px]] [http://www.slicer.org <br> Slicer]<br />
| align="center" | <ImageLink>http://www.itk.org/Wiki/images/8/81/ITK-PNG.png|http://www.itk.org</ImageLink><br> [http://www.itk.org <br> ITK]<br />
| align="center" | <ImageLink>http://public.kitware.com/Wiki/images/a/ac/Logo_optionVF-downsized.png|http://www.igstk.org</ImageLink><br> [http://www.igstk.org <br> IGSTK]<br />
| align="center" | <ImageLink>http://public.kitware.com/Wiki/images/a/ac/Plus.png|http://https://www.assembla.com/spaces/plus/wiki</ImageLink><br> [https://www.assembla.com/spaces/plus/wiki <br> PLUS]<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Team&diff=52948PET-CT/Team2013-06-12T13:33:51Z<p>Guillaume.sala: </p>
<hr />
<div>{| border="1" cellpadding="10" cellspacing="0"<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
{{:PET-CT/Panel}}<br />
| align="left" width="800px" | <br />
{{:PET-CT/Team/Main}}<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Team/Main&diff=52947PET-CT/Team/Main2013-06-12T13:32:49Z<p>Guillaume.sala: </p>
<hr />
<div>* Kitware Inc.<br />
** Andinet Enquobahrie (andinet.enquobahrie@kitware.com)<br />
** Danielle Pace (danielle.pace@kitware.com)<br />
** Guillaume Sala (guillaume.sala@kitware.com)<br />
<br />
* Children's National Medical Center<br />
** Kevin Cleary (KCleary@childrensnational.org)<br />
** Rahul Khare (RKhare@childrensnational.org)<br />
<br />
* Georgetown University<br />
** Fil Banovac (Banovac@isis.georgetown.edu)<br />
** Giuseppe Esposito (EXG11@gunet.georgetown.edu)</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Team/Main&diff=52946PET-CT/Team/Main2013-06-12T13:32:27Z<p>Guillaume.sala: Created page with "* Kitware Inc. ** Andinet Enquobahrie (julien.finet@kitware.com) ** Danielle Pace (danielle.pace@kitware.com) ** Guillaume Sala (guillaume.sala@kitware.com) * Children's Nation..."</p>
<hr />
<div>* Kitware Inc.<br />
** Andinet Enquobahrie (julien.finet@kitware.com)<br />
** Danielle Pace (danielle.pace@kitware.com)<br />
** Guillaume Sala (guillaume.sala@kitware.com)<br />
<br />
* Children's National Medical Center<br />
** Kevin Cleary (KCleary@childrensnational.org)<br />
** Rahul Khare (RKhare@childrensnational.org)<br />
<br />
* Georgetown University<br />
** Fil Banovac (Banovac@isis.georgetown.edu)<br />
** Giuseppe Esposito (EXG11@gunet.georgetown.edu)</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development/Main&diff=52945PET-CT/Development/Main2013-06-12T13:30:38Z<p>Guillaume.sala: </p>
<hr />
<div>==External Projects==<br />
The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes <br />
# PlusLib<br />
##SVN_REPOSITORY: "https://subversion.assembla.com/svn/plus/branches/Plus-1.8/PlusLib"<br />
##SVN_REVISION: "-r "2670"<br />
# PathPlanner <br />
##GIT_REPOSITORY: "[https://github.com/andinet/PathPlanner https://github.com/andinet/PathPlanner]"<br />
##GIT_TAG: "2d2ed19b89d477a8540ac4dd76468e4911c3f7de"<br />
# VisualLine<br />
##GIT_REPOSITORY "[https://github.com/andinet/VisuaLine https://github.com/andinet/VisuaLine]"<br />
##GIT_TAG "75b442fe6d81b230620e9c689766571dfc37e5c8"<br />
#VolumeResliceDrive<br />
##GIT_REPOSITORY "[https://github.com/andinet/VolumeResliceDriver https://github.com/andinet/VolumeResliceDriver]"<br />
##GIT_TAG "6f5b0e868f6f0a37404ee5cf09757de1ab7b43d4"<br />
<br />
==Video Tools==<br />
To produce the videos showing how the different modules work, we used the following tools:<br />
* On Windows:<br />
** We used [http://camstudio.org/ CamStudio], a tool that allows to record all screen and audio activity on the computer. To improve the quality of the videos, we boosted the video option of the tool to the maximum (Quality 100% and 1000 frame per second).<br />
** We used VLC to record the streaming video from a camera device.<br />
* On Mac:<br />
** We used iMovie for post-production, editing and voice-over<br />
<br />
==Upload packages==<br />
How to upload packages to [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]:<br />
* Create an account and join the PET-CT community<br />
* Download the following script : [http://public.kitware.com/Wiki/File:Upload-SlicerPET-to-packages-kitware-com.cmake Upload-SlicerPET-to-packages-kitware-com.cmake]<br />
** Change the MIDAS_USER and enter you MIDAS_API_KEY that you can generate in your packages.kitware.com profile.<br />
** Modify the following lines if you are uploading windows or linux executables to the appropriate values:<br />
file(GLOB packages "SlicerPET-*.exe")<br />
...<br />
PACKAGE_TYPE "NSIS installer"<br />
* Run the command line "cmake -P Upload-SlicerPET-to-packages-kitware-com.cmake"</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Images/Main&diff=52944PET-CT/Images/Main2013-06-11T19:43:44Z<p>Guillaume.sala: </p>
<hr />
<div>== Study of the guidance workflow ==<br />
<gallery widths=300px perrow=2><br />
File:PETCTWorkflowSystemDiagram.png<br />
File:PETCTStudyWorkflowChart.png<br />
</gallery><br />
<br />
== Videos ==<br />
<br />
<gallery widths=300px perrow=3><br />
File:PivotCalibration-video.png|[http://vimeo.com/68161539 PivotCalibration demo] (01:35)<br />
File:GuidedInterventionPETCT-video.png|[http://vimeo.com/68161954 Workflow demo] (02:59)<br />
</gallery><br />
<br />
== Guided Intervention Workflow ==<br />
<br />
<gallery widths=300px perrow=3><br />
Image:GuidedPETCTWorkflowStep1.png|Step 1: Load Data<br />
Image:GuidedPETCTWorkflowStep2.png|Step 2: Registration PET/CT and interventional CT<br />
Image:GuidedPETCTWorkflowStep3.png|Step 3: OpenIGTLinkIF<br />
Image:GuidedPETCTWorkflowStep4.png|Step 4: Pivot Calibration<br />
Image:GuidedPETCTWorkflowStep5.png|Step 5: CT to hardware registration<br />
Image:GuidedPETCTWorkflowStep6.png|Step 6: Reslicing with tracker<br />
</gallery></div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedInterventionPETCT-video.png&diff=52943File:GuidedInterventionPETCT-video.png2013-06-11T19:41:37Z<p>Guillaume.sala: First image in the GuidedInterventionPETCT video demo</p>
<hr />
<div>First image in the GuidedInterventionPETCT video demo</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:PivotCalibration-video.png&diff=52942File:PivotCalibration-video.png2013-06-11T19:40:44Z<p>Guillaume.sala: First image in the Pivot Calibration video demo</p>
<hr />
<div>First image in the Pivot Calibration video demo</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development/Main&diff=52941PET-CT/Development/Main2013-06-11T17:39:49Z<p>Guillaume.sala: </p>
<hr />
<div>==External Projects==<br />
The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes <br />
# PathPlanner <br />
##GIT_REPOSITORY: "github.com/Will-S/PathPlanner.git"<br />
##GIT_TAG: "2d2ed19b89d477a8540ac4dd76468e4911c3f7de"<br />
# PlusLib<br />
##SVN_REPOSITORY: "https://subversion.assembla.com/svn/plus/branches/Plus-1.8/PlusLib"<br />
##SVN_REVISION: "-r "2670"<br />
# VisualLine<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VisuaLine.git"<br />
##GIT_TAG "75b442fe6d81b230620e9c689766571dfc37e5c8"<br />
#VolumeResliceDrive<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VolumeResliceDriver.git"<br />
##GIT_TAG "6f5b0e868f6f0a37404ee5cf09757de1ab7b43d4"<br />
<br />
==Video Tools==<br />
To produce the videos showing how the different modules work, we used the following tools:<br />
* On Windows:<br />
** We used [http://camstudio.org/ CamStudio], a tool that allows to record all screen and audio activity on the computer. To improve the quality of the videos, we boosted the video option of the tool to the maximum (Quality 100% and 1000 frame per second).<br />
** We used VLC to record the streaming video from a camera device.<br />
* On Mac:<br />
** We used iMovie for post-production, editing and voice-over<br />
<br />
==Upload packages==<br />
How to upload packages to [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]:<br />
* Create an account and join the PET-CT community<br />
* Download the following script : [http://public.kitware.com/Wiki/File:Upload-SlicerPET-to-packages-kitware-com.cmake Upload-SlicerPET-to-packages-kitware-com.cmake]<br />
** Change the MIDAS_USER and enter you MIDAS_API_KEY that you can generate in your packages.kitware.com profile.<br />
** Modify the following lines if you are uploading windows or linux executables to the appropriate values:<br />
file(GLOB packages "SlicerPET-*.exe")<br />
...<br />
PACKAGE_TYPE "NSIS installer"<br />
* Run the command line "cmake -P Upload-SlicerPET-to-packages-kitware-com.cmake"</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development/Main&diff=52940PET-CT/Development/Main2013-06-11T17:39:16Z<p>Guillaume.sala: </p>
<hr />
<div>=External Projects=<br />
The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes <br />
# PathPlanner <br />
##GIT_REPOSITORY: "github.com/Will-S/PathPlanner.git"<br />
##GIT_TAG: "2d2ed19b89d477a8540ac4dd76468e4911c3f7de"<br />
# PlusLib<br />
##SVN_REPOSITORY: "https://subversion.assembla.com/svn/plus/branches/Plus-1.8/PlusLib"<br />
##SVN_REVISION: "-r "2670"<br />
# VisualLine<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VisuaLine.git"<br />
##GIT_TAG "75b442fe6d81b230620e9c689766571dfc37e5c8"<br />
#VolumeResliceDrive<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VolumeResliceDriver.git"<br />
##GIT_TAG "6f5b0e868f6f0a37404ee5cf09757de1ab7b43d4"<br />
<br />
=Video Tools=<br />
To produce the videos showing how the different modules work, we used the following tools:<br />
* On Windows:<br />
** We used [http://camstudio.org/ CamStudio], a tool that allows to record all screen and audio activity on the computer. To improve the quality of the videos, we boosted the video option of the tool to the maximum (Quality 100% and 1000 frame per second).<br />
** We used VLC to record the streaming video from a camera device.<br />
* On Mac:<br />
** We used iMovie for post-production, editing and voice-over<br />
<br />
=Upload packages=<br />
How to upload packages to [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]:<br />
* Create an account and join the PET-CT community<br />
* Download the following script : [http://public.kitware.com/Wiki/File:Upload-SlicerPET-to-packages-kitware-com.cmake Upload-SlicerPET-to-packages-kitware-com.cmake]<br />
** Change the MIDAS_USER and enter you MIDAS_API_KEY that you can generate in your packages.kitware.com profile.<br />
** Modify the following lines if you are uploading windows or linux executables to the appropriate values:<br />
file(GLOB packages "SlicerPET-*.exe")<br />
...<br />
PACKAGE_TYPE "NSIS installer"<br />
* Run the command line "cmake -P Upload-SlicerPET-to-packages-kitware-com.cmake"</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development&diff=52939PET-CT/Development2013-06-11T17:37:28Z<p>Guillaume.sala: </p>
<hr />
<div>{| border="1" cellpadding="10" cellspacing="0"<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
{{:PET-CT/Panel}}<br />
| align="left" width="800px" | <br />
{{:PET-CT/Development/Main}}<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development/Main&diff=52938PET-CT/Development/Main2013-06-11T17:36:28Z<p>Guillaume.sala: Created page with "==External Projects== The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes # PathPlanner ..."</p>
<hr />
<div>==External Projects==<br />
The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes <br />
# PathPlanner <br />
##GIT_REPOSITORY: "github.com/Will-S/PathPlanner.git"<br />
##GIT_TAG: "2d2ed19b89d477a8540ac4dd76468e4911c3f7de"<br />
# PlusLib<br />
##SVN_REPOSITORY: "https://subversion.assembla.com/svn/plus/branches/Plus-1.8/PlusLib"<br />
##SVN_REVISION: "-r "2670"<br />
# VisualLine<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VisuaLine.git"<br />
##GIT_TAG "75b442fe6d81b230620e9c689766571dfc37e5c8"<br />
#VolumeResliceDrive<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VolumeResliceDriver.git"<br />
##GIT_TAG "6f5b0e868f6f0a37404ee5cf09757de1ab7b43d4"<br />
<br />
==Video Tools==<br />
To produce the videos showing how the different modules work, we used the following tools:<br />
* On Windows:<br />
** We used [http://camstudio.org/ CamStudio], a tool that allows to record all screen and audio activity on the computer. To improve the quality of the videos, we boosted the video option of the tool to the maximum (Quality 100% and 1000 frame per second).<br />
** We used VLC to record the streaming video from a camera device.<br />
* On Mac:<br />
** We used iMovie for post-production, editing and voice-over<br />
<br />
== Upload packages ==<br />
How to upload packages to [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]:<br />
* Create an account and join the PET-CT community<br />
* Download the following script : [http://public.kitware.com/Wiki/File:Upload-SlicerPET-to-packages-kitware-com.cmake Upload-SlicerPET-to-packages-kitware-com.cmake]<br />
** Change the MIDAS_USER and enter you MIDAS_API_KEY that you can generate in your packages.kitware.com profile.<br />
** Modify the following lines if you are uploading windows or linux executables to the appropriate values:<br />
file(GLOB packages "SlicerPET-*.exe")<br />
...<br />
PACKAGE_TYPE "NSIS installer"<br />
* Run the command line "cmake -P Upload-SlicerPET-to-packages-kitware-com.cmake"</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development&diff=52937PET-CT/Development2013-06-11T16:11:12Z<p>Guillaume.sala: </p>
<hr />
<div>==External Projects==<br />
The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes <br />
# PathPlanner <br />
##GIT_REPOSITORY: "github.com/Will-S/PathPlanner.git"<br />
##GIT_TAG: "2d2ed19b89d477a8540ac4dd76468e4911c3f7de"<br />
# PlusLib<br />
##SVN_REPOSITORY: "https://subversion.assembla.com/svn/plus/branches/Plus-1.8/PlusLib"<br />
##SVN_REVISION: "-r "2670"<br />
# VisualLine<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VisuaLine.git"<br />
##GIT_TAG "75b442fe6d81b230620e9c689766571dfc37e5c8"<br />
#VolumeResliceDrive<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VolumeResliceDriver.git"<br />
##GIT_TAG "6f5b0e868f6f0a37404ee5cf09757de1ab7b43d4"<br />
<br />
==Video Tools==<br />
To produce the videos showing how the different modules work, we used the following tools:<br />
* On Windows:<br />
** We used [http://camstudio.org/ CamStudio], a tool that allows to record all screen and audio activity on the computer. To improve the quality of the videos, we boosted the video option of the tool to the maximum (Quality 100% and 1000 frame per second).<br />
** We used VLC to record the streaming video from a camera device.<br />
* On Mac:<br />
** We used iMovie for post-production, editing and voice-over<br />
<br />
== Upload packages ==<br />
How to upload packages to [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]:<br />
* Create an account and join the PET-CT community<br />
* Download the following script : [http://public.kitware.com/Wiki/File:Upload-SlicerPET-to-packages-kitware-com.cmake Upload-SlicerPET-to-packages-kitware-com.cmake]<br />
** Change the MIDAS_USER and enter you MIDAS_API_KEY that you can generate in your packages.kitware.com profile.<br />
** Modify the following lines if you are uploading windows or linux executables to the appropriate values:<br />
file(GLOB packages "SlicerPET-*.exe")<br />
...<br />
PACKAGE_TYPE "NSIS installer"<br />
* Run the command line "cmake -P Upload-SlicerPET-to-packages-kitware-com.cmake"</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:Upload-SlicerPET-to-packages-kitware-com.cmake&diff=52936File:Upload-SlicerPET-to-packages-kitware-com.cmake2013-06-11T15:54:16Z<p>Guillaume.sala: Use this script to upload SlicerPET packages to packages.kitware.com</p>
<hr />
<div>Use this script to upload SlicerPET packages to packages.kitware.com</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Installation/Main&diff=52933PET-CT/Installation/Main2013-06-10T22:07:00Z<p>Guillaume.sala: </p>
<hr />
<div>== System requirements ==<br />
SlicerPET requires 1GB of RAM minimum, with more highly recommended. Common data sets may require 4GB or more RAM for processing. A fast graphics card or GPU that supports OpenGL is also recommended.<br />
SlicerPET runs on Microsoft Windows 7 and a variety of Linux distributions.<br />
<br />
== Pre-compiled binaries ==<br />
<br />
* Download packages on [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]<br />
* Install SlicerPET<br />
** Execute SlicerPET-xxx.exe on Windows<br />
** Untar SlicerPET-xxx.tar.gz on Linux</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Installation&diff=52932PET-CT/Installation2013-06-10T22:05:57Z<p>Guillaume.sala: Created page with "{| border="1" cellpadding="10" cellspacing="0" |- | style="background:#efefef;" align="left" valign="top" width="150px" | {{:PET-CT/Panel}} | align="left" width="800px" | {{:PE..."</p>
<hr />
<div>{| border="1" cellpadding="10" cellspacing="0"<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
{{:PET-CT/Panel}}<br />
| align="left" width="800px" | <br />
{{:PET-CT/Installation/Main}}<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Installation/Main&diff=52931PET-CT/Installation/Main2013-06-10T22:04:10Z<p>Guillaume.sala: Created page with "=== System requirements === SlicerPET requires 1GB of RAM minimum, with more highly recommended. Common data sets may require 4GB or more RAM for processing. A fast graphics card..."</p>
<hr />
<div>=== System requirements ===<br />
SlicerPET requires 1GB of RAM minimum, with more highly recommended. Common data sets may require 4GB or more RAM for processing. A fast graphics card or GPU that supports OpenGL is also recommended.<br />
SlicerPET runs on Microsoft Windows 7 and a variety of Linux distributions.<br />
<br />
=== Pre-compiled binaries ===<br />
<br />
* Download packages on [http://packages.kitware.com/packages/application/view?applicationId=15 packages.kitware.com]<br />
* Install SlicerPET<br />
** Execute SlicerPET-xxx.exe on Windows<br />
** Untar SlicerPET-xxx.tar.gz on Linux</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Development&diff=52855PET-CT/Development2013-06-06T21:47:38Z<p>Guillaume.sala: </p>
<hr />
<div>===External Projects===<br />
The SlicerPET application is based on Slicer Framework. In addition to the external projects included by Slicer official, SlicerPET includes <br />
# PathPlanner <br />
##GIT_REPOSITORY: "github.com/Will-S/PathPlanner.git"<br />
##GIT_TAG: "2d2ed19b89d477a8540ac4dd76468e4911c3f7de"<br />
# PlusLib<br />
##SVN_REPOSITORY: "https://subversion.assembla.com/svn/plus/branches/Plus-1.8/PlusLib"<br />
##SVN_REVISION: "-r "2670"<br />
# VisualLine<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VisuaLine.git"<br />
##GIT_TAG "75b442fe6d81b230620e9c689766571dfc37e5c8"<br />
#VolumeResliceDrive<br />
##GIT_REPOSITORY "${git_protocol}://github.com/Will-S/VolumeResliceDriver.git"<br />
##GIT_TAG "6f5b0e868f6f0a37404ee5cf09757de1ab7b43d4"<br />
<br />
===Video Tools===<br />
To produce the videos showing how the different modules work, we used the following tools:<br />
* On Windows:<br />
** We used [http://camstudio.org/ CamStudio], a tool that allows to record all screen and audio activity on the computer. To improve the quality of the videos, we boosted the video option of the tool to the maximum (Quality 100% and 1000 frame per second).<br />
** We used VLC to record the streaming video from a camera device.<br />
* On Mac:<br />
** We used iMovie for post-production, editing and voice-over</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Documentation/Modules/GuidedInterventionPETCT&diff=52566PET-CT/Documentation/Modules/GuidedInterventionPETCT2013-04-22T19:49:44Z<p>Guillaume.sala: moved PET/CT/Documentation/1.0/Modules/GuidedInterventionPETCT to PET-CT/Documentation/1.0/Modules/GuidedInterventionPETCT: Moving the page to be logical with the hierarchy of the PET-CT wiki</p>
<hr />
<div>= Introduction and Acknowledgements =<br />
Authors: Andinet Enquobahrie [http://www.kitware.com Kitware], Guillaume Sala, [http://www.kitware.com Kitware], Rahul Khare, [http://www.childrensnational.org ChildrensNational]<br><br />
Acknowledgements: This work is supported by NIH grants 2R42CA153488-02A1 and R41CA153488-01 "Improving liver lesion biopsy in the CT suite through fusion with PET images"<br><br />
Contact: Andinet Enquobahrie, Guillaume Sala<br><br />
<br />
= Module Description =<br />
<br />
The GuidedInterventionPETCT is a workflow-based module that guides the user in a step-by-step interface to realize a guided biopsy after fusing respiratory-compensated PET/CT with images in the interventional CT suite.<br><br />
In each step of the workflow we prepare the necessary requirements to fulfill the end goal, following a given pipeline: Registration of the different volumes acquired, establishing the connection between the tracking device and Slicer, registration of the coordinate system of the tracking system and the registered volume and live tracking of the needle in Slicer.<br><br />
This module uses existing modules to accomplish some of the steps:<br><br />
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/OpenIGTLinkIF OpenIGTLinkIF]<br />
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/Annotations Annotations]<br />
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/FiducialRegistration Fiducial Registration]<br />
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/VolumeResliceDriver Volume Reslice Driver]<br />
*[http://public.kitware.com/Wiki/PET-CT/Documentation/1.0/Modules/Pivot_Calibration Pivot Calibration]<br />
<br />
= Use Cases =<br />
<br />
<gallery widths=300px perrow=3><br />
Image:GuidedPETCTWorkflowStep1.png|Step1: Load Data<br />
Image:GuidedPETCTWorkflowStep2.png|Step2: Registration PET/CT and interventional CT<br />
Image:GuidedPETCTWorkflowStep3.png|Step3: OpenIGTLinkIF<br />
Image:GuidedPETCTWorkflowStep4.png|Step4: Pivot Calibration<br />
Image:GuidedPETCTWorkflowStep5.png|Step5: CT to hardware registration<br />
Image:GuidedPETCTWorkflowStep6.png|Step6: Reslicing with tracker<br />
</gallery><br />
<br />
= Panels =<br />
<br />
== Loading Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
The loading step is the first step of the workflow. The user selects the data that is going to be used for the guided biopsy.<br><br />
Read [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/SlicerApplication/LoadingData here] the instructions to load data into Slicer.<br><br />
<br />
* '''MC PET Volume''': This combobox allows selecting the motion-compensated PET scans.<br />
* '''MC CT Volume''': This combobox allows selecting the motion-compensated CT scans.<br />
* '''CBCT Volume''': This combobox allows selecting the interventional CT Scan.<br />
<br />
The volumes in these comboboxes will be used to compute the image registration, between the pre-operative PET/CT acquisition and the interventional CT. The fused PET and interventional CT images will guide the biopsy procedure.<br />
<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep1Panel.png|thumb|300px|Loading data panel]]<br />
|}<br />
<br />
== Volume Registration Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
In this step we will compute the image registration with the motion-compensation PET/CT and interventional CT.<br><br />
For the time being we have place-holders while the software is developed.<br><br />
<br />
*Registration Parameters:<br />
** '''Registration parameter 1'''<br />
** '''Registration parameter 2'''<br />
** '''Registration parameter 3'''<br />
<br />
* '''Start Registration''': Push Button to start the registration with the volumes selected in the previous step.<br />
At this stage, a result volume is created and all other volumes are deleted from the scene.<br />
<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep2Panel.png|thumb|300px|Volume Registration panel]]<br />
|}<br />
<br />
== OpenIGTLinkIF Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
In this step of the workflow we establish the link between Slicer and the tracking system.<br><br />
To establish this connection we import the OpenIGTLinkIF module of Slicer.<br />
For more information about the use of this module please see the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/OpenIGTLinkIF OpenIGTLinkIF] documentation.<br><br />
One method to establish the connection is using IGSTK:<br><br />
*Run the executable [http://public.kitware.com/IGSTKWIKI/index.php/Using_OpenIGTLink_in_IGSTK#Broadcast_Tracking_data_using_OpenIGTLink OpenIGTLinkTrackerBroadcasting] giving a configuration file for the given tracking system (e.g [[Media:IGSTK_polarisHybridConfiguration.xml|Polaris configuration file]], [[Media:IGSTK_micronConfiguration.xml|Micron configuration file]])<br />
<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep3Panel.png|thumb|300px|OpenIGTLinkIF panel]]<br />
|}<br />
<br />
== Pivot Calibration Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
This section allows the user to run a pivot calibration algorithm on the tracker device (whose connection was establish on the previous step), to do this, we import the existing PivotCalibration module.<br><br />
For more information about the use of this module please see the [http://public.kitware.com/Wiki/PET-CT/Documentation/1.0/Modules/Pivot_Calibration Pivot Calibration] documentation.<br><br />
<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep4Panel.png|thumb|300px|Pivot calibration panel]]<br />
|}<br />
<br />
== Hardware Registration Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
This step allows the user to run a fiducial registration to transform the registered volume (PET/CT scans with the interventional CT scans) coordinate system to the tracker coordinate system.<br><br />
To run the fiducial registration we need to create two fiducial lists containing respective points in the different coordinate system.<br />
<br />
At this stage of the workflow two list are generated, the "CTMarkers" to place the fiducials on the registered Volume and the "TrackerMarkers" where the fiducials on the tracker coordinate system will be placed.<br><br />
For more information about the fiducial registration, please see the documentation [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/FiducialRegistration here].<br><br />
<br />
* '''Register''': The "Add Fiducial" button allows the user, by clicking on it, to create a new fiducial at the current position of the tracking device, and adding it to the "TrackerMarkers" list<br />
<br />
* '''Annotation''': This is the "Annotation" module where we can see the fiducial lists and manipulate them. The user needs to place the fiducials on the CT volume to be able to run the registration.<br> <br />
* '''Start Registration''': This button allows the user to call the fiducial registration CLI module with two fiducial lists previously filled.<br />
<br />
|[[File:GuidedPETCTWorkflowStep5Panel.png|thumb|300px|Hardware registration panel]]<br />
|}<br />
<br />
== Tracking Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
This is the last step of the workflow, it uses the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/VolumeResliceDriver Volume Reslice Driver] module, to reslice de volume according to the position of the tracker device<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep6Panel.png|thumb|300px|Pivot calibration panel]]<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Images/Main&diff=52565PET-CT/Images/Main2013-04-22T19:41:39Z<p>Guillaume.sala: Created page with "= Study of the guidance workflow = <gallery widths=300px perrow=2> File:PETCTWorkflowSystemDiagram.png File:PETCTStudyWorkflowChart.png </gallery> = Guided Intervention Workflo..."</p>
<hr />
<div>= Study of the guidance workflow = <br />
<gallery widths=300px perrow=2><br />
File:PETCTWorkflowSystemDiagram.png<br />
File:PETCTStudyWorkflowChart.png<br />
</gallery><br />
<br />
= Guided Intervention Workflow =<br />
<br />
<gallery widths=300px perrow=3><br />
Image:GuidedPETCTWorkflowStep1.png|Step1: Load Data<br />
Image:GuidedPETCTWorkflowStep2.png|Step2: Registration PET/CT and interventional CT<br />
Image:GuidedPETCTWorkflowStep3.png|Step3: OpenIGTLinkIF<br />
Image:GuidedPETCTWorkflowStep4.png|Step4: Pivot Calibration<br />
Image:GuidedPETCTWorkflowStep5.png|Step5: CT to hardware registration<br />
Image:GuidedPETCTWorkflowStep6.png|Step6: Reslicing with tracker<br />
</gallery></div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:PETCTWorkflowSystemDiagram.png&diff=52564File:PETCTWorkflowSystemDiagram.png2013-04-22T19:39:15Z<p>Guillaume.sala: System diagram of the proposed PET/CT guidance workflow</p>
<hr />
<div>System diagram of the proposed PET/CT guidance workflow</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:PETCTStudyWorkflowChart.png&diff=52563File:PETCTStudyWorkflowChart.png2013-04-22T19:35:59Z<p>Guillaume.sala: Workflow of the guided biopsy PET/CT project</p>
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<div>Workflow of the guided biopsy PET/CT project</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Images&diff=52562PET-CT/Images2013-04-22T19:30:53Z<p>Guillaume.sala: Created page with "{| border="1" cellpadding="10" cellspacing="0" |- | style="background:#efefef;" align="left" valign="top" width="150px" | {{:PET-CT/Panel}} | align="left" width="800px" | {{:PE..."</p>
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<div>{| border="1" cellpadding="10" cellspacing="0"<br />
|-<br />
| style="background:#efefef;" align="left" valign="top" width="150px" | <br />
{{:PET-CT/Panel}}<br />
| align="left" width="800px" | <br />
{{:PET-CT/Images/Main}}<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Documentation/Modules/GuidedInterventionPETCT&diff=52561PET-CT/Documentation/Modules/GuidedInterventionPETCT2013-04-22T19:27:12Z<p>Guillaume.sala: Created page with "= Introduction and Acknowledgements = Authors: Andinet Enquobahrie [http://www.kitware.com Kitware], Guillaume Sala, [http://www.kitware.com Kitware], Rahul Khare, [http://www.ch..."</p>
<hr />
<div>= Introduction and Acknowledgements =<br />
Authors: Andinet Enquobahrie [http://www.kitware.com Kitware], Guillaume Sala, [http://www.kitware.com Kitware], Rahul Khare, [http://www.childrensnational.org ChildrensNational]<br><br />
Acknowledgements: This work is supported by NIH grants 2R42CA153488-02A1 and R41CA153488-01 "Improving liver lesion biopsy in the CT suite through fusion with PET images"<br><br />
Contact: Andinet Enquobahrie, Guillaume Sala<br><br />
<br />
= Module Description =<br />
<br />
The GuidedInterventionPETCT is a workflow-based module that guides the user in a step-by-step interface to realize a guided biopsy after fusing respiratory-compensated PET/CT with images in the interventional CT suite.<br><br />
In each step of the workflow we prepare the necessary requirements to fulfill the end goal, following a given pipeline: Registration of the different volumes acquired, establishing the connection between the tracking device and Slicer, registration of the coordinate system of the tracking system and the registered volume and live tracking of the needle in Slicer.<br><br />
This module uses existing modules to accomplish some of the steps:<br><br />
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/OpenIGTLinkIF OpenIGTLinkIF]<br />
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/Annotations Annotations]<br />
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/FiducialRegistration Fiducial Registration]<br />
*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/VolumeResliceDriver Volume Reslice Driver]<br />
*[http://public.kitware.com/Wiki/PET-CT/Documentation/1.0/Modules/Pivot_Calibration Pivot Calibration]<br />
<br />
= Use Cases =<br />
<br />
<gallery widths=300px perrow=3><br />
Image:GuidedPETCTWorkflowStep1.png|Step1: Load Data<br />
Image:GuidedPETCTWorkflowStep2.png|Step2: Registration PET/CT and interventional CT<br />
Image:GuidedPETCTWorkflowStep3.png|Step3: OpenIGTLinkIF<br />
Image:GuidedPETCTWorkflowStep4.png|Step4: Pivot Calibration<br />
Image:GuidedPETCTWorkflowStep5.png|Step5: CT to hardware registration<br />
Image:GuidedPETCTWorkflowStep6.png|Step6: Reslicing with tracker<br />
</gallery><br />
<br />
= Panels =<br />
<br />
== Loading Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
The loading step is the first step of the workflow. The user selects the data that is going to be used for the guided biopsy.<br><br />
Read [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/SlicerApplication/LoadingData here] the instructions to load data into Slicer.<br><br />
<br />
* '''MC PET Volume''': This combobox allows selecting the motion-compensated PET scans.<br />
* '''MC CT Volume''': This combobox allows selecting the motion-compensated CT scans.<br />
* '''CBCT Volume''': This combobox allows selecting the interventional CT Scan.<br />
<br />
The volumes in these comboboxes will be used to compute the image registration, between the pre-operative PET/CT acquisition and the interventional CT. The fused PET and interventional CT images will guide the biopsy procedure.<br />
<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep1Panel.png|thumb|300px|Loading data panel]]<br />
|}<br />
<br />
== Volume Registration Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
In this step we will compute the image registration with the motion-compensation PET/CT and interventional CT.<br><br />
For the time being we have place-holders while the software is developed.<br><br />
<br />
*Registration Parameters:<br />
** '''Registration parameter 1'''<br />
** '''Registration parameter 2'''<br />
** '''Registration parameter 3'''<br />
<br />
* '''Start Registration''': Push Button to start the registration with the volumes selected in the previous step.<br />
At this stage, a result volume is created and all other volumes are deleted from the scene.<br />
<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep2Panel.png|thumb|300px|Volume Registration panel]]<br />
|}<br />
<br />
== OpenIGTLinkIF Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
In this step of the workflow we establish the link between Slicer and the tracking system.<br><br />
To establish this connection we import the OpenIGTLinkIF module of Slicer.<br />
For more information about the use of this module please see the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/OpenIGTLinkIF OpenIGTLinkIF] documentation.<br><br />
One method to establish the connection is using IGSTK:<br><br />
*Run the executable [http://public.kitware.com/IGSTKWIKI/index.php/Using_OpenIGTLink_in_IGSTK#Broadcast_Tracking_data_using_OpenIGTLink OpenIGTLinkTrackerBroadcasting] giving a configuration file for the given tracking system (e.g [[Media:IGSTK_polarisHybridConfiguration.xml|Polaris configuration file]], [[Media:IGSTK_micronConfiguration.xml|Micron configuration file]])<br />
<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep3Panel.png|thumb|300px|OpenIGTLinkIF panel]]<br />
|}<br />
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== Pivot Calibration Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
This section allows the user to run a pivot calibration algorithm on the tracker device (whose connection was establish on the previous step), to do this, we import the existing PivotCalibration module.<br><br />
For more information about the use of this module please see the [http://public.kitware.com/Wiki/PET-CT/Documentation/1.0/Modules/Pivot_Calibration Pivot Calibration] documentation.<br><br />
<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep4Panel.png|thumb|300px|Pivot calibration panel]]<br />
|}<br />
<br />
== Hardware Registration Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
This step allows the user to run a fiducial registration to transform the registered volume (PET/CT scans with the interventional CT scans) coordinate system to the tracker coordinate system.<br><br />
To run the fiducial registration we need to create two fiducial lists containing respective points in the different coordinate system.<br />
<br />
At this stage of the workflow two list are generated, the "CTMarkers" to place the fiducials on the registered Volume and the "TrackerMarkers" where the fiducials on the tracker coordinate system will be placed.<br><br />
For more information about the fiducial registration, please see the documentation [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/FiducialRegistration here].<br><br />
<br />
* '''Register''': The "Add Fiducial" button allows the user, by clicking on it, to create a new fiducial at the current position of the tracking device, and adding it to the "TrackerMarkers" list<br />
<br />
* '''Annotation''': This is the "Annotation" module where we can see the fiducial lists and manipulate them. The user needs to place the fiducials on the CT volume to be able to run the registration.<br> <br />
* '''Start Registration''': This button allows the user to call the fiducial registration CLI module with two fiducial lists previously filled.<br />
<br />
|[[File:GuidedPETCTWorkflowStep5Panel.png|thumb|300px|Hardware registration panel]]<br />
|}<br />
<br />
== Tracking Step ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
This is the last step of the workflow, it uses the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/VolumeResliceDriver Volume Reslice Driver] module, to reslice de volume according to the position of the tracker device<br />
| align="right"|<br />
|[[File:GuidedPETCTWorkflowStep6Panel.png|thumb|300px|Pivot calibration panel]]<br />
|}</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep6Panel.png&diff=52560File:GuidedPETCTWorkflowStep6Panel.png2013-04-22T19:13:16Z<p>Guillaume.sala: Sixth step of the Guided Intervention PET CT workflow module. Panel View.</p>
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<div>Sixth step of the Guided Intervention PET CT workflow module. Panel View.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep6.png&diff=52559File:GuidedPETCTWorkflowStep6.png2013-04-22T19:12:54Z<p>Guillaume.sala: Sixth step of the Guided Intervention PET CT workflow module.</p>
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<div>Sixth step of the Guided Intervention PET CT workflow module.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep5Panel.png&diff=52558File:GuidedPETCTWorkflowStep5Panel.png2013-04-22T19:12:11Z<p>Guillaume.sala: Fifth step of the Guided Intervention PET CT workflow module. Panel View.</p>
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<div>Fifth step of the Guided Intervention PET CT workflow module. Panel View.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep5.png&diff=52557File:GuidedPETCTWorkflowStep5.png2013-04-22T19:11:43Z<p>Guillaume.sala: Fifth step of the Guided Intervention PET CT workflow module.</p>
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<div>Fifth step of the Guided Intervention PET CT workflow module.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep4Panel.png&diff=52556File:GuidedPETCTWorkflowStep4Panel.png2013-04-22T19:10:55Z<p>Guillaume.sala: Forth step of the Guided Intervention PET CT workflow module. Panel View.</p>
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<div>Forth step of the Guided Intervention PET CT workflow module. Panel View.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep4.png&diff=52555File:GuidedPETCTWorkflowStep4.png2013-04-22T19:10:37Z<p>Guillaume.sala: Forth step of the Guided Intervention PET CT workflow module.</p>
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<div>Forth step of the Guided Intervention PET CT workflow module.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep3Panel.png&diff=52554File:GuidedPETCTWorkflowStep3Panel.png2013-04-22T19:10:16Z<p>Guillaume.sala: Third step of the Guided Intervention PET CT workflow module. Panel View.</p>
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<div>Third step of the Guided Intervention PET CT workflow module. Panel View.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep3.png&diff=52553File:GuidedPETCTWorkflowStep3.png2013-04-22T19:09:56Z<p>Guillaume.sala: Third step of the Guided Intervention PET CT workflow module.</p>
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<div>Third step of the Guided Intervention PET CT workflow module.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep2Panel.png&diff=52552File:GuidedPETCTWorkflowStep2Panel.png2013-04-22T19:09:27Z<p>Guillaume.sala: Second step of the Guided Intervention PET CT workflow module. Panel view</p>
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<div>Second step of the Guided Intervention PET CT workflow module. Panel view</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep2.png&diff=52551File:GuidedPETCTWorkflowStep2.png2013-04-22T19:09:02Z<p>Guillaume.sala: Second step of the Guided Intervention PET CT workflow module.</p>
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<div>Second step of the Guided Intervention PET CT workflow module.</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep1Panel.png&diff=52550File:GuidedPETCTWorkflowStep1Panel.png2013-04-22T19:08:38Z<p>Guillaume.sala: First step of the Guided Intervention PET CT workflow module. Panel view</p>
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<div>First step of the Guided Intervention PET CT workflow module. Panel view</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:GuidedPETCTWorkflowStep1.png&diff=52549File:GuidedPETCTWorkflowStep1.png2013-04-22T19:07:52Z<p>Guillaume.sala: First step of the Guided Intervention PET CT workflow module</p>
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<div>First step of the Guided Intervention PET CT workflow module</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=PET-CT/Documentation/Modules/Pivot_Calibration&diff=52546PET-CT/Documentation/Modules/Pivot Calibration2013-04-18T19:40:13Z<p>Guillaume.sala: Created page with "== Introduction and Acknowledgements == Author: Guillaume Sala, [http://www.kitware.com Kitware]<br> Contributor: Andinet Enquobahrie, [http://www.kitware.com Kitware]<br> Ackno..."</p>
<hr />
<div>== Introduction and Acknowledgements == <br />
Author: Guillaume Sala, [http://www.kitware.com Kitware]<br><br />
Contributor: Andinet Enquobahrie, [http://www.kitware.com Kitware]<br><br />
Acknowledgements: This work is supported by NIH grants 2R42CA153488-02A1 and R41CA153488-01 "Improving liver lesion biopsy in the CT suite through fusion with PET images"<br><br />
Contact: Andinet Enquobahrie, Guillaume Sala<br><br />
<br />
== Module Description ==<br />
<br />
The PivotCalibration module allows to run a pivot calibration algorithm (Using [https://www.assembla.com/spaces/plus/wiki Plus library]) for a given tracker device.<br><br />
When a tracking device connection is establish with Slicer, the coordinates of the system correspond to the markers on the tool.<br><br />
This module is useful when we want to determine and track the tip of the tool instead of the markers.<br><br />
It calculates the matrix needed to transform from the marker coordinates system to the tool tip coordinate system, which is the part of interest.<br><br />
<br />
{| border="1"<br />
|-<br />
|valign="middle"|<br />
[[File:PivotCalibration-GUI.png|thumb|center|500px|PivotCalibration Module]]<br />
|valign="middle"|<br />
[[File:ToolTipCalibrationIllustration.png|thumb|center|150px|Pivot Calibration Illustration]]<br />
|-<br />
|}<br />
<br><br />
<br />
== Panels ==<br />
{| width="100%"<br />
| valign="top"|<br />
<br />
* '''Pivot Transform''': The tracker selection combobox allows select the transform corresponding to the tracking device. The transform in this combobox will be used to compute the pivot calibration transform.<br />
<br />
* '''Number of points to acquire''': Choose the number of points to use to run the algorithm<br />
* '''Output''': The current coordinate of the tracker is displayed while acquiring the points and the computed transform is displayed when it is generated.<br />
| align="right"|<br />
|[[File:PivotCalibrationPanel.png|thumb|400px|Pivot calibration panel]]<br />
|}<br />
<br />
== Tutorial ==<br />
<br />
*Use [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/OpenIGTLinkIF OpenIGTLinkIF] to establish connection between Slicer and the tracker device.<br />
**Using IGSTK: run the executable [http://public.kitware.com/IGSTKWIKI/index.php/Using_OpenIGTLink_in_IGSTK#Broadcast_Tracking_data_using_OpenIGTLink OpenIGTLinkTrackerBroadcasting] giving a configuration file for the given tracking system (e.g [[Media:IGSTK_polarisHybridConfiguration.xml|Polaris configuration file]], [[Media:IGSTK_micronConfiguration.xml|Micron configuration file]])<br />
<br />
*In the PivotCalibration module<br />
**Select the transform node corresponding to the tracker.<br />
**Select the number of points to acquire for the pivot calibration<br />
**Start calibration and move the tracker around a fixed point while the module computes the transform</div>Guillaume.salahttps://public.kitware.com/Wiki/index.php?title=File:PivotCalibrationPanel.png&diff=52545File:PivotCalibrationPanel.png2013-04-18T19:30:01Z<p>Guillaume.sala: Pivot calibration module panel</p>
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<div>Pivot calibration module panel</div>Guillaume.sala