https://www.na-mic.org/w/api.php?action=feedcontributions&user=Sbengali&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T10:19:56ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=CardiacMRIToolkit_TutorialContestSummer2013&diff=90427CardiacMRIToolkit TutorialContestSummer20132015-10-23T20:45:53Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===Cardiac MRI Toolkit Tutorial===<br />
<br />
<br />
Material for the Slicer 4.1 Cardiac MRI Toolkit tutorial, Project Week Summer 2013:<br />
<br />
[[File: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pdf]]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:Cardiac_MRI_Toolkit_Tutorial_Data.zip Data: Cardiac_MRI_Toolkit_Tutorial_Data.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part1.zip Videos Part 1: Tutorial_Videos_Part1.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part2.zip Videos Part 2: Tutorial_Videos_Part2.zip]<br />
<br />
<table><br />
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Cardiac MRI Toolkit Extension || Mac OS || Slicer 4.2.2 || 2013/06/07 || Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 32 bit || Slicer 4.2.2 || || <br />
| <br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 64 bit || Slicer 4.2.2 || 2013/06/07 || Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Linux 64 bit || Slicer 4.2.2 || 2013/06/19 || Salma Bengali<br />
| Worked<br />
|-<br />
|}<br />
</table><br />
<br />
<br />
[http://www.na-mic.org/Wiki/index.php/2012_Tutorial_Contest Back to tutorial contest]</div>Sbengalihttps://www.na-mic.org/w/index.php?title=CardiacMRIToolkit_TutorialContestSummer2013&diff=90283CardiacMRIToolkit TutorialContestSummer20132015-08-12T02:48:25Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===Cardiac MRI Toolkit Tutorial===<br />
<br />
<br />
Material for the Slicer 4.1 Cardiac MRI Toolkit tutorial, Project Week Summer 2013:<br />
<br />
[[Tutorial: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pdf]]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:Cardiac_MRI_Toolkit_Tutorial_Data.zip Data: Cardiac_MRI_Toolkit_Tutorial_Data.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part1.zip Videos Part 1: Tutorial_Videos_Part1.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part2.zip Videos Part 2: Tutorial_Videos_Part2.zip]<br />
<br />
<table><br />
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Cardiac MRI Toolkit Extension || Mac OS || Slicer 4.2.2 || 2013/06/07 || Umme Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 32 bit || Slicer 4.2.2 || || <br />
| <br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 64 bit || Slicer 4.2.2 || 2013/06/07 || Umme Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Linux 64 bit || Slicer 4.2.2 || 2013/06/19 || Umme Salma Bengali<br />
| Worked<br />
|-<br />
|}<br />
</table><br />
<br />
<br />
[http://www.na-mic.org/Wiki/index.php/2012_Tutorial_Contest Back to tutorial contest]</div>Sbengalihttps://www.na-mic.org/w/index.php?title=CardiacMRIToolkit_TutorialContestSummer2013&diff=90282CardiacMRIToolkit TutorialContestSummer20132015-08-12T02:48:16Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===Cardiac MRI Toolkit Tutorial===<br />
<br />
<br />
Material for the Slicer 4.1 Cardiac MRI Toolkit tutorial, Project Week Summer 2013:<br />
<br />
[[Tutorial: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pdf]]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:Cardiac_MRI_Toolkit_Tutorial_Data.zip Data: Cardiac_MRI_Toolkit_Tutorial_Data.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part1.zip Videos Part 1: Tutorial_Videos_Part1.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part2.zip Videos Part 2: Tutorial_Videos_Part2.zip]<br />
<br />
<table><br />
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Cardiac MRI Toolkit Extension || Mac OS || Slicer 4.2.2 || 2013/06/07 || Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 32 bit || Slicer 4.2.2 || || <br />
| <br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 64 bit || Slicer 4.2.2 || 2013/06/07 || Umme Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Linux 64 bit || Slicer 4.2.2 || 2013/06/19 || Umme Salma Bengali<br />
| Worked<br />
|-<br />
|}<br />
</table><br />
<br />
<br />
[http://www.na-mic.org/Wiki/index.php/2012_Tutorial_Contest Back to tutorial contest]</div>Sbengalihttps://www.na-mic.org/w/index.php?title=CardiacMRIToolkit_TutorialContestSummer2013&diff=87598CardiacMRIToolkit TutorialContestSummer20132014-10-17T19:24:32Z<p>Sbengali: Added videos which are not included in PDF</p>
<hr />
<div>__NOTOC__<br />
===Cardiac MRI Toolkit Tutorial===<br />
<br />
<br />
Material for the Slicer 4.1 Cardiac MRI Toolkit tutorial, Project Week Summer 2013:<br />
<br />
[[Tutorial: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pdf]]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:Cardiac_MRI_Toolkit_Tutorial_Data.zip Data: Cardiac_MRI_Toolkit_Tutorial_Data.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part1.zip Videos Part 1: Tutorial_Videos_Part1.zip]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part2.zip Videos Part 2: Tutorial_Videos_Part2.zip]<br />
<br />
<table><br />
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| Cardiac MRI Toolkit Extension || Mac OS || Slicer 4.2.2 || 2013/06/07 || Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 32 bit || Slicer 4.2.2 || || <br />
| <br />
|-<br />
| Cardiac MRI Toolkit Extension || Windows 7 64 bit || Slicer 4.2.2 || 2013/06/07 || Salma Bengali<br />
| Worked<br />
|-<br />
| Cardiac MRI Toolkit Extension || Linux 64 bit || Slicer 4.2.2 || 2013/06/19 || Salma Bengali<br />
| Worked<br />
|-<br />
|}<br />
</table><br />
<br />
<br />
[http://www.na-mic.org/Wiki/index.php/2012_Tutorial_Contest Back to tutorial contest]</div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:CMRToolkit_SummerTutorialContest2013_Videos_Part2.zip&diff=87597File:CMRToolkit SummerTutorialContest2013 Videos Part2.zip2014-10-17T19:08:12Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:CMRToolkit_SummerTutorialContest2013_Videos_Part1.zip&diff=87596File:CMRToolkit SummerTutorialContest2013 Videos Part1.zip2014-10-17T18:52:55Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=CMRToolkitLAWorkflow_TutorialContestSummer2014&diff=86448CMRToolkitLAWorkflow TutorialContestSummer20142014-06-23T18:11:31Z<p>Sbengali: Added test results</p>
<hr />
<div>__NOTOC__<br />
===Cardiac MRI Toolkit Tutorial===<br />
<br />
Material for the Slicer 4.2 Cardiac MRI Toolkit, LA Segmentation Workflow tutorial, Project Week Summer 2014:<br />
<br />
[[File: CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf]]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip Data: CMRToolkitLAWorkflowData]<br />
<br />
<table><br />
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| CMRToolkitLAWorkflow Tutorial|| Mac OS || nightly || 2013/06/23 || Salma Bengali || Worked<br />
|<br />
|-<br />
| || Windows 7 32 bit || nightly || || <br />
|<br />
|-<br />
| CMRToolkitLAWorkflow Tutorial|| Windows 7 64 bit || nightly || 2013/06/23 || Salma Bengali || Worked<br />
|<br />
|-<br />
| CMRToolkitLAWorkflow Tutorial|| Linux 64 bit || nightly || 2013/06/23 || Salma Bengali || Worked<br />
|<br />
|-<br />
|}</div>Sbengalihttps://www.na-mic.org/w/index.php?title=2014_Tutorial_Contest&diff=859842014 Tutorial Contest2014-06-20T18:58:05Z<p>Sbengali: </p>
<hr />
<div>'''NA-MIC Tutorial Contest, Thursday June 26, 9-10:30 am'''<br />
<br />
[[2014_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]<br />
<br />
[http://www.slicer.org Slicer4] is used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer. <br />
<br />
The primary purpose of the Summer 2014 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe participants will be motivated to join this event to enhance the dissemination of their own algorithms that they have incorporated into the Slicer4 platform and/or to enhance training of Slicer4 functionality for their own laboratory groups.<br />
<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/2013_Tutorial_Contest 2013 Summer Tutorial 2013 Contest page]<br />
<br />
There will be three categories:<br />
*Category 0: '''EXTENSION TUTORIAL''' <br> In this category, the tutorial will teach a user how to use an Extension of Slicer.<br />
*Category 1: '''END TO END SOLUTION TUTORIAL''' <br> In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. <br> Example: [http://www.slicer.org/slicerWiki/images/f/f1/NeurosurgicalPlanning_SoniaPujol.pdf White Matter Exploration for Neurosurgical Planning]<br />
*Category 2: '''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data.<br> Examples: [http://www.slicer.org/slicerWiki/images/c/c6/Slicer4QuantitativeImaging.pdf Quantitative Imaging tutorial]<br><br />
*Category 3: '''METHODOLOGY TUTORIAL'''. Application-level tutorials for users and developers.<br> Examples:[[Slicer3:Fiducials_TutorialContestSummer2010 | '''Fiducials''']] <br />
<br />
<br />
Entries in each category require the following material: <br />
* scientific background and application motivation<br />
* step-by-step instructions<br />
* anonymized sample dataset<br />
<br />
=Rules=<br />
<br />
The [[Summer2014_Tutorial_Contest | evaluation criteria]] for the 2014 tutorial contest are below:<br />
*Tutorial must be based on the Slicer nightly build of June 2,2014:<br />
Windows: <br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-win-amd64.exe&checksum=f464d190dda72957d1ab7f43b58843e2 Slicer4.4.2014-06.03]<br />
Mac:<br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-macosx-amd64.dmg&checksum=b5c99307995cbb1292d1789a4cf6c7a9 Slicer4.4.2014-06.03]<br />
Linux:<br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-linux-amd64.tar.gz&checksum=eebf24ed14aaf46ccd0f47311e96f1fe Slicer4.4.2014-06.03]<br />
<br />
*To enter the contest, you must provide a self-test that can be run in Slicer and '''a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)+'''.<br />
Example of self-tests can be found in the RSNA2012Quant module of Slicer4.3.<br />
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br />
*Tutorial data must be anonymized<br />
*Tutorial must include contact information of the primary author (e-mail and phone number) <br />
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2014.ppt | Summer 2014 contest tutorial template]].<br />
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br><br />
+Applicants will work with the NA-MIC Training Core in advance to do the multi-platform testing.<br />
<br />
NOTE: If you plan on sending the DTI data, we are currently experiencing a [http://na-mic.org/Mantis/view.php?id=3723 bug] that is being worked on. Please refer to these useful debugging hints:<br />
*Load DTI and get bad display as shown in bug report<br />
*Go to volumes module<br />
*Select perpendicular diffusivity mode (possible others work too)<br />
*Switch back to Color Orientation and display is working<br />
*FA now works as well.<br />
<br />
=Submission Dead-line and Presentation=<br />
<br />
'''<span style="background-color: pink"> Submission dead-line: Monday June 23, 2014'''</span><br />
* '''Submission process''': to enter the contest, please follow the 5 steps below:<br />
**1. Create a wiki page for your tutorial on the NA-MIC wiki.<br />
**2. Upload your slides and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestSummer2014.pdf' and 'TutorialData_TutorialContestSummer2014.zip'<br />
**3. Add a link to the uploaded tutorial and datasets on your tutorial page. <br />
**4. Copy the template of the [http://wiki.na-mic.org/Wiki/index.php/Training:Summer_2014_Contest_Table Summer 2014 test table ] on your tutorial page, and enter the results of your cross-platform testing (Mac, Windows XP &7, Linux 64, Linux 32).<br />
**5. Once you have completed step 1-4, add a link to your tutorial page in the list below and send a notification email to Sonia Pujol (spujol at bwh.harvard.edu) to receive a confirmation of your submission.<br />
<br />
* '''Presentation at the NA-MIC Project week''': Brief highlights of tutorials will be presented by the authors at the Summer 2014 Project Week. Each presentation should be 5-minute summary of the submission.<br />
<br />
*Tutorial contest entries<br />
#[http://wiki.na-mic.org/Wiki/index.php/CMRToolkitLAWorkflow_TutorialContestSummer2014 Cardiac MRI Toolkit LA Segmentation Workflow. Salma Bengali, Josh Cates, SCI, Utah]<br />
<br />
Contest judges: <br />
*Randy Gollby, MD, PhD, Massachusetts General Hospital, Harvard Medical School<br />
*Greg Sharp, PhD, Massachusetts General Hospital, Harvard Medical School<br />
*Sidong Liu, MSc, Brigham and Women's Hospital, Harvard Medical School - University of Sydney <br />
*Sonia Pujol, PhD, Brigham and Women's Hospital, Harvard Medical School</div>Sbengalihttps://www.na-mic.org/w/index.php?title=2014_Tutorial_Contest&diff=859832014 Tutorial Contest2014-06-20T18:57:42Z<p>Sbengali: Added link to tutorial contest entry</p>
<hr />
<div>'''NA-MIC Tutorial Contest, Thursday June 26, 9-10:30 am'''<br />
<br />
[[2014_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]<br />
<br />
[http://www.slicer.org Slicer4] is used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer. <br />
<br />
The primary purpose of the Summer 2014 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe participants will be motivated to join this event to enhance the dissemination of their own algorithms that they have incorporated into the Slicer4 platform and/or to enhance training of Slicer4 functionality for their own laboratory groups.<br />
<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/2013_Tutorial_Contest 2013 Summer Tutorial 2013 Contest page]<br />
<br />
There will be three categories:<br />
*Category 0: '''EXTENSION TUTORIAL''' <br> In this category, the tutorial will teach a user how to use an Extension of Slicer.<br />
*Category 1: '''END TO END SOLUTION TUTORIAL''' <br> In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. <br> Example: [http://www.slicer.org/slicerWiki/images/f/f1/NeurosurgicalPlanning_SoniaPujol.pdf White Matter Exploration for Neurosurgical Planning]<br />
*Category 2: '''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data.<br> Examples: [http://www.slicer.org/slicerWiki/images/c/c6/Slicer4QuantitativeImaging.pdf Quantitative Imaging tutorial]<br><br />
*Category 3: '''METHODOLOGY TUTORIAL'''. Application-level tutorials for users and developers.<br> Examples:[[Slicer3:Fiducials_TutorialContestSummer2010 | '''Fiducials''']] <br />
<br />
<br />
Entries in each category require the following material: <br />
* scientific background and application motivation<br />
* step-by-step instructions<br />
* anonymized sample dataset<br />
<br />
=Rules=<br />
<br />
The [[Summer2014_Tutorial_Contest | evaluation criteria]] for the 2014 tutorial contest are below:<br />
*Tutorial must be based on the Slicer nightly build of June 2,2014:<br />
Windows: <br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-win-amd64.exe&checksum=f464d190dda72957d1ab7f43b58843e2 Slicer4.4.2014-06.03]<br />
Mac:<br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-macosx-amd64.dmg&checksum=b5c99307995cbb1292d1789a4cf6c7a9 Slicer4.4.2014-06.03]<br />
Linux:<br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-linux-amd64.tar.gz&checksum=eebf24ed14aaf46ccd0f47311e96f1fe Slicer4.4.2014-06.03]<br />
<br />
*To enter the contest, you must provide a self-test that can be run in Slicer and '''a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)+'''.<br />
Example of self-tests can be found in the RSNA2012Quant module of Slicer4.3.<br />
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br />
*Tutorial data must be anonymized<br />
*Tutorial must include contact information of the primary author (e-mail and phone number) <br />
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2014.ppt | Summer 2014 contest tutorial template]].<br />
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br><br />
+Applicants will work with the NA-MIC Training Core in advance to do the multi-platform testing.<br />
<br />
NOTE: If you plan on sending the DTI data, we are currently experiencing a [http://na-mic.org/Mantis/view.php?id=3723 bug] that is being worked on. Please refer to these useful debugging hints:<br />
*Load DTI and get bad display as shown in bug report<br />
*Go to volumes module<br />
*Select perpendicular diffusivity mode (possible others work too)<br />
*Switch back to Color Orientation and display is working<br />
*FA now works as well.<br />
<br />
=Submission Dead-line and Presentation=<br />
<br />
'''<span style="background-color: pink"> Submission dead-line: Monday June 23, 2014'''</span><br />
* '''Submission process''': to enter the contest, please follow the 5 steps below:<br />
**1. Create a wiki page for your tutorial on the NA-MIC wiki.<br />
**2. Upload your slides and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestSummer2014.pdf' and 'TutorialData_TutorialContestSummer2014.zip'<br />
**3. Add a link to the uploaded tutorial and datasets on your tutorial page. <br />
**4. Copy the template of the [http://wiki.na-mic.org/Wiki/index.php/Training:Summer_2014_Contest_Table Summer 2014 test table ] on your tutorial page, and enter the results of your cross-platform testing (Mac, Windows XP &7, Linux 64, Linux 32).<br />
**5. Once you have completed step 1-4, add a link to your tutorial page in the list below and send a notification email to Sonia Pujol (spujol at bwh.harvard.edu) to receive a confirmation of your submission.<br />
<br />
* '''Presentation at the NA-MIC Project week''': Brief highlights of tutorials will be presented by the authors at the Summer 2014 Project Week. Each presentation should be 5-minute summary of the submission.<br />
<br />
*Tutorial contest entries<br />
#[http://wiki.na-mic.org/Wiki/index.php/CMRToolkitLAWorkflow_TutorialContestSummer2014 Cardiac MRI Toolkit. Salma Bengali, Josh Cates, SCI, Utah]<br />
<br />
Contest judges: <br />
*Randy Gollby, MD, PhD, Massachusetts General Hospital, Harvard Medical School<br />
*Greg Sharp, PhD, Massachusetts General Hospital, Harvard Medical School<br />
*Sidong Liu, MSc, Brigham and Women's Hospital, Harvard Medical School - University of Sydney <br />
*Sonia Pujol, PhD, Brigham and Women's Hospital, Harvard Medical School</div>Sbengalihttps://www.na-mic.org/w/index.php?title=CMRToolkitLAWorkflow_TutorialContestSummer2014&diff=85982CMRToolkitLAWorkflow TutorialContestSummer20142014-06-20T18:57:27Z<p>Sbengali: Created page for tutorial</p>
<hr />
<div>__NOTOC__<br />
===Cardiac MRI Toolkit Tutorial===<br />
<br />
Material for the Slicer 4.2 Cardiac MRI Toolkit, LA Segmentation Workflow tutorial, Project Week Summer 2014:<br />
<br />
[[File: CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf]]<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip Data: CMRToolkitLAWorkflowData]<br />
<br />
<table><br />
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"<br />
|-<br />
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''<br />
|-<br />
| || Mac OS || || || <br />
|<br />
|-<br />
| || Windows 7 32 bit || || || <br />
|<br />
|-<br />
| || Windows 7 64 bit || || || <br />
|<br />
|-<br />
| || Linux 64 bit || || || <br />
|<br />
|-<br />
|}</div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf&diff=85980File:CMRToolkitLAWorkflow TutorialContestSummer2014.pdf2014-06-20T18:51:55Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip&diff=85978File:CMRToolkitLAWorkflowData TutorialContestSummer2014.zip2014-06-20T18:49:23Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:LAWorkflow_MRA.nrrd&diff=85977File:LAWorkflow MRA.nrrd2014-06-20T17:54:58Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:LAWorkflow_LGE.nrrd&diff=85976File:LAWorkflow LGE.nrrd2014-06-20T17:44:22Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=2014_Project_Week:MRAFusionRegistration&diff=848352014 Project Week:MRAFusionRegistration2014-01-10T03:26:45Z<p>Sbengali: Added progress</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Josh Cates, Salma Bengali<br />
[[File:MRAFusion_Step1.png|thumb|left|300px|Loading data into Slicer]]<br />
[[File:MRAFusion_Step2.png|thumb|center|300px|Segmenting the endo in the MRA]]<br />
==Project Description==<br />
We have been developing an approach to segmentation of cardiac DE-MRI images that uses the associated<br />
MRA to help define endocardial boundaries. This approach is possible because CARMA is now acquiring gated MRAs routinely for patients. The approach is to perform a quick, semi-automated segmentation of the LA in the MRA, register the MRA to the DE MRI, and then refine the registered segmentation based on the DE MRI data.<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* To design and implement a Slicer module or wizard that walks the user through segmentation of the LA using the MRA in conjunction with the DE MRI<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Refine and test MRA segmentation based on available slicer tools<br />
* Refine and test MRA to DE MRI segmentation in CMR toolkit extension<br />
* Design and build Wizard module for slicer<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* We have completed the first two steps for this wizard and will add the registration step.<br />
<br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be added to the CMR Toolkit extension as a Slicer loadable module.</div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:MRAFusion_Step2.png&diff=84830File:MRAFusion Step2.png2014-01-10T03:22:09Z<p>Sbengali: uploaded a new version of "File:MRAFusion Step2.png"</p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:MRAFusion_Step2.png&diff=84829File:MRAFusion Step2.png2014-01-10T03:20:19Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:MRAFusion_Step1.png&diff=84828File:MRAFusion Step1.png2014-01-10T03:20:05Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=2014_Project_Week:GraphCutsLASegmentationModule&diff=848222014 Project Week:GraphCutsLASegmentationModule2014-01-10T03:04:53Z<p>Sbengali: Added progress</p>
<hr />
<div>==Key Investigators==<br />
<br />
Gopalkrishna Veni (SCI Institute, University of Utah)<br />
<br />
Salma Bengali (CARMA center, University of Utah)<br />
<br />
Josh Cates (CARMA center, University of Utah)<br />
<br />
Rob Macleod (CARMA center, SCI Institute, University of Utah)<br />
<br />
Ross Whitaker(SCI Institute, University of Utah)<br />
[[File:LAsegment GraphCut.png|thumb|center|300px]]<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Develop a Slicer module that automatically segments the left atrial wall from a given LGE-MRI image.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Involves Bayesian formulation with Markov random field prior within a nested-layer 3D mesh which leads to surface-net problem [Veni ''et al'', IPMI 2013]. <br />
* Solved by using VCEnet strategy and graph-cuts [Wu and Chen, 2002]. <br />
* Uses training strategy in order to generate model shapes as well as to compute costs at each mesh point. <br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* The module now provides the ability to the user to select the approximate center of the left atrium and the model is aligned with that point. <br />
* The VCEnet technique produces better results than the Vnet technique that was used in previous versions of the module. <br />
* Module is now available in the Slicer. It could be downloaded from: https://github.com/carma-center/carma_slicer_extension/<br />
* The online documentation on its usage is available at: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/AutomatedLASegmentation<br />
* Model data could be downloaded from: http://slicer.kitware.com/midas3/folder/1550<br />
<br />
</div><br />
</div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=2014_Project_Week:LAFibrosisVisualizationModule&diff=848122014 Project Week:LAFibrosisVisualizationModule2014-01-10T02:19:45Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Utah: Salma Bengali, Josh Cates<br />
<br />
[[File:LAFibrosisVis2.png|thumb|center|300px|An example of a thresholded isosurface. Blue: Below threshold, Green: Above threshold, White: Highest intensity]]<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* The workflow at CARMA for generating fibrosis scores for patients involves creating an isosurface of the left atrium wall, with regions of scar overlaid. We have a preliminary module for visualization of scar / fibrosis, but need to expand with additional color maps. We would also like to add the calculation of the percent of scar in the left atrium wall.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
# Build slicer module for visualization of (1) fibrosis and (2) scar with custom color maps<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
# We have discussed with Nicole and have decided to add a custom color map that will be included with our extension. An example of what the wall model will look like is shown above. <br />
# The percentage of scar in the wall will be calculated and updated as the user changes the intensity threshold. <br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be added to what is already available as a Slicer loadable module. <br />
<br />
==References==<br />
*[http://www.na-mic.org/Wiki/index.php/DBP3:Utah Utah DBP]</div>Sbengalihttps://www.na-mic.org/w/index.php?title=2014_Project_Week:LAFibrosisVisualizationModule&diff=848112014 Project Week:LAFibrosisVisualizationModule2014-01-10T02:19:21Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Utah: Salma Bengali, Josh Cates<br />
<br />
[[File:LAFibrosisVis2.png|thumb|center|300px|An example of a thresholded isosurface. Blue: Below threshold, Green: Above threshold.]]<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* The workflow at CARMA for generating fibrosis scores for patients involves creating an isosurface of the left atrium wall, with regions of scar overlaid. We have a preliminary module for visualization of scar / fibrosis, but need to expand with additional color maps. We would also like to add the calculation of the percent of scar in the left atrium wall.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
# Build slicer module for visualization of (1) fibrosis and (2) scar with custom color maps<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
# We have discussed with Nicole and have decided to add a custom color map that will be included with our extension. An example of what the wall model will look like is shown above. <br />
# The percentage of scar in the wall will be calculated and updated as the user changes the intensity threshold. <br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be added to what is already available as a Slicer loadable module. <br />
<br />
==References==<br />
*[http://www.na-mic.org/Wiki/index.php/DBP3:Utah Utah DBP]</div>Sbengalihttps://www.na-mic.org/w/index.php?title=2014_Project_Week:LAFibrosisVisualizationModule&diff=848102014 Project Week:LAFibrosisVisualizationModule2014-01-10T02:19:04Z<p>Sbengali: Added progress</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Utah: Salma Bengali, Josh Cates<br />
<br />
[[File:LAFIbrosisVis2.png|thumb|center|300px|An example of a thresholded isosurface. Blue: Below threshold, Green: Above threshold.]]<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* The workflow at CARMA for generating fibrosis scores for patients involves creating an isosurface of the left atrium wall, with regions of scar overlaid. We have a preliminary module for visualization of scar / fibrosis, but need to expand with additional color maps. We would also like to add the calculation of the percent of scar in the left atrium wall.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
# Build slicer module for visualization of (1) fibrosis and (2) scar with custom color maps<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
# We have discussed with Nicole and have decided to add a custom color map that will be included with our extension. An example of what the wall model will look like is shown above. <br />
# The percentage of scar in the wall will be calculated and updated as the user changes the intensity threshold. <br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be added to what is already available as a Slicer loadable module. <br />
<br />
==References==<br />
*[http://www.na-mic.org/Wiki/index.php/DBP3:Utah Utah DBP]</div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:LAFibrosisVis2.png&diff=84809File:LAFibrosisVis2.png2014-01-10T02:15:18Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:LAFIbrosisVis.png&diff=84808File:LAFIbrosisVis.png2014-01-10T02:07:06Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah&diff=83030DBP3:Utah2013-07-29T20:02:05Z<p>Sbengali: /* Tutorials */</p>
<hr />
<div> Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]<br />
<br />
<br />
=== The CARMA DBP: MRI-based study and treatment of atrial fibrillation ===<br />
Tissue remodeling of the atrial wall is the hallmark of Atrial Fibrillation<br />
(AF), a progressive cardiac disease that develops over time (months to<br />
years). The mechanisms of of this transformation are only partially understood,<br />
but the current scientific focus on tissue remodeling and its putative role in<br />
AF suggests an MRI image-based approach to the study of AF.<br />
<br />
The Comprehensive Arrhythmia Research and MAnagement (CARMA) Center at the<br />
University of Utah is a world leader in the rapidly emerging field of<br />
MRI-managed evaluation and ablation of AF. Other groups have begun to recognize<br />
the potential of this approach and to investigate and validate some of our<br />
findings. Still others are developing new refinements of the MRI technique<br />
driven by the specific needs of this application domain.<br />
<br />
Preliminary investigation by CARMA has identified image processing and analysis<br />
as the rate-limiting step to the development of MRI-based therapies. Novel<br />
forms of MRI can be used to evaluate new patients, predict success before<br />
ablation, analyze outcomes post-ablation, and guide repeat ablations. Such<br />
MRI-based therapies, however, urgently require advanced tools and software to<br />
support efficient workflows and accelerate the quantification and analysis of<br />
images. The CARMA-NAMIC DBP project will address some of these needs with the<br />
development of algorithms and tools for the automated segmentation of heart<br />
structures and the MRI-based evaluation of AF progression and recovery.<br />
<br />
This remainder of this wiki page describes ongoing CARMA-NAMIC activities and<br />
specific plans. For more background information, references, and description of<br />
the specific scientific and clinical aims of this project,<br />
please see the project web page: http://www.na-mic.org/pages/DBP:Atrial_Fibrillation .<br />
<br />
<br />
=== DBP Specific Aims ===<br />
# Develop and validate image-based longitudinal diagnostic indices for AF<br />
# Develop automatic segmentation methods for the atrium and adjacent structures<br />
# Develop an AF scoring scheme to evaluate disease progression and recovery from therapy<br />
<br />
<br />
[[Image:TV1.jpg|center|thumb|400px|The CARMA Center's Utah classification for Atrial Fibrillation staging involves segmentation of the left atrial wall from MRI, followed by quantification of enhanced vs. non-enhanced voxels in the wall.]]<br />
<br />
==Activities==<br />
=== Slicer Modules ===<br />
* [[DBP3:Utah:SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
* [[DBP3:Utah:SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
* [[DBP3:Utah:SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
* [[DBP3:Utah:SlicerModuleAxialDilate|Axial Dilate Filter]]<br />
* [[DBP3:Utah:SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
* [[DBP3:Utah:SlicerModuleThresholdModel|Threshold Model]]<br />
* [[DBP3:Utah:SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutomatedLASegmentation|Automated Graph Cut LA Segmentation]]<br />
<br />
=== Tutorials ===<br />
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]<br />
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]<br />
* [[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI Registration Tutorial]]<br />
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|Cardiac MRI Registration Using BRAINSFit Tutorial]]<br />
* [[Media:Carma_PVAntrumCutFilter_Tutorial_New.pptx|PV Antrum Cut Filter Tutorial]]<br />
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]<br />
* [[Media:Carma_Boolean_Remove_Tutorial.pptx|Boolean REMOVE Filter Tutorial]]<br />
* [[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
* [[Media:Carma_Isolated_Connected_Filter_Tutorial.pptx|Isolated Connected Filter Tutorial]]<br />
* [[Media:Carma_Connected_Threshold_Filter_Tutorial.pptx|Connected Threshold Filter Tutorial]]<br />
* [[Media:CarmaWorkflowV2.pdf|Slicer Workflow Tutorial]]<br />
<br />
=== Other Projects ===<br />
* Image registration capabilities for longitudinal analysis: [[DBP3:Utah:RegSegPipeline|Registration & Segmentation pipeline pilots & workflow development (Dominik Meier, Alex Zaitsev)]]<br />
* Evaluation of BRAINSFit and fiducial-based registration tools for LA wall alignment and longitudinal registration of PV: [[DBP3:Utah:PV_BFReg|BRAINSFit Registration of PVs]]<br />
* Collaboration with GA Tech - <br />
** Test and evaluate Behnood's wall segmentation - results and analysis are here: [[DBP3:Utah:AutoWallSeg|Automatic Wall Segmentation]]<br />
** Test and evaluate Yi Gao's atlas-based endocardial segmentation algorithm: [[DBP3:Utah:AutoEndoSeg|Automatic Endocardial Segmentation]]<br />
** Test and evaluate Yi Gao's image and segmentation-driven registration algorithm: [[DBP3:Utah:VecReg|Image and Segmentation-Driven Registration]]<br />
<br />
=== Slicer4 Needs and Plans ===<br />
Summary of the Slicer4 needs to support CARMA workflows can be found [[DBP3:Utah:Slicer4 | here]].<br />
<br />
==Sample Data==<br />
* Sixty anonymized datasets containing LGE-MRI image data and segmentations of the left atrium from patients with atrial fibrillation: [http://hdl.handle.net/1926/1755 Pre and Post Radiofrequency Ablation LGE-MRI Collection]<br />
* Sixty segmentation datasets of the left atrium from patients with atrial fibrillation who have undergone radiofrequency catheter ablation for treatment: [http://hdl.handle.net/1926/1764 CARMA Longitudinal Left Atrial Shape Data]<br />
* Two subjects, two time points: [[Media:CardiacMRIs.zip|CardiacMRIs]].</div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:Carma_Connected_Threshold_Filter_Tutorial.pptx&diff=83029File:Carma Connected Threshold Filter Tutorial.pptx2013-07-29T20:01:51Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:Carma_Isolated_Connected_Filter_Tutorial.pptx&diff=83028File:Carma Isolated Connected Filter Tutorial.pptx2013-07-29T20:00:47Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah&diff=83027DBP3:Utah2013-07-29T19:59:51Z<p>Sbengali: /* Slicer Modules */</p>
<hr />
<div> Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]<br />
<br />
<br />
=== The CARMA DBP: MRI-based study and treatment of atrial fibrillation ===<br />
Tissue remodeling of the atrial wall is the hallmark of Atrial Fibrillation<br />
(AF), a progressive cardiac disease that develops over time (months to<br />
years). The mechanisms of of this transformation are only partially understood,<br />
but the current scientific focus on tissue remodeling and its putative role in<br />
AF suggests an MRI image-based approach to the study of AF.<br />
<br />
The Comprehensive Arrhythmia Research and MAnagement (CARMA) Center at the<br />
University of Utah is a world leader in the rapidly emerging field of<br />
MRI-managed evaluation and ablation of AF. Other groups have begun to recognize<br />
the potential of this approach and to investigate and validate some of our<br />
findings. Still others are developing new refinements of the MRI technique<br />
driven by the specific needs of this application domain.<br />
<br />
Preliminary investigation by CARMA has identified image processing and analysis<br />
as the rate-limiting step to the development of MRI-based therapies. Novel<br />
forms of MRI can be used to evaluate new patients, predict success before<br />
ablation, analyze outcomes post-ablation, and guide repeat ablations. Such<br />
MRI-based therapies, however, urgently require advanced tools and software to<br />
support efficient workflows and accelerate the quantification and analysis of<br />
images. The CARMA-NAMIC DBP project will address some of these needs with the<br />
development of algorithms and tools for the automated segmentation of heart<br />
structures and the MRI-based evaluation of AF progression and recovery.<br />
<br />
This remainder of this wiki page describes ongoing CARMA-NAMIC activities and<br />
specific plans. For more background information, references, and description of<br />
the specific scientific and clinical aims of this project,<br />
please see the project web page: http://www.na-mic.org/pages/DBP:Atrial_Fibrillation .<br />
<br />
<br />
=== DBP Specific Aims ===<br />
# Develop and validate image-based longitudinal diagnostic indices for AF<br />
# Develop automatic segmentation methods for the atrium and adjacent structures<br />
# Develop an AF scoring scheme to evaluate disease progression and recovery from therapy<br />
<br />
<br />
[[Image:TV1.jpg|center|thumb|400px|The CARMA Center's Utah classification for Atrial Fibrillation staging involves segmentation of the left atrial wall from MRI, followed by quantification of enhanced vs. non-enhanced voxels in the wall.]]<br />
<br />
==Activities==<br />
=== Slicer Modules ===<br />
* [[DBP3:Utah:SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
* [[DBP3:Utah:SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
* [[DBP3:Utah:SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
* [[DBP3:Utah:SlicerModuleAxialDilate|Axial Dilate Filter]]<br />
* [[DBP3:Utah:SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
* [[DBP3:Utah:SlicerModuleThresholdModel|Threshold Model]]<br />
* [[DBP3:Utah:SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutomatedLASegmentation|Automated Graph Cut LA Segmentation]]<br />
<br />
=== Tutorials ===<br />
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]<br />
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]<br />
* [[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI Registration Tutorial]]<br />
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|Cardiac MRI Registration Using BRAINSFit Tutorial]]<br />
* [[Media:Carma_PVAntrumCutFilter_Tutorial_New.pptx|PV Antrum Cut Filter Tutorial]]<br />
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]<br />
* [[Media:Carma_Boolean_Remove_Tutorial.pptx|Boolean REMOVE Filter Tutorial]]<br />
* [[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
* [[Media:CarmaWorkflowV2.pdf|Slicer Workflow Tutorial]]<br />
<br />
=== Other Projects ===<br />
* Image registration capabilities for longitudinal analysis: [[DBP3:Utah:RegSegPipeline|Registration & Segmentation pipeline pilots & workflow development (Dominik Meier, Alex Zaitsev)]]<br />
* Evaluation of BRAINSFit and fiducial-based registration tools for LA wall alignment and longitudinal registration of PV: [[DBP3:Utah:PV_BFReg|BRAINSFit Registration of PVs]]<br />
* Collaboration with GA Tech - <br />
** Test and evaluate Behnood's wall segmentation - results and analysis are here: [[DBP3:Utah:AutoWallSeg|Automatic Wall Segmentation]]<br />
** Test and evaluate Yi Gao's atlas-based endocardial segmentation algorithm: [[DBP3:Utah:AutoEndoSeg|Automatic Endocardial Segmentation]]<br />
** Test and evaluate Yi Gao's image and segmentation-driven registration algorithm: [[DBP3:Utah:VecReg|Image and Segmentation-Driven Registration]]<br />
<br />
=== Slicer4 Needs and Plans ===<br />
Summary of the Slicer4 needs to support CARMA workflows can be found [[DBP3:Utah:Slicer4 | here]].<br />
<br />
==Sample Data==<br />
* Sixty anonymized datasets containing LGE-MRI image data and segmentations of the left atrium from patients with atrial fibrillation: [http://hdl.handle.net/1926/1755 Pre and Post Radiofrequency Ablation LGE-MRI Collection]<br />
* Sixty segmentation datasets of the left atrium from patients with atrial fibrillation who have undergone radiofrequency catheter ablation for treatment: [http://hdl.handle.net/1926/1764 CARMA Longitudinal Left Atrial Shape Data]<br />
* Two subjects, two time points: [[Media:CardiacMRIs.zip|CardiacMRIs]].</div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah&diff=83026DBP3:Utah2013-07-29T19:59:25Z<p>Sbengali: /* Tutorials */</p>
<hr />
<div> Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]<br />
<br />
<br />
=== The CARMA DBP: MRI-based study and treatment of atrial fibrillation ===<br />
Tissue remodeling of the atrial wall is the hallmark of Atrial Fibrillation<br />
(AF), a progressive cardiac disease that develops over time (months to<br />
years). The mechanisms of of this transformation are only partially understood,<br />
but the current scientific focus on tissue remodeling and its putative role in<br />
AF suggests an MRI image-based approach to the study of AF.<br />
<br />
The Comprehensive Arrhythmia Research and MAnagement (CARMA) Center at the<br />
University of Utah is a world leader in the rapidly emerging field of<br />
MRI-managed evaluation and ablation of AF. Other groups have begun to recognize<br />
the potential of this approach and to investigate and validate some of our<br />
findings. Still others are developing new refinements of the MRI technique<br />
driven by the specific needs of this application domain.<br />
<br />
Preliminary investigation by CARMA has identified image processing and analysis<br />
as the rate-limiting step to the development of MRI-based therapies. Novel<br />
forms of MRI can be used to evaluate new patients, predict success before<br />
ablation, analyze outcomes post-ablation, and guide repeat ablations. Such<br />
MRI-based therapies, however, urgently require advanced tools and software to<br />
support efficient workflows and accelerate the quantification and analysis of<br />
images. The CARMA-NAMIC DBP project will address some of these needs with the<br />
development of algorithms and tools for the automated segmentation of heart<br />
structures and the MRI-based evaluation of AF progression and recovery.<br />
<br />
This remainder of this wiki page describes ongoing CARMA-NAMIC activities and<br />
specific plans. For more background information, references, and description of<br />
the specific scientific and clinical aims of this project,<br />
please see the project web page: http://www.na-mic.org/pages/DBP:Atrial_Fibrillation .<br />
<br />
<br />
=== DBP Specific Aims ===<br />
# Develop and validate image-based longitudinal diagnostic indices for AF<br />
# Develop automatic segmentation methods for the atrium and adjacent structures<br />
# Develop an AF scoring scheme to evaluate disease progression and recovery from therapy<br />
<br />
<br />
[[Image:TV1.jpg|center|thumb|400px|The CARMA Center's Utah classification for Atrial Fibrillation staging involves segmentation of the left atrial wall from MRI, followed by quantification of enhanced vs. non-enhanced voxels in the wall.]]<br />
<br />
==Activities==<br />
=== Slicer Modules ===<br />
* [[DBP3:Utah:SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
* [[DBP3:Utah:SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
* [[DBP3:Utah:SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
* [[DBP3:Utah:SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
* [[DBP3:Utah:SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
* [[DBP3:Utah:SlicerModuleThresholdModel|Threshold Model]]<br />
* [[DBP3:Utah:SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutomatedLASegmentation|Automated Graph Cut LA Segmentation]]<br />
<br />
=== Tutorials ===<br />
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]<br />
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]<br />
* [[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI Registration Tutorial]]<br />
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|Cardiac MRI Registration Using BRAINSFit Tutorial]]<br />
* [[Media:Carma_PVAntrumCutFilter_Tutorial_New.pptx|PV Antrum Cut Filter Tutorial]]<br />
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]<br />
* [[Media:Carma_Boolean_Remove_Tutorial.pptx|Boolean REMOVE Filter Tutorial]]<br />
* [[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
* [[Media:CarmaWorkflowV2.pdf|Slicer Workflow Tutorial]]<br />
<br />
=== Other Projects ===<br />
* Image registration capabilities for longitudinal analysis: [[DBP3:Utah:RegSegPipeline|Registration & Segmentation pipeline pilots & workflow development (Dominik Meier, Alex Zaitsev)]]<br />
* Evaluation of BRAINSFit and fiducial-based registration tools for LA wall alignment and longitudinal registration of PV: [[DBP3:Utah:PV_BFReg|BRAINSFit Registration of PVs]]<br />
* Collaboration with GA Tech - <br />
** Test and evaluate Behnood's wall segmentation - results and analysis are here: [[DBP3:Utah:AutoWallSeg|Automatic Wall Segmentation]]<br />
** Test and evaluate Yi Gao's atlas-based endocardial segmentation algorithm: [[DBP3:Utah:AutoEndoSeg|Automatic Endocardial Segmentation]]<br />
** Test and evaluate Yi Gao's image and segmentation-driven registration algorithm: [[DBP3:Utah:VecReg|Image and Segmentation-Driven Registration]]<br />
<br />
=== Slicer4 Needs and Plans ===<br />
Summary of the Slicer4 needs to support CARMA workflows can be found [[DBP3:Utah:Slicer4 | here]].<br />
<br />
==Sample Data==<br />
* Sixty anonymized datasets containing LGE-MRI image data and segmentations of the left atrium from patients with atrial fibrillation: [http://hdl.handle.net/1926/1755 Pre and Post Radiofrequency Ablation LGE-MRI Collection]<br />
* Sixty segmentation datasets of the left atrium from patients with atrial fibrillation who have undergone radiofrequency catheter ablation for treatment: [http://hdl.handle.net/1926/1764 CARMA Longitudinal Left Atrial Shape Data]<br />
* Two subjects, two time points: [[Media:CardiacMRIs.zip|CardiacMRIs]].</div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah&diff=83025DBP3:Utah2013-07-29T19:58:49Z<p>Sbengali: /* Tutorials */</p>
<hr />
<div> Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]<br />
<br />
<br />
=== The CARMA DBP: MRI-based study and treatment of atrial fibrillation ===<br />
Tissue remodeling of the atrial wall is the hallmark of Atrial Fibrillation<br />
(AF), a progressive cardiac disease that develops over time (months to<br />
years). The mechanisms of of this transformation are only partially understood,<br />
but the current scientific focus on tissue remodeling and its putative role in<br />
AF suggests an MRI image-based approach to the study of AF.<br />
<br />
The Comprehensive Arrhythmia Research and MAnagement (CARMA) Center at the<br />
University of Utah is a world leader in the rapidly emerging field of<br />
MRI-managed evaluation and ablation of AF. Other groups have begun to recognize<br />
the potential of this approach and to investigate and validate some of our<br />
findings. Still others are developing new refinements of the MRI technique<br />
driven by the specific needs of this application domain.<br />
<br />
Preliminary investigation by CARMA has identified image processing and analysis<br />
as the rate-limiting step to the development of MRI-based therapies. Novel<br />
forms of MRI can be used to evaluate new patients, predict success before<br />
ablation, analyze outcomes post-ablation, and guide repeat ablations. Such<br />
MRI-based therapies, however, urgently require advanced tools and software to<br />
support efficient workflows and accelerate the quantification and analysis of<br />
images. The CARMA-NAMIC DBP project will address some of these needs with the<br />
development of algorithms and tools for the automated segmentation of heart<br />
structures and the MRI-based evaluation of AF progression and recovery.<br />
<br />
This remainder of this wiki page describes ongoing CARMA-NAMIC activities and<br />
specific plans. For more background information, references, and description of<br />
the specific scientific and clinical aims of this project,<br />
please see the project web page: http://www.na-mic.org/pages/DBP:Atrial_Fibrillation .<br />
<br />
<br />
=== DBP Specific Aims ===<br />
# Develop and validate image-based longitudinal diagnostic indices for AF<br />
# Develop automatic segmentation methods for the atrium and adjacent structures<br />
# Develop an AF scoring scheme to evaluate disease progression and recovery from therapy<br />
<br />
<br />
[[Image:TV1.jpg|center|thumb|400px|The CARMA Center's Utah classification for Atrial Fibrillation staging involves segmentation of the left atrial wall from MRI, followed by quantification of enhanced vs. non-enhanced voxels in the wall.]]<br />
<br />
==Activities==<br />
=== Slicer Modules ===<br />
* [[DBP3:Utah:SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
* [[DBP3:Utah:SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
* [[DBP3:Utah:SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
* [[DBP3:Utah:SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
* [[DBP3:Utah:SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
* [[DBP3:Utah:SlicerModuleThresholdModel|Threshold Model]]<br />
* [[DBP3:Utah:SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutomatedLASegmentation|Automated Graph Cut LA Segmentation]]<br />
<br />
=== Tutorials ===<br />
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]<br />
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]<br />
* [[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI Registration Tutorial]]<br />
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|Cardiac MRI Registration Using BRAINSFit Tutorial]]<br />
* [[Media:Carma_PVAntrumCutFilter_Tutorial_New.pptx|PV Antrum Cut Filter Tutorial]]<br />
* [[Media:Carma_Boolean_Remove_Tutorial.pptx|Boolean REMOVE Filter Tutorial]]<br />
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]<br />
* [[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
* [[Media:CarmaWorkflowV2.pdf|Slicer Workflow Tutorial]]<br />
<br />
=== Other Projects ===<br />
* Image registration capabilities for longitudinal analysis: [[DBP3:Utah:RegSegPipeline|Registration & Segmentation pipeline pilots & workflow development (Dominik Meier, Alex Zaitsev)]]<br />
* Evaluation of BRAINSFit and fiducial-based registration tools for LA wall alignment and longitudinal registration of PV: [[DBP3:Utah:PV_BFReg|BRAINSFit Registration of PVs]]<br />
* Collaboration with GA Tech - <br />
** Test and evaluate Behnood's wall segmentation - results and analysis are here: [[DBP3:Utah:AutoWallSeg|Automatic Wall Segmentation]]<br />
** Test and evaluate Yi Gao's atlas-based endocardial segmentation algorithm: [[DBP3:Utah:AutoEndoSeg|Automatic Endocardial Segmentation]]<br />
** Test and evaluate Yi Gao's image and segmentation-driven registration algorithm: [[DBP3:Utah:VecReg|Image and Segmentation-Driven Registration]]<br />
<br />
=== Slicer4 Needs and Plans ===<br />
Summary of the Slicer4 needs to support CARMA workflows can be found [[DBP3:Utah:Slicer4 | here]].<br />
<br />
==Sample Data==<br />
* Sixty anonymized datasets containing LGE-MRI image data and segmentations of the left atrium from patients with atrial fibrillation: [http://hdl.handle.net/1926/1755 Pre and Post Radiofrequency Ablation LGE-MRI Collection]<br />
* Sixty segmentation datasets of the left atrium from patients with atrial fibrillation who have undergone radiofrequency catheter ablation for treatment: [http://hdl.handle.net/1926/1764 CARMA Longitudinal Left Atrial Shape Data]<br />
* Two subjects, two time points: [[Media:CardiacMRIs.zip|CardiacMRIs]].</div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah&diff=83024DBP3:Utah2013-07-29T19:58:39Z<p>Sbengali: /* Tutorials */</p>
<hr />
<div> Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]<br />
<br />
<br />
=== The CARMA DBP: MRI-based study and treatment of atrial fibrillation ===<br />
Tissue remodeling of the atrial wall is the hallmark of Atrial Fibrillation<br />
(AF), a progressive cardiac disease that develops over time (months to<br />
years). The mechanisms of of this transformation are only partially understood,<br />
but the current scientific focus on tissue remodeling and its putative role in<br />
AF suggests an MRI image-based approach to the study of AF.<br />
<br />
The Comprehensive Arrhythmia Research and MAnagement (CARMA) Center at the<br />
University of Utah is a world leader in the rapidly emerging field of<br />
MRI-managed evaluation and ablation of AF. Other groups have begun to recognize<br />
the potential of this approach and to investigate and validate some of our<br />
findings. Still others are developing new refinements of the MRI technique<br />
driven by the specific needs of this application domain.<br />
<br />
Preliminary investigation by CARMA has identified image processing and analysis<br />
as the rate-limiting step to the development of MRI-based therapies. Novel<br />
forms of MRI can be used to evaluate new patients, predict success before<br />
ablation, analyze outcomes post-ablation, and guide repeat ablations. Such<br />
MRI-based therapies, however, urgently require advanced tools and software to<br />
support efficient workflows and accelerate the quantification and analysis of<br />
images. The CARMA-NAMIC DBP project will address some of these needs with the<br />
development of algorithms and tools for the automated segmentation of heart<br />
structures and the MRI-based evaluation of AF progression and recovery.<br />
<br />
This remainder of this wiki page describes ongoing CARMA-NAMIC activities and<br />
specific plans. For more background information, references, and description of<br />
the specific scientific and clinical aims of this project,<br />
please see the project web page: http://www.na-mic.org/pages/DBP:Atrial_Fibrillation .<br />
<br />
<br />
=== DBP Specific Aims ===<br />
# Develop and validate image-based longitudinal diagnostic indices for AF<br />
# Develop automatic segmentation methods for the atrium and adjacent structures<br />
# Develop an AF scoring scheme to evaluate disease progression and recovery from therapy<br />
<br />
<br />
[[Image:TV1.jpg|center|thumb|400px|The CARMA Center's Utah classification for Atrial Fibrillation staging involves segmentation of the left atrial wall from MRI, followed by quantification of enhanced vs. non-enhanced voxels in the wall.]]<br />
<br />
==Activities==<br />
=== Slicer Modules ===<br />
* [[DBP3:Utah:SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
* [[DBP3:Utah:SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
* [[DBP3:Utah:SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
* [[DBP3:Utah:SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
* [[DBP3:Utah:SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
* [[DBP3:Utah:SlicerModuleThresholdModel|Threshold Model]]<br />
* [[DBP3:Utah:SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutomatedLASegmentation|Automated Graph Cut LA Segmentation]]<br />
<br />
=== Tutorials ===<br />
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]<br />
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]<br />
* [[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI Registration Tutorial]]<br />
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|Cardiac MRI Registration Using BRAINSFit Tutorial]]<br />
* [[Media:Carma_PVAntrumCutFilter_Tutorial_New.pptx|PV Antrum Cut Filter Tutorial]]<br />
* [[[Media:Carma_Boolean_Remove_Tutorial.pptx|Boolean REMOVE Filter Tutorial]]<br />
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]<br />
* [[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
* [[Media:CarmaWorkflowV2.pdf|Slicer Workflow Tutorial]]<br />
<br />
=== Other Projects ===<br />
* Image registration capabilities for longitudinal analysis: [[DBP3:Utah:RegSegPipeline|Registration & Segmentation pipeline pilots & workflow development (Dominik Meier, Alex Zaitsev)]]<br />
* Evaluation of BRAINSFit and fiducial-based registration tools for LA wall alignment and longitudinal registration of PV: [[DBP3:Utah:PV_BFReg|BRAINSFit Registration of PVs]]<br />
* Collaboration with GA Tech - <br />
** Test and evaluate Behnood's wall segmentation - results and analysis are here: [[DBP3:Utah:AutoWallSeg|Automatic Wall Segmentation]]<br />
** Test and evaluate Yi Gao's atlas-based endocardial segmentation algorithm: [[DBP3:Utah:AutoEndoSeg|Automatic Endocardial Segmentation]]<br />
** Test and evaluate Yi Gao's image and segmentation-driven registration algorithm: [[DBP3:Utah:VecReg|Image and Segmentation-Driven Registration]]<br />
<br />
=== Slicer4 Needs and Plans ===<br />
Summary of the Slicer4 needs to support CARMA workflows can be found [[DBP3:Utah:Slicer4 | here]].<br />
<br />
==Sample Data==<br />
* Sixty anonymized datasets containing LGE-MRI image data and segmentations of the left atrium from patients with atrial fibrillation: [http://hdl.handle.net/1926/1755 Pre and Post Radiofrequency Ablation LGE-MRI Collection]<br />
* Sixty segmentation datasets of the left atrium from patients with atrial fibrillation who have undergone radiofrequency catheter ablation for treatment: [http://hdl.handle.net/1926/1764 CARMA Longitudinal Left Atrial Shape Data]<br />
* Two subjects, two time points: [[Media:CardiacMRIs.zip|CardiacMRIs]].</div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:Carma_Boolean_Remove_Tutorial.pptx&diff=83023File:Carma Boolean Remove Tutorial.pptx2013-07-29T19:58:05Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah&diff=83022DBP3:Utah2013-07-29T19:57:25Z<p>Sbengali: </p>
<hr />
<div> Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]<br />
<br />
<br />
=== The CARMA DBP: MRI-based study and treatment of atrial fibrillation ===<br />
Tissue remodeling of the atrial wall is the hallmark of Atrial Fibrillation<br />
(AF), a progressive cardiac disease that develops over time (months to<br />
years). The mechanisms of of this transformation are only partially understood,<br />
but the current scientific focus on tissue remodeling and its putative role in<br />
AF suggests an MRI image-based approach to the study of AF.<br />
<br />
The Comprehensive Arrhythmia Research and MAnagement (CARMA) Center at the<br />
University of Utah is a world leader in the rapidly emerging field of<br />
MRI-managed evaluation and ablation of AF. Other groups have begun to recognize<br />
the potential of this approach and to investigate and validate some of our<br />
findings. Still others are developing new refinements of the MRI technique<br />
driven by the specific needs of this application domain.<br />
<br />
Preliminary investigation by CARMA has identified image processing and analysis<br />
as the rate-limiting step to the development of MRI-based therapies. Novel<br />
forms of MRI can be used to evaluate new patients, predict success before<br />
ablation, analyze outcomes post-ablation, and guide repeat ablations. Such<br />
MRI-based therapies, however, urgently require advanced tools and software to<br />
support efficient workflows and accelerate the quantification and analysis of<br />
images. The CARMA-NAMIC DBP project will address some of these needs with the<br />
development of algorithms and tools for the automated segmentation of heart<br />
structures and the MRI-based evaluation of AF progression and recovery.<br />
<br />
This remainder of this wiki page describes ongoing CARMA-NAMIC activities and<br />
specific plans. For more background information, references, and description of<br />
the specific scientific and clinical aims of this project,<br />
please see the project web page: http://www.na-mic.org/pages/DBP:Atrial_Fibrillation .<br />
<br />
<br />
=== DBP Specific Aims ===<br />
# Develop and validate image-based longitudinal diagnostic indices for AF<br />
# Develop automatic segmentation methods for the atrium and adjacent structures<br />
# Develop an AF scoring scheme to evaluate disease progression and recovery from therapy<br />
<br />
<br />
[[Image:TV1.jpg|center|thumb|400px|The CARMA Center's Utah classification for Atrial Fibrillation staging involves segmentation of the left atrial wall from MRI, followed by quantification of enhanced vs. non-enhanced voxels in the wall.]]<br />
<br />
==Activities==<br />
=== Slicer Modules ===<br />
* [[DBP3:Utah:SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
* [[DBP3:Utah:SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
* [[DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
* [[DBP3:Utah:SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
* [[DBP3:Utah:SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
* [[DBP3:Utah:SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
* [[DBP3:Utah:SlicerModuleThresholdModel|Threshold Model]]<br />
* [[DBP3:Utah:SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
* [[DBP3:Utah:SlicerModuleAutomatedLASegmentation|Automated Graph Cut LA Segmentation]]<br />
<br />
=== Tutorials ===<br />
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]<br />
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]<br />
* [[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI Registration Tutorial]]<br />
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|Cardiac MRI Registration Using BRAINSFit Tutorial]]<br />
* [[Media:Carma_PVAntrumCutFilter_Tutorial_New.pptx|PV Antrum Cut Filter Tutorial]]<br />
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]<br />
* [[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
* [[Media:CarmaWorkflowV2.pdf|Slicer Workflow Tutorial]]<br />
<br />
=== Other Projects ===<br />
* Image registration capabilities for longitudinal analysis: [[DBP3:Utah:RegSegPipeline|Registration & Segmentation pipeline pilots & workflow development (Dominik Meier, Alex Zaitsev)]]<br />
* Evaluation of BRAINSFit and fiducial-based registration tools for LA wall alignment and longitudinal registration of PV: [[DBP3:Utah:PV_BFReg|BRAINSFit Registration of PVs]]<br />
* Collaboration with GA Tech - <br />
** Test and evaluate Behnood's wall segmentation - results and analysis are here: [[DBP3:Utah:AutoWallSeg|Automatic Wall Segmentation]]<br />
** Test and evaluate Yi Gao's atlas-based endocardial segmentation algorithm: [[DBP3:Utah:AutoEndoSeg|Automatic Endocardial Segmentation]]<br />
** Test and evaluate Yi Gao's image and segmentation-driven registration algorithm: [[DBP3:Utah:VecReg|Image and Segmentation-Driven Registration]]<br />
<br />
=== Slicer4 Needs and Plans ===<br />
Summary of the Slicer4 needs to support CARMA workflows can be found [[DBP3:Utah:Slicer4 | here]].<br />
<br />
==Sample Data==<br />
* Sixty anonymized datasets containing LGE-MRI image data and segmentations of the left atrium from patients with atrial fibrillation: [http://hdl.handle.net/1926/1755 Pre and Post Radiofrequency Ablation LGE-MRI Collection]<br />
* Sixty segmentation datasets of the left atrium from patients with atrial fibrillation who have undergone radiofrequency catheter ablation for treatment: [http://hdl.handle.net/1926/1764 CARMA Longitudinal Left Atrial Shape Data]<br />
* Two subjects, two time points: [[Media:CardiacMRIs.zip|CardiacMRIs]].</div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleThresholdModel&diff=83021DBP3:Utah:SlicerModuleThresholdModel2013-07-29T19:56:51Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Threshold Model===<br />
<br />
{|<br />
|[[Image:CMRToolkit_ThresholdModel.png|thumb|400px|Thresholded Wall Model]]<br />
|[[Image:CMRToolkit_Threshold_Model.gif|thumb|400px|Changing the Threshold]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module can be used to threshold a model of the left atrium. It requires an input LGE-MRI image, an endocardium segmentation and a wall segmentation. The wall model can be thresholded in order to visualize regions of scar.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* This module is meant to be used to threshold the wall model produced from the wall segmentation of the left atrium. <br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs<br />
<br />
* Input Image Volume : Select an LGE-MRI image<br />
* Endo Label Map : Select the endo segmentation<br />
* Wall Label Map : Select the wall segmentation<br />
* Input Wall Model : Select the wall model created by the module<br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleAutomatedLASegmentation&diff=83020DBP3:Utah:SlicerModuleAutomatedLASegmentation2013-07-29T19:56:18Z<p>Sbengali: /* Quick Tour of Features and Use */</p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit LA Segmentation Using Graph Cuts===<br />
<br />
{|<br />
|[[File:CMRToolkit_GraphCut.png|thumb|center|Automated LA Segmentation]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Gopal Veni, Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module automatically segments the left atrium from a cardiac LGE-MRI image volume. The input to the module is a cardiac LGE-MRI image, a smoothness parameter and model data. The model is arbitrarily selected and can be changed to check if it improves the segmentation output. <br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* This module is meant to be used for segmenting the left atrium from cardiac LGE-MRI images.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs:<br />
<br />
* Input Image : Select the cardiac LGE-MRI image volume<br />
* Smoothness Parameter : Select the smoothness parameter value<br />
* Model Number: Select the model number<br />
* Output Endo Label Image: Create the output endo label image<br />
* Output Epi Label Image: Create the output epi label image<br />
* Model Data Directory: Select the directory of the input model<br />
* Epi Mesh: Create the output epi mesh<br />
* Endo Mesh: Create the output endo mesh<br />
* Center of Left Atrium: Select the approximate center of the left atrium by placing a fiducial<br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleAutomatedLASegmentation&diff=83019DBP3:Utah:SlicerModuleAutomatedLASegmentation2013-07-29T19:55:59Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit LA Segmentation Using Graph Cuts===<br />
<br />
{|<br />
|[[File:CMRToolkit_GraphCut.png|thumb|center|Automated LA Segmentation]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Gopal Veni, Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module automatically segments the left atrium from a cardiac LGE-MRI image volume. The input to the module is a cardiac LGE-MRI image, a smoothness parameter and model data. The model is arbitrarily selected and can be changed to check if it improves the segmentation output. <br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* This module is meant to be used for segmenting the left atrium from cardiac LGE-MRI images.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs<br />
<br />
* Input Image : Select the cardiac LGE-MRI image volume<br />
* Smoothness Parameter : Select the smoothness parameter value<br />
* Model Number: Select the model number<br />
* Output Endo Label Image: Create the output endo label image<br />
* Output Epi Label Image: Create the output epi label image<br />
* Model Data Directory: Select the directory of the input model<br />
* Epi Mesh: Create the output epi mesh<br />
* Endo Mesh: Create the output endo mesh<br />
* Center of Left Atrium: Select the approximate center of the left atrium by placing a fiducial<br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleConnectedThreshold&diff=83018DBP3:Utah:SlicerModuleConnectedThreshold2013-07-29T19:55:28Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Isolated Connected Image Filter===<br />
<br />
{|<br />
|[[Image:connectedThreshold.jpg|thumb|280px|Left:Segmented Image, Center: Original Gated MRA Image]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod <br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Tookit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module uses a single seed point to segment an image. The seed point (fiducial) is placed within the region to be segmented. The upper and lower thresholds are entered by the user. The segmented region will contain pixels that are connected to this seed, and lie in between this range. Multiple seed points can be used.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* This module is meant to be used for segmenting the entire endocardium region from a cardiac MRI or MRA image. It can also be used for segmentation of structures in other types of images.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs<br />
* Input image<br />
* Output image<br />
* Lower threshold<br />
* Upper threshold<br />
* Seed/s: User placed fiducial/s inside the region to be segmented <br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source code & documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<br />
</div><br />
</div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleIsolatedConnected&diff=83017DBP3:Utah:SlicerModuleIsolatedConnected2013-07-29T19:55:19Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Isolated Connected Image Filter===<br />
<br />
{|<br />
|[[Image:isolatedConnected.jpg|thumb|280px|Left:Segmented Image, Center: Original Gated MRA Image]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod <br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module uses two seed points to segment an image. One seed point (fiducial) is placed within the region to be segmented, and the other is placed outside that region. Multiple seed points can be used as well. The lower threshold is given as an input by the user. The isolated connected image filter will find the isolating upper threshold. If no isolating threshold can be found then the segmentation will fail.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* This module is meant to be used for segmenting the entire endocardium region from a cardiac MRI or MRA image. It can also be used for segmentation of structures in other types of images.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs<br />
* Input image<br />
* Output image<br />
* Lower threshold<br />
* Seed1: User placed fiducial/s inside the region to be segmented <br />
* Seed2: User placed fiducial/s outside the region to be segmented<br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source code & documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
</div><br />
</div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleAxialDilate&diff=83016DBP3:Utah:SlicerModuleAxialDilate2013-07-29T19:55:03Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Axial Dilate Filter===<br />
<br />
{|<br />
|[[Image:CarmaAxialDilate1.png|thumb|280px|Before Dilation]]<br />
|[[Image:CarmaAxialDilate2.png|thumb|280px|After Dilation]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Alan Morris, Salma Bengali, Greg Gardner, Josh Cates, Rob MacLeod <br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module performs a 4 pixel binary dilation in the axial plane only. This is needed for the CARMA segmentation pipeline as the segmentations are performed in the axial plane and a dilation to start the wall segmentation from an endo segmentation should be performed in the axial plane only.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* This module is meant to be used to create an initial wall segmentation from an endo segmentation.<br />
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|CARMA Axial Dilate Filter Tutorial]]<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs<br />
<br />
* Target Layer : Select the segmentation to dilate<br />
* Output Layer : The dilated output<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source code & documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== More Information == <br />
<br />
</div><br />
</div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModulePVAntrumCut&diff=83015DBP3:Utah:SlicerModulePVAntrumCut2013-07-29T19:54:54Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit PV Antrum Cut Filter===<br />
<br />
{|<br />
|[[Image:PVAntrumCutFilter.jpg|thumb|280px|(Clockwise from top right) LA Wall Layer, LA Endo Layer, and LA Endo Layer with Pulmonary Veins Removed]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Alan Morris, Salma Bengali, Greg Gardner, Josh Cates, Rob MacLeod <br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module creates a cardiac MRI segmentation mask called the PV Antrum Cut mask by removing the pulmonary veins (PVs) from the left atrium (LA) segmentation. The inputs are the LA endocardial segmentation and the LA endocardial wall segmentation. The output mask represents the entire LA endocardial layer minus the PVs. This mask can be used to calculate the early diastolic (peak) volume of the LA. <br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* This module is meant to be used for removing the PV regions from the LA endocardial segmentation. <br />
* [[Media:Carma_PVAntrumCutFilter_Tutorial_New.pptx|CARMA PV Antrum Cut Filter Tutorial]]<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs:<br />
* Endo Layer : Select the LA endocardial segmentation label mask<br />
* Wall Layer : Select the LA wall segmentation label mask<br />
* Endo Layer No Veins: The output label mask<br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source code & documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
</div><br />
</div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit&diff=83014DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit2013-07-29T19:54:46Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Cardiac MRI Registration Using BRAINSFit===<br />
<br />
{|<br />
|[[Image:Slicer_Carma_BrainsFit_Screenshot.jpg|thumb|280px|(L to R) Registered image, fixed image, and moving image]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Salma Bengali, Alan Morris, Greg Gardner, Josh Cates, Rob MacLeod<br />
<br />
<div style="margin: 20px; height: 345px"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module implements case-specific registration using BRAINSFit for cardiac LGE-MRI, MRA and CT images acquired at different time points or across different patients. The types of registration scenarios are described [[DBP3:Utah:RegCases|here]]. The inputs to this module are two image volumes: image volume one is the fixed volume, and image volume two is the moving volume. The user selects the imaging modalities based on the types of input image volumes. Registration parameters are tuned for the registration cases. Input image volumes that are cropped to the area around the left atrium can also be used to improve the final registration result. Advanced registration parameters can be changed to check if the registration result shows improvement. <br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|CARMA Registration Using BRAINSFit Tutorial]]<br />
<br />
* The image volumes in this dataset: [http://hdl.handle.net/1926/1765 CARMA Registration Tutorial Data] can be used as inputs to the module. The dataset contains anonymized LGE-MRI, MRA and CT images.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs:<br />
<br />
* Image Volume One (Fixed): Select the LGE-MRI, MRA or CT Image<br />
* Image Volume Two (Moving): Select the LGE-MRI or MRA image<br />
* Output Image Volume: The registration result<br />
* Imaging modality: The types of image volumes that are being registered (e.g LGE-MRI, MRA, CT, Acute Scar)<br />
<br />
===Advanced Registration Parameters===<br />
The advanced registration parameters are:<br />
* Initialization Type <br />
* Registration Type<br />
* Maximum Number of Iterations<br />
* Number of Samples<br />
* Minimum Step Length<br />
* Transform Scale<br />
* Reproportion Scale<br />
* Skew Scale<br />
* Interpolation Type<br />
* Metric Type<br />
The details about the advanced registration parameters can be found at http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit.<br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleCardiacRegistration&diff=83013DBP3:Utah:SlicerModuleCardiacRegistration2013-07-29T19:54:36Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Cardiac Registration===<br />
<br />
{|<br />
|[[Image:Cardiac_mri_registration_module.jpg|thumb|280px|(L to R) Registered image, fixed image, and moving image]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Alan Morris, Greg Gardner, Salma Bengali, Josh Cates, Rob MacLeod<br />
<br />
<div style="margin: 20px; height: 345px"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module implements case-specific registration for cardiac LGE-MRI, MRA and CT images acquired at different time points or across different patients. The types of registration scenarios are described [[DBP3:Utah:RegCases|here]]. The inputs to this module are two image volumes: image volume one is the fixed volume, and image volume two is the moving volume. The goal of registration is to find a spatial mapping that will align the moving volume with the fixed volume. The user selects the imaging modalities based on the types of input image volumes. Registration parameters are tuned for the registration cases. Input image volumes that are cropped to the area around the left atrium can be used as well, which would improve the final registration result. Advanced registration parameters can be changed to check if the registration result shows improvement. <br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
[[Media:Carma_Registration_Tutorial.pptx|CARMA Registration Tutorial]]<br />
<br />
The image volumes in this dataset: [http://hdl.handle.net/1926/1765 CARMA Registration Tutorial Data] can be used as inputs to the module. The dataset contains anonymized LGE-MRI, MRA and CT images.<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs:<br />
<br />
* Image Volume One (Fixed): Select the LGE-MRI, MRA or CT Image<br />
* Image Volume Two (Moving): Select the LGE-MRI or MRA image<br />
* Output Image Volume : The registration result<br />
* Imaging modality: The types of image volumes that are being registered (e.g LGE-MRI, MRA, CT, Acute Scar)<br />
<br />
===Advanced Registration Parameters===<br />
The advanced registration parameters are:<br />
* Registration Type<br />
* Metric Type<br />
* Initialization Type<br />
* Interpolation Type<br />
* Maximum Number of Iterations<br />
* Sampling Ratio<br />
* Sample from Fixed/Moving Image Overlap<br />
The details about the advanced registration parameters can be found at http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6.<br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source code & documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleAutoScar&diff=83012DBP3:Utah:SlicerModuleAutoScar2013-07-29T19:54:21Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Automatic Left Atrial Scar===<br />
<br />
{|<br />
|[[Image:carma_afib_auto_scar.png|thumb|280px|Automatic Left Atrial Scar]]<br />
|}<br />
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==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Alan Morris, Josh Cates, Rob MacLeod<br />
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<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
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== General Information ==<br />
===Module Type & Category===<br />
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Type: CLI<br />
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Category: Cardiac MRI Toolkit<br />
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</div><br />
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<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module determines left atrial scar automatically given the wall segmentation, in a post-ablation LGE-MRI. For details see: [http://healthsciences.utah.edu/carma/research/publications/pdf/automatic_lawall_scar_segmentation.pdf Perry, D. et al. "Automatic classification of scar tissue...", Proceedings of SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.]<br />
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</div><br />
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<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* This module automatically classifies scar tissue in post ablation DE-MRIs<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 CARMA Automatic Left Atrial Scar Tutorial]<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs<br />
<br />
* MRI image : Select the DE-MRI image<br />
* LA wall mask : Select the label map for the left atrial wall<br />
* Blood Pool mask : Select the label map for the blood pool<br />
* Result : The output label map denoting scar<br />
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</div><br />
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<div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
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<div style="width: 27%; float: left; padding-right: 3%;"><br />
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== More Information == <br />
<br />
===References===<br />
[http://healthsciences.utah.edu/carma/research/publications/pdf/automatic_lawall_scar_segmentation.pdf Perry, D. et al. "Automatic classification of scar tissue...", Proceedings of SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.]<br />
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</div><br />
</div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleInhomogeneity&diff=83011DBP3:Utah:SlicerModuleInhomogeneity2013-07-29T19:54:09Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Inhomogeneity Correction Filter===<br />
<br />
{|<br />
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Alan Morris, Eugene Kholmovski, Josh Cates, Rob MacLeod<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module implements a local intensity correction for inhomogeneities due to coil placement in cardiac LGE-MRI images. It fits a gradient function to the image data and normalizes accordingly. Note that this is not a whole image correction and it is specific to LGE MRI cardiac images. The input to this module is a segmented region on which to base the intensity gradient model and a segmentation of the region of interest to apply the correction. There are no parameters.<br />
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</div><br />
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<div style="width: 40%; float: left;"><br />
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== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* This module is meant to be used for MRI scans where local inhomogeneity has been detected<br />
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|CARMA Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs<br />
<br />
* MRI Image : Select the DE-MRI image<br />
* Blood Pool mask : Select the label map for the blood pool<br />
* ROI mask : Select the label map for the targeted region of interest<br />
* Corrected Output : The output volume<br />
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</div><br />
</div><br />
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<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
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<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleThresholdModel&diff=83010DBP3:Utah:SlicerModuleThresholdModel2013-07-29T19:53:09Z<p>Sbengali: Added documentation for module</p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Threshold Model===<br />
<br />
{|<br />
|[[Image:CMRToolkit_ThresholdModel.png|thumb|400px|Thresholded Wall Model]]<br />
|[[Image:CMRToolkit_Threshold_Model.gif|thumb|400px|Changing the Threshold]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This module can be used to threshold a model of the left atrium. It requires an input LGE-MRI image, an endocardium segmentation and a wall segmentation. The wall model can be thresholded in order to visualize regions of scar.<br />
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</div><br />
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<div style="width: 40%; float: left;"><br />
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== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* This module is meant to be used to threshold the wall model produced from the wall segmentation of the left atrium. <br />
* [[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the inputs and outputs<br />
<br />
* Input Image Volume : Select an LGE-MRI image<br />
* Endo Label Map : Select the endo segmentation<br />
* Wall Label Map : Select the wall segmentation<br />
* Input Wall Model : Select the wall model created by the module<br />
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</div><br />
</div><br />
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<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:CMRToolkit_Threshold_Model.gif&diff=83009File:CMRToolkit Threshold Model.gif2013-07-29T19:52:15Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:CMRToolkit_ThresholdModel.png&diff=83008File:CMRToolkit ThresholdModel.png2013-07-29T19:51:59Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=File:CMRToolkit_Threshold_Model_Tutorial.pptx&diff=83007File:CMRToolkit Threshold Model Tutorial.pptx2013-07-29T19:49:28Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleCMRToolkitWizard&diff=83006DBP3:Utah:SlicerModuleCMRToolkitWizard2013-07-29T19:48:03Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===CMR Toolkit Wizard===<br />
<br />
{|<br />
|[[Image:CMRToolkitWizard_1.png|thumb|280px|Choose image panel]]<br />
|[[Image:CMRToolkitWizard_2.png|thumb|280px|Segmentation panel]]<br />
|[[Image:CMRToolkitWizard_3.png|thumb|280px|Axial Dilate Module panel]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This wizard module takes the user through the steps involved in analyzing a cardiac LGE-MRI image for scar enhancement. The wizard uses modules from the Cardiac MRI Toolkit extension as well as core Slicer modules. Test data or other data can be used to run the wizard.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* This module is meant to be used for cardiac LGE-MRI scans. <br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the steps to use the module:<br />
<br />
1. Select the input cardiac MRI image.<br><br />
2. Manually segment the left atrial (LA) endocardium region.<br><br />
3. Axially dilate the endocardium segmentation to obtain the epicardium region.<br><br />
4. Subtract the endocardium segmentation from the epicardium segmentation to obtain the wall region.<br><br />
5. Remove the pulmonary veins (PVs) from the wall segmentation.<br><br />
6. Cut off the PVs from the endocardium segmentation created in step 2.<br><br />
7. Create the isosurface of the endocardium segmentation without the PVs.<br><br />
8. Run the automatic scar module to view regions of scar enhancement in the MRI. Create the isosurface of the scar to view it overlaid on the endocardium isosurface. <br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengalihttps://www.na-mic.org/w/index.php?title=DBP3:Utah:SlicerModuleCMRToolkitWizard&diff=83005DBP3:Utah:SlicerModuleCMRToolkitWizard2013-07-29T19:37:36Z<p>Sbengali: </p>
<hr />
<div>__NOTOC__<br />
===Cardiac MRI Toolkit Wizard===<br />
<br />
{|<br />
|[[Image:CMRToolkitWizard_1.png|thumb|280px|Choose image panel]]<br />
|[[Image:CMRToolkitWizard_2.png|thumb|280px|Segmentation panel]]<br />
|[[Image:CMRToolkitWizard_3.png|thumb|280px|Axial Dilate Module panel]]<br />
|}<br />
<br />
==Authors, Collaborators & Contact==<br />
* CARMA Center, University of Utah: Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==General Information==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Cardiac MRI Toolkit<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
==Module Description==<br />
This wizard module takes the user through the steps involved in analyzing a cardiac LGE-MRI image for scar enhancement. The wizard uses modules from the Cardiac MRI Toolkit extension as well as core Slicer modules. Test data or other data can be used to run the wizard.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* This module is meant to be used for cardiac LGE-MRI scans. <br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The following are the steps to use the module:<br />
<br />
1. Select the input cardiac MRI image.<br><br />
2. Manually segment the left atrial (LA) endocardium region.<br><br />
3. Axially dilate the endocardium segmentation to obtain the epicardium region.<br><br />
4. Subtract the endocardium segmentation from the epicardium segmentation to obtain the wall region.<br><br />
5. Remove the pulmonary veins (PVs) from the wall segmentation.<br><br />
6. Cut off the PVs from the endocardium segmentation created in step 2.<br><br />
7. Create the isosurface of the endocardium segmentation without the PVs.<br><br />
8. Run the automatic scar module to view regions of scar enhancement in the MRI. Create the isosurface of the scar to view it overlaid on the endocardium isosurface. <br />
<br />
</div><br />
</div><br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
== Development ==<br />
<br />
===Source Code & Documentation===<br />
<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Sbengali