https://www.slicer.org/w/api.php?action=feedcontributions&feedformat=atom&user=SbengaliSlicer Wiki - User contributions [en]2026-04-05T14:27:32ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=43092Documentation/Nightly/Extensions/CardiacMRIToolkit2015-10-27T00:09:24Z<p>Sbengali: </p>
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This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://capulet.med.utah.edu/namic/cmrslicer/ Slicer CMR Toolkit] <br> [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
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{|<br />
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The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
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*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Scar Visualization]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
*[[Documentation/{{documentation/version}}/Modules/LASegmentationWorkflow|LA Segmentation Workflow]]<br />
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*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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
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*[[Media: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pptx|Cardiac MRI Toolkit Tutorial]]<br />
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part1.zip Tutorial Videos Part 1]<br />
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkit_SummerTutorialContest2013_Videos_Part2.zip Tutorial Videos Part 2]<br />
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The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/LASegmentationWorkflow&diff=42384Documentation/Nightly/Modules/LASegmentationWorkflow2015-08-12T02:45:06Z<p>Sbengali: </p>
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Author: Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob McLeod, CARMA Center, University of Utah<br> <br />
Contact: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
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This wizard module takes the user through the steps involved in segmenting the left atrium from an LGE-MRI by using an MRA. 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 />
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This module is meant to be used for cardiac LGE-MRI scans. <br />
{|<br />
|[[Image:LASegmentationWorkflow_Step1.png|thumb|280px|Select the input images]]<br />
|[[Image:LASegmentationWorkflow_Step2.png|thumb|280px|Register the MRA to the LGE-MRI]]<br />
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# Select the input cardiac LGE-MRI image and MRA image.<br />
# Register the MRA image to the LGE-MRI.<br />
# Use the Slicer editor to segment the left atrium from the MRA. The CarreraSlice editor module is very useful for this task<br />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/AutomatedLASegmentation&diff=42383Documentation/Nightly/Modules/AutomatedLASegmentation2015-08-12T02:44:55Z<p>Sbengali: </p>
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Author: Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Gopal Veni, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker, CARMA Center, University of Utah<br> <br />
Contact: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
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'''Note: This module is licensed for research purposes only. This module relies on code made available by Vladimir Kolmogorov for research use only. See [http://vision.csd.uwo.ca/code/ this web site] for more information.'''<br />
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The 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 />
Model data to run this module can be downloaded from the [http://slicer.kitware.com/midas3/download/folder/1550/LA+Segmentation+using+Graph+Cuts.zip Slicer Midas repository]. <br />
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This module can be used to automatically segment the Left Atrium from a cardiac LGE-MRI image. <br />
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* 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 />
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*Boykov, Yuri, and Vladimir Kolmogorov. "An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision." Pattern Analysis and Machine Intelligence, IEEE Transactions on 26, no. 9 (2004): 1124-1137.<br />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleConnectedThreshold&diff=42382Documentation/Nightly/Modules/SlicerModuleConnectedThreshold2015-08-12T02:44:41Z<p>Sbengali: </p>
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Author: Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contacts: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
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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 />
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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 />
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* 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 />
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<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleIsolatedConnected&diff=42381Documentation/Nightly/Modules/SlicerModuleIsolatedConnected2015-08-12T02:44:30Z<p>Sbengali: </p>
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Author: Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contacts: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
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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 />
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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 />
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* 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 />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ScarVisualization&diff=42380Documentation/Nightly/Modules/ScarVisualization2015-08-12T02:44:17Z<p>Sbengali: </p>
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Author: Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
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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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This module is meant to be used to threshold the wall model produced from the wall segmentation of the left atrium. <br />
{|<br />
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|[[Image:CMRToolkit_Threshold_Model.gif|thumb|400px|Changing the Threshold]]<br />
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* 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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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleBooleanRemove&diff=42379Documentation/Nightly/Modules/SlicerModuleBooleanRemove2015-08-12T02:44:04Z<p>Sbengali: </p>
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Author: Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
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This module performs a subtraction of two label maps. This is needed for the CARMA segmentation pipeline to obtain the left atrium epicardium segmentation. This step follows the 2D axial dilate. <br />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
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{{documentation/{{documentation/version}}/module-description}}<br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used to create a initial wall segmentation from an endo segmentation and a dilated endo segmentation.<br />
{|<br />
|[[Image:Boolean-Remove.jpg|thumb|400px|Top row: Dilated endo segmentation and endo segmentation, Bottom row: Subtracted output (epicardial segmentation)]]<br />
|}<br />
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[[Media:Carma_Boolean_Remove_Tutorial.pptx|Boolean Remove Filter Tutorial]]<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
* Input Volume 1 : Select the dilated segmentation<br />
* Input Volume 2 : Select the endo segmentation<br />
* Output Volume : The subtraction output<br />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleAxialDilate&diff=42378Documentation/Nightly/Modules/SlicerModuleAxialDilate2015-08-12T02:43:53Z<p>Sbengali: </p>
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Author: Alan Morris, CARMA Center, University of Utah<br><br />
Contributors: Umme Salma Bengali, Greg Gardner, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Alan Morris: <email>alan.morris@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used to create an initial wall segmentation from an endo segmentation.<br />
{|<br />
|[[Image:CarmaAxialDilate1.png|thumb|400px|Before Dilation]]<br />
|[[Image:CarmaAxialDilate2.png|thumb|400px|After Dilation]]<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
* Target Layer : Select the segmentation to dilate<br />
* Output Layer : The dilated output<br />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModulePVAntrumCut&diff=42377Documentation/Nightly/Modules/SlicerModulePVAntrumCut2015-08-12T02:43:41Z<p>Sbengali: </p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Greg Gardner, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used for removing the PV regions from the LA endocardial segmentation.<br />
{|<br />
|[[Image:PVAntrumCutFilter.jpg|thumb|400px|(Clockwise from top right) LA Wall Layer, LA Endo Layer, and LA Endo Layer with Pulmonary Veins Removed]]<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:Carma_PVAntrumCutFilter_Tutorial.pptx|PV Antrum Cut Filter Tutorial]]<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleCardiacRegistrationBRAINSFit&diff=42376Documentation/Nightly/Modules/SlicerModuleCardiacRegistrationBRAINSFit2015-08-12T02:43:28Z<p>Sbengali: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Authors: Umme Salma Bengali, Alan Morris, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contacts: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email>, Alan Morris: <email>alan.morris@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:Slicer_Carma_BrainsFit_Screenshot.jpg|thumb|400px|(L to R) Registered image, fixed image, and moving image]]<br />
|}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
* [[Media:Carma_Registration_BrainsFit_Tutorial.pptx|Cardiac MRI 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 />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
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 />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleCardiacRegistration&diff=42375Documentation/Nightly/Modules/SlicerModuleCardiacRegistration2015-08-12T02:43:15Z<p>Sbengali: </p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Authors: Umme Salma Bengali, Alan Morris, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contacts: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email>, Alan Morris: <email>alan.morris@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:Cardiac_mri_registration_module.jpg|thumb|400px|(L to R) Registered image, fixed image, and moving image]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI 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 />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
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 />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleCMRToolkitWizard&diff=42374Documentation/Nightly/Modules/SlicerModuleCMRToolkitWizard2015-08-12T02:42:41Z<p>Sbengali: </p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contact: Umme Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{|<br />
[[Image:CMRToolkit_UofU_logo.jpg|center|280px]]<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used for cardiac LGE-MRI scans. <br />
{|<br />
|[[Image:CMRToolkitWizard_Panel1.png|thumb|280px|Loading input LGE-MRI image]]<br />
|[[Image:CMRToolkitWizard_Panel2.png|thumb|280px|Segment endocardium]]<br />
|[[Image:CMRToolkitWizard_Panel3.png|thumb|280px|Run axial dilate module]] <br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:]]<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
# Select the input cardiac MRI image.<br />
# Manually segment the left atrial (LA) endocardium region.<br />
# Axially dilate the endocardium segmentation to obtain the epicardium region.<br />
# Subtract the endocardium segmentation from the epicardium segmentation to obtain the wall region.<br />
# Remove the pulmonary veins (PVs) from the wall segmentation.<br />
# Cut off the PVs from the endocardium segmentation created in step 2.<br />
# Create the isosurface of the endocardium segmentation without the PVs.<br />
# 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 />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=42373Documentation/Nightly/Extensions/CardiacMRIToolkit2015-08-12T02:42:21Z<p>Sbengali: </p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Umme Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://capulet.med.utah.edu/namic/cmrslicer/ Slicer CMR Toolkit] <br> [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:CMRTK-logo.png]]<br />
|<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
|<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Scar Visualization]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
*[[Documentation/{{documentation/version}}/Modules/LASegmentationWorkflow|LA Segmentation Workflow]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Lookup Table}}<br />
*[[Documentation/{{documentation/version}}/Modules/CMRToolkitColorLUT|Lookup Table]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
[[Media: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pptx|Cardiac MRI Toolkit Tutorial]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=42301Documentation/Nightly/Extensions/CardiacMRIToolkit2015-08-03T02:35:24Z<p>Sbengali: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://capulet.med.utah.edu/namic/cmrslicer/ Slicer CMR Toolkit] <br> [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:CMRTK-logo.png]]<br />
|<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
|<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Scar Visualization]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
*[[Documentation/{{documentation/version}}/Modules/LASegmentationWorkflow|LA Segmentation Workflow]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Lookup Table}}<br />
*[[Documentation/{{documentation/version}}/Modules/CMRToolkitColorLUT|Lookup Table]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
[[Media: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pptx|Cardiac MRI Toolkit Tutorial]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=38488Documentation/Nightly/Extensions/CardiacMRIToolkit2014-07-02T17:25:21Z<p>Sbengali: Added tutorial link to page</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://capulet.med.utah.edu/namic/cmrslicer/ Slicer CMR Toolkit] <br> [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:CMRTK-logo.png]]<br />
|<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
|<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Threshold Model]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
*[[Documentation/{{documentation/version}}/Modules/LASegmentationWorkflow|LA Segmentation Workflow]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Lookup Table}}<br />
*[[Documentation/{{documentation/version}}/Modules/CMRToolkitColorLUT|Lookup Table]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
[[Media: Cardiac_MRI_Toolkit_Tutorial_Summer2013.pptx|Cardiac MRI Toolkit Tutorial]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:Cardiac_MRI_Toolkit_Tutorial_Summer2013.pptx&diff=38487File:Cardiac MRI Toolkit Tutorial Summer2013.pptx2014-07-02T17:20:43Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/CMRToolkitColorLUT&diff=38073Documentation/Nightly/Modules/CMRToolkitColorLUT2014-05-30T19:33:58Z<p>Sbengali: Added colors for LUT</p>
<hr />
<div>{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
! integer_label<br />
! text_label<br />
! color<br />
! notes<br />
|-<br />
|0<br />
|Left Atrium<br />
|style="background: #4daf4a; color:white"|#4daf4a<br />
|#4daf4a<br />
|-<br />
|1<br />
|Right Atrium<br />
|style="background: #ffff33; color:black"|#ffff33<br />
|#ffff33<br />
|-<br />
|2<br />
|Left Ventricle<br />
|style="background:#e41a1c; color:white"|#e41a1c<br />
|#e41a1c<br />
|-<br />
|3<br />
|Right Ventricle<br />
|style="background:#984ea3; color:white"|#984ea3<br />
|#984ea3<br />
|-<br />
|4<br />
|Left Atrium Wall<br />
|style="background:#377eb8; color:white"|#377eb8<br />
|#377eb8<br />
|-<br />
|5<br />
|Left Ventricle Wall<br />
|style="background:#a65628; color:white"|#a65628<br />
|#a65628<br />
|-<br />
|6<br />
|Aorta<br />
|style="background:#ff7f00; color:white"|#ff7f00<br />
|#ff7f00<br />
|-<br />
|}</div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=38072Documentation/Nightly/Extensions/CardiacMRIToolkit2014-05-30T19:11:03Z<p>Sbengali: Added lookup table page link</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://capulet.med.utah.edu/namic/cmrslicer/ Slicer CMR Toolkit] <br> [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:CMRTK-logo.png]]<br />
|<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
|<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Threshold Model]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
*[[Documentation/{{documentation/version}}/Modules/LASegmentationWorkflow|LA Segmentation Workflow]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Lookup Table}}<br />
*[[Documentation/{{documentation/version}}/Modules/CMRToolkitColorLUT|Lookup Table]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
Tutorials for the modules can be found on their respective pages. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:Lasegment_mra.nrrd&diff=37613File:Lasegment mra.nrrd2014-04-16T16:39:13Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/LASegmentationWorkflow&diff=37605Documentation/Nightly/Modules/LASegmentationWorkflow2014-04-15T22:00:11Z<p>Sbengali: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'</p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob McLeod, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{|<br />
[[Image:CMRToolkit_UofU_logo.jpg|center|280px]]<br />
|}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This wizard module takes the user through the steps involved in segmenting the left atrium from an LGE-MRI by using an MRA. 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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
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--><br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used for cardiac LGE-MRI scans. <br />
{|<br />
|[[Image:LASegmentationWorkflow_Step1.png|thumb|280px|Select the input images]]<br />
|[[Image:LASegmentationWorkflow_Step2.png|thumb|280px|Register the MRA to the LGE-MRI]]<br />
|[[Image:]] <br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:]]<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
# Select the input cardiac LGE-MRI image and MRA image.<br />
# Register the MRA image to the LGE-MRI.<br />
# Use the Slicer editor to segment the left atrium from the MRA. The CarreraSlice editor module is very useful for this task<br />
<!--<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:LASegmentationWorkflow_Step2.png&diff=37604File:LASegmentationWorkflow Step2.png2014-04-15T21:59:06Z<p>Sbengali: uploaded a new version of "File:LASegmentationWorkflow Step2.png"</p>
<hr />
<div></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:LASegmentationWorkflow_Step2.png&diff=37603File:LASegmentationWorkflow Step2.png2014-04-15T21:55:40Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:LASegmentationWorkflow_Step1.png&diff=37602File:LASegmentationWorkflow Step1.png2014-04-15T21:55:29Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=37601Documentation/Nightly/Extensions/CardiacMRIToolkit2014-04-15T21:27:35Z<p>Sbengali: Adding page for new module</p>
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://capulet.med.utah.edu/namic/cmrslicer/ Slicer CMR Toolkit] <br> [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:CMRTK-logo.png]]<br />
|<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
|<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Threshold Model]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
*[[Documentation/{{documentation/version}}/Modules/LASegmentationWorkflow|LA Segmentation Workflow]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
Tutorials for the modules can be found on their respective pages. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ScarVisualization&diff=37478Documentation/Nightly/Modules/ScarVisualization2014-03-11T20:34:02Z<p>Sbengali: moved Documentation/Nightly/Modules/SlicerModuleThresholdModel to Documentation/Nightly/Modules/ScarVisualization</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
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{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used to threshold the wall model produced from the wall segmentation of the left atrium. <br />
{|<br />
|[[Image:CMRToolkit Threshold Model.png|thumb|400px|Thresholded Wall Model]]<br />
|[[Image:CMRToolkit_Threshold_Model.gif|thumb|400px|Changing the Threshold]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
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{{documentation/{{documentation/version}}/module-section|References}}<br />
N/A<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleThresholdModel&diff=37479Documentation/Nightly/Modules/SlicerModuleThresholdModel2014-03-11T20:34:02Z<p>Sbengali: moved Documentation/Nightly/Modules/SlicerModuleThresholdModel to Documentation/Nightly/Modules/ScarVisualization</p>
<hr />
<div>#REDIRECT [[Documentation/Nightly/Modules/ScarVisualization]]</div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=36976Documentation/Nightly/Extensions/CardiacMRIToolkit2014-01-10T03:33:40Z<p>Sbengali: Added link to new webpage</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://capulet.med.utah.edu/namic/cmrslicer/ Slicer CMR Toolkit] <br> [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:CMRTK-logo.png]]<br />
|<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
|<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Threshold Model]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
Tutorials for the modules can be found on their respective pages. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=34056Documentation/Nightly/Extensions/CardiacMRIToolkit2013-07-30T20:04:33Z<p>Sbengali: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
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<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:CMRTK-logo.png]]<br />
|<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
|<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Threshold Model]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
Tutorials for the modules can be found on their respective pages. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=34055Documentation/Nightly/Extensions/CardiacMRIToolkit2013-07-30T20:02:12Z<p>Sbengali: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Threshold Model]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
Tutorials for the modules can be found on their respective pages. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleConnectedThreshold&diff=34054Documentation/Nightly/Modules/SlicerModuleConnectedThreshold2013-07-30T19:52:59Z<p>Sbengali: </p>
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contacts: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|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 />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<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 />
|[[Image:connectedThreshold.jpg|thumb|400px|Bottom Left:Segmentation overlaid on LGE-MRI image, Center: Segmentation output]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:Carma_Connected_Threshold_Filter_Tutorial.pptx|Connected Threshold Filter Tutorial]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
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{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleIsolatedConnected&diff=34053Documentation/Nightly/Modules/SlicerModuleIsolatedConnected2013-07-30T19:52:36Z<p>Sbengali: </p>
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Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contacts: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<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 />
|[[Image:isolatedConnected.jpg|thumb|400px|Bottom Left:Segmentation overlaid on LGE-MRI image, Center: Segmentation]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:Carma_Isolated_Connected_Filter_Tutorial.pptx|Isolated Connected Filter Tutorial]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ScarVisualization&diff=34052Documentation/Nightly/Modules/ScarVisualization2013-07-30T19:52:20Z<p>Sbengali: </p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used to threshold the wall model produced from the wall segmentation of the left atrium. <br />
{|<br />
|[[Image:CMRToolkit Threshold Model.png|thumb|400px|Thresholded Wall Model]]<br />
|[[Image:CMRToolkit_Threshold_Model.gif|thumb|400px|Changing the Threshold]]<br />
|}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:CMRToolkit_Threshold_Model_Tutorial.pptx|Threshold Model Tutorial]]<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleBooleanRemove&diff=34051Documentation/Nightly/Modules/SlicerModuleBooleanRemove2013-07-30T19:52:04Z<p>Sbengali: </p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module performs a subtraction of two label maps. This is needed for the CARMA segmentation pipeline to obtain the left atrium epicardium segmentation. This step follows the 2D axial dilate. <br />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used to create a initial wall segmentation from an endo segmentation and a dilated endo segmentation.<br />
{|<br />
|[[Image:Boolean-Remove.jpg|thumb|400px|Top row: Dilated endo segmentation and endo segmentation, Bottom row: Subtracted output (epicardial segmentation)]]<br />
|}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:Carma_Boolean_Remove_Tutorial.pptx|Boolean Remove Filter Tutorial]]<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
* Input Volume 1 : Select the dilated segmentation<br />
* Input Volume 2 : Select the endo segmentation<br />
* Output Volume : The subtraction output<br />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleAxialDilate&diff=34050Documentation/Nightly/Modules/SlicerModuleAxialDilate2013-07-30T19:51:49Z<p>Sbengali: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Alan Morris, CARMA Center, University of Utah<br><br />
Contributors: Salma Bengali, Greg Gardner, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Alan Morris: <email>alan.morris@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used to create an initial wall segmentation from an endo segmentation.<br />
{|<br />
|[[Image:CarmaAxialDilate1.png|thumb|400px|Before Dilation]]<br />
|[[Image:CarmaAxialDilate2.png|thumb|400px|After Dilation]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
* Target Layer : Select the segmentation to dilate<br />
* Output Layer : The dilated output<br />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModulePVAntrumCut&diff=34049Documentation/Nightly/Modules/SlicerModulePVAntrumCut2013-07-30T19:51:34Z<p>Sbengali: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Alan Morris, Greg Gardner, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used for removing the PV regions from the LA endocardial segmentation.<br />
{|<br />
|[[Image:PVAntrumCutFilter.jpg|thumb|400px|(Clockwise from top right) LA Wall Layer, LA Endo Layer, and LA Endo Layer with Pulmonary Veins Removed]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:Carma_PVAntrumCutFilter_Tutorial.pptx|PV Antrum Cut Filter Tutorial]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleCardiacRegistrationBRAINSFit&diff=34048Documentation/Nightly/Modules/SlicerModuleCardiacRegistrationBRAINSFit2013-07-30T19:51:15Z<p>Sbengali: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Authors: Salma Bengali, Alan Morris, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contacts: Salma Bengali: <email>salma.bengali@carma.utah.edu</email>, Alan Morris: <email>alan.morris@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:Slicer_Carma_BrainsFit_Screenshot.jpg|thumb|400px|(L to R) Registered image, fixed image, and moving image]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
* [[Media:Carma_Registration_BrainsFit_Tutorial.pptx|Cardiac MRI 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 />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
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 />
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N/A<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleCardiacRegistration&diff=34047Documentation/Nightly/Modules/SlicerModuleCardiacRegistration2013-07-30T19:50:58Z<p>Sbengali: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Authors: Salma Bengali, Alan Morris, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contacts: Salma Bengali: <email>salma.bengali@carma.utah.edu</email>, Alan Morris: <email>alan.morris@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|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 />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
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{{documentation/{{documentation/version}}/module-description}}<br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:Cardiac_mri_registration_module.jpg|thumb|400px|(L to R) Registered image, fixed image, and moving image]]<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI 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 />
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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 />
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 />
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The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
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{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleAutoScar&diff=34046Documentation/Nightly/Modules/SlicerModuleAutoScar2013-07-30T19:50:45Z<p>Sbengali: </p>
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Author: Alan Morris, CARMA Center, University of Utah<br><br />
Contributors: Josh Cates, Rob MacLeod, CARMA Center, University of Utah<br> <br />
Contact: Alan Morris: <email>alan.morris@carma.utah.edu</email> <br><br />
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{{documentation/{{documentation/version}}/module-section|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 />
<br />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module automatically classifies scar tissue in post ablation cardiac LGE-MRIs.<br />
{|<br />
|[[Image:carma_afib_auto_scar.png|thumb|400px|Automatic Left Atrial Scar]]<br />
|}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]<br />
<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
<!--<br />
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SlicerModuleInhomogeneity&diff=34045Documentation/Nightly/Modules/SlicerModuleInhomogeneity2013-07-30T19:50:26Z<p>Sbengali: </p>
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Alan Morris, CARMA Center, University of Utah<br><br />
Contributors: Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contact: Alan Morris: <email>alan.morris@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module is meant to be used for MRI scans where local inhomogeneity has been detected.<br />
{|<br />
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|400px|Inhomogeneity correction, original above, corrected below]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:CARMA_Inhomogenity_Correction_Tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
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{{documentation/{{documentation/version}}/module-section|References}}<br />
N/A<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/AutomatedLASegmentation&diff=34044Documentation/Nightly/Modules/AutomatedLASegmentation2013-07-30T19:49:40Z<p>Sbengali: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Gopal Veni, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|uofu}}|{{collaborator|longname|uofu}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module is licensed for research purposes only. <br />
The 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 />
Model data to run this module can be downloaded from the [http://slicer.kitware.com/midas3/download/folder/1550/LA+Segmentation+using+Graph+Cuts.zip Slicer Midas repository]. <br />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to automatically segment the Left Atrium from a cardiac LGE-MRI image. <br />
{|<br />
|[[Image:CMRToolkit_GraphCut.png|thumb|400px|The segmented left atrium with model displayed]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
*Boykov, Yuri, and Vladimir Kolmogorov. "An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision." Pattern Analysis and Machine Intelligence, IEEE Transactions on 26, no. 9 (2004): 1124-1137.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:CMRTK-logo.png&diff=34043File:CMRTK-logo.png2013-07-30T19:45:50Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/AutomatedLASegmentation&diff=34041Documentation/Nightly/Modules/AutomatedLASegmentation2013-07-30T16:51:42Z<p>Sbengali: Updated license information</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Gopal Veni, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{|<br />
[[Image:CMRToolkit_UofU_logo.jpg|center|280px]]<br />
|}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module is licensed for research purposes only. <br />
The 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 />
Model data to run this module can be downloaded from the [http://slicer.kitware.com/midas3/download/folder/1550/LA+Segmentation+using+Graph+Cuts.zip Slicer Midas repository]. <br />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to automatically segment the Left Atrium from a cardiac LGE-MRI image. <br />
{|<br />
|[[Image:CMRToolkit_GraphCut.png|thumb|400px|The segmented left atrium with model displayed]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
*Boykov, Yuri, and Vladimir Kolmogorov. "An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision." Pattern Analysis and Machine Intelligence, IEEE Transactions on 26, no. 9 (2004): 1124-1137.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/AutomatedLASegmentation&diff=34040Documentation/Nightly/Modules/AutomatedLASegmentation2013-07-30T16:17:32Z<p>Sbengali: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Gopal Veni, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{|<br />
[[Image:CMRToolkit_UofU_logo.jpg|center|280px]]<br />
|}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|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 />
Model data to run this module can be downloaded from the [http://slicer.kitware.com/midas3/download/folder/1550/LA+Segmentation+using+Graph+Cuts.zip Slicer Midas repository]. <br />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to automatically segment the Left Atrium from a cardiac LGE-MRI image. <br />
{|<br />
|[[Image:CMRToolkit_GraphCut.png|thumb|400px|The segmented left atrium with model displayed]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
*Boykov, Yuri, and Vladimir Kolmogorov. "An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision." Pattern Analysis and Machine Intelligence, IEEE Transactions on 26, no. 9 (2004): 1124-1137.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/AutomatedLASegmentation&diff=34038Documentation/Nightly/Modules/AutomatedLASegmentation2013-07-30T16:16:45Z<p>Sbengali: Updated references</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Gopal Veni, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{|<br />
[[Image:CMRToolkit_UofU_logo.jpg|center|280px]]<br />
|}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|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 />
Model data to run this module can be downloaded from the [http://slicer.kitware.com/midas3/download/folder/1550/LA+Segmentation+using+Graph+Cuts.zip Slicer Midas repository]. <br />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to automatically segment the Left Atrium from a cardiac LGE-MRI image. <br />
{|<br />
|[[Image:CMRToolkit_GraphCut.png|thumb|400px|The segmented left atrium with model displayed]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:]]<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
*"An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision." Yuri Boykov and Vladimir Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), September 2004<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CardiacMRIToolkit&diff=34035Documentation/Nightly/Extensions/CardiacMRIToolkit2013-07-30T16:12:45Z<p>Sbengali: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Authors: Alan Morris, Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Greg Gardner, Josh Cates, Rob MacLeod, Eugene Kholmovski, CARMA Center, University of Utah<br> <br />
Contacts: Alan Morris: <email>alan.morris@carma.utah.edu</email>, Salma Bengali: <email>salma.bengali@carma.utah.edu</email><br><br />
Website: [http://carmacenter.org http://carmacenter.org] <br><br />
[http://www.na-mic.org/Wiki/index.php/DBP3:Utah http://www.na-mic.org/Wiki/index.php/DBP3:Utah]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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|}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
The Cardiac MRI Toolkit extension consists of several modules that can be used in the analysis of cardiac LGE-MRI images for the purpose of studying cardiac arrhythmia. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
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*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCMRToolkitWizard|CMR Toolkit Wizard]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistration|Cardiac MRI Registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModulePVAntrumCut|PV Antrum Cut Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleAxialDilate|2D Axial Dilate Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleBooleanRemove|Boolean REMOVE Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleThresholdModel|Threshold Model]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleIsolatedConnected|Isolated Connected Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerModuleConnectedThreshold|Connected Threshold Image Filter]]<br />
*[[Documentation/{{documentation/version}}/Modules/AutomatedLASegmentation|Automated LA Segmentation]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<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 />
* Automatic scar detection from cardiac LGE-MRI scans<br />
* Segmentation of the heart<br />
* Cardiac LGE-MRI image registration<br />
* Various operations on segmentation masks<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
Tutorials for the modules can be found on their respective pages. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The source code for this extension can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
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{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=Template:Collaborator&diff=34029Template:Collaborator2013-07-29T22:36:27Z<p>Sbengali: Added U of U logo</p>
<hr />
<div><includeonly>{{#ifeq: {{{2|}}} | namic | <br />
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{{#ifeq: {{{1|}}} | name | Isomics, Inc. |}}<br />
{{#ifeq: {{{1|}}} | longname | Isomics, Inc. |}}<br />
{{#ifeq: {{{1|}}} | url | https://sites.google.com/a/isomics.com/www |}}<br />
|}}{{#ifeq: {{{2|}}} | ge | <br />
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|}}{{#ifeq: {{{2|}}} | itk | <br />
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{{#ifeq: {{{1|}}} | name | ITK |}}<br />
{{#ifeq: {{{1|}}} | longname | Insight Segmentation and Registration Toolkit (ITK) |}}<br />
{{#ifeq: {{{1|}}} | url | http://www.itk.org |}}<br />
|}}{{#ifeq: {{{2|}}} | ctk | <br />
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{{#ifeq: {{{1|}}} | name | Ctk |}}<br />
{{#ifeq: {{{1|}}} | longname | The Common Toolkit |}}<br />
{{#ifeq: {{{1|}}} | url | http://www.commontk.org |}}<br />
|}}{{#ifeq: {{{2|}}} | kitware | <br />
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{{#ifeq: {{{1|}}} | longname | Kitware, Inc. |}}<br />
{{#ifeq: {{{1|}}} | url | http://www.kitware.com |}}<br />
|}}{{#ifeq: {{{2|}}} | csail | <br />
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{{#ifeq: {{{1|}}} | name | CSAIL |}}<br />
{{#ifeq: {{{1|}}} | longname |MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) |}}<br />
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|}}{{#ifeq: {{{2|}}} | ncigt | <br />
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{{#ifeq: {{{1|}}} | name | NCIGT |}}<br />
{{#ifeq: {{{1|}}} | longname | National Center for Image Guided Therapy (NCIGT) |}}<br />
{{#ifeq: {{{1|}}} | url | http://www.ncigt.org |}}<br />
|}}{{#ifeq: {{{2|}}} | bsf | <br />
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|}}{{#ifeq: {{{2|}}} | unc | <br />
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|}}{{#ifeq: {{{2|}}} | martinos | <br />
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|}}{{#ifeq: {{{2|}}} | python | <br />
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{{#ifeq: {{{1|}}} | name | Python |}}<br />
{{#ifeq: {{{1|}}} | longname | Python Programming Language |}}<br />
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{{#ifeq: {{{1|}}} | url | http://www.nedo.go.jp/english |}}<br />
|}}{{#ifeq: {{{2|}}} | slicer4 | <br />
{{#ifeq: {{{1|}}} | logo | Image:Slicer4Announcement-HiRes.png |}}<br />
{{#ifeq: {{{1|}}} | name | Slicer4 |}}<br />
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{{#ifeq: {{{1|}}} | name | UPenn |}}<br />
{{#ifeq: {{{1|}}} | longname | University of Pennsylvania (UPenn) |}}<br />
{{#ifeq: {{{1|}}} | url | http://www.upenn.edu |}}<br />
|}}{{#ifeq: {{{2|}}} | cco | <br />
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{{#ifeq: {{{1|}}} | name | CCO |}}<br />
{{#ifeq: {{{1|}}} | longname | Cancer Care Ontario |}}<br />
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|}}{{#ifeq: {{{2|}}} | sparkit | <br />
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{{#ifeq: {{{1|}}} | name | SparKit |}}<br />
{{#ifeq: {{{1|}}} | longname | Software Platform and Adaptive Radiotherapy Kit |}}<br />
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{{#ifeq: {{{1|}}} | logo | Image:AFRLLogo.png |}}<br />
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{{#ifeq: {{{1|}}} | longname | Air Force Research Laboratories |}}<br />
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{{#ifeq: {{{1|}}} | logo | Image:UAB_MONOGRAM.png |}}<br />
{{#ifeq: {{{1|}}} | name | UAB |}}<br />
{{#ifeq: {{{1|}}} | longname | The University of Alabama at Birmingham |}}<br />
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|}}{{#ifeq: {{{2|}}} | nlm | <br />
{{#ifeq: {{{1|}}} | logo | File:Nlmlogo.gif |}}<br />
{{#ifeq: {{{1|}}} | name | NLM |}}<br />
{{#ifeq: {{{1|}}} | longname | The National Library of Medicine |}}<br />
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|}}{{#ifeq: {{{2|}}} | uofu | <br />
{{#ifeq: {{{1|}}} | logo | File:UofU_logo.jpg |}}<br />
{{#ifeq: {{{1|}}} | name | UofU |}}<br />
{{#ifeq: {{{1|}}} | longname | The University of Utah Health Sciences |}}<br />
{{#ifeq: {{{1|}}} | url | http://healthsciences.utah.edu/ |}}<br />
|}}</includeonly><noinclude><br />
<br />
== Usage ==<br />
<br />
{{collaborator/usage-start}}<br />
{{collaborator/usage-row|afrl}}<br />
{{collaborator/usage-row|bsf}}<br />
{{collaborator/usage-row|cco}}<br />
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{{collaborator/usage-row|isomics}}<br />
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{{collaborator/usage-row|kitware}}<br />
{{collaborator/usage-row|lmi}}<br />
{{collaborator/usage-row|martinos}}<br />
{{collaborator/usage-row|nac}}<br />
{{collaborator/usage-row|namic}}<br />
{{collaborator/usage-row|ncigt}}<br />
{{collaborator/usage-row|nedo}}<br />
{{collaborator/usage-row|pnl}}<br />
{{collaborator/usage-row|python}}<br />
{{collaborator/usage-row|sci}}<br />
{{collaborator/usage-row|slicer4}}<br />
{{collaborator/usage-row|sparkit}}<br />
{{collaborator/usage-row|spl}}<br />
{{collaborator/usage-row|uab}}<br />
{{collaborator/usage-row|uiowa}}<br />
{{collaborator/usage-row|unc}}<br />
{{collaborator/usage-row|nlm}}<br />
{{collaborator/usage-row|upenn}}<br />
{{collaborator/usage-row|uofu}}<br />
{{collaborator/usage-end}}<br />
<br />
[[Category:Templates|{{PAGENAME}}]]<br />
[[Category:Templates:Logos]]<br />
</noinclude></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:UofU_logo.jpg&diff=34028File:UofU logo.jpg2013-07-29T22:26:26Z<p>Sbengali: uploaded a new version of "File:UofU logo.jpg"</p>
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<div></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:UofU_logo.jpg&diff=34027File:UofU logo.jpg2013-07-29T22:13:03Z<p>Sbengali: </p>
<hr />
<div></div>Sbengalihttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/AutomatedLASegmentation&diff=34023Documentation/Nightly/Modules/AutomatedLASegmentation2013-07-29T18:10:28Z<p>Sbengali: Added documentation for graph cut module</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Author: Salma Bengali, CARMA Center, University of Utah<br><br />
Contributors: Gopal Veni, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker, CARMA Center, University of Utah<br> <br />
Contact: Salma Bengali: <email>salma.bengali@carma.utah.edu</email> <br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{|<br />
[[Image:CMRToolkit_UofU_logo.jpg|center|280px]]<br />
|}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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{{documentation/{{documentation/version}}/module-section|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 />
Model data to run this module can be downloaded from the [http://slicer.kitware.com/midas3/download/folder/1550/LA+Segmentation+using+Graph+Cuts.zip Slicer Midas repository]. <br />
<!--<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
--><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to automatically segment the Left Atrium from a cardiac LGE-MRI image. <br />
{|<br />
|[[Image:CMRToolkit_GraphCut.png|thumb|400px|The segmented left atrium with model displayed]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
[[Media:]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<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 />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ CARMA GitHub repository].<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Sbengalihttps://www.slicer.org/w/index.php?title=File:CMRToolkit_GraphCut.png&diff=34022File:CMRToolkit GraphCut.png2013-07-29T18:10:01Z<p>Sbengali: uploaded a new version of "File:CMRToolkit GraphCut.png"</p>
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<div></div>Sbengali