NAMIC Wiki - User contributions [en]

2013 Project Week:CARMA PV Antrum Cut

2013-01-10T18:28:35Z

Amorris:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Salma Bengali, Alan Morris, Greg Gardner, Josh Cates, Rob MacLeod

[[File:CARMA_PV_AntrumCut.png|thumb|center|Project Goal: A Slicer Module to compute the endocardial surface minus pulmonary veins (the light blue region). Requires an input endocardial surface (orange) and wall segmentation (green).]]

The standard CARMA clinical MRI processing workflow involves several segmentation steps, and we seek to implement our entire workflow in Slicer. The goal of this project is to fill one of the current gaps in the processing pipeline, which is to produce an LA endocardial surface segmentation that includes only the antrum regions of the pulmonary veins. There are no image features that define this boundary, but we have developed some heuristic criteria. Given a completed LA wall segmentation and a completed endocardial segmentation (blood pool), we have developed a simple algorithm to automatically compute the endocardium with PV antrum regions. The goal of this project is to implement this algorithm in Slicer.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
# Port existing CARMA C++ code for PV Antrum Cutting to command-line Slicer module
# Test and Document Module
# Deploy in CARMA Extension Module
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We plan to package existing C++ code as a command-line module. There are no parameters for the algorithm, so the user interface will be relatively straightforward. Some work in advance of the Programmer's Week has already been done. By the end of the week, we expect to have a working module to deploy online through our CARMA Extension.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [[DBP3:Utah:SlicerModulePVAntrumCut | Completed ]]
</div>
</div>

2013 Project Week:CARMA 2D Dilate

2013-01-10T18:17:11Z

Amorris: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker

[[Image:CarmaAxialDilate2.png|thumb|center|Axial Dilation]]

The goal of this project is to implement a 2D dilate filter that can be used to extend the left atrium endo layer segmentation to the left atrium epicardium boundary. The filter will extend the endo layer segmentation in the desired slice direction by 4 pixels. LGE-MRI images will be used as inputs to the filter. The output of this filter is further used to obtain a segmentation of only the wall of the left atrium by subtracting the endo layer segmentation from the epi layer segmentation. The implementation of this filter in Slicer would complete another part of our workflow.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
#Port existing CARMA C++ code for 2D dilate filter to command-line Slicer module
#Test and Document Module
#Deploy in CARMA Extension Module
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We plan to implement this algorithm as a Slicer command-line module. We will use the existing Slicer Editor tool as part of our implementation. We will decide whether this module should use real world or pixel space while dilating the endo layer segmentation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*[[DBP3:Utah:SlicerModuleAxialDilate|Completed]]
</div>
</div>

DBP3:Utah

2013-01-09T19:18:01Z

Amorris: /* Tutorials */

Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]

=== The CARMA DBP: MRI-based study and treatment of atrial fibrillation ===
Tissue remodeling of the atrial wall is the hallmark of Atrial Fibrillation
(AF), a progressive cardiac disease that develops over time (months to
years). The mechanisms of of this transformation are only partially understood,
but the current scientific focus on tissue remodeling and its putative role in
AF suggests an MRI image-based approach to the study of AF.

The Comprehensive Arrhythmia Research and MAnagement (CARMA) Center at the
University of Utah is a world leader in the rapidly emerging field of
MRI-managed evaluation and ablation of AF. Other groups have begun to recognize
the potential of this approach and to investigate and validate some of our
findings. Still others are developing new refinements of the MRI technique
driven by the specific needs of this application domain.

Preliminary investigation by CARMA has identified image processing and analysis
as the rate-limiting step to the development of MRI-based therapies. Novel
forms of MRI can be used to evaluate new patients, predict success before
ablation, analyze outcomes post-ablation, and guide repeat ablations. Such
MRI-based therapies, however, urgently require advanced tools and software to
support efficient workflows and accelerate the quantification and analysis of
images. The CARMA-NAMIC DBP project will address some of these needs with the
development of algorithms and tools for the automated segmentation of heart
structures and the MRI-based evaluation of AF progression and recovery.

This remainder of this wiki page describes ongoing CARMA-NAMIC activities and
specific plans. For more background information, references, and description of
the specific scientific and clinical aims of this project,
please see the project web page: http://www.na-mic.org/pages/DBP:Atrial_Fibrillation .

=== DBP Specific Aims ===
# Develop and validate image-based longitudinal diagnostic indices for AF
# Develop automatic segmentation methods for the atrium and adjacent structures
# Develop an AF scoring scheme to evaluate disease progression and recovery from therapy

[[Image:TV1.jpg|center|thumb|400px|The CARMA Center's Utah classification for Atrial Fibrillation staging involves segmentation of the left atrial wall from MRI, followed by quantification of enhanced vs. non-enhanced voxels in the wall.]]

==Activities==
=== Slicer Modules ===
* [[DBP3:Utah:SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]
* [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]
* [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration]]
* [[DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]
* [[DBP3:Utah:SlicerModulePVAntrumCut|PV Antrum Cut Filter]]
* [[DBP3:Utah:SlicerModuleAxialDilate|2D Axial Dilate Filter]]

=== Tutorials ===
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]
* [[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI Registration Tutorial]]
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|Cardiac MRI Registration Using BRAINSFit Tutorial]]
* [[Media:CARMA_Shrink_Wrap_Filter_Tutorial.pptx|PV Antrum Cut Filter Tutorial]]
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|Axial Dilate Filter Tutorial]]

=== Other Projects ===
* Image registration capabilities for longitudinal analysis: [[DBP3:Utah:RegSegPipeline|Registration & Segmentation pipeline pilots & workflow development (Dominik Meier, Alex Zaitsev)]]
* Evaluation of BRAINSFit and Fiducial-based registration tools for LA wall alignment and longitudinal registration of PV: [[DBP3:Utah:PV_BFReg|BRAINSFit Registration of PVs]]
* Collaboration with GA Tech -
** Test and Evaluate Behnood's wall segmentation - results and analysis are here: [[DBP3:Utah:AutoWallSeg|Automatic Wall Segmentation]]
** Test and Evaluate Yi Gao's atlas-based endocardial segmentation algorithm: [[DBP3:Utah:AutoEndoSeg|Automatic Endocardial Segmentation]]
** Test and Evaluate Yi Gao's image and segmentation-driven registration algorithm: [[DBP3:Utah:VecReg|Image and Segmentation-Driven Registration]]

==Sample Data==
* 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]
* 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]
* Two Subjects Two Time Points: [[Media:CardiacMRIs.zip|CardiacMRIs]].

File:CARMA Axial Dilate Filter Tutorial.pptx

2013-01-09T18:33:59Z

Amorris:

DBP3:Utah:SlicerModuleAxialDilate

2013-01-09T18:33:38Z

Amorris: /* Examples, Use Cases & Tutorials */

__NOTOC__
===CARMA Axial Dilate Filter===

{|
|[[Image:CarmaAxialDilate1.png|thumb|280px|Before Dilation]]
|[[Image:CarmaAxialDilate2.png|thumb|280px|After Dilation]]
|}

==Authors, Collaborators & Contact==
* CARMA Center, University of Utah: Alan Morris, Salma Bengali, Greg Gardner, Josh Cates, Rob MacLeod

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

==General Information==
===Module Type & Category===

Type: CLI

Category: CARMA

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

==Module Description==
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.

</div>

<div style="width: 40%; float: left;">

== Usage ==

===Examples, Use Cases & Tutorials===
* This module is meant to be used to create an initial wall segmentation from an endo segmentation.
* [[Media:CARMA_Axial_Dilate_Filter_Tutorial.pptx|CARMA Axial Dilate Filter Tutorial]]

===Quick Tour of Features and Use===

The following are the inputs and outputs

* Target Layer : Select the segmentation to dilate
* Output Layer : The dilated output
</div>
</div>

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

== Development ==

===Source code & documentation===

The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

== More Information ==

</div>
</div>

File:CarmaAxialDilate2.png

2013-01-09T16:28:56Z

Amorris:

File:CarmaAxialDilate1.png

2013-01-09T16:28:37Z

Amorris:

DBP3:Utah:SlicerModuleAxialDilate

2013-01-09T16:27:56Z

Amorris: Created page with '__NOTOC__ ===CARMA Axial Dilate Filter=== {| |Before Dilation |After Dilation |} ==Autho…'

__NOTOC__
===CARMA Axial Dilate Filter===

{|
|[[Image:CarmaAxialDilate1.png|thumb|280px|Before Dilation]]
|[[Image:CarmaAxialDilate2.png|thumb|280px|After Dilation]]
|}

==Authors, Collaborators & Contact==
* CARMA Center, University of Utah: Alan Morris, Salma Bengali, Greg Gardner, Josh Cates, Rob MacLeod

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

==General Information==
===Module Type & Category===

Type: CLI

Category: CARMA

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

==Module Description==
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.

</div>

<div style="width: 40%; float: left;">

== Usage ==

===Examples, Use Cases & Tutorials===
* This module is meant to be used to create an initial wall segmentation from an endo segmentation.

===Quick Tour of Features and Use===

The following are the inputs and outputs

* Target Layer : Select the segmentation to dilate
* Output Layer : The dilated output
</div>
</div>

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

== Development ==

===Source code & documentation===

The source code for this module can be found at the [https://github.com/carma-center/carma_slicer_extension/ GitHub repository].

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

== More Information ==

</div>
</div>

DBP3:Utah

2013-01-09T16:23:18Z

Amorris: /* Slicer Modules */

Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]

=== The CARMA DBP: MRI-based study and treatment of atrial fibrillation ===
Tissue remodeling of the atrial wall is the hallmark of Atrial Fibrillation
(AF), a progressive cardiac disease that develops over time (months to
years). The mechanisms of of this transformation are only partially understood,
but the current scientific focus on tissue remodeling and its putative role in
AF suggests an MRI image-based approach to the study of AF.

The Comprehensive Arrhythmia Research and MAnagement (CARMA) Center at the
University of Utah is a world leader in the rapidly emerging field of
MRI-managed evaluation and ablation of AF. Other groups have begun to recognize
the potential of this approach and to investigate and validate some of our
findings. Still others are developing new refinements of the MRI technique
driven by the specific needs of this application domain.

Preliminary investigation by CARMA has identified image processing and analysis
as the rate-limiting step to the development of MRI-based therapies. Novel
forms of MRI can be used to evaluate new patients, predict success before
ablation, analyze outcomes post-ablation, and guide repeat ablations. Such
MRI-based therapies, however, urgently require advanced tools and software to
support efficient workflows and accelerate the quantification and analysis of
images. The CARMA-NAMIC DBP project will address some of these needs with the
development of algorithms and tools for the automated segmentation of heart
structures and the MRI-based evaluation of AF progression and recovery.

This remainder of this wiki page describes ongoing CARMA-NAMIC activities and
specific plans. For more background information, references, and description of
the specific scientific and clinical aims of this project,
please see the project web page: http://www.na-mic.org/pages/DBP:Atrial_Fibrillation .

=== DBP Specific Aims ===
# Develop and validate image-based longitudinal diagnostic indices for AF
# Develop automatic segmentation methods for the atrium and adjacent structures
# Develop an AF scoring scheme to evaluate disease progression and recovery from therapy

[[Image:TV1.jpg|center|thumb|400px|The CARMA Center's Utah classification for Atrial Fibrillation staging involves segmentation of the left atrial wall from MRI, followed by quantification of enhanced vs. non-enhanced voxels in the wall.]]

==Activities==
=== Slicer Modules ===
* [[DBP3:Utah:SlicerModuleInhomogeneity|Automatic Cardiac MRI Inhomogeneity Correction Filter]]
* [[DBP3:Utah:SlicerModuleAutoScar|Automatic Left Atrial (Post-ablation) Scar Detection]]
* [[DBP3:Utah:SlicerModuleCardiacRegistration|Cardiac MRI Registration]]
* [[DBP3:Utah:SlicerModuleCardiacRegistrationBRAINSFit|Cardiac MRI Registration Using BRAINSFit]]
* [[DBP3:Utah:SlicerModulePVAntrumCut|PV Antrum Cut Filter]]
* [[DBP3:Utah:SlicerModuleAxialDilate|2D Axial Dilate Filter]]

=== Tutorials ===
* [[Media:CARMA_Inhomogeneity_correction_filter_tutorial.pptx|Automatic Cardiac MRI Inhomogeneity Correction Filter Tutorial]]
* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Tutorial]
* [[Media:Carma_Registration_Tutorial.pptx|Cardiac MRI Registration Tutorial]]
* [[Media:Carma_BrainsFit_Registration_Tutorial.pptx|Cardiac MRI Registration Using BRAINSFit Tutorial]]
* [[Media:CARMA_Shrink_Wrap_Filter_Tutorial.pptx|PV Antrum Cut Filter Tutorial]]

=== Other Projects ===
* Image registration capabilities for longitudinal analysis: [[DBP3:Utah:RegSegPipeline|Registration & Segmentation pipeline pilots & workflow development (Dominik Meier, Alex Zaitsev)]]
* Evaluation of BRAINSFit and Fiducial-based registration tools for LA wall alignment and longitudinal registration of PV: [[DBP3:Utah:PV_BFReg|BRAINSFit Registration of PVs]]
* Collaboration with GA Tech -
** Test and Evaluate Behnood's wall segmentation - results and analysis are here: [[DBP3:Utah:AutoWallSeg|Automatic Wall Segmentation]]
** Test and Evaluate Yi Gao's atlas-based endocardial segmentation algorithm: [[DBP3:Utah:AutoEndoSeg|Automatic Endocardial Segmentation]]
** Test and Evaluate Yi Gao's image and segmentation-driven registration algorithm: [[DBP3:Utah:VecReg|Image and Segmentation-Driven Registration]]

==Sample Data==
* 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]
* 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]
* Two Subjects Two Time Points: [[Media:CardiacMRIs.zip|CardiacMRIs]].

AHM2013-IGT

2013-01-09T00:30:14Z

Amorris:

[[AHM_2013#Agenda|Back to AHM_2013 Agenda]]

Attendees: Tina Kapur, Tamas Ungi, Adam Rankin, Alireza Mehrtash, Stephen Aylward, Matthew Toews, Sandy Wells, Andrey Fedorov, Noby Hata, Junichi Tokuda, Laurent Chauvin, Matt McCormick, Alan Morris

Agenda:
*new US-guided applications in Slicer (TU)
*what's new in PLUS (AR)
*iGyne Demo and plans (TK, AM)
*AMIGO Ultrasound Tracking for Neurosurgery (MT)
*Using PLUS for Prostate interventions (AF)
*Smart Template for Prostate Interventions (NH)
*EP ablation at Utah (Alan)
*OpenIGTLink (JT)

DBP3:Utah:SlicerModuleCardiacRegistration

2012-08-16T19:53:04Z

Amorris:

__NOTOC__
===CARMA Cardiac Registration Module===

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Greg Gardner: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Rob MacLeod: CARMA Center, University of Utah

===Module Description===
This module implements case-specific registration for cardiac LGE-MRI and CT images. The input to this module is two image volumes. The user then selects from a set of presets based on the type of images. Registration parameters are tuned for the cases listed [[DBP3:Utah:RegCases|registration case]].

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is meant to be used for cardiac LGE-MRI and CT scans acquired at different time points or across different patients.

===Quick Tour of Features and Use===

The following are the inputs and outputs

* Moving Volume : Select the LGE-MRI image
* Fixed Volume : Select the LGE-MRI Image
* Output Volume : The output volume
* Registration Type : Type of images (e.g LGE-MRI, MRA, CT, Acute Scar)

== More Information ==

===Acknowledgment===

===References===

File:Carma-logo-128.png

2012-08-08T22:48:36Z

Amorris:

File:Carma afib auto scar.png

2012-05-01T17:56:45Z

Amorris: uploaded a new version of "File:Carma afib auto scar.png"

File:Carma afib auto scar.png

2012-05-01T17:52:35Z

Amorris: uploaded a new version of "File:Carma afib auto scar.png"

File:Carma afib auto scar.png

2012-05-01T17:47:48Z

Amorris:

DBP3:Utah:SlicerModuleAutoScar

2012-05-01T17:24:02Z

Amorris:

__NOTOC__
===CARMA Automatic Left Atrial Scar===

{|
|[[Image:carma_afib_auto_scar.png|thumb|280px|Automatic Left Atrial Scar]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Danny Perry: CARMA Center, University of Utah
* Alan Morris: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Rob MacLeod: CARMA Center, University of Utah

===Module Description===
Determines Left Atrial Scar Automatically given the wall segmentation, in a post-ablation LGE-MRI. For details see: Perry, D. et al. "Automatic classification of scar tissue...", Proceedings of SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module automatically classifies scar tissue in post ablation DE-MRIs

===Quick Tour of Features and Use===

The following are the inputs and outputs

* MRI image : Select the DE-MRI image
* LA wall mask : Select the label map for the left atrial wall
* Blood Pool mask : Select the label map for the blood pool
* Result : The output label map denoting scar

== Development ==

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleAutoScar

2012-05-01T17:22:58Z

Amorris: /* Module Description */

__NOTOC__
===CARMA Automatic Left Atrial Scar===

{|
|[[Image:carma_afib_auto_scar.png|thumb|280px|Automatic Left Atrial Scar]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Danny Perry: CARMA Center, University of Utah
* Alan Morris: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Rob MacLeod: CARMA Center, University of Utah

===Module Description===
Determines Left Atrial Scar Automatically given the wall segmentation, in a post-ablation LGE-MRI. For details see: Perry, D. et al. "Automatic classification of scar tissue...", Proceedings of SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module automatically classifies scar tissue in post ablation DE-MRIs

===Quick Tour of Features and Use===

The following are the inputs and outputs

* MRI Image : Select the DE-MRI image
* Wall mask : Select the label map for the left atrial wall
* Blood Pool mask : Select the label map for the blood pool
* Output : The output label map denoting scar

== Development ==

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleAutoScar

2012-05-01T17:22:48Z

Amorris: Created page with '__NOTOC__ ===CARMA Automatic Left Atrial Scar=== {| |Automatic Left Atrial Scar |} == General Information == ===Module Type & Cat…'

__NOTOC__
===CARMA Automatic Left Atrial Scar===

{|
|[[Image:carma_afib_auto_scar.png|thumb|280px|Automatic Left Atrial Scar]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Danny Perry: CARMA Center, University of Utah
* Alan Morris: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Rob MacLeod: CARMA Center, University of Utah

===Module Description===
Determines Left Atrial Scar Automatically given the wall segmentation, in a post-ablation LGE-MRI. For details see: Perry, D. et al. "Automatic classification of scar tissue...", Proceedings of SPIE Medical Imaging: Computer Aided Diag\
nosis, Feb 2012.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module automatically classifies scar tissue in post ablation DE-MRIs

===Quick Tour of Features and Use===

The following are the inputs and outputs

* MRI Image : Select the DE-MRI image
* Wall mask : Select the label map for the left atrial wall
* Blood Pool mask : Select the label map for the blood pool
* Output : The output label map denoting scar

== Development ==

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:59:26Z

Amorris:

__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah
* Rob MacLeod: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is meant to be used for MRI scans where local inhomogeneity has been detected

===Quick Tour of Features and Use===

The following are the inputs and outputs

* MRI Image : Select the DE-MRI image
* Blood Pool mask : Select the label map for the blood pool
* ROI mask : Select the label map for the targeted region of interest
* Corrected Output : The output volume

== Development ==

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:59:16Z

Amorris:

__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah
* Rob Macleod: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is meant to be used for MRI scans where local inhomogeneity has been detected

===Quick Tour of Features and Use===

The following are the inputs and outputs

* MRI Image : Select the DE-MRI image
* Blood Pool mask : Select the label map for the blood pool
* ROI mask : Select the label map for the targeted region of interest
* Corrected Output : The output volume

== Development ==

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:58:35Z

Amorris:

__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is meant to be used for MRI scans where local inhomogeneity has been detected

===Quick Tour of Features and Use===

The following are the inputs and outputs

* MRI Image : Select the DE-MRI image
* Blood Pool mask : Select the label map for the blood pool
* ROI mask : Select the label map for the targeted region of interest
* Corrected Output : The output volume

== Development ==

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:57:48Z

Amorris: /* Development */

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is meant to be used for MRI scans where local inhomogeneity has been detected

===Quick Tour of Features and Use===

The following are the inputs and outputs

* MRI Image : Select the DE-MRI image
* Blood Pool mask : Select the label map for the blood pool
* ROI mask : Select the label map for the targeted region of interest
* Corrected Output : The output volume

== Development ==

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:57:39Z

Amorris: /* Development */

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:57:23Z

Amorris: /* Quick Tour of Features and Use */

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is meant to be used for MRI scans where local inhomogeneity has been detected

===Quick Tour of Features and Use===

The following are the inputs and outputs

* MRI Image : Select the DE-MRI image
* Blood Pool mask : Select the label map for the blood pool
* ROI mask : Select the label map for the targeted region of interest
* Corrected Output : The output volume

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:57:06Z

Amorris: /* Quick Tour of Features and Use */

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is meant to be used for MRI scans where local inhomogeneity has been detected

===Quick Tour of Features and Use===

* MRI Image : Select the DE-MRI image
* Blood Pool mask : Select the label map for the blood pool
* ROI mask : Select the label map for the targeted region of interest
* Corrected Output : The output volume

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:54:11Z

Amorris: /* Examples, Use Cases & Tutorials */

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is meant to be used for MRI scans where local inhomogeneity has been detected

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:53:09Z

Amorris:

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity correction, original above, corrected below]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

File:Carma afib inhomogeneity correction.png

2012-04-25T21:52:45Z

Amorris:

DBP3:Utah:SlicerModuleInhomogeneity

2012-04-25T21:52:33Z

Amorris:

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===CARMA Inhomogeneity Correction Filter===

{|
|[[Image:carma_afib_inhomogeneity_correction.png|thumb|280px|Inhomogeneity Correction]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: CARMA

===Authors, Collaborators & Contact===
* Alan Morris: CARMA Center, University of Utah
* Eugene Kholmovski: CARMA Center, University of Utah
* Josh Cates: CARMA Center, University of Utah
* Danny Perry: CARMA Center, University of Utah

===Module Description===
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 an 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.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.