NAMIC Wiki - User contributions [en]

2013 Project Week:CARMA PractialLASeg

2013-01-10T07:30:30Z

Ggardner:

__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

[[File:CarmaWorkflowSlide.jpeg|thumb|center|Workflow Overview]]

Automatic segmenation of the left atrium (LA) from LGE-MRI images continues to be challenging to automate. Recent work by Ross and Gopal looks promising, but will require further validation and some significant work to implement in Slicer in a useful format for CARMA technicians. In the meantime, we propose to explore some new approaches to a semi-automated segmentation, with the goal of reducing the necessary time for the manual process (the process is described in [[File:carmaWorkflowV2.pdf | carmaWorkflowV2.pdf]]).

CARMA has recently begun to acquire fully gated MRA images, along with the LGE-MRI protocol. Gated MRA can produce much sharper blood pool boundaries (LA endocardium) than standard, 1-pass MRA and may prove valuable for localizing endocardial contours.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
The objective of this project is to collaboratively brainstorm and (ideally) implement a semi-automated LA segmentation workflow (wizard?) within slicer. We plan to take advantage of available Slicer experts and provide a wish list to Slicer engineers of any missing pieces -- or nice to have features -- necessary for our proposed workflow.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
# Explore the use of Slicer to perform semi-automated segmentation of the LA Endocardium using gated MRA aligned with LGE-MRI
# Identify missing segmentation tools that may be useful in a proposed segmentation workflow (e.g. 3D editing?)
# Plan (or implement if time permits) a workflow (wizard) within CARMA based on what we learn from objectives 1-2

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

File:CarmaWorkflowSlide.jpeg

2013-01-10T07:29:50Z

Ggardner: Overview of the CARMA fibrosis/scar segmentation workflow in Slicer.

Overview of the CARMA fibrosis/scar segmentation workflow in Slicer.

2013 Project Week:CARMA PractialLASeg

2013-01-10T07:27:08Z

Ggardner:

__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

[[File:CarmaWorkflowSlide.png|thumb|center|Workflow Overview]]

Automatic segmenation of the left atrium (LA) from LGE-MRI images continues to be challenging to automate. Recent work by Ross and Gopal looks promising, but will require further validation and some significant work to implement in Slicer in a useful format for CARMA technicians. In the meantime, we propose to explore some new approaches to a semi-automated segmentation, with the goal of reducing the necessary time for the manual process (the process is described in [[File:carmaWorkflowV2.pdf | carmaWorkflowV2.pdf]]).

CARMA has recently begun to acquire fully gated MRA images, along with the LGE-MRI protocol. Gated MRA can produce much sharper blood pool boundaries (LA endocardium) than standard, 1-pass MRA and may prove valuable for localizing endocardial contours.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
The objective of this project is to collaboratively brainstorm and (ideally) implement a semi-automated LA segmentation workflow (wizard?) within slicer. We plan to take advantage of available Slicer experts and provide a wish list to Slicer engineers of any missing pieces -- or nice to have features -- necessary for our proposed workflow.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
# Explore the use of Slicer to perform semi-automated segmentation of the LA Endocardium using gated MRA aligned with LGE-MRI
# Identify missing segmentation tools that may be useful in a proposed segmentation workflow (e.g. 3D editing?)
# Plan (or implement if time permits) a workflow (wizard) within CARMA based on what we learn from objectives 1-2

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

File:CarmaWorkflowV2.pdf

2013-01-10T07:24:37Z

Ggardner: Overview of the CARMA fibrosis/scar segmentation workflow in Slicer.

Overview of the CARMA fibrosis/scar segmentation workflow in Slicer.

2013 Project Week:CARMA PractialLASeg

2013-01-10T07:23:49Z

Ggardner:

__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

[[File:CarmaWorkflowSlide.png|thumb|center|Workflow Overview]]

Automatic segmenation of the left atrium (LA) from LGE-MRI images continues to be challenging to automate. Recent work by Ross and Gopal looks promising, but will require further validation and some significant work to implement in Slicer in a useful format for CARMA technicians. In the meantime, we propose to explore some new approaches to a semi-automated segmentation, with the goal of reducing the necessary time for the manual process (the process is described in [[File:carmaWorkflowV2.pdf|carmaWorkflowV2.pdf]]).

CARMA has recently begun to acquire fully gated MRA images, along with the LGE-MRI protocol. Gated MRA can produce much sharper blood pool boundaries (LA endocardium) than standard, 1-pass MRA and may prove valuable for localizing endocardial contours.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
The objective of this project is to collaboratively brainstorm and (ideally) implement a semi-automated LA segmentation workflow (wizard?) within slicer. We plan to take advantage of available Slicer experts and provide a wish list to Slicer engineers of any missing pieces -- or nice to have features -- necessary for our proposed workflow.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
# Explore the use of Slicer to perform semi-automated segmentation of the LA Endocardium using gated MRA aligned with LGE-MRI
# Identify missing segmentation tools that may be useful in a proposed segmentation workflow (e.g. 3D editing?)
# Plan (or implement if time permits) a workflow (wizard) within CARMA based on what we learn from objectives 1-2

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2013 Project Week:CARMA PractialLASeg

2013-01-10T07:22:45Z

Ggardner:

__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

[[File:CarmaWorkflowSlide.png|thumb|center|Workflow Overview]]

Automatic segmenation of the left atrium (LA) from LGE-MRI images continues to be challenging to automate. Recent work by Ross and Gopal looks promising, but will require further validation and some significant work to implement in Slicer in a useful format for CARMA technicians. In the meantime, we propose to explore some new approaches to a semi-automated segmentation, with the goal of reducing the necessary time for the manual process (the process is described in [[file:carmaWorkflowV2.pdf]]).

CARMA has recently begun to acquire fully gated MRA images, along with the LGE-MRI protocol. Gated MRA can produce much sharper blood pool boundaries (LA endocardium) than standard, 1-pass MRA and may prove valuable for localizing endocardial contours.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
The objective of this project is to collaboratively brainstorm and (ideally) implement a semi-automated LA segmentation workflow (wizard?) within slicer. We plan to take advantage of available Slicer experts and provide a wish list to Slicer engineers of any missing pieces -- or nice to have features -- necessary for our proposed workflow.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
# Explore the use of Slicer to perform semi-automated segmentation of the LA Endocardium using gated MRA aligned with LGE-MRI
# Identify missing segmentation tools that may be useful in a proposed segmentation workflow (e.g. 3D editing?)
# Plan (or implement if time permits) a workflow (wizard) within CARMA based on what we learn from objectives 1-2

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2013 Project Week:CARMA PractialLASeg

2013-01-10T07:22:15Z

Ggardner:

__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

[[File:CarmaWorkflowSlide.png|thumb|center|Workflow Overview]]

Automatic segmenation of the left atrium (LA) from LGE-MRI images continues to be challenging to automate. Recent work by Ross and Gopal looks promising, but will require further validation and some significant work to implement in Slicer in a useful format for CARMA technicians. In the meantime, we propose to explore some new approaches to a semi-automated segmentation, with the goal of reducing the necessary time for the manual process (the process is described in [file:carmaWorkflowV2.pdf].

CARMA has recently begun to acquire fully gated MRA images, along with the LGE-MRI protocol. Gated MRA can produce much sharper blood pool boundaries (LA endocardium) than standard, 1-pass MRA and may prove valuable for localizing endocardial contours.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
The objective of this project is to collaboratively brainstorm and (ideally) implement a semi-automated LA segmentation workflow (wizard?) within slicer. We plan to take advantage of available Slicer experts and provide a wish list to Slicer engineers of any missing pieces -- or nice to have features -- necessary for our proposed workflow.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
# Explore the use of Slicer to perform semi-automated segmentation of the LA Endocardium using gated MRA aligned with LGE-MRI
# Identify missing segmentation tools that may be useful in a proposed segmentation workflow (e.g. 3D editing?)
# Plan (or implement if time permits) a workflow (wizard) within CARMA based on what we learn from objectives 1-2

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

File:CarmaWorkflowSlide.png

2013-01-10T07:20:42Z

Ggardner: uploaded a new version of "File:CarmaWorkflowSlide.png": Overview of the CARMA fibrosis segmentation workflow in Slicer.

Overview of the CARMA fibrosis segmentation workflow in Slicer.

File:CarmaWorkflowSlide.png

2013-01-10T07:18:30Z

Ggardner: uploaded a new version of "File:CarmaWorkflowSlide.png": Overview of the CARMA fibrosis segmentation workflow in Slicer.

Overview of the CARMA fibrosis segmentation workflow in Slicer.

File:CarmaWorkflowSlide.png

2013-01-10T07:17:50Z

Ggardner: Overview of the CARMA fibrosis segmentation workflow in Slicer.

Overview of the CARMA fibrosis segmentation workflow in Slicer.

2013 Project Week:CARMA PractialLASeg

2013-01-10T07:17:01Z

Ggardner:

__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

[[File:CarmaWorkflowSlide.png|thumb|center|Workflow Overview]]

Automatic segmenation of the left atrium (LA) from LGE-MRI images continues to be challenging to automate. Recent work by Ross and Gopal looks promising, but will require further validation and some significant work to implement in Slicer in a useful format for CARMA technicians. In the meantime, we propose to explore some new approaches to a semi-automated segmentation, with the goal of reducing the necessary time for the manual process.

CARMA has recently begun to acquire fully gated MRA images, along with the LGE-MRI protocol. Gated MRA can produce much sharper blood pool boundaries (LA endocardium) than standard, 1-pass MRA and may prove valuable for localizing endocardial contours.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
The objective of this project is to collaboratively brainstorm and (ideally) implement a semi-automated LA segmentation workflow (wizard?) within slicer. We plan to take advantage of available Slicer experts and provide a wish list to Slicer engineers of any missing pieces -- or nice to have features -- necessary for our proposed workflow.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
# Explore the use of Slicer to perform semi-automated segmentation of the LA Endocardium using gated MRA aligned with LGE-MRI
# Identify missing segmentation tools that may be useful in a proposed segmentation workflow (e.g. 3D editing?)
# Plan (or implement if time permits) a workflow (wizard) within CARMA based on what we learn from objectives 1-2

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

File:CarmaWorkflowSlide.pdf

2013-01-10T07:15:19Z

Ggardner: Overview of the CARMA scar detection algorithm in Slicer.

Overview of the CARMA scar detection algorithm in Slicer.

2012 Summer Project Week

2012-06-22T14:26:57Z

Ggardner:

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' [[2012 Project Week Breakout Session: Slicer4|What's new in Slicer4 (Charts - Jim, DICOM - Steve, Multivolume - Andrey)]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' [[2012 Project Week Breakout Session:Slicer4 Python Q&A|Slicer4 Python Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Slicer in Networked Environment|Slicer in Networked Environment]] (Junichi)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2012 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2012 Summer Project Week Breakout Session:Slicer DICOM|Breakout Session: DICOM, Networking, RT, Segmentations]] (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:QtTesting|QtTesting]] (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
<br>----------------------------------------<br>
'''3:00-4:00pm''' [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer (Andras)]]<br>
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Danielle Pace, Stephen Aylward, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:Intraoperative_Tract_Detection | Intraoperative White Matter Tract Detection Module]] (Lauren O'Donnell, Isaiah Norton)
# [[2012_Summer_Project_Week:Ultrasound_Aberration_Correction | An Ultrasound-based Method for Aberration Correction in TCFUS]] (Jason White, Greg Clement)
# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck| Atlas-based segmentation for head and neck]] (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
#[[2012_Summer_Project_Week:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, Steve Pieper, Jim Miller, Andras Lasso)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch loadable module]] (James Shackleford, Greg Sharp)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
#[[2012_Summer_Project_Week:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:PET_Image_Analysis | SUV Threshold Computation]] (Nadya Shusharina, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams, Hans Johnson)
# [[2012_Summer_Project_Week:Evaluation Module|QA Evaluation Module]] (Dave Welch, Hans Johnson, Steve Pieper, JC Fillion-Robin)
# [[2012_Summer_Project_Week:4D shape analysis|4D Shape Analysis: Software Tools]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Greg Gardner, Danny Perry, Rob MacLeod)
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:SlicerWeb|Web Interface to Slicer 4]] (Steve Pieper)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda, Laurent Chauvin)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Simrin Nagpal, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder and other IGT modules]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:iGyne|iGyne for Gynecological Cancer Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
#[[2012_Summer_Project_Week:Interactive_Needle_Segmentation|Interactive Needle Segmentation for Gynecological Cancer Brachytherapy]] (Nabgha Farhat, Neha Agrawal, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Saman Nouranian, Samira Sojoudi, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Needle Tip Tracking |Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Pietro Nardelli, Padraig Cantillon-Murphy, Raul San Jose Estepar)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer, Andrey Fedorov)
#[[2012_Summer_Project_Week:ABC_Slicer4|Porting ABC extension to Slicer 4]] (Marcel Prastawa, Bo Wang, Guido Gerig)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)

==='''General Registration'''===
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
#[[2012_Summer_Project_Week:ElastixIntegration|Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, Petter Risholm, Dominik Meier, William Wells)

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:CMake_for_AIM_API|CMake-fying AIM API]] (Pat Mongklowat, Vlad Kleper, Andrey Fedorov)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim, Brendan Moloney)
# [[2012_Summer_Project_Week:PythonCLIandWidget|Python CLI modules (Demian, JC, Julien, Steve)]].
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:GPUEditor|Editor Effects]] (Steve, Jim, Brad, Ivan, Yi)
# [[2012_Summer_Project_Week:XTK|XTK/WebGL Exporter]] (Daniel, Nicolas - Boston Children's Hospital)
# [[2012_Summer_Project_Week:EventOptimization|Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)]]
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony, Steve)
# [[2012_Summer_Project_Week:CUDA Volume Rendering Extension|CUDA Volume Rendering as Extension]] (J2, Elvis)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blevins, Scott, BWH, stblevins@gmail.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chambers, Micah, UCLA, micahcc@ucla.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gao, Yi, BWH, gaoyi@bwh.harvard.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Golland, Polina, MIT CSAIL, polina@csail.mit.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Gupta, Aditya, NIRAL UNC, aditya_gupta@med.unc.edu
#Irimia, Andrei, UCLA, andrei.irimia@loni.ucla.edu
#Jagadeesan, Jayender, SPL, jayender@bwh.harvard.edu
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kalpathy-Cramer, Jayashree, MGH, kalpathy@nmr.mgh.harvard.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, (cancelled registration) Erasmus MC, s.klein@erasmusmc.nl
#Kleper, Vladimir, Northwestern Univ, vkleper@northwestern.edu
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Mastrogiacomo, Katie, SPL, BWH, kmast@bwh.harvard.edu
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Mercea, Paul, SPL, pmercea@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Mizutani, Tatsushi, Nagoya Univ, tatsushi0207@me.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Montillo, Albert, GE Research, montillo@ge.com
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Norton, Isaiah, BWH, inorton@partners.org
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#O'Donnell, Lauren, BWH, odonnell@bwh.harvard.edu
#Oyama, Rie, BWH, royama@bwh.harvard.edu
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Penzkofer, Tobias, SPL, pt@bwh.harvard.edu
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Rannou, Nicolas, Childrens Hospital, nicolas.rannou@childrens.harvard.edu
#Razzaque, Sharif, InnerOptic Technology, sharif@inneroptic.com
#Risholm, Petter, Harvard, pettri@bwh.harvard.edu
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Schroeder, William, Kitware, will.schroeder@kitware.com
#Shackleford, James, MGH, jshackleford@partners.org
#Sharp, Greg, MGH, gcsharp@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
#Sridharan, Ramesh, MIT CSAIL, rameshvs@MIT.EDU
#State, Andrei, InnerOptic Technology, andrei@inneroptic.com
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Tokuda, Junichi, BWH, tokuda@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wang, Kevin, Princess Margaret Hospital, kevin.wang@rmp.uhn.on.ca
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Wells, William, HMS BWH, sw@bwh.harvard.edu
#Whitaker, Ross, SCI, whitaker@cs.utah.edu
#White, Phillip, BWH HMS, white@bwh.harvard.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Summer Project Week:UtahAutoScar

2012-06-21T20:07:28Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-scar-snapshot-module.png|Updated module with logos/acknowledgements
Image:carma_afib_auto_scar.png|Automatic Left Atrial Scar Segmentation
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for automatically detecting post-procedural scar in LGE-MRI images. The goal is to make statistical group comparisons based on the spatial distribution and amount of scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach for automatic scar segmentation is summarized in the SPIE 2012 reference below. Briefly, we are using k-means clustering to tease apart the normalized pixel intensities corresponding to different tissue types (e.g., healthy, scar, blood).

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples. We will present a tutorial on this module during the project week tutorial contest [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012]

</div>

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

<h3>Progress</h3>
Software for the automatic scar segmentation has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleAutoScar]. We have created documentation/tutorial for the module. Lastly, we have updated the acknowledgements section to include the appropriate logos and information. The module is now available as a loadable extension in Slicer 4.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==
*Daniel Perry, Alan Morris, Nathan Burgon, Christopher McGann, Robert MacLeod, Joshua Cates. "Automatic classiﬁcation of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation". SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

2012 Summer Project Week:UtahInhomogeneity

2012-06-21T20:07:03Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-scar-snapshot-module.png|Updated module with logos and acknowledgements
Image:carma_afib_inhomogeneity_correction.png|Cardiac-Specific Inhomogeneity Correction Example
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Eugene Kholmovski, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for localized inhomogeneity correction for cardiac LGE-MRI images. The goal is to be able to reduce some of the noise inherent in cardiac LGE-MRI scans to improve clinical diagnoses and statistical comparisons.

</div>

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

<h3>Approach, Plan</h3>

Our approach for inhomogeneity correction is a gradient function to the image data that normalizes accordingly.

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples.

</div>

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

<h3>Progress</h3>
Software for the inhomogeneity correction has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleInhomogeneity]. We have created documentation/tutorial for the module. Lastly, we have updated the acknowledgements section to include the appropriate logos and information. The module is now available as a loadable extension in Slicer 4.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

2012 Summer Project Week:UtahAutoScar

2012-06-21T20:05:26Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-scar-snapshot-module.png|Updated module with logos/acknowledgements
Image:carma_afib_auto_scar.png|Automatic Left Atrial Scar Segmentation
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for automatically detecting post-procedural scar in LGE-MRI images. The goal is to make statistical group comparisons based on the spatial distribution and amount of scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach for automatic scar segmentation is summarized in the SPIE 2012 reference below. Briefly, we are using k-means clustering to tease apart the normalized pixel intensities corresponding to different tissue types (e.g., healthy, scar, blood).

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples. We will present a tutorial on this module during the project week tutorial contest [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012]

</div>

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

<h3>Progress</h3>
Software for the automatic scar segmentation has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleAutoScar]. We have created documentation/tutorial for the module. Lastly, we have updated the acknowledgements section to include the appropriate logos and information.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==
*Daniel Perry, Alan Morris, Nathan Burgon, Christopher McGann, Robert MacLeod, Joshua Cates. "Automatic classiﬁcation of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation". SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

2012 Summer Project Week:UtahCardiacRegistration

2012-06-21T20:03:06Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-registration-snapshot-module.png|Initial layout of CARMA registration module.
Image:CARMA-registration-snapshot-window.png|View of Slicer4 with initial CARMA registration module.

Image:CARMA_VecReg_Seg3.png|Current Registration Example - needs some work
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Greg Gardner, Rob MacLeod

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

<h3>Objective</h3>
We are developing a case-specific registration module capable of handling the different image types used at the CARMA Center (e.g., LGE-MRI, MRA, CT) [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases] [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleCardiacRegistration]. The goal is to improve the accuracy of the current registration methods by defining case-specific parameters.

</div>

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

<h3>Approach, Plan</h3>

Our approach for registration is parameter optimization for the current ITK registration approaches.

Our plan for the project week is to further define the registration cases and begin implementation in Slicer 4.

</div>

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

<h3>Progress</h3>
We have defined some preliminary registration cases [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases]. We have designed an initial layout for the module, but will have to refine the design as we have realized that the registration algorithm will require both images and segmentations to drive the registration.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

2012 Summer Project Week:UtahInhomogeneity

2012-06-21T19:38:02Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-scar-snapshot-module.png|Updated module with logos and acknowledgements
Image:carma_afib_inhomogeneity_correction.png|Cardiac-Specific Inhomogeneity Correction Example
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Eugene Kholmovski, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for localized inhomogeneity correction for cardiac LGE-MRI images. The goal is to be able to reduce some of the noise inherent in cardiac LGE-MRI scans to improve clinical diagnoses and statistical comparisons.

</div>

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

<h3>Approach, Plan</h3>

Our approach for inhomogeneity correction is a gradient function to the image data that normalizes accordingly.

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples.

</div>

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

<h3>Progress</h3>
Software for the inhomogeneity correction has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleInhomogeneity]. We need to create documentations and tutorials as well as finalize the migration to Slicer 4. We have begun validation of the module.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

File:CARMA-inhomogeneity-snapshot-module.png

2012-06-21T19:37:58Z

Ggardner: A view of the updated CARMA inhomogeneity correction module that includes the desired logos, acknowledgements, and a clarification of the difference between this algorithm and the existing N4 bias field correction algorithm.

A view of the updated CARMA inhomogeneity correction module that includes the desired logos, acknowledgements, and a clarification of the difference between this algorithm and the existing N4 bias field correction algorithm.

2012 Summer Project Week:UtahAutoScar

2012-06-21T19:36:04Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-scar-snapshot-module.png|Updated module with logos/acknowledgements
Image:carma_afib_auto_scar.png|Automatic Left Atrial Scar Segmentation
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for automatically detecting post-procedural scar in LGE-MRI images. The goal is to make statistical group comparisons based on the spatial distribution and amount of scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach for automatic scar segmentation is summarized in the SPIE 2012 reference below. Briefly, we are using k-means clustering to tease apart the normalized pixel intensities corresponding to different tissue types (e.g., healthy, scar, blood).

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples. We will present a tutorial on this module during the project week tutorial contest [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012]

</div>

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

<h3>Progress</h3>
Software for the automatic scar segmentation has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleAutoScar]. We need to create documentations and tutorials as well as finalize the migration to Slicer 4. We have begun statistical analysis and validation of the module.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==
*Daniel Perry, Alan Morris, Nathan Burgon, Christopher McGann, Robert MacLeod, Joshua Cates. "Automatic classiﬁcation of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation". SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

File:CARMA-scar-snapshot-module.png

2012-06-21T19:35:31Z

Ggardner: This is a view of the updated CARMA automate LA scar detection module. The acknowledgement section has been updated to include the appropriate information and logos.

This is a view of the updated CARMA automate LA scar detection module. The acknowledgement section has been updated to include the appropriate information and logos.

2012 Summer Project Week:UtahCardiacRegistration

2012-06-21T19:33:52Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-registration-snapshot-module.png|Initial layout of CARMA registration module.
Image:CARMA-registration-snapshot-window.png|View of Slicer4 with initial CARMA registration module.

Image:CARMA_VecReg_Seg3.png|Current Registration Example - needs some work
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Greg Gardner, Rob MacLeod

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

<h3>Objective</h3>
We are developing a case-specific registration module capable of handling the different image types used at the CARMA Center (e.g., LGE-MRI, MRA, CT) [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases] [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleCardiacRegistration]. The goal is to improve the accuracy of the current registration methods by defining case-specific parameters.

</div>

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

<h3>Approach, Plan</h3>

Our approach for registration is parameter optimization for the current ITK registration approaches.

Our plan for the project week is to further define the registration cases and begin implementation in Slicer 4.

</div>

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

<h3>Progress</h3>
We have defined some preliminary registration cases [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases].

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

File:CARMA-registration-snapshot-window.png

2012-06-21T19:33:10Z

Ggardner: This is an initial layout for our case-specific registration module. There are inputs for the moving and fixed images; the user also selects a registration case from the drop-down menu containing the supported variations. The module returns the registered

This is an initial layout for our case-specific registration module. There are inputs for the moving and fixed images; the user also selects a registration case from the drop-down menu containing the supported variations. The module returns the registered image relative to the fixed image.

2012 Summer Project Week:UtahCardiacRegistration

2012-06-21T19:32:33Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-registration-snapshot-module.png|Initial layout of CARMA registration module.

Image:CARMA_VecReg_Seg3.png|Current Registration Example - needs some work
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Greg Gardner, Rob MacLeod

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

<h3>Objective</h3>
We are developing a case-specific registration module capable of handling the different image types used at the CARMA Center (e.g., LGE-MRI, MRA, CT) [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases] [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleCardiacRegistration]. The goal is to improve the accuracy of the current registration methods by defining case-specific parameters.

</div>

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

<h3>Approach, Plan</h3>

Our approach for registration is parameter optimization for the current ITK registration approaches.

Our plan for the project week is to further define the registration cases and begin implementation in Slicer 4.

</div>

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

<h3>Progress</h3>
We have defined some preliminary registration cases [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases].

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

2012 Summer Project Week:UtahCardiacRegistration

2012-06-21T19:31:41Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA-registration-snapshot-module.png|Initial layout of CARMA registration module.
Image:CARMA_VecReg_Check1-2.png|Current Registration Example - needs some work
Image:CARMA_VecReg_Seg3.png|Current Registration Example - needs some work
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Greg Gardner, Rob MacLeod

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

<h3>Objective</h3>
We are developing a case-specific registration module capable of handling the different image types used at the CARMA Center (e.g., LGE-MRI, MRA, CT) [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases] [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleCardiacRegistration]. The goal is to improve the accuracy of the current registration methods by defining case-specific parameters.

</div>

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

<h3>Approach, Plan</h3>

Our approach for registration is parameter optimization for the current ITK registration approaches.

Our plan for the project week is to further define the registration cases and begin implementation in Slicer 4.

</div>

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

<h3>Progress</h3>
We have defined some preliminary registration cases [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases].

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

File:CARMA-registration-snapshot-module.png

2012-06-21T19:31:00Z

2012 Summer Project Week

2012-06-21T17:08:00Z

Ggardner:

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' [[2012 Project Week Breakout Session: Slicer4|What's new in Slicer4 (Charts - Jim, DICOM - Steve, Multivolume - Andrey)]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' [[2012 Project Week Breakout Session:Slicer4 Python Q&A|Slicer4 Python Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Slicer in Networked Environment|Slicer in Networked Environment]] (Junichi)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2012 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2012 Summer Project Week Breakout Session:Slicer DICOM|Breakout Session: DICOM, Networking, RT, Segmentations]] (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:QtTesting|QtTesting]] (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
<br>----------------------------------------<br>
'''3:00-4:00pm''' [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer (Andras)]]<br>
[[MIT_Project_Week_Rooms#Kiva_32-G449|Grier Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Danielle Pace, Stephen Aylward, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# [[2012_Summer_Project_Week:Intraoperative_Tract_Detection | Intraoperative White Matter Tract Detection Module]] (Lauren O'Donnell, Isaiah Norton)
# [[2012_Summer_Project_Week:Ultrasound_Aberration_Correction | An Ultrasound-based Method for Aberration Correction in TCFUS]] (Jason White, Greg Clement)
# [[2012_Summer_Project_Week:TimeSeriesMonitoringIntracranialBones| Monitoring time series images of intracranial bones in meningioma ]] (Karl Diedrich)
# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck| Atlas-based segmentation for head and neck]] (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
#[[2012_Summer_Project_Week:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, James Shackleford, Steve Pieper)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch loadable module]] (James Shackleford, Greg Sharp)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
#[[2012_Summer_Project_Week:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:PET_Image_Analysis | SUV Threshold Computation]] (Nadya Shusharina, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D Shape Analysis: Software Tools]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Greg Gardner, Alan Morris, Danny Perry, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Greg Gardner, Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Greg Gardner, Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:SlicerWeb|Web Interface to Slicer 4]] (Steve Pieper)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda, Laurent Chauvin)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder and other IGT modules]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:iGyne|iGyne for Gynecological Cancer Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
#[[2012_Summer_Project_Week:Interactive_Needle_Segmentation|Interactive Needle Segmentation for Gynecological Cancer Brachytherapy]] (Nabgha Farhat, Neha Agrawal, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Needle Tip Tracking |Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Pietro Nardelli, Padraig Cantillon-Murphy, Raul San Jose Estepar)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer, Andrey Fedorov)
#[[2012_Summer_Project_Week:ABC_Slicer4|Porting ABC extension to Slicer 4]] (Marcel Prastawa, Bo Wang, Guido Gerig)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#[[2012_Summer_Project_Week:SegmentationWithLabelFusion|Segmentation with Label Fusion]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)

==='''General Registration'''===
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
#[[2012_Summer_Project_Week:ElastixIntegration|Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, Petter Risholm, Dominik Meier, William Wells)

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:CMake_for_AIM_API|CMake-fying AIM API]] (Pat Mongklowat, Vlad Kleper, Andrey Fedorov)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim, Brendan Moloney)
# [[2012_Summer_Project_Week:PythonCLIandWidget|Python CLI modules (Demian, JC, Julien, Steve)]].
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:GPUEditor|GPU Editor Effects]] (Steve, Jim)
# [[2012_Summer_Project_Week:XTK|XTK/WebGL Exporter]] (Daniel, Nicolas - Boston Children's Hospital)
# [[2012_Summer_Project_Week:EventOptimization|Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)]]
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)
# [[2012_Summer_Project_Week:CUDA Volume Rendering Extension|CUDA Volume Rendering as Extension]] (J2, Elvis)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blevins, Scott, BWH, stblevins@gmail.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chambers, Micah, UCLA, micahcc@ucla.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gao, Yi, BWH, gaoyi@bwh.harvard.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Golland, Polina, MIT CSAIL, polina@csail.mit.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Gupta, Aditya, NIRAL UNC, aditya_gupta@med.unc.edu
#Irimia, Andrei, UCLA, andrei.irimia@loni.ucla.edu
#Jagadeesan, Jayender, SPL, jayender@bwh.harvard.edu
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kalpathy-Cramer, Jayashree, MGH, kalpathy@nmr.mgh.harvard.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, (cancelled registration) Erasmus MC, s.klein@erasmusmc.nl
#Kleper, Vladimir, Northwestern Univ, vkleper@northwestern.edu
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Mastrogiacomo, Katie, SPL, BWH, kmast@bwh.harvard.edu
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Mercea, Paul, SPL, pmercea@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Mizutani, Tatsushi, Nagoya Univ, tatsushi0207@me.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Montillo, Albert, GE Research, montillo@ge.com
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Norton, Isaiah, BWH, inorton@partners.org
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#O'Donnell, Lauren, BWH, odonnell@bwh.harvard.edu
#Oyama, Rie, BWH, royama@bwh.harvard.edu
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Penzkofer, Tobias, SPL, pt@bwh.harvard.edu
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Rannou, Nicolas, Childrens Hospital, nicolas.rannou@childrens.harvard.edu
#Razzaque, Sharif, InnerOptic Technology, sharif@inneroptic.com
#Risholm, Petter, Harvard, pettri@bwh.harvard.edu
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Schroeder, William, Kitware, will.schroeder@kitware.com
#Shackleford, James, MGH, jshackleford@partners.org
#Sharp, Greg, MGH, gcsharp@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
#Sridharan, Ramesh, MIT CSAIL, rameshvs@MIT.EDU
#State, Andrei, InnerOptic Technology, andrei@inneroptic.com
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Tokuda, Junichi, BWH, tokuda@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wang, Kevin, Princess Margaret Hospital, kevin.wang@rmp.uhn.on.ca
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Wells, William, HMS BWH, sw@bwh.harvard.edu
#Whitaker, Ross, SCI, whitaker@cs.utah.edu
#White, Phillip, BWH HMS, white@bwh.harvard.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Tutorial Contest

2012-06-19T18:12:46Z

Ggardner:

[[Media:Example.ogg]][http://www.slicer.org Slicer4] is used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer.

The primary purpose of the Summer 2012 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe participants will be motivated to join this event to enhance the dissemination of their own algorithms that they have incorporated into the Slicer4 platform and/or to enhance training of Slicer4 functionality for their own laboratory groups.

There will be three categories:
*Category 1: '''END TO END SOLUTION TUTORIAL''' <br> In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. <br> Example: [http://www.slicer.org/slicerWiki/images/f/f1/NeurosurgicalPlanning_SoniaPujol.pdf White Matter Exploration for Neurosurgical Planning]
*Category 2: '''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data.<br> Examples: [http://www.slicer.org/slicerWiki/images/c/c6/Slicer4QuantitativeImaging.pdf Quantitative Imaging tutorial]<br>
*Category 3: '''METHODOLOGY TUTORIAL'''. Application-level tutorials for users and developers.<br> Examples:[[Slicer3:Fiducials_TutorialContestSummer2010 | '''Fiducials''']]

Entries in each category require the following material:
* scientific background and application motivation
* step-by-step instructions
* anonymized sampel dataset

=Rules=
*Tutorial must be based on the [http://download.slicer.org/ Slicer4.1 release version ].
*To enter the contest, you must provide '''a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)+'''.
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Tutorial data must be anonymized
*Tutorial must include contact information of the primary author (e-mail and phone number)
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2012.ppt‎ | Summer 2012 contest tutorial template]].
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br>
+Applicants will work with the NA-MIC Training and Dissemination Cores in advance to do the multi-platform testing.

=Submission Dead-line and Presentation=

'''<span style="background-color: yellow"> Submission dead-line: Monday June 11, 2012'''</span>
* '''Submission process''': to enter the contest, please follow the 5 steps below:
**1. Create a wiki page for your tutorial on the NA-MIC wiki.
**2. Upload your slides and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestSummer2012.pdf' and 'TutorialData_TutorialContestSummer2012.zip'
**3. Add a link to the uploaded tutorial and datasets on your tutorial page.
**4. Copy the template of the [http://wiki.na-mic.org/Wiki/index.php/Training:Summer_2012_Contest_Table Summer 2012 test table ] on your tutorial page, and enter the results of your cross-platform testing (Mac, Windows XP &7, Linux 64, Linux 32).
**5. Once you have completed step 1-4, add a link to your tutorial page in the list below and send a notification email to Sonia Pujol (spujol at bwh.harvard.edu) to receive a confirmation of your submission.

* '''Presentation at the NA-MIC Project week''': Brief highlights of tutorials will be presented by the authors at 3 pm on Tuesday June 19 at the Summer 2012 Project Week. Each presentation should be 10-minute summary of the submission.

*Tutorial contest entries
#[http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.pdf Automatic Left Atrial Scar Segmenter. Greg Gardner, Josh Cates, SCI, Utah]
#[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of two RT dose distributions. James Shackleford, Nadya Shusharina, Greg Sharp, MGH]
#[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy. Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's]
#[http://www.na-mic.org/Wiki/index.php/WebGLExport_TutorialContestSummer2012 WebGL Export ]
#[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLinkIF Junichi Tokuda, BWH]

Judging will be done immediately following the presentations and winners will be announced Wednesday June 20 at 12:45 PM in the Grier Room.

Contest judges:
* Nicole Aucoin
* Guillaume Pernelle
* Nabgha Farhat
* Sonia Pujol

2012 Summer Project Week

2012-06-12T19:14:11Z

Ggardner:

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' What's new in Slicer4 (Group. Multivolumes, Charts.) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> <br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' Slicer4 Extensions (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font>Qt Testing (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# An Intraoperative Transcranial Ultrasound Brain Shift Monitor (Jason White, Alex Golby, Isaiah Norton)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT|Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
# [[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch integration]] (James Shackleford, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D shape analysis]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# OpenIGT for realtime MRI-guided RF ablation (Rob MacLeod, and Junichi Tokuda) ??
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Padraig Cantillon-Murphy, Raul San Jose Estepar, Pietro Nardelli)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer)
#[[2012_Summer_Project_Week:ABC_Slicer4|Porting ABC extension to Slicer 4]] (Marcel Prastawa, Bo Wang, Guido Gerig)

==='''General Registration'''===
# Interactive registration (Kunlin Cao GRC, Guillaume Pernelle BWH, Simrin Nagpal Queens)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, William Wells)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim)
# Python CLI modules (Demian, JC, Julien). See [http://www.na-mic.org/Bug/view.php?id=2039 #2039]
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html |hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blevins, Scott, BWH, stblevins@gmail.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Golland, Polina, MIT CSAIL, polina@csail.mit.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Montillo, Albert, GE Research, montillo@ge.com
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Shackleford, James, MGH, jshackleford@partners.org
#Sharp, Greg, MGH, gcsharp@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
#Sridharan, Ramesh, MIT CSAIL, rameshvs@MIT.EDU
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#White, Phillip, BWH HMS, white@bwh.harvard.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

2012 Summer Project Week

2012-06-12T18:14:44Z

Ggardner:

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' What's new in Slicer4 (Group. Multivolumes, Charts.) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> <br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' Slicer4 Extensions (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font>Qt Testing (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# An Intraoperative Transcranial Ultrasound Brain Shift Monitor (Jason White, Alex Golby, Isaiah Norton)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT|Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
# [[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch integration]] (James Shackleford, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D shape analysis]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Padraig Cantillon-Murphy, Raul San Jose Estepar, Pietro Nardelli)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer)

==='''General Registration'''===
# Interactive registration (Kunlin Cao GRC, Guillaume Pernelle BWH, Simrin Nagpal Queens)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, William Wells)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim)
# Python CLI modules (Demian, JC, Julien). See [http://www.na-mic.org/Bug/view.php?id=2039 #2039]
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html |hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Montillo, Albert, GE Research, montillo@ge.com
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Shackleford, James, MGH, jshackleford@partners.org
#Sharp, Greg, MGH, gcsharp@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

File:CARMA-LA-Scar TutorialContestSummer2012.pdf

2012-06-11T16:13:24Z

Ggardner: uploaded a new version of "File:CARMA-LA-Scar TutorialContestSummer2012.pdf": Tutorial slides for CARMA automatic LA scar segmentation module -- Project Week Summer 2012.

Tutorial slides for CARMA automatic LA scar segmentation module -- Project Week Summer 2012.

2012 Summer Project Week:UtahCardiacRegistration

2012-06-10T00:40:45Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA_VecReg_Check1-2.png|Current Registration Example - needs some work
Image:CARMA_VecReg_Seg3.png|Current Registration Example - needs some work
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Greg Gardner, Rob MacLeod

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

<h3>Objective</h3>
We are developing a case-specific registration module capable of handling the different image types used at the CARMA Center (e.g., LGE-MRI, MRA, CT) [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases] [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleCardiacRegistration]. The goal is to improve the accuracy of the current registration methods by defining case-specific parameters.

</div>

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

<h3>Approach, Plan</h3>

Our approach for registration is parameter optimization for the current ITK registration approaches.

Our plan for the project week is to further define the registration cases and begin implementation in Slicer 4.

</div>

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

<h3>Progress</h3>
We have defined some preliminary registration cases [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases].

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

2012 Summer Project Week:VecReg

2012-06-10T00:40:14Z

Ggardner: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List Image:CARMA_VecReg_Check1-2.png|Current Registration Example - needs some work Image:…'

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA_VecReg_Check1-2.png|Current Registration Example - needs some work
Image:CARMA_VecReg_Seg3.png|Current Registration Example - needs some work
</gallery>

==Key Investigators==
* BWH: Yi Gao, Sylvain Bouix
* Utah: Danny Perry, Alan Morris, Josh Cates, Greg Gardner, Rob MacLeod
* BU: Allen Tannenbaum
* GaTech: Liang-Jia Zhu

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

<h3>Objective</h3>
We are developing a vector-valued registration module capable of registering pre- and post-ablation images, using the information from the MRI images and corresponding segmentations. The goal is to improve the accuracy of the current registration methods.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to use the information in the LGE-MRI images and the blood pool segmentations to drive the registration.

Our plan for the project week is to evaluate the existing method and develop an approach to improve the current accuracy.

</div>

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

<h3>Progress</h3>
We have generated some initial registration examples [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:VecReg]. We need to improve the spatial accuracy of the current methods.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

2012 Summer Project Week:UtahAutoScar

2012-06-10T00:33:13Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:carma_afib_auto_scar.png|Automatic Left Atrial Scar Segmentation
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for automatically detecting post-procedural scar in LGE-MRI images. The goal is to make statistical group comparisons based on the spatial distribution and amount of scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach for automatic scar segmentation is summarized in the SPIE 2012 reference below. Briefly, we are using k-means clustering to tease apart the normalized pixel intensities corresponding to different tissue types (e.g., healthy, scar, blood).

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples. We will present a tutorial on this module during the project week tutorial contest [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012]

</div>

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

<h3>Progress</h3>
Software for the automatic scar segmentation has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleAutoScar]. We need to create documentations and tutorials as well as finalize the migration to Slicer 4. We have begun statistical analysis and validation of the module.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==
*Daniel Perry, Alan Morris, Nathan Burgon, Christopher McGann, Robert MacLeod, Joshua Cates. "Automatic classiﬁcation of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation". SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

2012 Summer Project Week:UtahCardiacRegistration

2012-06-10T00:31:38Z

Ggardner: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List Image:CARMA_VecReg_Check1-2.png|Current Registration Example - needs some work Image:…'

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:CARMA_VecReg_Check1-2.png|Current Registration Example - needs some work
Image:CARMA_VecReg_Seg3.png|Current Registration Example - needs some work
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Greg Gardner, Rob MacLeod

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

<h3>Objective</h3>
We are developing a case-specific registration module capable of handling the different image types used at the CARMA Center (e.g., LGE-MRI, MRA, CT) [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases]. The goal is to improve the accuracy of the current registration methods by defining case-specific parameters.

</div>

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

<h3>Approach, Plan</h3>

Our approach for registration is parameter optimization for the current ITK registration approaches.

Our plan for the project week is to further define the registration cases and begin implementation in Slicer 4.

</div>

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

<h3>Progress</h3>
We have defined some preliminary registration cases [http://www.na-mic.org/Wiki/index.php/DBP3:Utah:RegCases].

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

2012 Summer Project Week:UtahAutoScar

2012-06-10T00:23:21Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:carma_afib_auto_scar.png|Automatic Left Atrial Scar Segmentation
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for automatically detecting post-procedural scar in LGE-MRI images. The goal is to be able to make statistical group comparisons based on the spatial distribution and amount of scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach for automatic scar segmentation is summarized in the SPIE 2012 reference below. Briefly, we are using k-means clustering to tease apart the normalized pixel intensities corresponding to different tissue types (e.g., healthy, scar, blood).

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples. We will present a tutorial on this module during the project week tutorial contest [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012]

</div>

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

<h3>Progress</h3>
Software for the automatic scar segmentation has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleAutoScar]. We need to create documentations and tutorials as well as finalize the migration to Slicer 4. We have begun statistical analysis and validation of the module.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==
*Daniel Perry, Alan Morris, Nathan Burgon, Christopher McGann, Robert MacLeod, Joshua Cates. "Automatic classiﬁcation of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation". SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

2012 Summer Project Week:UtahInhomogeneity

2012-06-10T00:22:49Z

Ggardner: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List Image:carma_afib_inhomogeneity_correction.png|Cardiac-Specific Inhomogeneity Correcti…'

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:carma_afib_inhomogeneity_correction.png|Cardiac-Specific Inhomogeneity Correction Example
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Eugene Kholmovski, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for localized inhomogeneity correction for cardiac LGE-MRI images. The goal is to be able to reduce some of the noise inherent in cardiac LGE-MRI scans to improve clinical diagnoses and statistical comparisons.

</div>

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

<h3>Approach, Plan</h3>

Our approach for inhomogeneity correction is a gradient function to the image data that normalizes accordingly.

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples.

</div>

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

<h3>Progress</h3>
Software for the inhomogeneity correction has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleInhomogeneity]. We need to create documentations and tutorials as well as finalize the migration to Slicer 4. We have begun validation of the module.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==

2012 Summer Project Week:UtahAutoScar

2012-06-10T00:17:54Z

Ggardner:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:carma_afib_auto_scar.png|Automatic Left Atrial Scar Segmentation
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for automatically detecting post-procedural scar in LGE-MRI images. The goal is to be able to make statistical group comparisons based on the spatial distribution and amount of scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the SPIE 2012 reference below. Briefly, we are using k-means clustering to tease apart the normalized pixel intensities corresponding to different tissue types (e.g., healthy, scar, blood).

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples. We will present a tutorial on this module during the project week tutorial contest [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012]

</div>

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

<h3>Progress</h3>
Software for the automatic scar segmentation has been implemented [http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleAutoScar]. We need to create documentations and tutorials as well as finalize the migration to Slicer 4. We have begun statistical analysis and validation of the module.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==
*Daniel Perry, Alan Morris, Nathan Burgon, Christopher McGann, Robert MacLeod, Joshua Cates. "Automatic classiﬁcation of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation". SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

2012 Summer Project Week:UtahAutoScar

2012-06-10T00:17:05Z

Ggardner: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List Image:carma_afib_auto_scar.png|Automatic Left Atrial Scar Segmentation </gallery> ==…'

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:carma_afib_auto_scar.png|Automatic Left Atrial Scar Segmentation
</gallery>

==Key Investigators==
* Utah: Danny Perry, Alan Morris, Josh Cates, Rob MacLeod

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

<h3>Objective</h3>
We are developing methods for automatically detecting post-procedural scar in LGE-MRI images. The goal is to be able to make statistical group comparisons based on the spatial distribution and amount of scar.

</div>

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

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the SPIE 2012 reference below. Briefly, we are using k-means clustering to tease apart the normalized pixel intensities corresponding to different tissue types (e.g., healthy, scar, blood).

Our plan for the project week is to test our module, and ensure that it meets "Ron's Rules" and develop supporting documentation/examples. We will present a tutorial on this module during the project week tutorial contest [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012]

</div>

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

<h3>Progress</h3>
Software for the automatic scar segmentation has been implemented. We need to create documentations and tutorials as well as finalize the migration to Slicer 4. We have begun statistical analysis and validation of the module.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module - NO
#Slicer Module
##Built-in - NO
##Extension -- commandline - YES
##Extension -- loadable - NO
#Other (Please specify)

==References==
*Daniel Perry, Alan Morris, Nathan Burgon, Christopher McGann, Robert MacLeod, Joshua Cates. "Automatic classiﬁcation of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation". SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.

2012 Summer Project Week

2012-06-09T23:59:08Z

Ggardner:

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' What's new in Slicer4 (Group. Multivolumes, Charts.) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> <br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' Slicer4 Extensions (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font>Qt Testing (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# An Intraoperative Transcranial Ultrasound Brain Shift Monitor (Jason White, Alex Golby, Isaiah Norton)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT|Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D shape analysis]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# OpenIGT for realtime MRI-guided RF ablation (Rob MacLeod, Junichi Tokuda)
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Padraig Cantillon-Murphy, Raul San Jose Estepar, Pietro Nardelli)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer)

==='''General Registration'''===
# Interactive registration (Kunlin Cao GRC, Guillaume Pernelle BWH, Simrin Nagpal Queens)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, William Wells)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim)
# Python CLI modules (Demian, JC, Julien). See [http://www.na-mic.org/Bug/view.php?id=2039 #2039]
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html |hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Datar, Manasi, Utah SCI, brenda@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Miller, Jim, GE Research, millerjv@ge.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

DBP3:Utah:SlicerModuleAutoScar

2012-06-09T23:10:10Z

Ggardner:

__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

* [http://wiki.na-mic.org/Wiki/index.php?title=CARMA-LA-Scar_TutorialContestSummer2012 Tutorial]

===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.

CARMA-LA-Scar TutorialContestSummer2012

2012-06-09T23:08:07Z

Ggardner:

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

Material for the Slicer 4.1 CARMA automatic left atrial scar segmentation tutorial, Project Week Summer 2012:

[http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.pdf PDF: CARMA-LA-Scar_TutorialContestSummer2012.pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip Data: CARMA-LA-Scar_TutorialContestSummer2012.zip]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''
|-
| CARMA LA Scar Segmentation || Mac OS || 2012/06/06 || ||
| Worked
|-
| CARMA LA Scar Segmentation || Windows 7 32 bit || Slicer 4.1 || ||
| Worked
|-
| CARMA LA Scar Segmentation || Windows 7 64 bit || 2012/06/06 || ||
| Worked
|-
| CARMA LA Scar Segmentation || Linux 64 bit || || ||
|
|-
|}
</table>

[http://www.na-mic.org/Wiki/index.php/2012_Tutorial_Contest Back to tutorial contest]

CARMA-LA-Scar TutorialContestSummer2012

2012-06-09T23:04:25Z

Ggardner: Created page with 'Material for the Slicer 4.1 CARMA automatic left atrial scar segmentation tutorial, Project Week Summer 2012: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialC…'

Material for the Slicer 4.1 CARMA automatic left atrial scar segmentation tutorial, Project Week Summer 2012:

[http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.pdf PDF: CARMA-LA-Scar_TutorialContestSummer2012.pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip Data: CARMA-LA-Scar_TutorialContestSummer2012.zip]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Author''' ||'''Test results (Mantis Links if tests failed)'''
|-
| CARMA LA Scar Segmentation || Mac OS || 2012/06/06 || ||
| Worked
|-
| CARMA LA Scar Segmentation || Windows 7 32 bit || Slicer 4.1 || ||
| Worked
|-
| CARMA LA Scar Segmentation || Windows 7 64 bit || 2012/06/06 || ||
| Worked
|-
| CARMA LA Scar Segmentation || Linux 64 bit || || ||
|
|-
|}
</table>

[http://www.na-mic.org/Wiki/index.php/2012_Tutorial_Contest Back to tutorial contest]

File:CARMA-LA-Scar TutorialContestSummer2012.pdf

2012-06-09T22:51:27Z

Ggardner: Tutorial slides for CARMA automatic LA scar segmentation module -- Project Week Summer 2012.

Tutorial slides for CARMA automatic LA scar segmentation module -- Project Week Summer 2012.

File:CARMA-LA-Scar TutorialContestSummer2012.zip

2012-06-08T22:22:49Z

Ggardner: This is data set for the CARMA Left Atrial Scar module tutorial. This tutorial was submitted for the 2012 summer project week.

This is data set for the CARMA Left Atrial Scar module tutorial. This tutorial was submitted for the 2012 summer project week.

DBP3:Utah:RegCases

2012-05-10T18:21:22Z

Ggardner:

Back to [[DBP3:Utah|Utah AFib DBP]]
__NOTOC__

== Background ==

* The CARMA Center uses late gadolinium enhanced MRI (LGE-MRI) images to evaluate new patients, predict procedural success, and evaluate therapeutic outcomes. The MRI images for each patient are further accompanied by MR angiographic images (MRA) and manual segmentations of relevant structures. These images are acquired longitudinally over the course of a patient's evaluation, treatment, and follow-up (i.e. months or years). Registration is often necessary to compare images from different time points in a patient's treatment, different patients at the same stage of disease progression or treatment, and different image types. Registration is needed for a variety of combinations of common image types encountered at CARMA:

{| class="wikitable"
|-
! Pre-ablation LGE-MRI Image
! Post-ablation LGE-MRI Image
! Segmentation of LGE-MRI Image
|-
| [[File:carma_ex_pre.png|thumb|center]]
| [[File:carma_ex_post.png|thumb|center]]
| [[File:carma_ex_pre_seg.png|thumb|center]]
|-
|}

{| class="wikitable"
|-
! MRA Image
! Immediately Post-ablation LGE-MRI Image
! CT Image
|-
| [[File:carma_ex_mra.png|thumb|center]]
| [[File:Carma_no_reflow.png|thumb|center]]
| [[File:Carma_reg_CT.jpg|thumb|center]]
|-
|}

* Pre-ablation scans are acquired before the procedural. Bright portions in the LA wall is indicative of fibrosis; fibrosis scores are used to stratify and triage patients based on their Utah score.
* Post-ablation scans are acquired 3 months and later after the procedure. These scans have higher contrast (brighter regions) in the LA wall indicative of scaring from the ablation procedure.
* Segmentations will be binary label masks manually-contoured by experts at CARMA.
* MRAs have a bright blood pool, the bounds of which indicate the endocardial surface of the LA wall.
* Immediately-post ablation scans exhibit large, bright areas in and around the LA walls, reflecting edema and shape changes caused by the ablation procedures.
* CT scans are less common but can be acquired with a contrast agent to delineate the bounds of the blood pool. Many of our CT scans are acquired with a C-arm fluoroscopy unit rather than a traditional CT scanner.

== Registration Case Types ==

These are current projects at CARMA which could be aided by improved, case-specific registration algorithms. The projects are sorted according to the types of images to be registered.

=== Pre to Post LGE-MRI ===

* Residual fibrosis project -- Nazem Akoum
Registration of pre to post (at least 3 months) LGE-MRI to examine the overlap of fibrosis and post-procedural scar. Findings may support targeting ablations to areas of intense fibrosis. Registration may be complicated as LA volume will decrease after ablation.

=== Pre to Pre LGE-MRI ===

* AF progression -- UMAC
Registration of images from animals with induced AF to examine the progression of the disease. There will be multiple time points for each animal; scans are often acquired monthly. Registration will allow for changes in shape, volume, and fibrosis distribution to be examined. We may also look at registering images across different animals.

* Logitudinal pre-ablation scans -- Nathan Burgon/Chris McGann
Similar to the UMAC AF progression study, examining the progression of AF in humans. Scans will all be longitudinal pre-ablation; these scans typically come from patients who opt not to be ablated. The time between scans will likely be irregular and possibly as much as a couple years.

=== Post to Post LGE-MRI ===

* Permanent scar formation -- Koji Higuchi
This study examines at lost 2 post-ablation scans (likely 3 months and 2 years post-ablation). This allows us to assess the permanence of scar after the blanking period (3 months) to more stable, long-term scar formation.

=== MRA to LGE-MRI ===

* MRA threshold-based segmentation -- Image processing group
The MRA captures the extent of the blood pool and roughly corresponds to the endocardial surface of the LA wall. The MRA is also much easier to automatically segment. Registration of the MRA to LGE-MRI would allow for segmentation of the MRA blood pool as an initial guess in segmentation of the LGE-MRI blood pool. We will likely need gated MRAs.

=== MRA to MRA ===

* Shape-analysis studies -- Image processing group
The MRA is a quick and dirty way of capturing the bounds of the blood pool for shape studies. Alignment of the MRAs will allow for alignment of the blood pool masks for input into shape analysis pipelines (i.e., ShapeWorks)

=== Immediately-Post to Post LGE-MRI ===

* Ablation gaps -- Ravi Ranjan
Registration of animal scans or patient scans to look for the appearance of gaps in the lesion sets after ablation and how that impacts scar development.

* No-reflow studies -- Chris McGann
A more general variation of the gap study; how do no-reflow regions spatially correlate to permanent scar formation. Challenges will include major inflammation, variable wall thickness, and deformation.

=== Vector-Valued Registration ===

* Cardiac-specific image registration -- Yi Gao/Josh Cates
A collaboration with Yi Gao et al. to use blood pool segmentation and raw images before and after ablation to more accurately register the cardiac anatomy from the images.

=== CT to LGE-MRI ===

* Shape-analysis studies -- Image processing group
CT better captures the shape of the LA and is more easily segmented. We hope to compare the volumes and shapes of CT-derived LA segmentations to those of MRI-segmented images. We will need to register the CT and MRI images to make this work. A potential challenge here is the scarcity of CT scans (namely normal CT scans, although, DynaCT scans are also not commonly acquired).

== Implementation ==

* We are currently defining an optimized set of registration parameters for each of the above cases
* We will develop a Slicer extension module with the pre-defined registration parameters for each of the above scenarios
* The module will take as input two images; a drop-down menu will let the user select the appropriate registration scenario
* The module will return a registered output image

File:Carma reg CT.jpg

2012-05-10T18:20:38Z

Ggardner: Example CARMA CT image (likely DynaCT).

Example CARMA CT image (likely DynaCT).

File:Carma no reflow.jpg

2012-05-10T18:20:06Z

Ggardner: Example CARMA CT image (likely DynaCT).

Example CARMA CT image (likely DynaCT).

DBP3:Utah:RegCases

2012-05-10T00:14:25Z

Ggardner:

Back to [[DBP3:Utah|Utah AFib DBP]]
__NOTOC__

== Background ==

* The CARMA Center uses late gadolinium enhanced MRI (LGE-MRI) images to evaluate new patients, predict procedural success, and evaluate therapeutic outcomes. The MRI images for each patient are further accompanied by MR angiographic images (MRA) and manual segmentations of relevant structures. These images are acquired longitudinally over the course of a patient's evaluation, treatment, and follow-up (i.e. months or years). Registration is often necessary to compare images from different time points in a patient's treatment, different patients at the same stage of disease progression or treatment, and different image types. Registration is needed for a variety of combinations of common image types encountered at CARMA:

{| class="wikitable"
|-
! Pre-ablation LGE-MRI Image
! Post-ablation LGE-MRI Image
! Segmentation of LGE-MRI Image
|-
| [[File:carma_ex_pre.png|thumb|center]]
| [[File:carma_ex_post.png|thumb|center]]
| [[File:carma_ex_pre_seg.png|thumb|center]]
|-
|}

{| class="wikitable"
|-
! MRA Image
! Immediately Post-ablation (IPA) LGE-MRI Image
|-
| [[File:carma_ex_mra.png|thumb|center]]
| [[File:Carma_no_reflow.png|thumb|center]]
|-
|}

* Pre-ablation scans are acquired before the procedural. Bright portions in the LA wall is indicative of fibrosis; fibrosis scores are used to stratify and triage patients based on their Utah score.
* Post-ablation scans are acquired 3 months and later after the procedure. These scans have higher contrast (brighter regions) in the LA wall indicative of scaring from the ablation procedure.
* Segmentations will be binary label masks manually-contoured by experts at CARMA.
* MRAs have a bright blood pool, the bounds of which indicate the endocardial surface of the LA wall.
* Immediately-post ablation scans exhibit large, bright areas in and around the LA walls, reflecting edema and shape changes caused by the ablation procedures.
* CT scans are less common but can be acquired with a contrast agent to delineate the bounds of the blood pool. Many of our CT scans are acquired with a C-arm fluoroscopy unit rather than a traditional CT scanner.

== Registration Case Types ==

These are current projects at CARMA which could be aided by improved, case-specific registration algorithms. The projects are sorted according to the types of images to be registered.

=== Pre to Post LGE-MRI ===

* Residual fibrosis project -- Nazem Akoum
Registration of pre to post (at least 3 months) LGE-MRI to examine the overlap of fibrosis and post-procedural scar. Findings may support targeting ablations to areas of intense fibrosis. Registration may be complicated as LA volume will decrease after ablation.

=== Pre to Pre LGE-MRI ===

* AF progression -- UMAC
Registration of images from animals with induced AF to examine the progression of the disease. There will be multiple time points for each animal; scans are often acquired monthly. Registration will allow for changes in shape, volume, and fibrosis distribution to be examined. We may also look at registering images across different animals.

* Logitudinal pre-ablation scans -- Nathan Burgon/Chris McGann
Similar to the UMAC AF progression study, examining the progression of AF in humans. Scans will all be longitudinal pre-ablation; these scans typically come from patients who opt not to be ablated. The time between scans will likely be irregular and possibly as much as a couple years.

=== Post to Post LGE-MRI ===

* Permanent scar formation -- Koji Higuchi
This study examines at lost 2 post-ablation scans (likely 3 months and 2 years post-ablation). This allows us to assess the permanence of scar after the blanking period (3 months) to more stable, long-term scar formation.

=== MRA to LGE-MRI ===

* MRA threshold-based segmentation -- Image processing group
The MRA captures the extent of the blood pool and roughly corresponds to the endocardial surface of the LA wall. The MRA is also much easier to automatically segment. Registration of the MRA to LGE-MRI would allow for segmentation of the MRA blood pool as an initial guess in segmentation of the LGE-MRI blood pool. We will likely need gated MRAs.

=== MRA to MRA ===

* Shape-analysis studies -- Image processing group
The MRA is a quick and dirty way of capturing the bounds of the blood pool for shape studies. Alignment of the MRAs will allow for alignment of the blood pool masks for input into shape analysis pipelines (i.e., ShapeWorks)

=== Immediately-Post to Post LGE-MRI ===

* Ablation gaps -- Ravi Ranjan
Registration of animal scans or patient scans to look for the appearance of gaps in the lesion sets after ablation and how that impacts scar development.

* No-reflow studies -- Chris McGann
A more general variation of the gap study; how do no-reflow regions spatially correlate to permanent scar formation. Challenges will include major inflammation, variable wall thickness, and deformation.

=== Vector-Valued Registration ===

* Cardiac-specific image registration -- Yi Gao/Josh Cates
A collaboration with Yi Gao et al. to use blood pool segmentation and raw images before and after ablation to more accurately register the cardiac anatomy from the images.

=== CT to LGE-MRI ===

* Shape-analysis studies -- Image processing group
CT better captures the shape of the LA and is more easily segmented. We hope to compare the volumes and shapes of CT-derived LA segmentations to those of MRI-segmented images. We will need to register the CT and MRI images to make this work. A potential challenge here is the scarcity of CT scans (namely normal CT scans, although, DynaCT scans are also not commonly acquired).

== Implementation ==

* We are currently defining an optimized set of registration parameters for each of the above cases
* We will develop a Slicer extension module with the pre-defined registration parameters for each of the above scenarios
* The module will take as input two images; a drop-down menu will let the user select the appropriate registration scenario
* The module will return a registered output image

DBP3:Utah:RegCases

2012-05-10T00:14:03Z

Ggardner:

Back to [[DBP3:Utah|Utah AFib DBP]]
__NOTOC__

== Background ==

* The CARMA Center uses late gadolinium enhanced MRI (LGE-MRI) images to evaluate new patients, predict procedural success, and evaluate therapeutic outcomes. The MRI images for each patient are further accompanied by MR angiographic images (MRA) and manual segmentations of relevant structures. These images are acquired longitudinally over the course of a patient's evaluation, treatment, and follow-up (i.e. months or years). Registration is often necessary to compare images from different time points in a patient's treatment, different patients at the same stage of disease progression or treatment, and different image types. Registration is needed for a variety of combinations of common image types encountered at CARMA:

{| class="wikitable"
|-
! Pre-ablation LGE-MRI Image
! Post-ablation LGE-MRI Image
! Segmentation of LGE-MRI Image
|-
| [[File:carma_ex_pre.png|thumb|center]]
| [[File:carma_ex_post.png|thumb|center]]
| [[File:carma_ex_pre_seg.png|thumb|center]]
|-
|}

{| class="wikitable"
|-
! MRA Image
! Immediately Post-ablation (IPA) LGE-MRI Image
|-
| [[File:carma_ex_mra.png|thumb|center]]
| [[File:Carma_no_reflow.png|thumb|center]]
|-
|}

* Pre-ablation scans are acquired before the procedural. Bright portions in the LA wall is indicative of fibrosis; fibrosis scores are used to stratify and triage patients based on their Utah score.
* Post-ablation scans are acquired 3 months and later after the procedure. These scans have higher contrast (brighter regions) in the LA wall indicative of scaring from the ablation procedure.
* Segmentations will be binary label masks manually-contoured by experts at CARMA.
* MRAs have a bright blood pool, the bounds of which indicate the endocardial surface of the LA wall.
* Immediately-post ablation scans exhibit large, bright areas in and around the LA walls, reflecting edema and shape changes caused by the ablation procedures.
* CT scans are less common but can be acquired with a contrast agent to delineate the bounds of the blood pool. Many of our CT scans are acquired with a C-arm fluoroscopy unit rather than a traditional CT scanner.

== Registration Case Types ==

These are current projects at CARMA which could be aided by improved, case-specific registration algorithms. The projects are sorted according to the types of images to be registered.

=== Pre to Post LGE-MRI ===

* Residual fibrosis project -- Nazem Akoum
Registration of pre to post (at least 3 months) LGE-MRI to examine the overlap of fibrosis and post-procedural scar. Findings may support targeting ablations to areas of intense fibrosis. Registration may be complicated as LA volume will decrease after ablation.

=== Pre to Pre LGE-MRI ===

* AF progression -- UMAC
Registration of images from animals with induced AF to examine the progression of the disease. There will be multiple time points for each animal; scans are often acquired monthly. Registration will allow for changes in shape, volume, and fibrosis distribution to be examined. We may also look at registering images across different animals.

* Logitudinal pre-ablation scans -- Nathan Burgon/Chris McGann
Similar to the UMAC AF progression study, examining the progression of AF in humans. Scans will all be longitudinal pre-ablation; these scans typically come from patients who opt not to be ablated. The time between scans will likely be irregular and possibly as much as a couple years.

=== Post to Post LGE-MRI ===

* Permanent scar formation -- Koji Higuchi
This study examines at lost 2 post-ablation scans (likely 3 months and 2 years post-ablation). This allows us to assess the permanence of scar after the blanking period (3 months) to more stable, long-term scar formation.

=== MRA to LGE-MRI ===

* MRA threshold-based segmentation -- Image processing group
The MRA captures the extent of the blood pool and roughly corresponds to the endocardial surface of the LA wall. The MRA is also much easier to automatically segment. Registration of the MRA to LGE-MRI would allow for segmentation of the MRA blood pool as an initial guess in segmentation of the LGE-MRI blood pool. We will likely need gated MRAs.

=== MRA to MRA ===

* Shape-analysis studies -- Image processing group
The MRA is a quick and dirty way of capturing the bounds of the blood pool for shape studies. Alignment of the MRAs will allow for alignment of the blood pool masks for input into shape analysis pipelines (i.e., ShapeWorks)

=== Immediately-Post to Post LGE-MRI ===

* Ablation gaps -- Ravi Ranjan
Registration of animal scans or patient scans to look for the appearance of gaps in the lesion sets after ablation and how that impacts scar development.

* No-reflow studies -- Chris McGann
A more general variation of the gap study; how do no-reflow regions spatially correlate to permanent scar formation. Challenges will include major inflammation, variable wall thickness, and deformation.

=== Vector-Valued Registration ===

* Cardiac-specific image registration -- Yi Gao/Josh Cates
A collaboration with Yi Gao et al. to use blood pool segmentation and raw images before and after ablation to more accurately register the cardiac anatomy from the images.

=== CT to LGE-MRI ===

* Shape-analysis studies -- Image processing group
CT better captures the shape of the LA and is more easily segmented. We hope to compare the volumes and shapes of CT-derived LA segmentations to those of MRI-segmented images. We will need to register the CT and MRI images to make this work. A potential challenge here is the scarcity of CT scans (namely normal CT scans, although, DynaCT scans are also not commonly acquired).

== Implementation ==

* We are currently defining an optimized set of registration parameters for each of the above cases
* We will develop a Slicer extension module with the pre-defined registration parameters for each of the above scenarios
* The module will take as input two images; a drop-down menu will let the user select the appropriate registration scenario
* The module will return a registered output image