NAMIC Wiki - User contributions [en]

2014 Project Week Breakout Session: Slicer for users

2014-06-24T14:04:49Z

Ivan.kolesov:

[[2014_Summer_Project_Week|Back to project week]]

Wednesday, 11-12

This will be an informal discussion of new features in 3D Slicer. Some of the extensions will be mentioned as well.

*Data Store
**Registration library

*Extensions:
**Slicer RT
**IASEM
**Carrera - Ivan Kolesov

2014 Summer Project Week:InteractiveRegistration

2014-06-23T02:14:56Z

Ivan.kolesov: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List Image:PW-MIT2014.png|Projects List </gallery> …'

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Ivan Kolesov, Greg Sharp, Allen Tannenbaum

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Define the interface between existing automatic algorithm and the interactive version.
* Investigate using the plastimatch software as the main building block.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Summer Project Week

2014-06-23T02:10:34Z

Ivan.kolesov: /* Head and Neck Cancer */

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|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'''
|
|'''10-11:30pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[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''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==

==Huntington's Disease==
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp)
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)

==Cardiac==

==Stroke==
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Nobuhiko Hata)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer(WPI), Nirav Patel(WPI), Nobuhiko Hata (BWH) )
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

==Radiation Therapy==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques, ?)
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)

==Chronic Obstructive Pulmonary Disease ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)

==[http://qiicr.org QIICR]==
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim, ...)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim? Dirk?)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras?, ?)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc, ?)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba, ?)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

==Feature Extraction==
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)

==Other==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, University College Cork (UCC), Ireland)
*[[2014_Summer_Project_Week:Intraoperative_Registration_of_preoperative_CT_and_C-arm_CT_of_the_lung | Intraoperative Registration of preoperative CT and C-arm CT of the lung]] (Katharina Breininger, Jay Jagadeesan)
*[[2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders | CAD Toolbox for Neurological Disorders]] (Sidong Liu, Siqi Liu, Fan Zhang, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis)
*[[2014_Summer_Project_Week:Longitudinal_patient_specific_DTI_analysis | Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia]] (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Saskia Camps, SPL, saskiacamps@gmail.com
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Robin Kouver, BWH/SPL, r.kouver@gmail.com
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
#Yangming Li, University of Washington, ymli81@uw.edu
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week

2014-06-23T02:09:59Z

Ivan.kolesov: /* Head and Neck Cancer */

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|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'''
|
|'''10-11:30pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[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''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==

==Huntington's Disease==
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)

==Cardiac==

==Stroke==
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Nobuhiko Hata)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer(WPI), Nirav Patel(WPI), Nobuhiko Hata (BWH) )
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

==Radiation Therapy==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques, ?)
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)

==Chronic Obstructive Pulmonary Disease ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)

==[http://qiicr.org QIICR]==
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim, ...)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim? Dirk?)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras?, ?)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc, ?)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba, ?)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

==Feature Extraction==
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)

==Other==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, University College Cork (UCC), Ireland)
*[[2014_Summer_Project_Week:Intraoperative_Registration_of_preoperative_CT_and_C-arm_CT_of_the_lung | Intraoperative Registration of preoperative CT and C-arm CT of the lung]] (Katharina Breininger, Jay Jagadeesan)
*[[2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders | CAD Toolbox for Neurological Disorders]] (Sidong Liu, Siqi Liu, Fan Zhang, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis)
*[[2014_Summer_Project_Week:Longitudinal_patient_specific_DTI_analysis | Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia]] (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Saskia Camps, SPL, saskiacamps@gmail.com
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Robin Kouver, BWH/SPL, r.kouver@gmail.com
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
#Yangming Li, University of Washington, ymli81@uw.edu
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Project Week:CarreraSlice

2014-01-10T16:14:38Z

Ivan.kolesov:

__NOTOC__

<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:FGCsnapshot.png‎| Guide.
</gallery>

==Key Investigators==

* Ivan Kolesov, LiangJia Zhu, Allen Tannenbaum, Stony Brook University
* Nadya Shusharina, Gregory Sharp, MGH
* Yi Gao, University of Alabama Birmingham

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We have created an editor extension for quickly initializing, interactively segmenting targets. Currently, a portion of the module is based on a command line function. We will improve the speed, re-usability of the module by moving the command line portion to a slicer loadable module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a loadable module from an existing command line module

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Creeated loadable module; now, debugging
*Made a 'Guide' to help user with the pipeline
*Fixed scenario with user accidentally selecting zero label for segmentation

File:FGCsnapshot.png

2014-01-10T16:13:14Z

Ivan.kolesov:

2014 Project Week:CarreraSlice

2014-01-10T16:10:50Z

Ivan.kolesov:

__NOTOC__

<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:FGCsnapshot.png‎| Initialization.
</gallery>

==Key Investigators==

* Ivan Kolesov, LiangJia Zhu, Allen Tannenbaum, Stony Brook University
* Nadya Shusharina, Gregory Sharp, MGH
* Yi Gao, University of Alabama Birmingham

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We have created an editor extension for quickly initializing, interactively segmenting targets. Currently, a portion of the module is based on a command line function. We will improve the speed, re-usability of the module by moving the command line portion to a slicer loadable module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a loadable module from an existing command line module

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Creeated loadable module; now, debugging
*Made a 'Guide' to help user with the pipeline
*Fixed scenario with user accidentally selecting zero label for segmentation

2014 Project Week:CarreraSlice

2014-01-10T15:57:35Z

Ivan.kolesov: /* Project Description */

__NOTOC__

<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:CarreraSlice1.png‎| Initialization.
Image:CarreraSlice2.png | Refinement.
</gallery>

==Key Investigators==

* Ivan Kolesov, LiangJia Zhu, Allen Tannenbaum, Stony Brook University
* Nadya Shusharina, Gregory Sharp, MGH
* Yi Gao, University of Alabama Birmingham

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We have created an editor extension for quickly initializing, interactively segmenting targets. Currently, a portion of the module is based on a command line function. We will improve the speed, re-usability of the module by moving the command line portion to a slicer loadable module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a loadable module from an existing command line module

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Creeated loadable module; now, debugging
*Made a 'Guide' to help user with the pipeline
*Fixed scenario with user accidentally selecting zero label for segmentation

2014 Project Week:CarreraSlice

2013-12-26T19:42:09Z

Ivan.kolesov: Created page with '__NOTOC__ <gallery> Image:PW-SLC2014.png|Projects List Image:CarreraSlice1.png‎| Initialization. Image:CarreraSlice2.png | Refinement. </…'

2014 Winter Project Week

2013-12-26T19:41:58Z

Ivan.kolesov: /* Head and Neck Cancer */

Back to [[Project Events]], [[AHM_2014]], [[Events]]

__NOTOC__
[[image:PW-SLC2014.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

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

Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Project_Week:TBIatrophy|Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:TBIdemyelination|Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:BrainAging|Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer]] (Andrei Irimia, John D. Van Horn)
*[[2014_Project_Week:LongitudinalDTI|Patient-specific longitudinal DTI analysis in traumatic brain injury]] (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
*[[2014_Project_Week:TBISegmentation|Testing the interactive segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)

==Slicer4 Extensions==
*[[2014_Project_Week:ShapePopulationViewer|Surface Visualization - ShapePopulationViewer]] (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion]] (Hans, CF, Peter Savadjiev)
*[[2014_Project_Week:DTIAnalysis|DTI Compressed Sensing?]] (Hans, CF, Peter Savadjiev)
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent, Peter Savadjiev)
*[[2014_Project_Week:Slicer_Based_Surface_Template_Estimation|Slicer Based Surface Template Estimation]] (Saurabh JHU, Steve Pieper, Hans Johnson, Josh Cates)
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)
*[[2014_Project_Week:CarreraSlice|Interactive Segmentation]] (Ivan, LiangJia, Nadya, Yi, Greg, Allen)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Ramesh, Polina B., Polina G.)

==Image-Guided Interventions==
*[[2014_Project_Week:Ultrasound Visualization and Navigation in Neurosurgery|Ultrasound Visualization and Navigation in Neurosurgery]] (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, Steve Pieper, William M. Wells III)
*[[2014_Project_Week:OpenIGTLink| OpenIGTLink Interface: New data types and structures]] (Junichi Tokuda, Andras Lasso, Steve Piper, ???)
*[[2014_Project_Week:Statistical Shape Model for robotic spine surgery| Statistical Shape Model for robotic spine surgery]] (Marine Clogenson, ???)

==Radiation Therapy==
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Greg Sharp, others??)
*[[2014_Project_Week:External_Beam_Planning|External Beam Planning Visualization]] (Kevin Wang, Greg Sharp, Csaba Pinter)

==Medical Robotics==
==[http://qiicr.org QIICR]==

*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)
*[[2014_Project_Week:BatchConvertDICOM|Python Scripting Slicer DICOM read/write to convert segmentation objects]] (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)
*[[2014_Project_Week:Quantitative_Index_Computation|Quantitative Index Computation]] (Ethan Ulrich)
*[[2014_Project_Week:TCIA Browser Extension in Slicer|TCIA Browser Extension in Slicer]] (Alireza, Andrey, Steve, Ron)

==TMJ-OA==
* [[2014_Winter_Project_Week:Constrain Fiducial along Suface|Constrain Fiducial along Suface]] (Vinicius Boen, Nicole Aucoin, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Cropping Multiple Surfaces|Cropping multiple surfaces simultaneously]] (Alexander, Jc, Steve, Vinicius, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Color Code Tables|Color Coded Tables]] (Beatriz Paniagua, Vinicius Boen, Nicole Aucoin, Steve Pieper, Francois Budin)
* [[2014_Winter_Project_Week:4DShape Analysis of mandibular changes|4DShape Analysis of mandibular changes]] (James Fishbaugh, Guido Gerig, Vinicius Boen)

==Infrastructure==
*[[2014_Project_Week:SlicerSpeedUp|Slicer speed up]] (Jc, Andras Lasso, Steve Pieper)
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*CLI - Resources? Conditionals? Autonaming? Provenance? CTK unification? (Jim Miller)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonlinearTransforms|Integration nonlinear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Nicole Aucoin, Steve Pieper, Jc, Andras Lasso, Csaba Pinter, ???)

2014 Project Week:KSlice

2013-12-26T19:39:42Z

Ivan.kolesov: Created page with '__NOTOC__ <gallery> Image:PW-SLC2014.png|Projects List Image:CarreraSlice1.png‎| Initialization. Image:CarreraSlice2.png | Refinement. </…'

2014 Winter Project Week

2013-12-26T19:34:58Z

Ivan.kolesov: /* Head and Neck Cancer */

Back to [[Project Events]], [[AHM_2014]], [[Events]]

__NOTOC__
[[image:PW-SLC2014.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

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

Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Project_Week:TBIatrophy|Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:TBIdemyelination|Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:BrainAging|Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer]] (Andrei Irimia, John D. Van Horn)
*[[2014_Project_Week:LongitudinalDTI|Patient-specific longitudinal DTI analysis in traumatic brain injury]] (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
*[[2014_Project_Week:TBISegmentation|Testing the interactive segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)

==Slicer4 Extensions==
*[[2014_Project_Week:ShapePopulationViewer|Surface Visualization - ShapePopulationViewer]] (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion]] (Hans, CF, Peter Savadjiev)
*[[2014_Project_Week:DTIAnalysis|DTI Compressed Sensing?]] (Hans, CF, Peter Savadjiev)
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent, Peter Savadjiev)
*[[2014_Project_Week:Slicer_Based_Surface_Template_Estimation|Slicer Based Surface Template Estimation]] (Saurabh JHU, Steve Pieper, Hans Johnson, Josh Cates)
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)
*[[2014_Project_Week:KSlice|Interactive Segmentation]] (Ivan, LiangJia, Nadya, Yi, Greg, Allen)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Ramesh, Polina B., Polina G.)

==Image-Guided Interventions==
*[[2014_Project_Week:Ultrasound Visualization and Navigation in Neurosurgery|Ultrasound Visualization and Navigation in Neurosurgery]] (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, Steve Pieper, William M. Wells III)
*[[2014_Project_Week:OpenIGTLink| OpenIGTLink Interface: New data types and structures]] (Junichi Tokuda, Andras Lasso, Steve Piper, ???)
*[[2014_Project_Week:Statistical Shape Model for robotic spine surgery| Statistical Shape Model for robotic spine surgery]] (Marine Clogenson, ???)

==Radiation Therapy==
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Greg Sharp, others??)
*[[2014_Project_Week:External_Beam_Planning|External Beam Planning Visualization]] (Kevin Wang, Greg Sharp, Csaba Pinter)

==Medical Robotics==
==[http://qiicr.org QIICR]==

*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)
*[[2014_Project_Week:BatchConvertDICOM|Python Scripting Slicer DICOM read/write to convert segmentation objects]] (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)
*[[2014_Project_Week:Quantitative_Index_Computation|Quantitative Index Computation]] (Ethan Ulrich)
*[[2014_Project_Week:TCIA Browser Extension in Slicer|TCIA Browser Extension in Slicer]] (Alireza, Andrey, Steve, Ron)

==TMJ-OA==
* [[2014_Winter_Project_Week:Constrain Fiducial along Suface|Constrain Fiducial along Suface]] (Vinicius Boen, Nicole Aucoin, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Cropping Multiple Surfaces|Cropping multiple surfaces simultaneously]] (Alexander, Jc, Steve, Vinicius, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Color Code Tables|Color Coded Tables]] (Beatriz Paniagua, Vinicius Boen, Nicole Aucoin, Steve Pieper, Francois Budin)
* [[2014_Winter_Project_Week:4DShape Analysis of mandibular changes|4DShape Analysis of mandibular changes]] (James Fishbaugh, Guido Gerig, Vinicius Boen)

==Infrastructure==
*[[2014_Project_Week:SlicerSpeedUp|Slicer speed up]] (Jc, Andras Lasso, Steve Pieper)
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*CLI - Resources? Conditionals? Autonaming? Provenance? CTK unification? (Jim Miller)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonlinearTransforms|Integration nonlinear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Nicole Aucoin, Steve Pieper, Jc, Andras Lasso, Csaba Pinter, ???)

NA-MIC KSliceInteractiveSegmentor

2013-04-16T23:04:43Z

Ivan.kolesov:

Back to [[NA-MIC_External_Collaborations]]

[[Image:KSliceLogo.png|thumb|right|300px|KSlice Interactive Segmentation]]
__TOC__

==Abstract==
This is an interactive segmentation approach that is guided by the user throughout the task.

==Usage==
*Parameter Explanation:
*List of Keypresses:

*Step 1: with supporting pictures
...
*Step N:

==Applications==
*Orthpedic examples
*Adaptive Radiotherapy examples
*Huntingtons examples

==Key Personnel==
*Georgia Institute of Technology: Ivan Kolesov and Peter Karasev
*University of Alabama Birmingham: Allen Tannenbaum

== References ==
*CDC Paper
*TMI Paper
*Orthopedic paper

NA-MIC KSliceInteractiveSegmentor

2013-04-16T23:03:19Z

Ivan.kolesov:

Back to [[NA-MIC_External_Collaborations]]

[[Image:KSliceLogo.png|thumb|right|300px|KSlice Interactive Segmentation]]
__TOC__

==Abstract==
This is an interactive segmentation approach that is guided by the user throughout the task.

==Usage==
*Parameter Explanation:
*Step 1: with supporting pictures
...
*Step N:

==Applications==
*Orthpedic examples
*Adaptive Radiotherapy examples
*Huntingtons examples

==Key Personnel==
*Georgia Institute of Technology: Ivan Kolesov and Peter Karasev
*University of Alabama Birmingham: Allen Tannenbaum

== References ==
*CDC Paper
*TMI Paper
*Orthopedic paper

NA-MIC KSliceInteractiveSegmentor

2013-04-16T22:59:13Z

Ivan.kolesov:

Back to [[NA-MIC_External_Collaborations]]

[[Image:KSliceLogo.png|thumb|right|300px|KSlice Interactive Segmentation]]
__TOC__

==Abstract==

==Usage==
*Parameter Explanation:
*Step 1: with supporting pictures
...
*Step N:

==Applications==

==Key Personnel==
*Georgia Institute of Technology: Ivan Kolesov and Peter Karasev
*University of Alabama Birmingham: Allen Tannenbaum

== References ==
*CDC Paper
*TMI Paper
*Orthopedic paper

NA-MIC KSliceInteractiveSegmentor

2013-04-16T22:56:56Z

Ivan.kolesov:

Back to [[NA-MIC_External_Collaborations]]

[[Image:KSliceLogo.png|thumb|right|300px|KSlice Interactive Segmentation]]
__TOC__

==Abstract==

==Usage==

==Applications==

==Key Personnel==
*Georgia Institute of Technology: Ivan Kolesov and Peter Karasev
*University of Alabama Birmingham: Allen Tannenbaum

== References ==
*CDC Paper
*TMI Paper
*Orthopedic paper

NA-MIC KSliceInteractiveSegmentor

2013-04-16T22:56:08Z

Ivan.kolesov: Created page with 'Back to NA-MIC_External_Collaborations __TOC__ KSlice Interactive Segmentation ==Abstract== ==Usage== ==Applications== =…'

Back to [[NA-MIC_External_Collaborations]]
__TOC__

[[Image:KSliceLogo.png|thumb|right|300px|KSlice Interactive Segmentation]]

==Abstract==

==Usage==

==Applications==

==Key Personnel==
*Georgia Institute of Technology: Ivan Kolesov and Peter Karasev
*University of Alabama Birmingham: Allen Tannenbaum

== References ==
*CDC Paper
*TMI Paper
*Orthopedic paper

2013 Winter Project Week:PointSetRegistration

2013-01-10T23:10:36Z

Ivan.kolesov:

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

==Key Investigators==

* Ivan Kolesov, Peter Karasev, Allen Tannenbaum, UAB
* Gregory Sharp, MGH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We are working on registering CT images for head and neck non-rigidly with minimal input from the user. This is currently done with a sequential procedure by registering point sets obtained from rough segmentations.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We will work on reducing the number of user set parameters in our existing approach.
* We will determine what pieces from the pipeline are present in Slicer and what can be added as a module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Examined point set based image registration
*Created a plan for adding point set registration to within Plastimatch (integrated into Slicer)

File:SkeletonOp.png

2013-01-10T23:09:43Z

Ivan.kolesov:

2013 Winter Project Week:PointSetRegistration

2013-01-10T23:06:56Z

Ivan.kolesov: /* Project Description */

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

</gallery>

==Key Investigators==

* Ivan Kolesov, Peter Karasev, Allen Tannenbaum, UAB
* Gregory Sharp, MGH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We are working on registering CT images for head and neck non-rigidly with minimal input from the user. This is currently done with a sequential procedure by registering point sets obtained from rough segmentations.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We will work on reducing the number of user set parameters in our existing approach.
* We will determine what pieces from the pipeline are present in Slicer and what can be added as a module.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Examined point set based image registration
*Created a plan for adding point set registration to within Plastimatch (integrated into Slicer)

2013 Winter Project Week:PointSetRegistration

2013-01-10T23:04:49Z

Ivan.kolesov:

2013 Winter Project Week:PointSetRegistration

2013-01-04T22:23:10Z

Ivan.kolesov:

2013 Winter Project Week:PointSetRegistration

2013-01-04T22:21:48Z

Ivan.kolesov:

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

==Key Investigators==

* Ivan Kolesov, Peter Karasev, Allen Tannenbaum, UAB
* Gregory Sharp, MGH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We are working on registering CT images for head and neck non-rigidly with minimal input from the user. This is currently done with a sequential procedure by registering point sets obtained from rough segmentations.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We will work on reducing the number of user set parameters in our existing approach.
* We will determine what pieces from the pipeline are present in Slicer and what can be added as a module.

2013 Winter Project Week:PointSetRegistration

2013-01-04T22:21:36Z

Ivan.kolesov:

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

==Key Investigators==

* Ivan Kolesov, Peter Karasev, Allen Tannenbaum, UAB
* Gregory Sharp, MGH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We are working on registering CT images for head and neck non-rigidly with minimal input from the user. This is currently done with a sequential procedure by registering point sets obtained from rough segmentations.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We will work on reducing the number of user set parameters in our existing approach.
* We will determine what pieces from the pipeline are present in Slicer and what can be added as a module.

2013 Winter Project Week:PointSetRegistration

2013-01-04T22:21:24Z

Ivan.kolesov: /* Project Description */

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

==Key Investigators==

* Ivan Kolesov, Peter Karasev, Allen Tannenbaum, UAB
* Gregory Sharp, MGH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We are working on registering CT images for head and neck non-rigidly with minimal input from the user. This is currently done with a sequential procedure by registering point sets obtained from rough segmentations.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We will work on reducing the number of user set parameters in our existing approach.
* We will determine what pieces from the pipeline are present in Slicer and what can be added as a module.

2013 Winter Project Week:PointSetRegistration

2013-01-04T22:20:02Z

Ivan.kolesov: Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List Image:ScarSeg_EM.png‎| Scar tissue identification. </gallery> ==Key Investigators=…'

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

==Key Investigators==

* Ivan Kolesov, Peter Karasev, Allen Tannenbaum, UAB
* Gregory Sharp, MGH

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We are working on registering CT images for head and neck non-rigidly with minimal input from the user.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We will work on reducing the number of user set parameters in our existing approach.
* We will determine what pieces from the pipeline are present in Slicer and what can be added as a module.

2013 Winter Project Week

2013-01-04T22:02:25Z

Ivan.kolesov:

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2013]], [[Events]]

__NOTOC__
[[image:PW-SLC2013.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please [[AHM_2013#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2013#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2013#Agenda|'''Click here for the agenda for AHM 2013 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

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

Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2013_Project_Week_Template | Template for project pages]]

==TBI==
* [[4D DTI tractography in Slicer for TBI | Coregistration of structural and diffusion MRI towards 4D modeling of TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented TBI connectivity analysis in Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Geometric metamorphosis for TBI]] (Danielle Pace, Stephen Aylward, Andrei Irimia, Micah Chambers)
* [[UKF Tractography in Slicer 4]] (Ryan Eckbo, Yogesh Rathi, Demian Wassermann, C.F Westin, Ron Kikinis)
* [[4D DTI analysis via longitudinal modeling of tract diffusivities]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)

==Atrial Fibrillation==
* [[2013_Project_Week:CARMA_Scar_Segmentation|Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)]]
* [[2013_Project_Week:CARMA_PV_Antrum_Cut|SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_LA_Seg_Gopal|SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_2D_Dilate|SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_PractialLASeg|SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_RT_MRI|PROJECT PLANNING: Real Time MRI in Slicer with OpenIGT (Alan Morris, Ashvin George, Josh Cates, Rob MacLeod)]]

==Slicer4 Extensions==
* [[2013_Project_Week:DTIExtension|Diffusion Tensor Images processing tools as Slicer4 extensions (Francois Budin, Adrien Kaiser, Martin Styner)]]

==Huntington's Disease==
* [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson)
* [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch)
* [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch, Nicole Aucoin)
* [[2013_Project_Week:4DShapeAnalysis | 4D shape analysis: application to HD]] (James Fishbaugh, Marcel Prastawa, Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
* [[2013_Winter_Project_Week:MABS|Multi atlas-based segmentation]] (Sharp, Shusharina, Golland)
* [[2013_Winter_Project_Week:Hybrid_registration|Hybrid interactive-automatic registration]] (Shusharina, Sharp, Pieper)
* [[2013_Winter_Project_Week:PointSetRegistration|Constrained Point Set Registration]] (Kolesov, Karasev, Sharp, Tannenbaum)

==Stroke==
* [[2013_Project_Week:WMH_Segmentation_for_Stroke|White Matter Hyperintensity Segmentation in Stroke (Adrian Dalca, Ramesh Sridharan, Polina Golland)]]
* [[2013_Project_Week:Imaging_Genetic_for_Stroke|Imaging Genetics for Stroke (Adrian Dalca, Kayhan Batmanghelich, Polina Golland)]]

==Prostate Interventions==
* [[2013_Project_Week:BRAINSFit_new_features|BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)]]
* [[2013_Project_Week:PkModeling_for_prostate_DCE_MRI|PkModeling for prostate DCE MRI (Jim, Andrey)]]

==Abdominal Interventions==
* [[2013_Project_Week:AbdominalNavigationModule|Abdominal navigation module (Junichi Tokuda, Atsushi Yamada)]]

==Medical Robotics==
* [[Configurable fiducial-based device to image registration]] (Junichi Tokuda)
* Reviving ultrasound integration for visual servoing (Laurent Chauvin, Noby Hata)
* [[2013_Project_Week:AgileMedicalRobot | Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)]]
* [[2013_Project_Week:InvestigatingRoleOfOpenSourceInTranslationalResearch | Investigating role of open source in translational research (Miki Kumekawa)]]

==General Image Guided Therapy==
* [[2013_Project_Week:UnitedSlicerIGTExtension|United SlicerIGT extension, repository, website]] (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* [[2013_Project_Week:MobileImageOverlay|Mobile image overlay augmented reality needle guidance]] (Adam Rankin, Tamas Ungi)
* [[2013_Project_Week:TemperatureMonitoring|Temperature Monitoring for Laser Ablation intervention]] (Laurent Chauvin, Noby Hata)

==Radiation Therapy==
* [[2013_Project_Week:DicomRtExport|SlicerRT: DICOM RT export]] (Kevin Wang, Greg Sharp, Csaba Pinter)
* [[2013_Project_Week:RtBeamGeometry|SlicerRT: Beam geometry widgets]] (Csaba Pinter, Greg Sharp)
* [[2013_Project_Week:MRIAblation|Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor]] (Laurent Chauvin)

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc?, Bill Lorensen,Bradley Lowekamp)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov?, Nicole Aucoin, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Nicole Aucoin Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper, Csaba Pinter)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and Sample Data Refactor]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?, Greg Sharp)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao)
*[[2013_Project_Week:Threaded SimpleITK Modules|Threaded SimpleITK Modules]] (Brad Lowekamp, Steve Pieper)

Algorithm:BU

2012-11-19T03:39:22Z

Ivan.kolesov:

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Boston University Algorithms (PI: Allen Tannenbaum) =

At Boston University and the Comprehensive Cancer Center of UAB, we are broadly interested in a range of mathematical image analysis algorithms for segmentation, registration, diffusion-weighted MRI analysis, and statistical analysis. For many applications, we cast the problem in an energy minimization framework wherein we define a partial differential equation whose numeric solution corresponds to the desired algorithmic outcome. The following are many examples of PDE techniques applied to medical image analysis.

= Boston University/UAB Projects =

{| cellpadding="10" style="text-align:left;"

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== [[Projects:RegistrationTBI|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] ==

Time-efficient processing and analysis of magnetic resonance imaging (MRI) volumes is desirable is for the neurocritical care and monitoring of traumatic brain injury (TBI) patients. An important problem of TBI neuroimaging data analysis is the task of co-registering MR volumes acquired using distinct sequences in the presence of widely variable pixel intensities that are due to the presence of pathology. Here we address this important and challenging problems using an implementation of multimodal deformable registration on graphics processing units (GPU). We follow a viscous fluid model framework and replace mutual information with the Bhattacharyya distance as the measure of similarity between image volumes. The proposed algorithm is implemented on a GPU and its robustness is illustrated using a longitudinal multimodal TBI dataset. [[Projects:RegistrationTBI|More...]]

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| | [[Image:MultiScaleHippoSegmentationHausdorf.png|200px]]
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== [[Projects:MultiScaleShapeSegmentation|Multi-scale Shape Representation, Registration, and Segmentation With Applications to Radiotherapy]] ==

We present in this work a multiscale representation for shapes with arbitrary topology, and a method to segment the target organ/tissue from medical images having very low contrast with respect to surrounding regions using multiscale shape information and local image features. In a number of previous papers, shape knowledge was incorporated by first constructing a shape space from training data, and then constraining the segmentation process to be within the resulting shape space. However, such an approach has certain limitations including the fact that small scale shape variances may be overwhelmed by those on larger scale, and therefore the local shape information is lost. In this work, first we handle this problem by providing a multiscale shape representation using the wavelet transform. Consequently, the shape variances captured by the statistical learning step are also represented at various scales. In doing so, not only is the diversity of shape enriched, but also small scale changes are nicely captured. [[Projects:MultiScaleShapeSegmentation|More...]]

<font color="red">'''New: '''</font> Yifei Lou, Tianye Niu, Xun Jia, Patricio Vela, Lei Zhu, Allen Tannenbaum, Joint CT/CBCT Deformable Registration and CBCT Enhancement for Cancer Radiotherapy, MedIA (in submission), 2012.

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| | [[Image:GT-SPD-img1.png|200px|]]
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== [[Projects:SoftPlaqueDetection|Soft Plaque Detection in CTA Imagery]] ==

The ability to detect and measure non-calciﬁed plaques (also known as soft plaques) may improve physicians’ ability to predict cardiac events. This work automatically detects soft plaques in CTA imagery using active contours driven by spatially localized probabilistic models. Plaques are identified by simultaneously segmenting the vessel from the inside-out and the outside-in using carefully chosen localized energies [[Projects:SoftPlaqueDetection|More...]]

<font color="red">'''New: '''</font> Soft Plaque Detection and Automatic Vessel Segmentation. PMMIA Workshop in MICCAI, Sep. 2009.
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| | [[Image:3D_Segmentation_LA.png|200px]]
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== [[Projects:AFibSegmentationRegistration|Segmentation and Registration for Atrial Fibrillation Ablation Therapy]] ==

Magnetic resonance imaging (MRI) has been used for both pre- and and post-ablation assessment of the atrial wall. MRI can aid in selecting the right candidate for the ablation procedure and assessing post-ablation scar formations. Image processing techniques can be used for automatic segmentation of the atrial wall, which facilitates an accurate statistical assessment of the region. As a first step towards the general solution to the computer-assisted segmentation of the left atrial wall, in this research we propose a shape-based image segmentation framework to segment the endocardial wall of the left atrium.[[Projects:SegmentationEpicardialWall|More...]]

<font color="red">'''New: '''</font> Y. Gao, B. Gholami, R. S. MacLeod, J, Blauer, W. M. Haddad, and A. R. Tannenbaum, Segmentation of the Endocardial Wall of the Left Atrium using Local Region-Based Active Contours and Statistical Shape Learning, SPIE Medical Imaging, San Diego, CA, 2010.

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| | [[Image:Pain1.JPG|200px]]
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== [[Projects:PainAssessment|Agitation and Pain Assessment Using Digital Imaging]] ==

Pain assessment in patients who are unable to verbally
communicate with medical staff is a challenging problem
in patient critical care. The fundamental limitations in sedation
and pain assessment in the intensive care unit (ICU) stem
from subjective assessment criteria, rather than quantifiable,
measurable data for ICU sedation and analgesia. This often
results in poor quality and inconsistent treatment of patient
agitation and pain from nurse to nurse. Recent advancements in
pattern recognition techniques using a relevance vector machine
algorithm can assist medical staff in assessing sedation and pain
by constantly monitoring the patient and providing the clinician
with quantifiable data for ICU sedation. In this paper, we show
that the pain intensity assessment given by a computer classifier
has a strong correlation with the pain intensity assessed by
expert and non-expert human examiners.[[Projects:PainAssessment|More...]]

<font color="red">'''New: '''</font> B. Gholami, W. M. Haddad, and A. Tannenbaum, Relevance Vector Machine Learning for Neonate Pain Intensity Assessment Using Digital Imaging. IEEE Trans. Biomed. Eng., vol. 57, pp. 1457-1466, 2012.

<font color="red">'''New: '''</font> B. Gholami, W. M. Haddad, and A. R. Tannenbaum, Agitation and Pain Assessment Using Digital Imaging. Proc. IEEE Eng. Med. Biolog. Conf., Minneapolis, MN, pp. 2176-2179, 2009 (Awarded National Institute of Biomedical Imaging and Bioengineering/National Institute of Health Student Travel Fellowship).

<font color="red">'''New: '''</font> Wassim M. Haddad, James M. Bailey, Behnood Gholami, and Allen Tannenbaum. Optimal Drug Dosing Control for Intensive Care Unit Sedation Using a Hybrid Deterministic-Stochastic Pharmacokinetic and Pharmacodynamic
Model. Optimal Control, Applications and Methods}, 2012, DOI: 10.1002/oca.2038.

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| | [[Image:MultiObjSeg.png|200px|]]
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== [[RobustStatisticsSegmentation|Simultaneous Multiple Object Segmentation using Robust Statistics Features ]] ==

Multiple objects are segmented simultaneously using several interactive active contours based on the feature image which utilizes the robust statistics of the image. [[RobustStatisticsSegmentation|More...]]

<font color="red">'''New: '''</font> Y. Gao, S. Bouix, M. Shenton, R. Kikinis, A. Tannenbaum. A 3D interactive multi-object segmentation tool using local robust statistics driven active contours. MedIA, volume 16, 2012, pp. 1216-1227.
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| | [[Image:ShapeBasePstSegSlicer.png|200px|]]
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== [[Projects:ProstateSegmentation|Prostate Segmentation]] ==

The 3D prostate MRI images are collected by collaborators at Queen’s University. With a little manual initialization, the algorithm provided the results give to the left. The method mainly uses Random Walk algorithm. [[Projects:ProstateSegmentation|More...]]

<font color="red">'''New: '''</font> Y. Gao, R. Sandhu, G. Fichtinger, A. Tannenbaum. A coupled global registration and segmentation framework with application to magnetic resonance prostate imagery. IEEE Trans. Medical Imaging, volume 29, 2010, pp. 1781-1794.

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| | [[Image:ProstateRegSupineToProneInParaview.png|200px|]]
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== [[Projects:pfPtSetImgReg|Particle Filter Registration of Medical Imagery]] ==

3D volumetric image registration is performed. The method is based on registering the images through point sets, which is able to handle long distance between as well as registration between Supine and Prone pose prostate. [[Projects:pfPtSetImgReg|More...]]

<font color="red">'''New: '''</font> Y. Gao, R. Sandhu, G. Fichtinger, A. Tannenbaum; A coupled global registration and segmentation framework with application to magnetic resonance prostate imagery. IEEE TMI vol.29, 2010, pp. 1781-1794.

<font color="red">'''New: '''</font> Y. Gao, Y. Rathi, S. Bouix, A. Tannenbaum; Filtering in the diffeomorphism group and the registration of point sets. IEEE Transactions Image Processing, vol. 21, 2012, pp. 4383-4396 .

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| | [[Image:GT-DWI-Reorientation-1.jpg|200px]]
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== [[Projects:DWIReorientation|Re-Orientation Approach for Segmentation of DW-MRI]] ==

This work proposes a methodology to segment tubular fiber bundles from diffusion weighted magnetic resonance images (DW-MRI). Segmentation is simplified by locally reorienting diffusion information based on large-scale fiber bundle geometry. [[Projects:DWIReorientation|More...]]

<font color="red">'''New: '''</font> Near-tubular fiber bundle segmentation for diffusion weighted imaging: segmentation through frame reorientation. Neuroimage, Mar 2009.

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| | [[Image:GTTubSurfaceSeg-Img1.png|200px]]
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== [[Projects:TubularSurfaceSegmentation|Tubular Surface Segmentation Framework]] ==

We have proposed a new model for tubular surfaces that transforms the problem of detecting a surface in 3D space, to detecting a curve in 4D space. Besides allowing us to impose a "soft" tubular shape prior, this also leads to computational efficiency over conventional surface segmentation approaches. [[Projects:TubularSurfaceSegmentation|More...]]

<font color="red">'''New: '''</font> V. Mohan, G. Sundaramoorthi, A. Stillman and A. Tannenbaum. Vessel Segmentation with Automatic Centerline Extraction using Tubular Surface Segmentation. September 2009. Proceedings of the Workshop on Cardiac Interventional Imaging and Biophysical Modelling (CI2BM'09), Int Conf Med Image Comput Comput Assist Interv. 2009.

<font color="red">'''New: '''</font> V. Mohan, G. Sundaramoorthi and A. Tannenbaum. Tubular Surface Segmentation for Extracting Anatomical Structures from Medical Imagery, IEEE Transactions on Medical Imaging, volume 29, 2011, pp. 1945-1958.

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| | [[Image:GT-PopStudyVis OnCBs Case19-View2.jpg|200px]]
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== [[Projects:TubularSurfaceSegmentationPopStudy|Group Study on DW-MRI using the Tubular Surface Model]] ==

We have proposed a new framework for performing group studies on DW-MRI data sets using the Tubular Surface Model of Mohan et al. We successfully apply this framework to discriminating schizophrenic cases from normal controls, as well as towards visualizing the regions of the Cingulum Bundle that are affected by Schizophrenia. [[Projects:TubularSurfaceSegmentationPopStudy|More...]]

<font color="red">'''New: '''</font> V. Mohan, G. Sundaramoorthi, M. Kubicki, D. Terry and A. Tannenbaum. Population Analysis of the Cingulum Bundle using the Tubular Surface Model for Schizophrenia Detection. SPIE Medical Imaging 2010.

<font color="red">'''New: '''</font> V. Mohan, G. Sundaramoorthi, M. Kubicki and A. Tannenbaum. Population Analysis of neural fiber bundles towards schizophrenia detection and characterization, using the Tubular Surface model. Neuroimage (in submission)

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| | [[Image:KVoutSegTightMod.png|200px]]
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== [[Projects:InteractiveSegmentation|Interactive Image Segmentation With Active Contours]] ==

An approach for tightly coupling the user into a semi-automatic segmentation framework is proposed in this work. A human guides the automatic segmentation by iteratively providing input until convergence to the desired segmentation. The result is a segmentation of manual quality in a fraction of the time; the whole process is intuitive and highly flexible [[Projects:InteractiveSegmentation|More...]]

<font color="red">'''New: '''</font> I. Kolesov, P.Karasev, G.Muller, K.Chudy, J.Xerogeanes, and A. Tannenbaum. Human Supervisory Control Framework for Interactive Medical Image Segmentation. MICCAI Workshop on Computational Biomechanics for Medicine 2011.

<font color="red">'''New: '''</font> P.Karasev, I.Kolesov, K.Chudy, G.Muller, J.Xerogeanes, and A. Tannenbaum. Interactive MRI Segmentation with Controlled Active Vision. IEEE CDC-ECC 2011.

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| | [[Image:PostRegFleshSkeleton.png|200px]]
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== [[Projects:MGH-HeadAndNeck-PtSetReg|Constrained Registration for Adaptive Radiotherapy]] ==

A hierarchical approach is described to register two CT scans from different patients. The registration process extracts point clouds representing anatomical structures and aligns them sequentially. The proposed method for registering point clouds can incorporate a variety of constraints including restriction on the injectivity of the deformation field and stationarity of selected landmarks. [[Projects:MGH-HeadAndNeck-PtSetReg|More...]]

<font color="red">'''New: '''</font> I. Kolesov, J. Lee, P.Vela, G. Sharp and A. Tannenbaum. Diffeomorphic Point Set Registration with Landmark Constraints. In Preparation for PAMI.

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| | [[Image:Model3D_upTrans.png|200px]]
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== [[Projects:MGH-HeadAndNeck-RT|Adaptive Radiotherapy for head, neck and thorax]] ==

We proposed an algorithm to include prior knowledge in previously segmented anatomical structures to help in the segmentation of the next structure. This will add enough prior information to allow the Graph Cuts algorithm to segment structures with fuzzy boundaries. [[Projects:MGH-HeadAndNeck-RT|More...]]

<font color="red">'''New: '''</font> I. Kolesov, V. Mohan, G. Sharp and A. Tannenbaum. Coupled Segmentation for Anatomical Structures by Combining Shape and Relational Spatial Information. MTNS 2010.

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| | [[Image:Circle seg.PNG|200px|]]
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== [[Projects:KPCASegmentation|Kernel PCA for Segmentation]] ==

Segmentation performances using active contours can be drastically improved if the possible shapes of the object of interest are learnt. The goal of this work is to use Kernel PCA to learn shape priors. Kernel PCA allows for learning non linear dependencies in data sets, leading to more robust shape priors. [[Projects:KPCASegmentation|More...]]

<font color="red">'''New: '''</font> S. Dambreville, Y. Rathi, and A. Tannenbaum. A Framework for Image Segmentation using Image Shape Models and Kernel PCA Shape Priors. IEEE Trans Pattern Anal Mach Intell. 2008 Aug;30(8):1385-99

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| | [[Image:ZoomedResultWithModel.png|200px]]
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== [[Projects:GeodesicTractographySegmentation|Geodesic Tractography Segmentation]] ==

In this work, we provide an energy minimization framework which allows one to find fiber tracts and volumetric fiber bundles in brain diffusion-weighted MRI (DW-MRI). [[Projects:GeodesicTractographySegmentation|More...]]

<font color="red">'''New: '''</font> J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, March 2008, Vol 30, Num 3.

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| | [[Image:P1_small.png|200px|]]
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== [[Projects:LabelSpace|Label Space: A Coupled Multi-Shape Representation]] ==

Many techniques for multi-shape representation may often develop inaccuracies stemming from either approximations or inherent variation. Label space is an implicit representation that offers unbiased algebraic manipulation and natural expression of label uncertainty. We demonstrate smoothing and registration on multi-label brain MRI. [[Projects:LabelSpace|More...]]

<font color="red">'''New: '''</font> J. Malcolm, Y. Rathi, S. Bouix, M. Shenton, A. Tannenbaum. Affine registration of label maps in label space. Journal of Computing, volume 2, 2010, pp, 1-11.

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| | [[Image:BasePair3DModel.JPG|200px|]]
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== [[Projects:NonParametricClustering|Non Parametric Clustering for Biomolecular Structural Analysis]] ==

High accuracy imaging and image processing techniques allow for collecting structural information of biomolecules with atomistic accuracy. Direct interpretation of the dynamics and the functionality of these structures with physical models, is yet to be developed. Clustering of molecular conformations into classes seems to be the first stage in recovering the formation and the functionality of these molecules. [[Projects:NonParametricClustering|More...]]

<font color="red">'''New: '''</font> X. LeFaucheur, E. Hershkovits, R. Tannenbaum, and A. Tannenbaum. Non-parametric clustering for studying RNA conformations. IEEE Trans. Computational Biology and Bioinformatics, volume 8, 2011, pp. 1604-1618.

<font color="red">'''New: '''</font> Il Tae Kim, A. Tannenbaum, R. Tannenbaum. Anisotropic conductivity of magnetic carbon nanotubes
embedded in epoxy matrices. Carbon, volume 49, 2011, pp. 54-61.

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| | [[Image:TruckInitialization.png|200px|]]
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== [[Projects:PointSetRigidRegistration|Point Set Rigid Registration]] ==

In this work, we propose a particle filtering approach for the problem of registering two point sets that differ by
a rigid body transformation. Experimental results are provided that demonstrate the robustness of the algorithm to initialization, noise, missing structures or differing point densities in each sets, on challenging 2D and 3D registration tasks. [[Projects:PointSetRigidRegistration|More...]]

<font color="red">'''New: '''</font> R. Sandhu, S. Dambreville, A. Tannenbaum. Point set registration via particle filtering and stochastic dynamics. IEEE TPAMI, volume 32, 2010, pp. 1459-1473.

<font color="red">'''New: '''</font> R. Sandhu, S. Dambreville, A. Tannenbaum. A non-rigid kernel based framework for 2D/3D pose estimation and 2D image segmentation. IEEE TPAMI, volume 33, 2011, pp. 1098-1115.

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| | [[Image:Results brain sag.JPG|200px]]
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== [[Projects:OptimalMassTransportRegistration|Optimal Mass Transport Registration]] ==

The goal of this project is to implement a computationally efficient Elastic/Non-rigid Registration algorithm based on the Monge-Kantorovich theory of optimal mass transport for 3D Medical Imagery. Our technique is based on Multigrid and Multiresolution techniques. This method is particularly useful because it is parameter free and utilizes all of the grayscale data in the image pairs in a symmetric fashion and no landmarks need to be specified for correspondence. [[Projects:OptimalMassTransportRegistration|More...]]

<font color="red">'''New: '''</font> Eldad Haber, Tauseef Rehman, and Allen Tannenbaum. An Efficient Numerical Method for the Solution of the L2 Optimal Mass Transfer Problem. SIAM Journal of Scientific Computing, volume 32, 2011, pp. 197-211.

<font color="red">'''New: '''</font> Tauseef Rehman, Eldad Haber, Gallagher Pryor, and Allen Tannenbaum. 3D nonrigid registration via optimal mass transport on the GPU. MedIA, volume 13, 2010, pp. 931-940.

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| | [[Image:Gatech caudateBands.PNG|200px]]
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== [[Projects:MultiscaleShapeSegmentation|Multiscale Shape Segmentation Techniques]] ==

To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus. [[Projects:MultiscaleShapeSegmentation|More...]]

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| | [[Image:Caudate Nucleus Denoising.JPG|200px|]]
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== [[Projects:WaveletShrinkage|Wavelet Shrinkage for Shape Analysis]] ==

Shape analysis has become a topic of interest in medical imaging since local variations of a shape could carry relevant information about a disease that may affect only a portion of an organ. We developed a novel wavelet-based denoising and compression statistical model for 3D shapes. [[Projects:WaveletShrinkage|More...]]

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| | [[Image:Basis membership.png|200px]]
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== [[Projects:MultiscaleShapeAnalysis|Multiscale Shape Analysis]] ==

We present a novel method of statistical surface-based morphometry based on the use of non-parametric permutation tests and a spherical wavelet (SWC) shape representation. [[Projects:MultiscaleShapeAnalysis|More...]]

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| | [[Image:Dlpfc1.jpg|200px|]]
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== [[Projects:RuleBasedDLPFCSegmentation|Rule-Based DLPFC Segmentation]] ==

In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules for the dorsolateral prefrontal cortex. [[Projects:RuleBasedDLPFCSegmentation|More...]]

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| | [[Image:Striatum1.png|200px|]]
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== [[Projects:RuleBasedStriatumSegmentation|Rule-Based Striatum Segmentation]] ==

In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules for the striatum. [[Projects:RuleBasedStriatumSegmentation|More...]]

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| | [[Image:Brain-flat.PNG|200px]]
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== [[Projects:ConformalFlatteningRegistration|Conformal Surface Flattening]] ==

The goal of this project is for better visualizing and computation of neural activity from fMRI brain imagery. Also, with this technique, shapes can be mapped to shperes for shape analysis, registration or other purposes. Our technique is based on conformal mappings which map genus-zero surface: in fmri case cortical or other surfaces, onto a sphere in an angle preserving manner. [[Projects:ConformalFlatteningRegistration|More...]]

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| | [[Image:Fig1yan.PNG|200px|]]
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== [[Projects:BloodVesselSegmentation|Blood Vessel Segmentation]] ==

The goal of this work is to develop blood vessel segmentation techniques for 3D MRI and CT data. The methods have been applied to coronary arteries and portal veins, with promising results. [[Projects:BloodVesselSegmentation|More...]]

<font color="red">'''New: '''</font> V.Mohan, G. Sundaramoorthi, A. Stillman and A. Tannenbaum. Vessel Segmentation with Automatic Centerline Extraction Using Tubular Tree Segmentation. CI2BM at MICCAI 2009, September 2009.

|-

| | [[Image:Fig67.png|200px|]]
| |

== [[Projects:KnowledgeBasedBayesianSegmentation|Knowledge-Based Bayesian Segmentation]] ==

This ITK filter is a segmentation algorithm that utilizes Bayes's Rule along with an affine-invariant anisotropic smoothing filter. [[Projects:KnowledgeBasedBayesianSegmentation|More...]]

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| | [[Image:Stochastic-snake.png|200px|]]
| |

== [[Projects:StochasticMethodsSegmentation|Stochastic Methods for Segmentation]] ==

New stochastic methods for implementing curvature driven flows for various medical tasks such as segmentation. [[Projects:StochasticMethodsSegmentation|More...]]

|-

| | [[Image:GT-SulciOutlining1.jpg|200px]]
| |

== [[Projects:SulciOutlining|Automatic Outlining of sulci on the brain surface]] ==

We present a method to automatically extract certain key features on a surface. We apply this technique to outline sulci on the cortical surface of a brain. [[Projects:SulciOutlining|More...]]

|-

| | [[Image:Table1.png|200px|]]
| |

== [[Projects:KPCA_LLE_KLLE_ShapeAnalysis|KPCA, LLE, KLLE Shape Analysis]] ==

The goal of this work is to study and compare shape learning techniques. The techniques considered are Linear Principal Components Analysis (PCA), Kernel PCA, Locally Linear Embedding (LLE) and Kernel LLE. [[Projects:KPCA_LLE_KLLE_ShapeAnalysis|More...]]

|-

| | [[Image:Gatech SlicerModel2.jpg|200px]]
| |

== [[Projects:StatisticalSegmentationSlicer2|Statistical/PDE Methods using Fast Marching for Segmentation]] ==

This Fast Marching based flow was added to Slicer 2. [[Projects:StatisticalSegmentationSlicer2|More...]]

|}

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:34:46Z

Ivan.kolesov:

Back to [[Algorithm:BU|Boston University Algorithms]]
__NOTOC__
= Semi-Automatic Image Registration =

We recognize that the difference between a failure of an automatic image registration approach and a success of a semi-automatic method can be a small amount of user input. The goal of this work is to register two CT volumes of different patients that are related by a large misalignment. The user sets two thresholds for each image: one for the bone mask and another for the flesh tissue. This operation is not time consuming but simplifies the registration task dramatically for the automatic algorithm.

= Description =
In this example, large misalignment is present between the two patients.

* [[Image:PreRegFleshSkeleton.png | PreRegFleshSkeleton| 400px]]
Original Misalignment of the volumes.

Point clouds are generated from label maps of bone. The computed registration field, which is guaranteed to be injective, is applied to the original CT volumes.

* [[Image:SkeletonMisalignedView1.png | SkeletonMisalignedView1| 400px]] [[Image:SkeletonAlignedView1.png | SkeletonMisalignedView1| 400px]]
Point clouds representing bone tissue of the patients (before and after registration).

Another set of point clouds is generated by sampling from label maps of flesh. To avoid undoing the previous registration, regions belonging to the registered bone tissue from above are constrained not to move. Again, an injective deformation field is computed.

* [[Image:FleshMis.png | FleshMis| 400px]] [[Image:FleshAlignedView1.png | FleshAlignedView1| 400px]]
Point clouds representing flesh tissue of the patients (before and after registration). This step is constrained.

The result of applying the two deformations computed by the proposed process are shown below.

* [[Image:PostRegFleshSkeleton.png | PostRegFleshSkeleton| 400px]]
Aligned images using the two step registration process.

== Current State of Work ==
A pipeline composed of Matlab and mex-ed C++ code has been implemented.

= Key Investigators =

* Georgia Tech: Ivan Kolesov, Patricio Vela
* Boston University: Jehoon Lee, Allen Tannenbaum
* MGH: Gregory Sharp

= Publications =

''In Press''

I. Kolesov, J. Lee, P.Vela, G. Sharp and A. Tannenbaum. Diffeomorphic Point Set Registration with Landmark Constraints. In Preparation for PAMI.

File:FleshMis.png

2012-11-19T03:34:04Z

Ivan.kolesov: uploaded a new version of "File:FleshMis.png"

File:FleshAlignedView1.png

2012-11-19T03:33:44Z

Ivan.kolesov: uploaded a new version of "File:FleshAlignedView1.png"

File:SkeletonMisalignedView1.png

2012-11-19T03:33:04Z

Ivan.kolesov: uploaded a new version of "File:SkeletonMisalignedView1.png"

File:SkeletonAlignedView1.png

2012-11-19T03:32:41Z

Ivan.kolesov: uploaded a new version of "File:SkeletonAlignedView1.png"

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:26:45Z

Ivan.kolesov:

Back to [[Algorithm:BU|Boston University Algorithms]]
__NOTOC__
= Semi-Automatic Image Registration =

We recognize that the difference between a failure of an automatic image registration approach and a success of a semi-automatic method can be a small amount of user input. The goal of this work is to register two CT volumes of different patients that are related by a large misalignment. The user sets two thresholds for each image: one for the bone mask and another for the flesh tissue. This operation is not time consuming but simplifies the registration task dramatically for the automatic algorithm.

= Description =
In this example, large misalignment is present between the two patients.

* [[Image:PreRegFleshSkeleton.png | PreRegFleshSkeleton| 400px]]
Original Misalignment of the volumes.

Point clouds are generated from label maps of bone. The computed registration field, which is guaranteed to be injective, is applied to the original CT volumes.

* [[Image:SkeletonMisalignedView1.png | SkeletonMisalignedView1| 400px]] [[Image:SkeletonAlignedView1.png | SkeletonMisalignedView1| 400px]]
Point clouds representing bone tissue of the patients (before and after registration).

Another set of point clouds is generated by sampling from label maps of flesh. To avoid undoing the previous registration, regions belonging to the registered bone tissue from above are constrained not to move. Again, an injective deformation field is computed.

* [[Image:FleshMis.png | FleshMis| 600px]] [[Image:FleshAlignedView1.png | FleshAlignedView1| 400px]]
Point clouds representing flesh tissue of the patients (before and after registration). This step is constrained.

The result of applying the two deformations computed by the proposed process are shown below.

* [[Image:PostRegFleshSkeleton.png | PostRegFleshSkeleton| 400px]]
Aligned images using the two step registration process.

== Current State of Work ==
A pipeline composed of Matlab and mex-ed C++ code has been implemented.

= Key Investigators =

* Georgia Tech: Ivan Kolesov, Patricio Vela
* Boston University: Jehoon Lee, Allen Tannenbaum
* MGH: Gregory Sharp

= Publications =

''In Press''

I. Kolesov, J. Lee, P.Vela, G. Sharp and A. Tannenbaum. Diffeomorphic Point Set Registration with Landmark Constraints. In Preparation for PAMI.

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:25:57Z

Ivan.kolesov:

Back to [[Algorithm:BU|Boston University Algorithms]]
__NOTOC__
= Semi-Automatic Image Registration =

We recognize that the difference between a failure of an automatic image registration approach and a success of a semi-automatic method can be a small amount of user input. The goal of this work is to register two CT volumes of different patients that are related by a large misalignment. The user sets two thresholds for each image: one for the bone mask and another for the flesh tissue. This operation is not time consuming but simplifies the registration task dramatically for the automatic algorithm.

= Description =
In this example, large misalignment is present between the two patients.

* [[Image:PreRegFleshSkeleton.png | PreRegFleshSkeleton| 400px]]
Original Misalignment of the volumes.

Point clouds are generated from label maps of bone. The computed registration field, which is guaranteed to be injective, is applied to the original CT volumes.

* [[Image:SkeletonMisalignedView1.png | SkeletonMisalignedView1| 400px]] [[Image:SkeletonAlignedView1.png | SkeletonMisalignedView1| 400px]]
Point clouds representing bone tissue of the patients (before and after registration).

Another set of point clouds is generated by sampling from label maps of flesh. To avoid undoing the previous registration, regions belonging to the registered bone tissue from above are constrained not to move. Again, an injective deformation field is computed.

* [[Image:FleshMis.png | FleshMis| 600px]] [[Image:FleshAlignedView1.png | FleshAlignedView1| 400px]]
Point clouds representing flesh tissue of the patients (before and after registration). This step is constrained.

The results of applying the two deformation computed by the proposed process are shown below.

* [[Image:PostRegFleshSkeleton.png | PostRegFleshSkeleton| 400px]]
Aligned images using the two step registration process.

== Current State of Work ==
A pipeline composed of Matlab and mex-ed C++ code has been implemented.

= Key Investigators =

* Georgia Tech: Ivan Kolesov, Patricio Vela
* Boston University: Jehoon Lee, Allen Tannenbaum
* MGH: Gregory Sharp

= Publications =

''In Press''

I. Kolesov, J. Lee, P.Vela, G. Sharp and A. Tannenbaum. Diffeomorphic Point Set Registration with Landmark Constraints. In Preparation for PAMI.

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:21:17Z

Ivan.kolesov:

Back to [[Algorithm:BU|Boston University Algorithms]]
__NOTOC__
= Semi-Automatic Image Registration =

We recognize that the difference between a failure of an automatic image registration approach and a success of a semi-automatic method can be a small amount of user input. The goal of this work is to register two CT volumes of different patients that are related by a large deformation. The user sets two thresholds for each image: one for the bone mask and another for flesh tissue. This operation is not time consuming but simplifies the registration task dramatically for the automatic algorithm.

= Description =
In this example, large misalignment is present between the two patients.

* [[Image:PreRegFleshSkeleton.png | PreRegFleshSkeleton| 400px]]
Original Misalignment of the volumes.

Point clouds are generated from label maps of bone. The computed registration field, which is guaranteed to be injective, is applied to the original CT volumes.

* [[Image:SkeletonMisalignedView1.png | SkeletonMisalignedView1| 400px]] [[Image:SkeletonAlignedView1.png | SkeletonMisalignedView1| 400px]]
Point clouds representing bone tissue of the patients (before and after registration).

Another set of point clouds is generated by sampling from label maps of flesh created for the images from the previous step. To avoid undoing the previous registration, regions belonging to the registered bone tissue from above are constrained not to move. Again, an injective deformation field is computed.

* [[Image:FleshMis.png | FleshMis| 400px]] [[Image:FleshAlignedView1.png | FleshAlignedView1| 400px]]
Point clouds representing flesh tissue of the patients (before and after registration). This step is constrained.

The results of applying the two deformation computed by the proposed process are shown below.

* [[Image:PostRegFleshSkeleton.png | PostRegFleshSkeleton| 400px]]
Aligned images using the two step registration process.

== Current State of Work ==
A pipeline composed of Matlab and mex-ed C++ code has been implemented.

= Key Investigators =

* Georgia Tech: Ivan Kolesov, Patricio Vela
* Boston University: Jehoon Lee, Allen Tannenbaum
* MGH: Gregory Sharp

= Publications =

''In Press''

I. Kolesov, J. Lee, P.Vela, G. Sharp and A. Tannenbaum. Diffeomorphic Point Set Registration with Landmark Constraints. In Preparation for PAMI.

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:17:51Z

Ivan.kolesov:

Back to [[Algorithm:BU|Boston University Algorithms]]
__NOTOC__
= Semi-Automatic Image Registration =

We recognize that the difference between a failure of an automatic image registration approach and a success of a semi-automatic method can be a small amount of user input. The goal of this work is to register two CT volumes of different patients that are related by a large deformation. The user sets two thresholds for each image: one for the bone mask and another for flesh tissue. This operation is not time consuming but simplifies the registration task dramatically for the automatic algorithm.

= Description =
In this example, large misalignment is present between the two patients.

* [[Image:PreRegFleshSkeleton.png | PreRegFleshSkeleton| 400px]]
Original Misalignment of the volumes.

Point clouds are generated from label maps of bone. The computed registration field, which is guaranteed to be injective, is applied to the original CT volumes.

* [[Image:SkeletonMisalignedView1.png | SkeletonMisalignedView1| 400px]] [[Image:SkeletonAlignedView1.png | SkeletonMisalignedView1| 400px]]
Point clouds representing bone tissue of the patients (before and after registration).

Another set of point clouds is generated by sampling from label maps of flesh. To avoid undoing the previous registration, regions belonging to the registered bone tissue from above are constrained not to move. Again, an injective deformation field is computed.

* [[Image:FleshMis.png | FleshMis| 400px]] [[Image:FleshAlignedView1.png | FleshAlignedView1| 400px]]
Point clouds representing flesh tissue of the patients (before and after registration). This step is constrained.

The result of

== Current State of Work ==
A pipeline composed of Matlab and mex-ed C++ code has been implemented.

= Key Investigators =

* Georgia Tech: Ivan Kolesov, Patricio Vela
* Boston University: Jehoon Lee, Allen Tannenbaum
* MGH: Gregory Sharp

= Publications =

''In Press''

I. Kolesov, J. Lee, P.Vela, G. Sharp and A. Tannenbaum. Diffeomorphic Point Set Registration with Landmark Constraints. In Preparation for PAMI.

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:16:09Z

Ivan.kolesov:

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:15:38Z

Ivan.kolesov:

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:14:48Z

Ivan.kolesov:

File:FleshMis.png

2012-11-19T03:12:04Z

Ivan.kolesov:

File:FleshAlignedView1.png

2012-11-19T03:06:31Z

Ivan.kolesov:

File:SkeletonAlignedView1.png

2012-11-19T03:05:21Z

Ivan.kolesov:

File:SkeletonMisalignedView1.png

2012-11-19T03:05:07Z

Ivan.kolesov:

File:PostRegFleshSkeleton.png

2012-11-19T03:03:21Z

Ivan.kolesov:

File:PreRegFleshSkeleton.png

2012-11-19T03:02:59Z

Ivan.kolesov:

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T03:02:21Z

Ivan.kolesov:

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T02:55:46Z

Ivan.kolesov: /* Current State of Work */

Back to [[Algorithm:BU|Boston University Algorithms]]
__NOTOC__
= Semi-Automatic Image Registration =

We recognize that the difference between a failure of an automatic image registration approach and a success of a semi-automatic method can be a small amount of user input. The goal of this work is to register two CT volumes of different patients that are related by a large deformation. The user sets two thresholds for each image: one for the bone mask and another for flesh tissue. This operation is not time consuming but simplifies the registration task dramatically for the automatic algorithm.

= Description =
In this work, interactive segmentation is integrated with an active contour model and segmentation is posed as a human-supervisory control problem. User input is tightly coupled with an automatic segmentation algorithm leveraging the user's high-level anatomical knowledge and the automated method's speed. Real-time visualization enables the user to quickly identify and correct the result in a sub-domain where the variational model's statistical assumptions do not agree with his expert knowledge. Methods developed in this work are applied to magnetic resonance imaging (MRI) volumes as part of a population study of human skeletal development. Segmentation time is reduced by approximately five times over similarly accurate manual segmentation of large bone structures.

* [[Image:KSliceFlowChart.png | Rel Pred| 800px]]
Flowchart for the interactive segmentation approach. Notice the user's pivotal role in the process.
* [[Image:KSliceInptTimeChart.png | Eye Seg| 800px]]
Time-line of user input into the system. Note that user input is sparse, has local effect only, and decreases in frequency and magnitude over time.
* [[Image:KVoutSegTightMod.png | Eye Seg| 300px]]
Result of the segmentation.

== Current State of Work ==
A pipeline composed of Matlab and mex-ed C++ code has been implemented.

= Key Investigators =

* Georgia Tech: Ivan Kolesov, Patricio Vela
* Boston University: Jehoon Lee, Allen Tannenbaum
* MGH: Gregory Sharp

= Publications =

''In Press''

I. Kolesov, J. Lee, P.Vela, G. Sharp and A. Tannenbaum. Diffeomorphic Point Set Registration with Landmark Constraints. In Preparation for PAMI.

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T02:46:16Z

Ivan.kolesov:

Back to [[Algorithm:BU|Boston University Algorithms]]
__NOTOC__
= Semi-Automatic Image Registration =

We recognize that the difference between a failure of an automatic image registration approach and a success of a semi-automatic method can be a small amount of user input. The goal of this work is to register two CT volumes of different patients that are related by a large deformation. The user sets two thresholds for each image: one for the bone mask and another for flesh tissue. This operation is not time consuming but simplifies the registration task dramatically for the automatic algorithm.

= Description =
In this work, interactive segmentation is integrated with an active contour model and segmentation is posed as a human-supervisory control problem. User input is tightly coupled with an automatic segmentation algorithm leveraging the user's high-level anatomical knowledge and the automated method's speed. Real-time visualization enables the user to quickly identify and correct the result in a sub-domain where the variational model's statistical assumptions do not agree with his expert knowledge. Methods developed in this work are applied to magnetic resonance imaging (MRI) volumes as part of a population study of human skeletal development. Segmentation time is reduced by approximately five times over similarly accurate manual segmentation of large bone structures.

* [[Image:KSliceFlowChart.png | Rel Pred| 800px]]
Flowchart for the interactive segmentation approach. Notice the user's pivotal role in the process.
* [[Image:KSliceInptTimeChart.png | Eye Seg| 800px]]
Time-line of user input into the system. Note that user input is sparse, has local effect only, and decreases in frequency and magnitude over time.
* [[Image:KVoutSegTightMod.png | Eye Seg| 300px]]
Result of the segmentation.

== Current State of Work ==
The described algorithm is implemented in c++ and delivered to physicians. We have begun to analyze the data they created by segmenting the knee with out tool. Future work incorporates shape prior into the segmentation and improves user interaction(according to feedback physician's provide us).

= Key Investigators =

* Georgia Tech: Ivan Kolesov, Patricio Vela
* Boston University: Jehoon Lee, Allen Tannenbaum
* MGH: Gregory Sharp

= Publications =

''In Press''

I. Kolesov, J. Lee, P.Vela, G. Sharp and A. Tannenbaum. Diffeomorphic Point Set Registration with Landmark Constraints. In Preparation for PAMI.

Projects:MGH-HeadAndNeck-PtSetReg

2012-11-19T02:45:28Z

Ivan.kolesov: /* Interactive Image Segmentation With Active Contours */

Back to [[Algorithm:BU|Boston University Algorithms]]
__NOTOC__
= Semi-Automatic Image Registration =

We recognize that the difference between a failure of an automatic image registration approach and a success of a semi-automatic method can be a small amount of user input. The goal of this work is to register two CT volumes of different patients that are related by a large deformation. The user sets two thresholds for each image: one for the bone mask and another for flesh tissue. This operation is not time consuming but simplifies the registration task dramatically for the automatic algorithm.

= Description =
In this work, interactive segmentation is integrated with an active contour model and segmentation is posed as a human-supervisory control problem. User input is tightly coupled with an automatic segmentation algorithm leveraging the user's high-level anatomical knowledge and the automated method's speed. Real-time visualization enables the user to quickly identify and correct the result in a sub-domain where the variational model's statistical assumptions do not agree with his expert knowledge. Methods developed in this work are applied to magnetic resonance imaging (MRI) volumes as part of a population study of human skeletal development. Segmentation time is reduced by approximately five times over similarly accurate manual segmentation of large bone structures.

* [[Image:KSliceFlowChart.png | Rel Pred| 800px]]
Flowchart for the interactive segmentation approach. Notice the user's pivotal role in the process.
* [[Image:KSliceInptTimeChart.png | Eye Seg| 800px]]
Time-line of user input into the system. Note that user input is sparse, has local effect only, and decreases in frequency and magnitude over time.
* [[Image:KVoutSegTightMod.png | Eye Seg| 300px]]
Result of the segmentation.

== Current State of Work ==
The described algorithm is implemented in c++ and delivered to physicians. We have begun to analyze the data they created by segmenting the knee with out tool. Future work incorporates shape prior into the segmentation and improves user interaction(according to feedback physician's provide us).

= Key Investigators =

* Georgia Tech: Ivan Kolesov, Patricio Vela
* Boston University: Jehoon Lee, Allen Tannenbaum
* MGH: Gregory Sharp

= Publications =

''In Press''

I. Kolesov, P.Karasev, G.Muller, K.Chudy, J.Xerogeanes, and A. Tannenbaum. Human Supervisory Control Framework for Interactive Medical Image Segmentation. MICCAI Workshop on Computational Biomechanics for Medicine 2011.

P.Karasev, I.Kolesov, K.Chudy, G.Muller, J.Xerogeanes, and A. Tannenbaum. Interactive MRI Segmentation with Controlled Active Vision. IEEE CDC-ECC 2011.