NAMIC Wiki - User contributions [en]

2014 Summer Project Week:Intelligent Steering

2014-06-27T04:18:21Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Steered_rotations0_h.png| 2D slice views of fixed image using different PCA axis combinations
Image:Steered_rotations1_h.png| 2D slice views of moving image using different PCA axis combinations
</gallery>

==Key Investigators==
* Marcel Prastawa, GE
* Jim Miller, GE
* Steve Pieper, Isomics

==Project Description==
Steered image registration in Slicer using intelligent interaction rather than direct interaction where user specifies deformation changes.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop interaction schemes that allows users to indicate incorrect regions
* Provide intelligent interfaces so users provide minimal interaction without detailed control of image deformations
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate data exploration techniques for highlighting common registration errors (local rotation, shift, and scaling)
* Implement efficient, responsive extensions using the Slicer 4 Python extension platform and PyOpenCL
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Testing the use of robust PCA for providing hints on rotational misalignment
* Investigating the modeling of appropriate correction steps given the possible misalignments
</div>
</div>

==References==
[https://www.youtube.com/watch?v=sfAMD5wSvlQ Video of Direct Steering Interaction]

2014 Summer Project Week:Intelligent Steering

2014-06-27T04:17:35Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Steered_rotations0_h.png| 2D slice views of fixed image using different PCA axis combinations
Image:Steered_rotations1_h.png| 2D slice views of moving image using different PCA axis combinations
</gallery>

==Key Investigators==
* Marcel Prastawa, GE
* Jim Miller, GE
* Steve Pieper, Isomics

==Project Description==
Steered image registration in Slicer using intelligent interaction rather than direct interaction where user specifies deformation changes.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop interaction schemes that allows users to indicate incorrect regions
* Provide intelligent interfaces so users provide minimal interaction without detailed control of image deformations
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate data exploration techniques for highlighting rotational errors
* Implement efficient, responsive extensions using the Slicer 4 Python extension platform and PyOpenCL
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Testing the use of robust PCA for providing hints on rotational misalignment
* Investigating the modeling of appropriate correction steps given the possible misalignments
</div>
</div>

==References==
[https://www.youtube.com/watch?v=sfAMD5wSvlQ Video of Direct Steering Interaction]

File:Steered rotations1 h.png

2014-06-27T04:16:22Z

Prastawa:

File:Steered rotations0 h.png

2014-06-27T04:16:03Z

Prastawa:

2014 Summer Project Week:Intelligent Steering

2014-06-27T04:12:21Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
[[File:steered_rotations0_h.png]]| 2D slice views of fixed image
[[File:steered_rotations1_h.png]]| 2D slice views of moving image
</gallery>

==Key Investigators==
* Marcel Prastawa, GE
* Jim Miller, GE
* Steve Pieper, Isomics

==Project Description==
Steered image registration in Slicer using intelligent interaction rather than direct interaction where user specifies deformation changes.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop interaction schemes that allows users to indicate incorrect regions
* Provide intelligent interfaces so users provide minimal interaction without detailed control of image deformations
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate data exploration techniques for highlighting rotational errors
* Implement efficient, responsive extensions using the Slicer 4 Python extension platform and PyOpenCL
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Testing the use of robust PCA for providing hints on rotational misalignment
* Investigating the modeling of appropriate correction steps given the possible misalignments
</div>
</div>

==References==
[https://www.youtube.com/watch?v=sfAMD5wSvlQ Video of Direct Steering Interaction]

2014 Summer Project Week:Intelligent Steering

2014-06-27T04:11:18Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
File:steered_rotations0_h.png| 2D slice views of fixed image
Image:steered_rotations1_h.png| 2D slice views of moving image
</gallery>

==Key Investigators==
* Marcel Prastawa, GE
* Jim Miller, GE
* Steve Pieper, Isomics

==Project Description==
Steered image registration in Slicer using intelligent interaction rather than direct interaction where user specifies deformation changes.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop interaction schemes that allows users to indicate incorrect regions
* Provide intelligent interfaces so users provide minimal interaction without detailed control of image deformations
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate data exploration techniques for highlighting rotational errors
* Implement efficient, responsive extensions using the Slicer 4 Python extension platform and PyOpenCL
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Testing the use of robust PCA for providing hints on rotational misalignment
* Investigating the modeling of appropriate correction steps given the possible misalignments
</div>
</div>

==References==
[https://www.youtube.com/watch?v=sfAMD5wSvlQ Video of Direct Steering Interaction]

2014 Summer Project Week:Intelligent Steering

2014-06-27T04:09:32Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:steered_rotations0_h.png| 2D slice views of fixed image
Image:steered_rotations1_h.png| 2D slice views of moving image
</gallery>

==Key Investigators==
* Marcel Prastawa, GE
* Jim Miller, GE
* Steve Pieper, Isomics

==Project Description==
Steered image registration in Slicer using intelligent interaction rather than direct interaction where user specifies deformation changes.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop interaction schemes that allows users to indicate incorrect regions
* Provide intelligent interfaces so users provide minimal interaction without detailed control of image deformations
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate data exploration techniques for highlighting rotational errors
* Implement efficient, responsive extensions using the Slicer 4 Python extension platform and PyOpenCL
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Testing the use of robust PCA for providing hints on rotational misalignment
* Investigating the modeling of appropriate correction steps given the possible misalignments
</div>
</div>

==References==
[https://www.youtube.com/watch?v=sfAMD5wSvlQ Video of Direct Steering Interaction]

2014 Summer Project Week:Intelligent Steering

2014-06-27T04:08:42Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:steered_rotations0_h.png | 2D slice views of fixed image
Image:steered_rotations1_h.png | 2D slice views of moving image
</gallery>

==Key Investigators==
* Marcel Prastawa, GE
* Jim Miller, GE
* Steve Pieper, Isomics

==Project Description==
Steered image registration in Slicer using intelligent interaction rather than direct interaction where user specifies deformation changes.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop interaction schemes that allows users to indicate incorrect regions
* Provide intelligent interfaces so users provide minimal interaction without detailed control of image deformations
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate data exploration techniques for highlighting rotational errors
* Implement efficient, responsive extensions using the Slicer 4 Python extension platform and PyOpenCL
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Testing the use of robust PCA for providing hints on rotational misalignment
* Investigating the modeling of appropriate correction steps given the possible misalignments
</div>
</div>

==References==
[https://www.youtube.com/watch?v=sfAMD5wSvlQ Video of Direct Steering Interaction]

2014 Summer Project Week:Intelligent Steering

2014-06-20T21:00:35Z

Prastawa:

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

==Key Investigators==
* Marcel Prastawa, GE
* Jim Miller, GE
* Steve Pieper, Isomics

==Project Description==
Steered image registration in Slicer using intelligent interaction rather than direct interaction where user specifies deformation changes.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop interaction schemes that allows users to indicate incorrect regions
* Provide intelligent interfaces so users provide minimal interaction without detailed control of image deformations
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate data exploration techniques for highlighting rotational errors
* Implement efficient, responsive extensions using PyOpenCL
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==
[https://www.youtube.com/watch?v=sfAMD5wSvlQ Video of Direct Steering Interaction]

2014 Summer Project Week:Intelligent Steering

2014-06-20T20:55:57Z

Prastawa: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List </gallery> ==Key Investigators== * Marcel Prastawa, GE * Jim Miller, GE * Steve Piep…'

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

==Key Investigators==
* Marcel Prastawa, GE
* Jim Miller, GE
* Steve Pieper, Isomics

==Project Description==
Steered image registration in Slicer
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop interaction schemes that allows users to indicate incorrect regions
* Provide intelligent interfaces so users provide minimal interaction without detailed control of image deformations
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate data exploration techniques for highlighting rotational errors
* Implement efficient, responsive extensions using PyOpenCL
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Summer Project Week

2014-06-20T20:51:35Z

Prastawa: /* Image-Guided Therapy */

__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/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_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==

==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)

==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==

==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 ==

==[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})

==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
#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
#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
#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

2014-04-24T19:22:37Z

Prastawa: /* Image-Guided Therapy */

2014 Project Week:TBISegmentation

2014-01-06T14:29:00Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Active_4D.png| Interactive process
</gallery>

==Key Investigators==
* GE: Marcel Prastawa
* Utah: Bo Wang, Guido Gerig
* USC: Andrei Irimia, Jack Van Horn

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a pipeline combining our TBI segmentation algorithm with other Slicer modules.
* Study and gain understanding of the manual process for segmenting TBI.
* Test the algorithm with users from USC.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Wrap existing code into a Slicer extension.
* Determine approaches for user interaction for semi-automatic segmentation.
* Test and evaluate Slicer modules for TBI processing:
** Intra and inter time points coregistration.
** Initial atlas alignment using affine transformation.
** Skull stripping to obtain initial brain mask.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

== Reference ==
* [http://www.nitrc.org/projects/parser_4d 4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration) Code Repo]
* [http://www.cs.utah.edu/~bowang/projects/active4D/4D_Active_Cut.html 4D Active Cut]
* [http://link.springer.com/chapter/10.1007/978-3-319-02126-3_4 Modeling 4D changes in TBI]

2014 Project Week:TBISegmentation

2014-01-06T14:28:23Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Active_4D.png| Interactive process
</gallery>

==Key Investigators==
* GE: Marcel Prastawa
* Utah: Bo Wang, Guido Gerig
* USC: Andrei Irimia, Jack Van Horn

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a pipeline combining our TBI segmentation algorithm with other Slicer modules.
* Study and gain understanding of the manual process for segmenting TBI
* Test the algorithm with users from USC.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Wrap existing code into a Slicer extension.
* Determine approaches for user interaction for semi-automatic segmentation.
* Test and evaluate Slicer modules for TBI processing:
** Intra and inter time points coregistration.
** Initial atlas alignment using affine transformation.
** Skull stripping to obtain initial brain mask.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

== Reference ==
* [http://www.nitrc.org/projects/parser_4d 4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration)]
* [http://www.cs.utah.edu/~bowang/projects/active4D/4D_Active_Cut.html 4D Active Cut]
* [http://link.springer.com/chapter/10.1007/978-3-319-02126-3_4 Modeling 4D changes in TBI]

2014 Project Week:TBISegmentation

2014-01-06T14:24:47Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Active_4D.png| Interactive process
</gallery>

==Key Investigators==
* GE: Marcel Prastawa
* Utah: Bo Wang, Guido Gerig
* USC: Andrei Irimia, Jack Van Horn

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a pipeline combining our TBI segmentation algorithm with other Slicer modules.
* Study and gain understanding of the manual process for segmenting TBI
* Test the algorithm with users from USC.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Wrap existing code into a Slicer extension
* Determine approaches for user interaction for semi-automatic segmentation segmentation.
* Test and evaluate Slicer modules for TBI processing:
** Intra and inter time points coregistration
** Initial atlas alignment using affine transformation
** Skull stripping to obtain initial brain mask
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

== Reference ==
* [http://www.nitrc.org/projects/parser_4d 4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration)]

2014 Winter Project Week:Steered Registration

2013-12-13T17:40:18Z

Prastawa:

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

==Key Investigators==

* Isomics: Steve Pieper
* MGH: Greg Sharp
* GE: Marcel Prastawa, Jim Miller
* Princess Margaret Hospital: Kevin Wang
* Queen's University: Csaba Pinter

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Review various use cases for interactive registration
* Review current work-in-progress
** RegistrationPlugin architecture
** Integration with Hybrid BSpline HNC DBP Project
* Identify high priority fixes / features
* Make a long-term plan

</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>

== Reference ==

* [[2013_Summer_Project_Week:Landmark_Registration|Summer Project Week page]]
* Source code
** [https://github.com/pieper/LandmarkRegistration Landmark Registration]
*** [https://github.com/pieper/LandmarkRegistration/tree/refactor-RegistrationLib Branch with RegistrationPlugin support]
*** [https://github.com/pieper/LandmarkRegistration/blob/refactor-RegistrationLib/RegistrationLib/AffinePlugin.py Example plugin]
** [https://github.com/dirkpadfield/steeredReg Steered affine registration]
** [https://github.com/prastawa/SteeredFluidRegistration Steered fluid registration]
* Videos
** [http://www.youtube.com/watch?v=IOJ0yLG5QEE Screen capture of landmark registration] (note that the screen recording is much slower than using the tool in real life)
** [http://www.youtube.com/watch?v=LRA2wldGeEk Screen capture of steered fluid registration]

2012 Summer Project Week:ABC Slicer4

2012-06-22T13:58:17Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University of Utah: Marcel Prastawa, Bo Wang, Guido Gerig

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

<h3>Objective</h3>
Port the Atlas Based Classification (ABC) Slicer 3 command line extension to Slicer 4.
</div>

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

<h3>Approach, Plan</h3>

We will use the SkullStripper extension as a starting point for adapting the old code, together with the instructions at http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/Build_Module

</div>

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

<h3>Progress</h3>

Compilation of Slicer 4 ABC extension using the new framework is successful. Further testing still needed.

Module wrapper files are committed to the NITRC svn repository:
https://www.nitrc.org/svn/abc/trunk/Slicer4CommandLine

Need to determine procedure for submitting module to the ExtensionManager.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
* ABC: [http://www.nitrc.org/projects/abc]

</div>

2012 Summer Project Week:ABC Slicer4

2012-06-21T19:27:16Z

Prastawa: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University of Utah: Marcel Prastawa, Bo Wang, Guido Gerig

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

<h3>Objective</h3>
Port the Atlas Based Classification (ABC) Slicer 3 command line extension to Slicer 4.
</div>

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

<h3>Approach, Plan</h3>

We will use the SkullStripper extension as a starting point for adapting the old code, together with the instructions at http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/Build_Module

</div>

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

<h3>Progress</h3>

Compilation of Slicer 4 ABC extension using the new Slicer 4 CMake framework is successful. Further testing still needed.

Module wrapper files are committed to:
https://www.nitrc.org/svn/abc/trunk/Slicer4CommandLine

Need to determine procedure for submitting module to the ExtensionManager.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
* ABC: [http://www.nitrc.org/projects/abc]

</div>

2012 Summer Project Week:ABC Slicer4

2012-06-21T19:25:16Z

Prastawa: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University of Utah: Marcel Prastawa, Bo Wang, Guido Gerig

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

<h3>Objective</h3>
Port the Atlas Based Classification (ABC) Slicer 3 command line extension to Slicer 4.
</div>

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

<h3>Approach, Plan</h3>

We will use the SkullStripper extension as a starting point for adapting the old code, together with the instructions at http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/Build_Module

</div>

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

<h3>Progress</h3>

Compilation of Slicer 4 ABC extension using the new Slicer 4 CMake framework is successful. Further testing still needed.

Module wrapper files are committed to:
https://www.nitrc.org/svn/abc/trunk/Slicer4CommandLine

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
* ABC: [http://www.nitrc.org/projects/abc]

</div>

2012 Summer Project Week:ABC Slicer4

2012-06-14T18:51:23Z

Prastawa: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University of Utah: Marcel Prastawa, Bo Wang, Guido Gerig

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

<h3>Objective</h3>
Port the Atlas Based Classification (ABC) Slicer 3 command line extension to Slicer 4.
</div>

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

<h3>Approach, Plan</h3>
We will use the SkullStripper extension as a starting point for adapting the old code.
</div>

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

<h3>Progress</h3>
TBA
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
* ABC: [http://www.nitrc.org/projects/abc]

</div>

2012 Summer Project Week:ABC Slicer4

2012-06-12T18:51:20Z

Prastawa: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List </gallery> ==Key Investigators== * University of Utah: Marcel Prastawa, Bo Wang, Gu…'

2012 Summer Project Week

2012-06-12T18:46:58Z

Prastawa: /* General Segmentation */

Back to [[Events]]

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

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

==Agenda==

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

==Projects==

This is where the list of projects goes...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

==Background==

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

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

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

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

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

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

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

==Registrants==

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

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

2012 Winter Project Week

2011-11-28T15:57:38Z

Prastawa: /* Traumatic Brain Injury DBP */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===IGT===
*MR guided laser ablation for neurosurgery (Dan Orringer, MD BWH, Jason Stafford, MD Anderson, Isaiah Norton BWH)
*Pelvic Registration (Sandy Wells, Firdaus Janoos, Mehdi Moradi UBC/BWH, jan egger, andrey fedorov)
*OpenIGTLink interface for Slicer4(Junichi, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*Needle tracking (atushi yamada, radhika tibrewal, a needle navigation person)
*?mr susceptability (clare poynton, mr physics person?)
* [[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)

===Traumatic Brain Injury DBP===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
* [[2012_Winter_Project_Week:TBIDTI|Analysis of DTI data in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa)

===Predict Huntington's Disease DBP===
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation DBP===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer DBP===
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)

===Radiation therapy===
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)

===NA-MIC Kit Internals===
*Slicer4 Scene Views Module (Nicole Aucoin)
*Slicer4 Annotations Module
** File format refactor (Nicole Aucoin)
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)
* DICOM Networking, Database, and Slicer Integration (Steve Pieper)
* Editor Extension Examples and Debugging (Steve Pieper)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* Automated Testing (Sonia Pujol, Steve Pieper)

=== Preparation ===

#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]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week

2011-11-17T20:25:06Z

Prastawa: /* Traumatic Brain Injury DBP */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===IGT===
*MR guided laser ablation for neurosurgery (Dan Orringer, MD BWH, Jason Stafford, MD Anderson, Isaiah Norton BWH)
*Pelvic Registration (Sandy Wells, Firdaus Janoos, Mehdi Moradi UBC/BWH, jan egger, andrey fedorov)
*OpenIGTLink interface for Slicer4(Junichi, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*Needle tracking (atushi yamada, radhika tibrewal, a needle navigation person)
*?mr susceptability (clare poynton, mr physics person?)
* [[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)

===Traumatic Brain Injury DBP===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Quantitative clinical analysis of longitudinal TBI using current registration and segmentation algorithms]] (Marcel Prastawa, Bo Wang, Andrei Irimia, Jack van Horn, Guido Gerig)
* [[2012_Winter_Project_Week:TBIDTI|Analysis of DTI data in TBI]] (Marcel Prastawa, Bo Wang, Andrei Irimia, Jack van Horn, Guido Gerig)
* [[2012_Winter_Project_Week:TBIValidation|Validation of analysis algorithms for TBI]] (Marcel Prastawa, Bo Wang, Andrei Irimia, Jack van Horn, Guido Gerig)

===Predict Huntington's Disease DBP===
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)

===Atrial fibrillation DBP===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer DBP===
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)

===Radiation therapy===
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)

===NA-MIC Kit Internals===
*Slicer4 Scene Views Module (Nicole Aucoin)
*Slicer4 Annotations Module
** File format refactor (Nicole Aucoin)
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)
* Editor Extension Examples and Debugging (Steve Pieper)

=== Preparation ===

#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]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

File:NAMIC-ABC-UCLA-08Nov2010.ppt

2010-11-12T20:08:57Z

Prastawa:

Events:UCLA-Slicer-Training-11-2010

2010-11-12T20:08:18Z

Prastawa:

== Logistics ==

Location: Neuroscience Research Building (NRB), Room 470, UCLA campus.

Date: Monday November 8, 2010

'''Registration''': To sign-up for this event, please fill in the [[media:RegistrationForm_SlicerWorkshop_UCLA_Nov8_2010.doc‎ | registration form]] and send it by e-mail to Jack Van Horn, PhD [jack.vanhorn at loni.ucla.edu] before Friday November 5.

== Agenda ==
*9:00-10:00 am Computer setup assistance by the instructors
*10:00-10:30 am [[media:Kikinis-NA-MIC-2010-09-20.ppt|Introduction to NA-MIC]] and [[media:Kikinis-Slicer Community-2010-09-20.ppt|the Slicer community]] (Ron Kikinis)
*10:30-12:15 pm [[media:Slicer3_DataLoadingAndVisualization_UCLA2010_SoniaPujol.pdf | Data Loading and 3D Visualization ]](Sonia Pujol)
*12:15-1:00 pm Lunch
*1:00-2:15 pm [[media:ManualRegistration_UCLA2010.pdf | Image Registration ]] and [[media:InteractiveEditorTutorial_UCLA2010_SoniaPujol.pdf | Interactive Editing ]](Sonia Pujol)
*2:15-2:45 pm [[media:NAMIC-ABC-UCLA-08Nov2010.ppt|Atlas-Based Classification]] (Marcel Prastawa)
*2:45-3:00 pm [[media:TBIDataAnalysis_SoniaPujol.pdf | TBI Cases]] (Sonia Pujol)[http://www.na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C31 TBI Registration Case Library]
*2:45-3:00 pm Questions from the Audience and Discussion (Ron Kikinis/Sonia Pujol)

== Notes on the Nrrd file format==

The Nrrd file format, which is part of the NA-MIC kit, accurately represents N-dimensional raster information for scientific visualization and medical image processing.
This format is used in Slicer to represent the necessary information about a DWI image volume, its anatomical orientation, and all the DWI-specific acquisition parameters for estimating the diffusion tensors. A detailed description of the Nrrd file format usage for DWI images and DTI data can be found [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format here].

The [http://www.slicer.org/slicerWiki/index.php/Modules:DicomToNRRD-3.6 DicomToNrrd module] in Slicer can be used to convert Dicom data into Nrrd. A detailed [http://www.na-mic.org/Wiki/images/7/77/SlicerTraining9_DTI-FromDicomToNrrd.ppt tutorial] describes how to construct a nhdr file from a set of images, which can be in Dicom or in other format such as Nifti, and a list of known gradients, using the Teem Library.

== Local Organizer==
*Jack Van Horn, PhD, Laboratory of Neuro Imaging, UCLA School of Medicine

== Teaching Faculty==
*[http://www.spl.harvard.edu/pages/People/kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
*[http://lmi.bwh.harvard.edu/~spujol Sonia Pujol, Ph.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
*[http://www.spl.harvard.edu/~noby Nobuhiko Hata, Ph.D.], Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School
* [http://www.sci.utah.edu/~prastawa/ Marcel Prastawa, Ph.D.], Scientific Computing and Imaging Institute, University of Utah

== Preparation for the Workshop ==

<span style="background-color: yellow"> The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers.
All participants are required to come with their own laptop computer and install the software and datasets prior to the event.</span>. A minimum of 1 GB of RAM (2 GB if possible) and a dedicated graphic accelerator with 64mb of on board graphic memory are required.

Please install the '''Slicer3.6.1''' version appropriate to the laptop computer you'll be bringing to the tutorial:

* Windows: [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23-win32.exe]
* Linux 64: [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23-linux-x86_64]
* Linux 32: [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20-linux-x86 ]
* Mac Darwin: [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20-darwin-x86]

Please download the [[media:Slicer3VisualizationDataset.zip | 3D Visualization dataset]], [http://www.slicer.org/slicerWiki/index.php/File:EditorTutorialDataset.zip Editor dataset], and [http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Registration dataset] in preparation for the workshop.

== Slicer3 Training Survey ==
[http://www.surveymonkey.com/s/GZDXKXQ Please click here to take the Slicer3 Training Survey]

== Slicer Community ==
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] for questions and feature requests related to the software.
[[Events#2010|Back to Events 2010]]

AlgorithmRetreat2010

2010-10-20T22:07:08Z

Prastawa:

[[2010-09-Leadership-Brainstroming#Computer_Science|Back to brainstorming page]]
[[Events|Back to events page]]

= Nov 5-6, Chapel Hill, NC =

==Introduction==
*The NA-MIC algorithm core holds an annual retreat
*The 2010 event will begin on 8:30 am on Friday the 5th of Nov and finish at approximately 2pm on Saturday the 6th.

==Topics==
*Plans, Needs, Expectations of and Interactions with DBPs (Core-1 contacts, all)
*Segmentation
*Registration
**Upcoming event: [[Event:2011_Registration_Retreat|New Directions in Registration Workshop]]

*Interaction with the Engineering Core
*Slicer

===Suggested Hotels===

Nice for walking to campus & Franklin Street, but rather expensive (ask for the University/Computer Science rate of 159 USD per night):
* [http://www.carolinainn.com/ Carolina Inn], 211 Pittsboro Street, Chapel Hill, NC
* [http://www.franklinhotelnc.com/ Franklin Hotel], 311 W Franklin St, Chapel Hill, NC (mention that you are traveling for a meeting with Kitware, and receive Kitware's corporate rate)

Best suggestions (need taxi or rental car to campus & Franklin Street):
* [http://www.courtyardchapelhill.com/ Courtyard Marriott], 100 Marriott Way, Chapel Hill, NC
* [http://www.daysinn.com/DaysInn/control/Booking/property_info?propertyId=10275&as_srp=SP2&cid=carat_search-Days_Inn/ Days Inn], 15-501 & Fordham Blvd, Chapel Hill, NC 27514 US

== Attendees ==
* Ross Whitaker
* Guido Gerig
* Polina Golland
* Allen Tannenbaum
* Martin Styner
* Ron Kikinis (Saturday)
* Michal Depa, MIT
* Archana Venkataraman, MIT
* Sam Gerber, Utah
* Marcel Prastawa

Projects:UtahAtlasSegmentation

2010-05-11T19:01:30Z

Prastawa:

Back to [[Algorithm:Utah2|Utah 2 Algorithms]]
__NOTOC__

= Atlas Based Classification (ABC) for Healthy Brain MRI =

Automatic segmentation of brain MR images can be performed reliably using priors from brain atlases and an image generative model. We have developed a tool called ABC that provides an automatic segmentation pipeline in a modular framework.
The processing pipeline is composed of tasks such as filtering the input images, registering the multimodal input images and the brain atlas to a common space, followed by iterative steps which interleave segmentation, inhomogeneity correction, and atlas warping.

Our tool generates bias corrected images, fuzzy classification maps, and discrete segmentation labels. The tool has been used to automatically segment thousands of adult and toddler images from the University of North Carolina (UNC), and is also being used as a skull stripping mechanism for DTI processing at UNC and Utah. An example of the output of the tool is shown below.

{|
|-
| [[Image:UtahSegPlugin_result.png|thumb|center|400px|Output of the segmentation plugin, showing the bias corrected image and the probabilities for white and gray matter.]]
| [[Image:TBI-seg.jpg|thumb|center|400px|ABC tool applied to TBI MRI data.]]
|}

The ABC tool has been integrated into Slicer as an extension, and it can also be executed as a stand-alone application. Both versions are available for download through NITRC: http://www.nitrc.org/projects/abc .
{|
|-
| [[Image:UtahSegPlugin_screen.png|thumb|center|200px|Screen shot of the segmentation plugin in Slicer.]]
| [[Image:UtahSegGUI_screen.png|thumb|center|400px|Screen shot of the stand-alone segmentation GUI.]]
|}

== External Use and Modifications of ABC ==

An earlier version of ABC has been distributed to a large number of other research groups associated with ongoing image analysis projects at the University of North Carolina - Chapel Hill and the University of Utah, and to research groups linked to these investigators. High profile projects include the Silvio Conte Center (http://www.psychiatry.unc.edu/conte/, PI John H. Gilmore, UNC) involving the processing of over 1000 infant MRI, and the Autism Centers of Excellence Project IBIS (http://www.ibis-network.org/, PI Joseph Piven, UNC) where over 650 infant brain MRI will be processed with this tool. In order to segment infant brains with age range of 6 months to 2 years as part of this longitudinal study, new age-specific atlases have been developed to be used as spatial priors for ABC.

The ABC method has also been modified and extensively used by the Hans Johnson from University of Iowa, as part of a large, multi-center Huntington Disease study. Experience with a couple of hundred datasets at Iowa demonstrated the excellent robustness and reliability of the methodology.

{|
|-
| [[Image:ABC-MIND1.png|thumb|center|250px|Output of the segmentation plugin, showing the bias corrected image and the probabilities for white and gray matter.]]
| [[Image:ABC-MIND2.png|thumb|center|250px|BRAINSABC expanded prior class images.]]
| [[Image:ABC-MIND3.png|thumb|center|250px|BRAINSABC expanded prior class images.]]
|}

The probability maps for the atlas were created from a set of 729 3T multi-modal image data sets (Iowa, Hans Johnson). Improvements made were to include a measure of Venus Blood as a part of the model, and to add explicit tissue regions outside the head for tissue types that are not part of the brain. This atlas definitions are available from
svn co https://www.nitrc.org/svn/brains/BRAINS/trunk/BRAINSTools/BRAINSABC/Atlas_20100510

Under guidance of Hans Johnson, a branch of the ABC NITRC code has been modified to meet the needs of the Iowa group. This includes integration of a new Bspline-based registration from BRAINSFit, integration of BRAINSROIAuto, and to make it work with data with arbitrary orientation, and modifications of the interface (svn to https://www.nitrc.org/svn/brains/BRAINS/trunk/BRAINSTools/BRAINSABC).

== ABC Bias Correction Module ==

In order to meet existing strong demands for a stand-alone MRI bias correction method with FLASH images, part of the ABC code has been made available as a separate module and distributed via NITRC (http://www.nitrc.org/projects/probbiascor) by the MIND Institute group lead by Mark Skully and Jeremy Bockholt.

= Publications related to this software development =

* Marcel Prastawa, John H. Gilmore, Weili Lin, and Guido Gerig. Automatic Segmentation of MR Images of the Developing Newborn Brain. Medical Image Analysis (MedIA). Vol 9, Issue 5, October 2005, Pages 457-466.
* Marcel Prastawa, Elizabeth Bullitt, Sean Ho, and Guido Gerig. A Brain Tumor Segmentation Framework Based on Outlier Detection . Medical Image Analysis (MedIA). Vol 8, Issue 3, September 2004, Pages 275-283.
* Marcel Prastawa, John Gilmore, Weili Lin, and Guido Gerig. Automatic Segmentation of Neonatal Brain MRI. Medical Image Computing and Computer Assisted Intervention (MICCAI) 2004. Lecture Notes in Computer Science (LNCS) 3216, Pages 10-17.
* Marcel Prastawa, Elizabeth Bullitt, Nathan Moon, Koen van Leemput, and Guido Gerig. Automatic Brain Tumor Segmentation by Subject Specific Modification of Atlas Priors. Academic Radiology. Vol 10, Issue 12, December 2003, Pages 1341-1348.
* Marcel Prastawa, Elizabeth Bullitt, Sean Ho, and Guido Gerig. Robust Estimation for Brain Tumor Segmentation. Medical Image Computing and Computer Assisted Intervention (MICCAI) 2003. Lecture Notes in Computer Science (LNCS) 2879, Pages 530-537.

= Key Investigators =

*Utah Algorithms: Marcel Prastawa, Guido Gerig
*UNC Algorithms: Martin Styner
*External research collaboration: Hans Johnson, The University of Iowa
*External research collaboration: Jeremy Bockholt, MIND Institute

File:UtahSegGUI screen.png

2010-05-06T00:29:03Z

Prastawa:

File:UtahSegPlugin screen.png

2010-05-06T00:28:36Z

Prastawa: uploaded a new version of "File:UtahSegPlugin screen.png"

Projects:UtahAtlasSegmentation

2010-05-06T00:28:10Z

Prastawa:

Back to [[Algorithm:Utah2|Utah 2 Algorithms]]
__NOTOC__

= Atlas Based Brain Segmentation =

Automatic segmentation can be performed reliably using priors from brain atlases and an image generative model. We have developed a tool that provides an automatic segmentation pipeline in a modular framework.
The processing pipeline is composed tasks such as filtering the input images, registering the multimodal input images and the brain atlas to a common space, followed by iterative steps which interleave segmentation, inhomogeneity correction, and atlas warping.

Our tool generates bias corrected images, fuzzy classification maps, and discrete segmentation labels. The tool has been used to automatically segment thousands of adult and toddler images from the University of North Carolina (UNC), and is also being used as a skull stripping mechanism for DTI processing at UNC and Utah. An example of the output of the tool is shown below.
[[Image:UtahSegPlugin_result.png|thumb|center|600px|Output of the segmentation plugin, showing the bias corrected image and the probabilities for white and gray matter.]]

The tool has been integrated into Slicer as an extension, and it can also be executed as a stand-alone application. Both versions are available for download through NITRC: http://www.nitrc.org/projects/abc
{|
|-
| [[Image:UtahSegPlugin_screen.png|thumb|center|400px|Screen shot of the segmentation plugin in Slicer.]]
| [[Image:UtahSegGUI_screen.png|thumb|center|400px|Screen shot of the stand-alone segmentation GUI.]]
|}

The bias correction module that we develop as part of our tool is available separately from NITRC: http://www.nitrc.org/projects/probbiascor.

= Key Investigators =

*Utah Algorithms: Marcel Prastawa, Guido Gerig

File:TBI lesion shunt.png

2009-12-08T21:18:13Z

Prastawa:

File:TBI modalities.png

2009-12-08T21:17:56Z

Prastawa:

2010 Winter Project Week TBISegmentation

2009-12-08T21:17:21Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:TBI_modalities.png | TBI modalities
Image:TBI_lesion_shunt.png | Segmentation result with lesion and shunt
</gallery>

==Key Investigators==
* Marcel Prastawa, Guido Gerig, University of Utah
* Ron Kikinis, BWH
* UCLA

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

<h3>Objective</h3>
Traumatic Brain Injury (TBI) is caused by severe impact to the brain, which may result in skull fracture, lesions, and internal bleeding. Full assessment of these injuries is possible via multi-modality imaging, here T1w, T2, T1-postcontrast, Flair (fluid attenuated inversion recovery), SWI (susceptibility weighted imaging), DTI). Joint analysis of these modalities requires co-registration of these sets which come with different orientations, spatial resolution and head coverage. Segmentation of brain tissue, fluid and pathology requires efficient procedures for multi-modal analysis of images with classification of lesions.

</div>

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

<h3>Approach, Plan</h3>
Preferably, such a procedure should be automatic given the presence of small-scale pathology such as lesions, bleedings and ventricular shape alterations, or involve efficient, easy and intuitive expert interaction to support an automated classification algorithm. We propose an atlas based multi-modal segmentation method (''ABC: Atlas-Based Classification''), which makes use of normative data (spatial and intensity) for isolating abnormal regions that are likely due to injury.

</div>

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

<h3>Progress</h3>
We have a working ptototype program of ''ABC'' written in C++ using ITK. ''ABC'' incorporates image co-registration, atlas template registration, bias field correction, and tissue classification into an efficient workflow. We will wrap it as a Slicer module and will systematically test its performance on various TBI datasets. These tests will include co-registration of DTI and structural MRI for joint analysis of white matter tracts, brain anatomy and lesions.

</div>
</div>

<div style="width: 97%; float: left;">

==References==
[http://www.nitrc.org/projects/abc NITRC Project Page]

</div>

2010 Winter Project Week TBISegmentation

2009-12-08T21:07:29Z

Prastawa:

2010 Winter Project Week TBISegmentation

2009-12-08T20:51:02Z

Prastawa:

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:TBI_modalities.png|TBI modalities
Image:TBI_lesion_shunt.png|Segmentation result with lesion and shunt
</gallery>

==Key Investigators==
* Marcel Prastawa, Guido Gerig, University of Utah
* Ron Kikinis, BWH
* UCLA

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

<h3>Objective</h3>
Traumatic Brain Injury (TBI) is caused by severe impact to the brain, which may result in skull fracture, lesions, and internal bleeding. Full assessment of these injuries is possible via multi-modality imaging, here T1w, T2, T1-postcontrast, Flair (fluid attenuated inversion recovery), SWI (susceptibility weighted imaging), DTI). Joint analysis of these modalities requires co-registration of these sets which come with different orientations, spatial resolution and head coverage. Segmentation of brain tissue, fluid and pathology requires efficient procedures for multi-modal analysis of images with classification of lesions.

</div>

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

<h3>Approach, Plan</h3>
Preferably, such a procedure should be automatic given the presence of small-scale pathology such as lesions, bleedings and ventricular shape alterations, or involve efficient, easy and intuitive expert interaction to support an automated classification algorithm. We propose an atlas based multi-modal segmentation method (''ABC: Atlas-Based Classification''), which makes use of normative data (spatial and intensity) for isolating abnormal regions that are likely due to injury.

</div>

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

<h3>Progress</h3>
We have a working ptototype program of ''ABC'' written in C++ using ITK. ''ABC'' incorporates image co-registration, atlas template registration, bias field correction, and tissue classification into an efficient workflow. We will wrap it as a Slicer module and will systematically test its performance on various TBI datasets. These tests will include co-registration of DTI and structural MRI for joint analysis of white matter tracts, brain anatomy and lesions.

</div>
</div>

<div style="width: 97%; float: left;">

==References==
[http://www.nitrc.org/projects/abc NITRC Project Page]

</div>

2010 Winter Project Week TBISegmentation

2009-12-07T23:59:58Z

Prastawa: Created page with '__NOTOC__ <gallery> Image:PW-SLC2010.png|Projects List </gallery> ==Key Investigators== * Marcel Prastawa, Guido Gerig, University of Uta…'

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Marcel Prastawa, Guido Gerig, University of Utah
* Ron Kikinis, BWH
* UCLA

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

<h3>Objective</h3>
Traumatic Brain Injury (TBI) is caused by severe impact to the brain, which may result in skull fracture, lesions, and internal bleeding. Treatment for TBI involves significant surgery. The complication involved necessitates multiple imaging scans, such as CT for planning the surgeries and multimodal MRI for assessing the surgical treatment. We plan to study the process that occur in typical TBI patients and determine regions that are damaged and how they behave. The first step in analyzing these patient data is the segmentation of the different regions (edema, bleeding, etc) from multiple MRI modalities (T1w, T2w, T2w-blood, SWI).

</div>

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

<h3>Approach, Plan</h3>
We propose an atlas based segmentation method, which makes use of normative data (spatial and intensity) for isolating abnormal regions that are likely due to injury.

</div>

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

<h3>Progress</h3>
We have a working program written in C++ using ITK. We will wrap it as a Slicer module.

</div>
</div>

<div style="width: 97%; float: left;">

==References==

</div>

2010 Winter Project Week

2009-12-07T23:47:37Z

Prastawa: /* Segmentation */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Yi Gao)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Petter Risholm, Sandy Wells)

=== IGT ===
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp)

=== Analysis ===

=== Informatics ===
#XNAT Desktop User Interface (Dan M, Wendy P, Ron K)
#Slicer 3 XNAT Performance Tuning (Wendy P, Dan M, Tim Olson, Nicole Aucoin)

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen)
#VTK 3D Widgets in Slicer3 (Nicole Aucoin, Karthik, Will)
#Updates to Slicer3 Colors Module (Nicole Aucoin)
#Whole Body CT/MR open source data set publishing (Dan Marcus)
#CMAKE Build process (Dave Partyka, Katie Hayes)
#Integration of XNAT Packaging for Slicer Internals (Dan, Tim Olsen, Dave Partyka, Wendy, Randy)

=== Execution Model ===

=== Preparation ===

# 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]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

Algorithm:Utah2

2009-10-07T19:37:20Z

Prastawa:

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah 2 Algorithms (PI: Guido Gerig) =

At Utah, we are interested in a range of algorithms and solutions for the analysis of DTI and the segmentation of healthy brains and brains with lupus lesions from structural MRI.

= Utah 2 Projects =

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

| style="width:15%" | [[Image:Cbg-dtiatlas-tracts.png|200px]]
| style="width:85%" |

== [[Projects:DTIPopulationAnalysis|Group Analysis of DTI Fiber Tracts]] ==

Analysis of populations of diffusion images typically requires time-consuming manual segmentation of structures of interest to obtain correspondance for statistics. This project uses non-rigid registration of DTI images to produce a common coordinate system for hypothesis testing of diffusion properties. [[Projects:DTIPopulationAnalysis|More...]]

<font color="red">'''New: '''</font> Casey B. Goodlett, P. Thomas Fletcher, John H. Gilmore, Guido Gerig. Group Analysis of DTI Fiber Tract Statistics with Application to Neurodevelopment. NeuroImage 45 (1) Supp. 1, 2009. p. S133-S142.

|-

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

== [[Projects:LesionSegmentation|Lesion Segmentation]] ==

Quantification, analysis and display of brain pathology such as white matter lesions as observed in MRI is important for diagnosis, monitoring of disease progression, improved understanding of pathological processes and for developing new therapies.
[[Projects:LesionSegmentation|More...]]

<font color="red">'''New: '''</font> Marcel Prastawa and Guido Gerig. Automatic MS Lesion Segmentation by Outlier Detection and Information Theoretic Region Partitioning. 3D Segmentation in the Clinic: A Grand Challenge II Workshop at Medical Image Computing and Computer Assisted Intervention (MICCAI) 2008.

|-

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

== [[Projects:DTINoiseStatistics|Influence of Imaging Noise on DTI Statistics]] ==

Clinical acquisition of diffusion weighted images with high signal to noise ratio remains a challenge. The goal of this project is to understand the impact of MR noise on quantiative statistics of diffusion properties such as anisotropy measures, trace, etc. [[Projects:DTINoiseStatistics|More...]]

|-

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

== [[Projects:UtahAtlasSegmentation|Atlas Based Brain Segmentation]] ==

Automatic segmentation can be performed reliably using priors from brain atlases and an image generative model. We have developed a tool that provides an automatic segmentation pipeline in a modular framework.
[[Projects:UtahAtlasSegmentation|More...]]

|-

|-

| | [[Image:Meningiomasim_iter1.jpg|200px]]
| |

== [[Projects:UtahTumorSimulation|Tumor Simulation for Validating Change Tracking Applications]] ==

Determining extent of pathology as it changes over time is an important clinical task.
However, there is a lack of a reliable, objective ground truth for evaluating automatic tracking methods. We have developed a simulation tool that can generate MR images with known
tumor and edema.
[[Projects:UtahTumorSimulation|More...]]

|-

| |
| |

== [[Projects:RegistrationEvaluation|Evaluation of Registration Algorithms]] ==

We are interested in comparing existing registration packages to determine how registration in Slicer3 can be improved. This work focuses on examining various packages researchers are currently using for registration and comparing results on a set of examples representative of common registration tasks.
[[Projects:RegistrationEvaluation|More...]]

|-

|}

Projects:UtahTumorSimulation

2009-10-07T19:34:49Z

Prastawa:

Back to [[Algorithm:Utah2|Utah 2 Algorithms]]
__NOTOC__

= Tumor Simulation for Validating Change Tracking Applications =

Determining extent of pathology as it changes over time is an important clinical task. However, there is a lack of a reliable, objective ground truth for evaluating automatic tracking methods. We have developed a simulation tool that can generate MR images with known tumor and edema. This tool provides test MR image data along with the underlying ground truth, that can be used for performing objective, repeatable assessment of the performance of segmentation or change tracking systems.

We are exploring the use of the simulated datasets for validating the meningioma change tracking project at BWH. The simulations are performed using a modified version of our simulator that was developed previously. We provide extensions for the dura modelling and more exposure of internal modeling parameters. A summary of our simulation scheme is shown in the figure below.

[[Image:UtahTumorSimulationSummary.png|thumb|center|600px|Overview of the tumor simulation pipeline.]]

Project Activities:
[http://wiki.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Meningioma_growth_simulation 2009 Project Week]
[http://wiki.na-mic.org/Wiki/index.php/Meningioma_growth_modeling_with_TumorSim Followup Project]

= Key Investigators =

*Utah Algorithms: Marcel Prastawa, Guido Gerig
*Brigham and Women's Hospital: Andriy Fedorov, Ron Kikinis

File:UtahTumorSimulationSummary.png

2009-10-07T19:33:02Z

Prastawa:

Projects:UtahTumorSimulation

2009-10-07T19:32:15Z

Prastawa:

Back to [[Algorithm:Utah2|Utah 2 Algorithms]]
__NOTOC__

= Tumor Simulation for Validating Change Tracking Applications =

Determining extent of pathology as it changes over time is an important clinical task. However, there is a lack of a reliable, objective ground truth for evaluating automatic tracking methods. We have developed a simulation tool that can generate MR images with known tumor and edema. This tool provides test MR image data along with the underlying ground truth, that can be used for performing objective, repeatable assessment of the performance of segmentation or change tracking systems.

We are exploring the use of the simulated datasets for validating the meningioma change tracking project at BWH. The simulations are performed using a modified version of our simulator that was developed previously. We provide extensions for the dura modelling and more exposure of internal modeling parameters. A summary of our simulation scheme is shown in the figure below.

[[File:UtahTumorSimulationSummary.png]]

Project Activities:
[http://wiki.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Meningioma_growth_simulation 2009 Project Week]
[http://wiki.na-mic.org/Wiki/index.php/Meningioma_growth_modeling_with_TumorSim Followup Project]

= Key Investigators =

*Utah Algorithms: Marcel Prastawa, Guido Gerig
*Brigham and Women's Hospital: Andriy Fedorov, Ron Kikinis

Projects:UtahTumorSimulation

2009-10-05T19:42:35Z

Prastawa: Created page with ' Back to Utah 2 Algorithms __NOTOC__ = Tumor Simulation for Validating Change Tracking Applications = Determining extent of pathology as it changes over tim…'

Back to [[Algorithm:Utah2|Utah 2 Algorithms]]
__NOTOC__

= Tumor Simulation for Validating Change Tracking Applications =

Determining extent of pathology as it changes over time is an important clinical task. However, there is a lack of a reliable, objective ground truth for evaluating automatic tracking methods. We have developed a simulation tool that can generate MR images with known tumor and edema. This tool provides test MR image data along with the underlying ground truth, that can be used for performing objective, repeatable assessment of the performance of segmentation or change tracking systems.

We are exploring the use of the simulated datasets for validating the meningioma change tracking project at BWH.

Project Activities:
[http://wiki.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Meningioma_growth_simulation 2009 Project Week]
[http://wiki.na-mic.org/Wiki/index.php/Meningioma_growth_modeling_with_TumorSim Followup Project]

= Key Investigators =

*Utah Algorithms: Marcel Prastawa, Guido Gerig
*Brigham and Women's Hospital: Andriy Fedorov, Ron Kikinis

Algorithm:Utah2

2009-10-05T19:34:46Z

Prastawa:

2009 Summer Project Week Automatic Brain MRI Pipeline

2009-06-25T16:48:29Z

Prastawa: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:UtahSegPlugin_result.png|Example Utah segmentation output
</gallery>

==Key Investigators==
* Utah: Marcel Prastawa
* Iowa: Hans Johnson
* Wash U: Dan Marcus
<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Automatic processing of multimodal brain MRI datasets from large populations is a fundamental step for population based analysis. The processing pipeline typically involves registration, segmentation, noise reduction, artifact removal, etc. The Utah registration-segmentation tool is currently being used in Iowa and North Carolina. We plan to further develop the tool to ease integration with Iowa's processing pipeline, and perhaps add new features to the tool.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, plan</h3>
We will discuss how the tool is currently used, and find possible customizations that would make it easier to use.

We will design general test cases to simulate how the tool would be used and to ensure consistent stability as we collaborate and exchange code.
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
Designed a CLP-based interface for a more flexible connection with other processing steps.
This will also allow the loading/saving of program parameters as an XML file (possible future feature in CLP).

Started extending the segmentation parameters to allow testing of bias correction and integration of the BRAINSFit registration tool.
</div>

</div>

2009 Summer Project Week Automatic Brain MRI Pipeline

2009-06-25T16:45:08Z

Prastawa: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:UtahSegPlugin_result.png|Example Utah segmentation output
</gallery>

==Key Investigators==
* Utah: Marcel Prastawa
* Iowa: Hans Johnson
* Wash U: Dan Marcus
<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Automatic processing of multimodal brain MRI datasets from large populations is a fundamental step for population based analysis. The processing pipeline typically involves registration, segmentation, noise reduction, artifact removal, etc. The Utah registration-segmentation tool is currently being used in Iowa and North Carolina. We plan to further develop the tool to ease integration with Iowa's processing pipeline, and perhaps add new features to the tool.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, plan</h3>
<p>
We will discuss how the tool is currently used, and find possible customizations that would make it easier to use.

<p>
We will design general test cases to simulate how the tool would be used and to ensure consistent stability as we collaborate and exchange code.
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
<p>
Designed a CLP-based interface for a more flexible connection with other processing steps.
This will also allow the loading/saving of program parameters as an XML file (possible future feature in CLP).

<p>
Started extending the segmentation parameters to allow testing of bias correction and integration of BRAINSFit.
</div>

</div>

2009 Summer Project Week Automatic Brain MRI Pipeline

2009-06-04T17:32:43Z

Prastawa: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:UtahSegPlugin_result.png|Example Utah segmentation output </gallery> ==Key ...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:UtahSegPlugin_result.png|[[Example Utah segmentation output]]
</gallery>

==Key Investigators==
* Utah: Marcel Prastawa
* Iowa: Hans Johnson

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Automatic processing of multimodal brain MRI datasets from large populations is a fundamental step for population based analysis. The processing pipeline typically involves registration, segmentation, noise reduction, artifact removal, etc. The Utah registration-segmentation tool is currently being used in Iowa and North Carolina. We plan to further develop the tool to ease integration with Iowa's processing pipeline, and perhaps add new features to the tool.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, plan</h3>
We will discuss how the tool is currently used, and find possible customizations that would make it easier to use.

We will design general test cases to simulate how the tool would be used and to ensure consistent stability as we collaborate and exchange code.
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>

</div>

</div>

2009 Summer Project Week

2009-06-04T17:22:19Z

Prastawa:

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

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (1st day only)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

2009 Summer Project Week

2009-05-18T18:47:51Z

Prastawa:

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

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: TBD
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#4D Imaging - currently used for Lung Perfusion (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Georgetown?)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Xnat user clinic - combine with data clinic
#xnat programmer clinic
#Grid Wizard+xnat clinic (Clement)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement, Ipek)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiaodong, Snehashis Roy)
#FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)

===IGT Projects:===
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#slicer integration of mri compatible prostate biopsy robot(sid, queens)
#breakout session on Dynamic Patient Models (James Balter)
#gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# VTK 3d Widgets in Slicer3 (Nicole, Will/Karthik)
# Update to Slicer3 Colors module (Nicole)
# EM Segmenter (Sylvain, Nicolas)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# Informatics workflow Design (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Jim Miller, Ross Whitaker, Samuel Gerber)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal, Ran Tao )
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH
#Ferenc Jolesz, BWH
#Clare Tempany, BWH
#Tina Kapur, BWH
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH
#Haiying Liu BWH
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

Projects:UtahAtlasSegmentation

2009-05-05T23:21:56Z

Prastawa:

Back to [[Algorithm:Utah2|Utah 2 Algorithms]]
__NOTOC__

= Atlas Based Brain Segmentation =

Automatic segmentation can be performed reliably using priors from brain atlases and an image generative model. We have developed a tool that provides an automatic segmentation pipeline in a modular framework.
The processing pipeline is composed tasks such as filtering the input images, registering the multimodal input images and the brain atlas to a common space, followed by iterative steps which interleave segmentation, inhomogeneity correction, and atlas warping.

Our tool generates bias corrected images, fuzzy classification maps, and discrete segmentation labels. The tool has been used to automatically segment thousands of adult and toddler images from the University of North Carolina (UNC), and is also being used as a skull stripping mechanism for DTI processing at UNC and Utah. An example of the output of the tool is shown below.
[[Image:UtahSegPlugin_result.png|thumb|center|600px|Output of the segmentation plugin, showing the bias corrected image and the probabilities for white and gray matter.]]

The tool is being integrated into Slicer as a plugin, and a screenshot of the prototype is shown below.
[[Image:UtahSegPlugin_screen.png|thumb|center|400px|Screen shot of the segmentation plugin in Slicer.]]

The bias correction module that we develop as part of our tool is available separately from NITRC: http://www.nitrc.org/projects/probbiascor.

= Key Investigators =

*Utah Algorithms: Marcel Prastawa, Guido Gerig