NAMIC Wiki - User contributions [en]

2014 Summer Project Week:Slicer LDDMM Shape Analysis

2014-06-27T03:31:24Z

Saurabhjain:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:LDDMM-Plugin-Screen-Shot.png
Image:ScreenShot_2014-06-26.png
</gallery>

==Key Investigators==
* JHU: Saurabh Jain
* Isomics: Steve Pieper
* Iowa: Hans Johnson
* Iowa: Regina Young

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Develop a Slicer interface to various remote processing services
for shape analysis of human brain sub-cortical structures offered by
Center for Imaging Science (CIS) through our portal.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The pipeline accepts surfaces stored in the BYU format, or binary masks stored in the ANALYZE format. The processing is done on one of the clusters available to CIS, and upon completion the user receives an e-mail with a link to the results stored on the ftp site.

* At the previous project week, we created a simple interface, which accepts the directory location, and e-mail address (which must be registered with http://www.MRIStudio.org), and sends a template estimation job if the directory contains .byu files. To receive the estimated template, the user copies the md5 checksum from the e-mail, which reports the job completion, to the md5 box in slicer and hit receive.

* The template estimation is performed using a variant of the approach described in:

J. Ma, M. I. Miller, and L. Younes,
“A Bayesian Generative Model for Surface
Template Estimation,” Intl. J. Bio. Img.,
vol. 2010, Article ID 974957.

* We now plan to create interfaces to other services including LDDMM surface matching, and geodesic time series matching and template estimation for longitudinal data.

* In addition, we plan to make the interface more user friendly, which includes support for multiple segmentation labels stored as NiFTI files for data such as Han's (see 'Progress' tab), getting input from Slicer scenes, and importing the processed results to scenes.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Hans shared datasets for testing:
https://www.dropbox.com/sh/5w2ls8b4j9ihpze/51IkhaXbTJ
* Added interface for LDDMM mappings, in addition to the template estimation interface developed last time.
* Regina used the plugin to send a test job.
* Made the interface a bit more user friendly.
</div>
</div>

File:ScreenShot 2014-06-26.png

2014-06-27T03:30:18Z

Saurabhjain:

File:LDDMM-Plugin-Screen-Shot.png

2014-06-27T03:28:21Z

Saurabhjain: uploaded a new version of "File:LDDMM-Plugin-Screen-Shot.png": Reverted to version as of 04:49, 10 January 2014

2014 Summer Project Week:Slicer LDDMM Shape Analysis

2014-06-27T03:27:57Z

Saurabhjain:

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

==Key Investigators==
* JHU: Saurabh Jain
* Isomics: Steve Pieper
* Iowa: Hans Johnson
* Iowa: Regina Young

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Develop a Slicer interface to various remote processing services
for shape analysis of human brain sub-cortical structures offered by
Center for Imaging Science (CIS) through our portal.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The pipeline accepts surfaces stored in the BYU format, or binary masks stored in the ANALYZE format. The processing is done on one of the clusters available to CIS, and upon completion the user receives an e-mail with a link to the results stored on the ftp site.

* At the previous project week, we created a simple interface, which accepts the directory location, and e-mail address (which must be registered with http://www.MRIStudio.org), and sends a template estimation job if the directory contains .byu files. To receive the estimated template, the user copies the md5 checksum from the e-mail, which reports the job completion, to the md5 box in slicer and hit receive.

* The template estimation is performed using a variant of the approach described in:

J. Ma, M. I. Miller, and L. Younes,
“A Bayesian Generative Model for Surface
Template Estimation,” Intl. J. Bio. Img.,
vol. 2010, Article ID 974957.

* We now plan to create interfaces to other services including LDDMM surface matching, and geodesic time series matching and template estimation for longitudinal data.

* In addition, we plan to make the interface more user friendly, which includes support for multiple segmentation labels stored as NiFTI files for data such as Han's (see 'Progress' tab), getting input from Slicer scenes, and importing the processed results to scenes.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Hans shared datasets for testing:
https://www.dropbox.com/sh/5w2ls8b4j9ihpze/51IkhaXbTJ
* Added interface for LDDMM mappings, in addition to the template estimation interface developed last time.
* Regina used the plugin to send a test job.
* Made the interface a bit more user friendly.
</div>
</div>

2014-05-22T16:31:54Z

Saurabhjain: /* Other */

__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 and RT 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'''
|
|'''10-12pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11am: <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session:Registration Algorithms|Registration Algorithms]]'''(Sandy Wells)
[[MIT_Project_Week_Rooms#Star|Star]]
|
'''9:30-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations]] <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|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)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Tina Kapur)
<br>----------------------------------------<br>
'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
|
|-
|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==

==Atrial Fibrillation==

==Huntington's Disease==

==Head and Neck Cancer==

==Slicer4 Extensions==

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Junichi Tokuda)
* Gestural Point of Care Interface for IGT (Saskia, Franklin, Tobias)
* MR-Ultrasound Registration for Prostate Interventions (Chenxi Zhang, Andriy Fedorov, Andras)
* Surface approximation from contour points (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)

==Radiation Therapy==

==TMJ-OA==

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Andras, Steve, Jim, ...)
* Segmentation object support (Andrey, Csaba, Steve, ...)

==Infrastructure==
*Chronicle (Steve Pieper)
*Volume Registration (Steve Pieper)
*OpenCL (Steve Pieper, Marcel Prastawa)
*Markups (Nicole Aucoin)
*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, ?)

==Feature Extraction==
*Breast Tumor Segmentation and Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)

==Other==
*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; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)

== '''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 before May 27th. See [[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
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Adam Rankin, Queen's University, rankin@queensu.ca
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week:Slicer LDDMM Shape Analysis

2014-05-22T16:30:29Z

Saurabhjain: Created page with 'Image:LDDMM-Plugin-Screen-Shot.png </gallery> ==Key Investigators== * JHU: Saurabh Jain * Isomics: Steve Pieper * Iowa: Hans Johnson * Utah: Josh Cates ==Project Description==…'

2014 Summer Project Week

2014-05-22T16:29:58Z

Saurabhjain: /* Other */

__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 and RT 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'''
|
|'''10-12pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11am: <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session:Registration Algorithms|Registration Algorithms]]'''(Sandy Wells)
[[MIT_Project_Week_Rooms#Star|Star]]
|
'''9:30-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations]] <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|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)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Tina Kapur)
<br>----------------------------------------<br>
'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
|
|-
|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==

==Atrial Fibrillation==

==Huntington's Disease==

==Head and Neck Cancer==

==Slicer4 Extensions==

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Junichi Tokuda)
* Gestural Point of Care Interface for IGT (Saskia, Franklin, Tobias)
* MR-Ultrasound Registration for Prostate Interventions (Chenxi Zhang, Andriy Fedorov, Andras)
* Surface approximation from contour points (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)

==Radiation Therapy==

==TMJ-OA==

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Andras, Steve, Jim, ...)
* Segmentation object support (Andrey, Csaba, Steve, ...)

==Infrastructure==
*Chronicle (Steve Pieper)
*Volume Registration (Steve Pieper)
*OpenCL (Steve Pieper, Marcel Prastawa)
*Markups (Nicole Aucoin)
*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, ?)

==Feature Extraction==
*Breast Tumor Segmentation and Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)

==Other==
*Shape Analysis for the developing murine skull (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)

== '''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 before May 27th. See [[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
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Adam Rankin, Queen's University, rankin@queensu.ca
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week

2014-05-15T21:38:00Z

Saurabhjain: /* Other */

__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 and RT 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'''
|
|'''10-12pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11am: <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session:Registration Algorithms|Registration Algorithms]]'''(Sandy Wells)
[[MIT_Project_Week_Rooms#Star|Star]]
|
'''9:30-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations]] <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|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)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Tina Kapur)
<br>----------------------------------------<br>
'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD
[[MIT_Project_Week_Rooms#Star|Star]]
|
|-
|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==

==Atrial Fibrillation==

==Huntington's Disease==

==Head and Neck Cancer==

==Slicer4 Extensions==

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Junichi Tokuda)
* Gestural Point of Care Interface for IGT (Saskia, Franklin, Tobias)
* MR-Ultrasound Registration for Prostate Interventions (Chenxi Zhang, Andriy Fedorov, Andras)
* Surface approximation from contour points (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)

==Radiation Therapy==

==TMJ-OA==

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Andras, Steve, Jim, ...)
* Segmentation object support (Andrey, Csaba, Steve, ...)

==Infrastructure==
*Chronicle (Steve Pieper)
*Volume Registration (Steve Pieper)
*OpenCL (Steve Pieper, Marcel Prastawa)
* Markups (Nicole Aucoin)
* Pluggable Label Statistics (Andrey , Ethan, Steve, Brad?, Jim? Dirk?)

==Feature Extraction==
*Breast Tumor Segmentation and Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)

==Other==
*Shape Analysis for the developing murine skull (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*Slicer Interface to LDDMM shape anlaysis (Saurabh Jain, JHU; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)

== '''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 before May 27th. See [[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
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Project Week:Slicer Based Surface Template Estimation

2014-01-10T19:05:18Z

Saurabhjain: /* Project Description */

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

==Key Investigators==
* JHU: Saurabh Jain
* Isomics: Steve Pieper
* Iowa: Hans Johnson
* Utah: Josh Cates

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Develop a Slicer interface to the remote processing service
for template estimation of sub cortical structures offered by
Center for Imaging Science (CIS) through our ftp site.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The template estimation is performed using a variant of the approach described in:

J. Ma, M. I. Miller, and L. Younes,
“A Bayesian Generative Model for Surface
Template Estimation,” Intl. J. Bio. Img.,
vol. 2010, Article ID 974957.

* The pipeline accepts surfaces stored in the BYU format, or binary masks stored in the ANALYZE format. The processing is done on one of the clusters available to CIS, and upon completion the user receives an e-mail with a link to the results stored on the ftp site.

* We plan to provide an interface to browse the surfaces in Slicer, and an interface to send jobs to and receive results from the remote processing server.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Created a simple interface, which accepts the directory location, and e-mail address (which must be registered with http://www.MRIStudio.org), and sends the remote processing job if the directory contains .byu files.
* To receive the results copy the md5 checksum from the e-mail, which reports the job completion, to the md5 box in slicer and hit receive.
* In the near future, make it more user friendly, and put it up on the extension manager.
* Hans shared datasets for testing:
https://www.dropbox.com/sh/5w2ls8b4j9ihpze/51IkhaXbTJ
</div>
</div>

2014 Project Week:Slicer Based Surface Template Estimation

2014-01-10T18:15:39Z

Saurabhjain: /* Project Description */

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

==Key Investigators==
* JHU: Saurabh Jain
* Isomics: Steve Pieper
* Iowa: Hans Johnson
* Utah: Josh Cates

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Develop a Slicer interface to the remote processing service
for template estimation of sub cortical structures offered by
Center for Imaging Science (CIS) through our ftp site.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The template estimation is performed using a variant of the approach described in:

J. Ma, M. I. Miller, and L. Younes,
“A Bayesian Generative Model for Surface
Template Estimation,” Intl. J. Bio. Img.,
vol. 2010, Article ID 974957.

* The pipeline accepts surfaces stored in the BYU format, or binary masks stored in the ANALYZE format. The processing is done on one of the clusters available to CIS, and upon completion the user receives an e-mail with a link to the results stored on the ftp site.

* We plan to provide an interface to browse the surfaces in Slicer, and an interface to send jobs to and receive results from the remote processing server.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Created a simple interface, which accepts the directory location, and e-mail address (which must be registered with http://www.MRIStudio.org), and sends the remote processing job if the directory contains .byu files.
* To receive the results copy the md5 checksum from the e-mail, which reports the job completion, to the md5 box in slicer and hit receive.
* In the near future, make it more user friendly, and put it up on the extension manager.
* Hans shared datasets for testing:
</div>
</div>

2014 Project Week:Slicer Based Surface Template Estimation

2014-01-10T04:58:42Z

Saurabhjain:

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

==Key Investigators==
* JHU: Saurabh Jain
* Isomics: Steve Pieper
* Iowa: Hans Johnson
* Utah: Josh Cates

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Develop a Slicer interface to the remote processing service
for template estimation of sub cortical structures offered by
Center for Imaging Science (CIS) through our ftp site.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The template estimation is performed using a variant of the approach described in:

J. Ma, M. I. Miller, and L. Younes,
“A Bayesian Generative Model for Surface
Template Estimation,” Intl. J. Bio. Img.,
vol. 2010, Article ID 974957.

* The pipeline accepts surfaces stored in the BYU format, or binary masks stored in the ANALYZE format. The processing is done on one of the clusters available to CIS, and upon completion the user receives an e-mail with a link to the results stored on the ftp site.

* We plan to provide an interface to browse the surfaces in Slicer, and an interface to send jobs to and receive results from the remote processing server.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Created a simple interface, which accepts the directory location, and e-mail address (which must be registered with http://www.MRIStudio.org), and sends the remote processing job if the directory contains .byu files.
* To receive the results copy the md5 checksum from the e-mail which reports the job completion, to the md5 box in slicer and hit receive.
* In the near future, make it more user friendly, and put it up on the extension manager.
</div>
</div>

File:LDDMM-Plugin-Screen-Shot.png

2014-01-10T04:49:06Z

Saurabhjain:

2014 Project Week:Slicer Based Surface Template Estimation

2013-12-20T17:28:40Z

Saurabhjain: /* Project Description */

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

==Key Investigators==
* JHU: Saurabh Jain
* Isomics: Steve Pieper
* Iowa: Hans Johnson
* Utah: Josh Cates

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Develop a Slicer interface to the remote processing service
for template estimation of sub cortical structures offered by
Center for Imaging Science (CIS) through our ftp site.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The template estimation is performed using a variant of the approach described in:

J. Ma, M. I. Miller, and L. Younes,
“A Bayesian Generative Model for Surface
Template Estimation,” Intl. J. Bio. Img.,
vol. 2010, Article ID 974957.

* The pipeline accepts surfaces stored in the BYU format, or binary masks stored in the ANALYZE format. The processing is done on one of the clusters available to CIS, and upon completion the user receives an e-mail with a link to the results stored on the ftp site.

* We plan to provide an interface to browse the surfaces in Slicer, and an interface to send jobs to and receive results from the remote processing server.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Project Week:Slicer Based Surface Template Estimation

2013-12-20T17:24:50Z

Saurabhjain: /* Project Description */

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

==Key Investigators==
* JHU: Saurabh Jain
* Isomics: Steve Pieper
* Iowa: Hans Johnson
* Utah: Josh Cates

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Develop a Slicer interface to the remote processing service
for template estimation of sub cortical structures offered by
Center for Imaging Science (CIS) through our ftp site.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The template estimation is performed using a variant of the approach described in:

J. Ma, M. I. Miller, and L. Younes,
“A Bayesian Generative Model for Surface
Template Estimation,” Intl. J. Bio. Img.,
vol. 2010, Article ID 974957.

* The pipeline accepts surfaces stored in the BYU format, or binary masks stored in the ANALYZE format. The processing is done on one of the clusters available to CIS, and upon completion the user receives an e-mail with a link to the results stored on the ftp site.

* We plan to provide an interface to browse the surfaces in Slicer, and the capability to send jobs to the remote processing server from Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Winter Project Week

2013-12-19T20:34:53Z

Saurabhjain: /* Huntington's Disease */

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

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

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

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

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

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

=Background and Preparation=

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

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

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

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

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

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

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

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

==Stroke==

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

==Image-Guided Interventions==
*[[2014_Project_Week:Ultrasound Visualization and Navigation in Neurosurgery|Ultrasound Visualization and Navigation in Neurosurgery]] (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, William M. Wells III)

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

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

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

==TMJ-OA==

==Infrastructure==
*[[2014_Project_Week:SlicerSpeedUp|Slicer speed up]] (Jc, Andras Lasso, Steve Pieper)
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Steve Pieper)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*CLI - Resources? Conditionals? Autonaming? Provenance? CTK unification? (Jim Miller)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:Constrain Fiducial along Suface|Constrain Fiducial along Suface]] (Vinicius Boen, Nicole Aucoin)
* [[2014_Winter_Project_Week:Cropping Multiple Surfaces|Cropping multiple surfaces simultaneously]] (Alexander, Jc, Steve, Vinicius)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject Hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonLinearTransforms|Integration non-linear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)

2014 Project Week:Slicer Based Surface Template Estimation

2013-12-19T20:32:21Z

Saurabhjain: Created page with '__NOTOC__ <gallery> Image:PW-SLC2014.png|Projects List </gallery> ==Key Investigators== * JHU: Saurabh Jain * Isomics: Steve Pieper * Iowa:…'