https://www.na-mic.org/w/api.php?action=feedcontributions&user=Dmwelch&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T13:51:16ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:ManualSegmentationQA&diff=870352014 Summer Project Week:ManualSegmentationQA2014-06-27T14:11:56Z<p>Dmwelch: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
Image:ManualSegmentationQAmodule.png| GUI<br />
Image:ManSeg2.png| In action<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a Slicer module/extension to connect to a segmentation database and que 'bad' segmentations for QA raters review and editing<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Identify bad segmentations from PostgreSQL database of QA reviews<br />
* Load corresponding label map, T1, and T2 (if available)<br />
* Color label map s.t. 'good' labels are in green and bad labels in high-contrast colors<br />
* Include Editor widgets within module for label manipulation<br />
* Give users ability to:<br />
** leave bad regions unchanged with confirmation<br />
** edit good regions if desired<br />
** leave notes in database<br />
** toggle specific regions on/off in scene<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Complete<br />
* TODO: reviewers have requested hotkeys similar to Slicer 3 for Editor which we haven't implemented yet<br />
* TODO: Integrate with Subject Hierarchy module<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:ManualSegmentationQA&diff=869972014 Summer Project Week:ManualSegmentationQA2014-06-27T13:57:16Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
Image:ManualSegmentationQAmodule.png| GUI<br />
Image:ManSeg2.png| In action<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a Slicer module/extension to connect to a segmentation database and que 'bad' segmentations for QA raters review and editing<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Identify bad segmentations from PostgreSQL database of QA reviews<br />
* Load corresponding label map, T1, and T2 (if available)<br />
* Color label map s.t. 'good' labels are in green and bad labels in high-contrast colors<br />
* Include Editor widgets within module for label manipulation<br />
* Give users ability to:<br />
** leave bad regions unchanged with confirmation<br />
** edit good regions if desired<br />
** leave notes in database<br />
** toggle specific regions on/off in scene<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Complete<br />
* TODO: reviewers have requested hotkeys similar to Slicer 3 for Editor which we haven't implemented yet<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=File:ManSeg2.png&diff=86993File:ManSeg2.png2014-06-27T13:56:36Z<p>Dmwelch: Manual segmentation QA module screenshot</p>
<hr />
<div>Manual segmentation QA module screenshot</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Pipeline_Visualization&diff=869742014 Summer Project Week:Pipeline Visualization2014-06-27T13:26:49Z<p>Dmwelch: Added BRAINSTools screenshot</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
Image:Pipeline_visualization_sketch.png| Visualization of pipeline from code<br />
Image:atlas_pipeline.png|BRAINSTools Template pipeline<br />
</gallery><br />
<br />
==Key Investigators==<br />
<br />
* Ramesh Sridharan, Adrian Dalca, Polina Golland, MIT<br />
<br />
==Project Description==<br />
We have developed an extension to nipype (http://nipy.sourceforge.net/nipype/) that allows for visualization of pipelines and their results.<br />
At the project week, we plan to improve the visualization and features and release our code. <br />
<br />
Live demo (temporary link): http://shoutkey.com/grant<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
We plan to show our demo and get feedback to improve the visualization. Additionally, if time permits, we want to start work on combining this with our lightweight interface to nipype for prototyping pipelines.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Release code / integrate with nipype codebase<br />
* Discuss wishlist for visualization (come see me if you have any thoughts!)<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=File:Atlas_pipeline.png&diff=86973File:Atlas pipeline.png2014-06-27T13:25:18Z<p>Dmwelch: Visualization of template workflow from BRAINSTools AutoWorkup workflow</p>
<hr />
<div>Visualization of template workflow from BRAINSTools AutoWorkup workflow</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:ManualSegmentationQA&diff=869722014 Summer Project Week:ManualSegmentationQA2014-06-27T13:22:05Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
Image:ManualSegmentationQAmodule.png| GUI<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a Slicer module/extension to connect to a segmentation database and que 'bad' segmentations for QA raters review and editing<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Identify bad segmentations from PostgreSQL database of QA reviews<br />
* Load corresponding label map, T1, and T2 (if available)<br />
* Color label map s.t. 'good' labels are in green and bad labels in high-contrast colors<br />
* Include Editor widgets within module for label manipulation<br />
* Give users ability to:<br />
** leave bad regions unchanged with confirmation<br />
** edit good regions if desired<br />
** leave notes in database<br />
** toggle specific regions on/off in scene<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Complete<br />
* TODO: reviewers have requested hotkeys similar to Slicer 3 for Editor which we haven't implemented yet<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=File:ManualSegmentationQAmodule.png&diff=86971File:ManualSegmentationQAmodule.png2014-06-27T13:21:19Z<p>Dmwelch: Screenshot from manual segmentation QA module (Project Week Summer 2014)</p>
<hr />
<div>Screenshot from manual segmentation QA module (Project Week Summer 2014)</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:AutomatedSegmentationQA&diff=869702014 Summer Project Week:AutomatedSegmentationQA2014-06-27T13:18:40Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
Image:roboRater.png|[http://brainsia.github.io/roboRater/ Github site]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Eun Young (Regina) Kim, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a database-driven script to compare results of segmentation workflow experiments validating results on a per-region basis<br />
* Comparisons will use DICE<br />
* Script will register patient scans from a baseline experiment to the 'new' experiment<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Identify the DICE threshold for automatic QA entry<br />
* Interface with our PostgreSQL database for QA access and recording<br />
* Validate automated responses on 20 test cases<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Complete <br />
* Source code on [http://brainsia.github.io/roboRater Github]<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=File:RoboRater.png&diff=86969File:RoboRater.png2014-06-27T13:16:04Z<p>Dmwelch: Screenshot from roboRater page</p>
<hr />
<div>Screenshot from roboRater page</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:ManualSegmentationQA&diff=868022014 Summer Project Week:ManualSegmentationQA2014-06-27T02:56:09Z<p>Dmwelch: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a Slicer module/extension to connect to a segmentation database and que 'bad' segmentations for QA raters review and editing<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Identify bad segmentations from PostgreSQL database of QA reviews<br />
* Load corresponding label map, T1, and T2 (if available)<br />
* Color label map s.t. 'good' labels are in green and bad labels in high-contrast colors<br />
* Include Editor widgets within module for label manipulation<br />
* Give users ability to:<br />
** leave bad regions unchanged with confirmation<br />
** edit good regions if desired<br />
** leave notes in database<br />
** toggle specific regions on/off in scene<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Complete<br />
* TODO: reviewers have requested hotkeys similar to Slicer 3 for Editor which we haven't implemented yet<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:AutomatedSegmentationQA&diff=868002014 Summer Project Week:AutomatedSegmentationQA2014-06-27T02:48:19Z<p>Dmwelch: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Eun Young (Regina) Kim, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a database-driven script to compare results of segmentation workflow experiments validating results on a per-region basis<br />
* Comparisons will use DICE<br />
* Script will register patient scans from a baseline experiment to the 'new' experiment<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Identify the DICE threshold for automatic QA entry<br />
* Interface with our PostgreSQL database for QA access and recording<br />
* Validate automated responses on 20 test cases<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Complete <br />
* Source code on [http://brainsia.github.io/roboRater Github]<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:AutomatedSegmentationQA&diff=867992014 Summer Project Week:AutomatedSegmentationQA2014-06-27T02:46:52Z<p>Dmwelch: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Eun Young (Regina) Kim, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a database-driven script to compare results of segmentation workflow experiments validating results on a per-region basis<br />
* Comparisons will use DICE<br />
* Script will register patient scans from a baseline experiment to the 'new' experiment<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Identify the DICE threshold for automatic QA entry<br />
* Interface with our PostgreSQL database for QA access and recording<br />
* Validate automated responses on 20 test cases<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Complete<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:AutomatedSegmentationQA&diff=867982014 Summer Project Week:AutomatedSegmentationQA2014-06-27T02:46:26Z<p>Dmwelch: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a database-driven script to compare results of segmentation workflow experiments validating results on a per-region basis<br />
* Comparisons will use DICE<br />
* Script will register patient scans from a baseline experiment to the 'new' experiment<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Identify the DICE threshold for automatic QA entry<br />
* Interface with our PostgreSQL database for QA access and recording<br />
* Validate automated responses on 20 test cases<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Complete<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=863962014 Summer Project Week2014-06-23T17:14:18Z<p>Dmwelch: /* Huntington's Disease */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms|Grier Room (Left)]] <br />
|<br />
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
<br />
<br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)<br />
*[[2014_Summer_Prioject_Week:AgatstonScoring | Cardiac Agatston Scoring Extension]] (Jessica Forbes, Hans Johnson)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week: Quantitative image feature extraction | Quantitative image feature extraction in Non-Small Cell Lung Cancer]] (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistani, Sonia Pujol)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:ManualSegmentationQA&diff=863942014 Summer Project Week:ManualSegmentationQA2014-06-23T17:10:42Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a Slicer module/extension to connect to a segmentation database and que 'bad' segmentations for QA raters review and editing<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:ManualSegmentationQA&diff=863932014 Summer Project Week:ManualSegmentationQA2014-06-23T17:09:21Z<p>Dmwelch: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:AutomatedSegmentationQA&diff=863922014 Summer Project Week:AutomatedSegmentationQA2014-06-23T17:09:09Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a database-driven script to compare results of segmentation workflow experiments validating results on a per-region basis<br />
* Comparisons will use DICE<br />
* Script will register patient scans from a baseline experiment to the 'new' experiment<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Prioject_Week:AgatstonScoring&diff=863882014 Summer Prioject Week:AgatstonScoring2014-06-23T17:06:43Z<p>Dmwelch: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=863872014 Summer Project Week2014-06-23T17:06:34Z<p>Dmwelch: /* Huntington's Disease */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms|Grier Room (Left)]] <br />
|<br />
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
<br />
<br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Hans Johnson, Dave Welch)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Hans Johnson, Dave Welch)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)<br />
*[[2014_Summer_Prioject_Week:AgatstonScoring | Cardiac Agatston Scoring Extension]] (Hans Johnson, Jessica Forbes)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week: Quantitative image feature extraction | Quantitative image feature extraction in Non-Small Cell Lung Cancer]] (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistani)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:AutomatedSegmentationQA&diff=863852014 Summer Project Week:AutomatedSegmentationQA2014-06-23T17:05:02Z<p>Dmwelch: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List </gallery> ==Key Investigators== * IOWA: Dave Welch, Hans Johnson ==Project Descrip…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Create a database driven script to compare results of a segmentation workflow experiment <br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=863822014 Summer Project Week2014-06-23T17:03:26Z<p>Dmwelch: /* Huntington's Disease */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms|Grier Room (Left)]] <br />
|<br />
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
<br />
<br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Hans Johnson, Dave Welch)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Hans Johnson, Dave Welch)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week: Quantitative image feature extraction | Quantitative image feature extraction in Non-Small Cell Lung Cancer]] (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistani)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:UpdateBRAINSTools&diff=863812014 Summer Project Week:UpdateBRAINSTools2014-06-23T17:03:09Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* IOWA: Hans, Dave, Kent<br />
* Kitware: JC<br />
* NLM: Brad<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Update Slicer build to include BRAINSTools bbased on ITKv4 registation fravework<br />
* Ensure all BRAINSTools regression tests pass in the Slicer environment<br />
* Test ITK thread pool implemation in Slicer build<br />
* ITKv4 registation in SimpleITK<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* <br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:UpdateBRAINSTools&diff=863752014 Summer Project Week:UpdateBRAINSTools2014-06-23T17:00:18Z<p>Dmwelch: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=863732014 Summer Project Week2014-06-23T17:00:05Z<p>Dmwelch: /* Huntington's Disease */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms|Grier Room (Left)]] <br />
|<br />
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
<br />
<br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Hans Johnson, Dave Welch)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Hans Johnson, Dave Welch)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistani)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=863662014 Summer Project Week2014-06-23T16:58:17Z<p>Dmwelch: /* Huntington's Disease */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms|Grier Room (Left)]] <br />
|<br />
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
<br />
<br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Hans Johnson, Dave Welch)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Hans Johnson, Dave Welch)<br />
<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistani)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Project_Week:QA_module&diff=850732014 Project Week:QA module2014-01-10T17:25:18Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
Image:QAModule_filtered.png<br />
Image:QAModuleCloseup.png<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Iowa: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<div style="width: 100%;"><br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* We have an automatic QA application that compares old experiment results with manual QA measures to new experiment results. For some comparisons, the automated QA application cannot determine the quality and needs manual intervention. The SlicerQA module <ref>[https://github.com/BRAINSia/SlicerQAExtension.git QA module on Github]</ref> needs to be updated s.t. only the undetermined images/regions are evaluated manually by our QA raters.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Update helper.py with new PostgreSQL commands<br />
* Disable region/image buttons that have automated reviews<br />
* Force QA comments on failing regions<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* [COMPLETE]<br />
</div><br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
<div style="float: left; padding-right: 3%;"><br />
<h3>Source Code</h3><br />
<references/><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Project_Week:QA_module&diff=850702014 Project Week:QA module2014-01-10T17:10:08Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
Image:QAModule_filtered.png<br />
Image:QAModuleCloseup.png<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Iowa: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* We have an automatic QA application that compares old experiment results with manual QA measures to new experiment results. For some comparisons, the automated QA application cannot determine the quality and needs manual intervention. The QA module needs to be updated s.t. only the undetermined images/regions are evaluated manually by our QA raters.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Update helper.py with new PostgreSQL commands<br />
* Disable region/image buttons that have automated reviews<br />
* Force QA comments on failing regions<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* [COMPLETE]<br />
</div><br />
</div><br />
<br />
==References==<br />
<div style="float: left; padding-right: 3%;"><br />
<h3>Source Code</h3><br />
[https://github.com/BRAINSia/SlicerQAExtension.git QA module on Github]<br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Project_Week:QA_module&diff=850352014 Project Week:QA module2014-01-10T16:22:03Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
Image:QAModule_filtered.png<br />
Image:QAModuleCloseup.png<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Iowa: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* We have an automatic QA application that compares old experiment results with manual QA measures to new experiment results. For some comparisons, the automated QA application cannot determine the quality and needs manual intervention. The QA module needs to be updated s.t. only the undetermined images/regions are evaluated manually by our QA raters.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Update helper.py with new PostgreSQL commands<br />
* Disable region/image buttons that have automated reviews<br />
* Force QA comments on failing regions<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* [COMPLETE]<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=File:QAModuleCloseup.png&diff=85032File:QAModuleCloseup.png2014-01-10T16:21:24Z<p>Dmwelch: </p>
<hr />
<div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Project_Week:QA_module&diff=850262014 Project Week:QA module2014-01-10T16:20:24Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
Image:QAModule_filtered.png<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Iowa: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* We have an automatic QA application that compares old experiment results with manual QA measures to new experiment results. For some comparisons, the automated QA application cannot determine the quality and needs manual intervention. The QA module needs to be updated s.t. only the undetermined images/regions are evaluated manually by our QA raters.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Update helper.py with new PostgreSQL commands<br />
* Disable region/image buttons that have automated reviews<br />
* Force QA comments on failing regions<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* [COMPLETE]<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=File:QAModule_filtered.png&diff=85022File:QAModule filtered.png2014-01-10T16:19:24Z<p>Dmwelch: </p>
<hr />
<div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Project_Week:QA_module&diff=850092014 Project Week:QA module2014-01-10T16:14:59Z<p>Dmwelch: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Iowa: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* We have an automatic QA application that compares old experiment results with manual QA measures to new experiment results. For some comparisons, the automated QA application cannot determine the quality and needs manual intervention. The QA module needs to be updated s.t. only the undetermined images/regions are evaluated manually by our QA raters.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Update helper.py with new PostgreSQL commands<br />
* Disable region/image buttons that have automated reviews<br />
* Force QA comments on failing regions<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* [COMPLETE]<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Project_Week:QA_module&diff=849912014 Project Week:QA module2014-01-10T16:07:25Z<p>Dmwelch: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Iowa: Dave Welch, Hans Johnson<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* <br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* <br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* <br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Project_Week:QA_module&diff=849902014 Project Week:QA module2014-01-10T16:07:05Z<p>Dmwelch: Created page with '__NOTOC__ <gallery> Image:PW-SLC2014.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* <br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* <br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* <br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Winter_Project_Week&diff=849882014 Winter Project Week2014-01-10T16:06:50Z<p>Dmwelch: /* Huntington's Disease */</p>
<hr />
<div> Back to [[Project Events]], [[AHM_2014]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2014.png|300px]]<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
= Dates.Venue.Registration =<br />
<br />
Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=<br />
<br />
Please:<br />
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].<br />
* [[#Projects|'''Click here to jump to Project list''']]<br />
<br />
=Background and Preparation=<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
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]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==TBI==<br />
*[[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)<br />
*[[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)<br />
*[[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)<br />
*[[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)<br />
*[[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)<br />
<br />
==Atrial Fibrillation==<br />
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Salma, Josh, Alan)<br />
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Salma, Josh, Alan)<br />
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Salma, Josh)<br />
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)<br />
*[[2014_Project_Week:AblationSuccessRatePredictionUsingJointImageAndShapeAnalysis|Ablation Success Rate Prediction Using Joint Image And Shape Analysis]](Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)<br />
*[[2014_Project_Week:GrowCutLevelSetLA|Grow cut, level set integration for interactive LA segmentation]] ( Liangjia Zhu, Ivan Kolesov, Yi Gao, Allen Tannenbaum)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Project_Week:DWIDispersion|DWI Dispersion & Compressed Sensing Conversions]] (Hans, CF, Peter Savadjiev, Kent, Dave Welch)<br />
*[[2014_Project_Week:Modules scripting|Slicer module scripting]] (Dave, Bradley Lowekamp)<br />
*[[2014_Project_Week:QA module| QA module]] (Dave)<br />
*[[2014_Project_Week:DWIConverter|DWIConverter]] (Hans, Kent)<br />
*[[2014_Project_Week:Slicer_Based_Surface_Template_Estimation|Slicer Based Surface Template Estimation]] (Saurabh Jain, Steve Pieper, Hans Johnson, Josh Cates)<br />
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)<br />
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)<br />
*[[2014_Project_Week:WMQLExtension|WMQL implementation as a Slicer extension]] (Lichen Liang, Peter Savadjiev, Lauren O'Donnell, Steve Pieper)<br />
<br />
==Head and Neck Cancer==<br />
*[[2014_Project_Week:DIR_Validation|DIR Validation: Landmark Mismatch Error]] (Nadya and Greg)<br />
*[[2014_Project_Week:Vector_Field|DIR Validation: Vector Field Analysis]] (Nadya and Greg)<br />
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)<br />
*[[2014_Project_Week:CarreraSlice|Interactive Segmentation]] (Ivan, LiangJia, Nadya, Yi, Greg, Allen)<br />
<br />
==Slicer4 Extensions==<br />
*[[2014_Project_Week:ShapePopulationViewer|Surface Visualization - ShapePopulationViewer]] (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)<br />
*[[2014_Project_Week:DTIAnalysisPipeline|DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin, Martin Styner)<br />
<br />
==Cardiac==<br />
*[[2014_Project_Week:CardiacStemCellMonitoring|Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI]] (Karl Diedrich)<br />
*[[2014_Project_Week:CardiacCongenitalSegmentation|Whole-heart segmentation of cardiac MR images in congenital heart defect cases]] (Danielle Pace, Polina Golland)<br />
<br />
==Stroke==<br />
<br />
*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Polina Binder, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Project_Week:Processing_Pipelines|Processing Pipelines]] (Ramesh Sridharan, Polina Golland)<br />
<br />
==Brain Segmentation==<br />
*[[2014_Project_Week:MultiAtlas_MultiImage_Segmentation|Multi-Atlas based Multi-Image Segmentation]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)<br />
<br />
==Image-Guided Interventions==<br />
*[[2014_Project_Week:OpenIGTLink| OpenIGTLink Interface: New data types and structures]] (Junichi Tokuda, Andras Lasso, Steve Piper, ???)<br />
*[[2014_Project_Week:Ultrasound Visualization and Navigation in Neurosurgery|Ultrasound Visualization and Navigation in Neurosurgery]] (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, Steve Pieper, William M. Wells III)<br />
*[[2014_Project_Week:PercutaneousApproachAnalysis| Percutaneous Approach Analysis]] (Atsushi Yamada, Junichi Tokuda, Koichiro Murakami)<br />
*[[2014_Project_Week:EndoscopeConsole| Endoscope Console]] (Atsushi Yamada, Junichi Tokuda, Laurent Chauvin)<br />
*[[2014_Project_Week:Statistical Shape Model for robotic spine surgery| Statistical Shape Model for robotic spine surgery]] (Marine Clogenson, ???)<br />
*[[2014_Project_Week:ImmersiveVR| Immersive VR devices]] (Franklin King, Andras Lasso)<br />
<br />
==Radiation Therapy==<br />
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg Sharp, Kevin Wang)<br />
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg Sharp, Kevin Wang)<br />
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Steve Pieper, Greg Sharp)<br />
*[[2014_Project_Week:External_Beam_Planning|External Beam Planning Visualization]] (Kevin Wang, Greg Sharp, Csaba Pinter)<br />
<br />
==TMJ-OA==<br />
* [[2014_Winter_Project_Week:Constrain Fiducial along Suface|Constrain Fiducial along Suface]] (Vinicius Boen, Nicole Aucoin, Beatriz Paniagua)<br />
* [[2014_Winter_Project_Week:Cropping Multiple Surfaces|Cropping multiple surfaces simultaneously]] (Alexander, Jc, Steve, Vinicius, Beatriz Paniagua)<br />
* [[2014_Winter_Project_Week:Color Code Tables|Color Coded Tables]] (Vinicius Boen, Beatriz Paniagua, Nicole Aucoin, Steve Pieper, Francois Budin)<br />
* [[2014_Winter_Project_Week:4DShape Analysis of mandibular changes|4DShape Analysis of mandibular changes]] (Vinicius Boen, James Fishbaugh, Guido Gerig)<br />
<br />
==Chronic Obstructive Pulmonary Disease ==<br />
* [[2014_Winter_Project_Week:CIP Core|Chest Imaging Platform (CIP) - Core Infrastructure]] (Raul San Jose, Rola Harmouche, Pietro Nardelli, James Ross)<br />
* [[2014_Winter_Project_Week:CIP Infrastructure Testing and SuperBuild|CIP Testing and SuperBuild]] (James Ross, Raul San Jose)<br />
* [[2014_Winter_Project_Week:Slicer CIP Slicer MRML| Slicer CIP- MRML consolidation]] (Pietro Nardelli, Rola Harmouche, James Ross, Raul San Jose)<br />
* [[2014_Winter_Project_Week:Slicer CIP Modules| Slicer CIP- Modules]] (Rola Harmouche, Pietro Nardelli, James Ross, Raul San Jose)<br />
<br />
==[http://qiicr.org QIICR]==<br />
<br />
*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)<br />
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)<br />
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)<br />
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim, Rick Herrick)<br />
*[[2014_Project_Week:Quantitative_Index_Computation|Quantitative Index Computation]] (Ethan Ulrich, Reinhard Beichel, Nicole, Andrey, Jim)<br />
*[[2014_Project_Week:TCIA Browser Extension in Slicer|TCIA Browser Extension in Slicer]] (Alireza, Andrey, Steve, Ron)<br />
*[[2014_Project_Week:Slicer DICOM Module Interface Redesign|Slicer DICOM Module Interface Redesign]] (Alireza, Andrey, Steve, Ron, Rick Herrick)<br />
<br />
==Infrastructure==<br />
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)<br />
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang, Rick Herrick)<br />
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin, Rick Herrick)<br />
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Andras Lasso, Nicole Aucoin, Steve Pieper, Jc, Csaba Pinter, ???, Rick Herrick)<br />
*[[2014_Project_Week:CLI|CLI]] (Jim Miller, Matt McCormick, Nicole Aucoin, Steve Pieper, Jc)<br />
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration (LandmarkRegistration module)]] (Steve, Greg, Kevin, Vinicius, Marcel)<br />
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)<br />
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)<br />
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)<br />
* [[2014_Winter_Project_Week:NonlinearTransforms|Integration nonlinear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)<br />
* [[2014_Winter_Project_Week:ParameterSerialization | JSON Parameter Serialization]] (Matt McCormick, Steve Pieper, Jim Miller)<br />
* [[2014_Winter_Project_Week:XNATSlicerLink| 3DSlicer annotations in XNAT]] (Erwin Vast, Nicole Aucoin, Andrey Fedorov, Rick Herrick)<br />
* [[2014_Winter_Project_Week:PlanarImage|Planar Images]] (Franklin King, Csaba Pinter, Andras Lasso)</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Project_Week:Modules_scripting&diff=849802014 Project Week:Modules scripting2014-01-10T16:02:41Z<p>Dmwelch: /* Project Description */ FINAL status</p>
<hr />
<div>==Key Investigators==<br />
* Iowa: David Welch<br />
* NLM: Brad Lowekamp<br />
* Iowa: Hans Johnson<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Enhance the integration of SimpleITK with Slicer and expand the documentation for building modules from SimpleITK<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Enhance the interface for the existing "SimpleFilters" module to allow for label maps and image types to be better handled.<br />
** [BRAD] Explain how the SimpleFilters module works<br />
** [DAVE] Make outputs default to NOT overwriting the inputs<br />
** [Brad] For binary image outputs, set them as labelmaps<br />
<br />
* Add python output code generation and display<br />
** [DAVE] Introspect SimpleITK functions for get/set options<br />
** [DAVE] Add text output to SimpleFilters GUI<br />
** [DAVE] Verify code in external environment<br />
<br />
* Convert SimpleITK functions to user interface modules<br />
** [DAVE] Create a SimpleITK function that histogram equalizes one image to another. "outimage=histEQ(refImage,inputImage,numberOfBins)"<br />
** [DAVE] Convert that simple function to a Slicer GUI interface<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* [DONE] Enhance the interface for the existing "SimpleFilters" module to allow for label maps and image types to be better handled.<br />
* [NEEDS TESTING] Add python output code generation and display<br />
* [INCOMPLETE] Convert SimpleITK functions to user interface modules<br />
<br />
</div><br />
</div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Winter_Project_Week&diff=838852014 Winter Project Week2013-12-03T21:36:46Z<p>Dmwelch: /* Huntington's Disease */</p>
<hr />
<div> Back to [[Project Events]], [[AHM_2014]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2014.png|300px]]<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
= Dates.Venue.Registration =<br />
<br />
Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=<br />
<br />
Please:<br />
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].<br />
* [[#Projects|'''Click here to jump to Project list''']]<br />
<br />
=Background and Preparation=<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
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]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==TBI==<br />
<br />
==Atrial Fibrillation==<br />
*[[2014_Project_Week:GraphCutsLASegmentation|LA Segmentation via Graph Cuts]] (Josh, Salma, Gopal)<br />
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)<br />
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)<br />
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Project_Week:DWIDispersion|DWI Dispersion]] (Hans, CF)<br />
*[[2014_Project_Week:DTIAnalysis|DTI Compressed Sensing?]] (Hans, CF)<br />
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)<br />
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent)<br />
<br />
==Head and Neck Cancer==<br />
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)<br />
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)<br />
*[[2014_Project_Week:KSlice|Interactive Segmentation]] (Ivan, Nadya, Greg, Allen)<br />
<br />
==Stroke==<br />
<br />
==Image-Guided Interventions==<br />
<br />
==Radiation Therapy==<br />
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg, Kevin Wang, others)<br />
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg, Kevin Wang, others)<br />
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Greg, others)<br />
<br />
==Medical Robotics==<br />
==[http://qiicr.org QIICR]==<br />
<br />
==TMJ-OA==<br />
<br />
==Infrastructure==<br />
*[[2014_Project_Week:SlicerSpeedUp|Slicer speed up]] (Jc, Andras Lasso, Steve Pieper)<br />
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)<br />
*[[2014_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Steve Pieper)<br />
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)<br />
*CLI - Resources? Conditionals? Autonaming? Provenance? (Jim Miller)<br />
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)<br />
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)<br />
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)<br />
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject Hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc)<br />
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2014_Winter_Project_Week&diff=838202014 Winter Project Week2013-11-21T20:12:04Z<p>Dmwelch: /* Huntington's Disease */</p>
<hr />
<div> Back to [[Project Events]], [[AHM_2014]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2014.png|300px]]<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
= Dates.Venue.Registration =<br />
<br />
Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=<br />
<br />
Please:<br />
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].<br />
* [[#Projects|'''Click here to jump to Project list''']]<br />
<br />
=Background and Preparation=<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
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]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==TBI==<br />
<br />
==Atrial Fibrillation==<br />
<br />
==Huntington's Disease==<br />
*[[2014_Project_Week:DTIAnalysis|DTI Compressed Sensing?]] (Hans, Joy, ?)<br />
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)<br />
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent)<br />
<br />
==Head and Neck Cancer==<br />
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)<br />
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)<br />
*[[2014_Project_Week:DICOM_RT|DICOM RT]] (Greg, others)<br />
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration]] (Greg, others)<br />
<br />
==Stroke==<br />
<br />
==Image-Guided Interventions==<br />
<br />
==Radiation Therapy==<br />
<br />
==Medical Robotics==<br />
==[http://qiicr.org QIICR]==<br />
<br />
==Infrastructure==<br />
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)<br />
*[[2014_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Steve Pieper)<br />
*Multiobject (Andras Lasso, Andriy Fedorov, Steve Pieper, JC)<br />
*CLI (Jim Miller)<br />
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)<br />
* Steered Registration (Steve, Jim, Greg)</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=BRAINS_CAMP&diff=82954BRAINS CAMP2013-07-24T20:43:26Z<p>Dmwelch: Added registration link</p>
<hr />
<div>*Date: August 1-2, 2013<br />
*Local organizer: Hans Johnson, Iowa University<br />
*Location: Iowa University, Iowa City<br />
*[http://dev.sitenow.uiowa.edu/hpc/research/event/brainscamp-2013 BRAINSCamp website]<br />
*[http://www.regonline.com/BRAINSCamp2013 BRAINSCamp registration]<br />
<br />
* 3D Slicer tutorials:<br />
** 3D Visualization of DICOM Images for Radiology Applications<br />
** [http://www.slicer.org/slicerWiki/images/f/f1/NeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial ]<br />
<br />
* 3D Slicer data:<br />
**[[media:Dcmtk-db.zip| Dataset 1: DCMTK Database Folder Data]]<br />
** Dataset2: DICOM Dataset<br />
**[[media:WhiteMatterExplorationData.zip|Dataset 3: Neurosurgical Planning Tutorial Data]]<br />
<br />
<br />
[[Image:BRAINS_Camp_2013.jpeg| 500 px|Right]]</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:Enhance_and_update_SPL_atlas&diff=827092013 Summer Project Week:Enhance and update SPL atlas2013-06-21T14:05:34Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
Image:GrayMatter_bad.png|Gray Matter Prior<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* UIowa: Hans Johnson, Dave Welch<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Add spatial and tissue class priors, AC-PC alignment, all images and labels at same resolution (0.75 mm isotropic) <br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
# Register latest SPL atlas to AC-PC aligned space<br />
# Resample label image to 0.75mm resolution<br />
# Create new tissue prior probability images from 1457 subjects in HD dataset<br />
# Clean and fix prior images (cerebellum WM vs. cerebral WM, etc.)<br />
# Register and resample prior images to 0.75mm<br />
# Create basal ganglia region<br />
# Reconcile overlapping prior maps to normalized probability<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Completed:<br />
# Register latest SPL atlas to AC-PC aligned space<br />
# Resample label image to 0.75mm resolution<br />
# Create new tissue prior probability images from 1457 subjects in HD dataset<br />
In progress:<br />
# Clean and fix prior images (cerebellum WM vs. cerebral WM, etc.)<br />
<br />
<br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify) '''YES, atlas and label files'''<br />
<br />
==References==</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=File:GrayMatter_bad.png&diff=82708File:GrayMatter bad.png2013-06-21T14:05:02Z<p>Dmwelch: </p>
<hr />
<div></div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:Enhance_and_update_SPL_atlas&diff=827072013 Summer Project Week:Enhance and update SPL atlas2013-06-21T14:04:30Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
Image:WhiteMatterPrior_bad.png|White matter prior<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* UIowa: Hans Johnson, Dave Welch<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Add spatial and tissue class priors, AC-PC alignment, all images and labels at same resolution (0.75 mm isotropic) <br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
# Register latest SPL atlas to AC-PC aligned space<br />
# Resample label image to 0.75mm resolution<br />
# Create new tissue prior probability images from 1457 subjects in HD dataset<br />
# Clean and fix prior images (cerebellum WM vs. cerebral WM, etc.)<br />
# Register and resample prior images to 0.75mm<br />
# Create basal ganglia region<br />
# Reconcile overlapping prior maps to normalized probability<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Completed:<br />
# Register latest SPL atlas to AC-PC aligned space<br />
# Resample label image to 0.75mm resolution<br />
# Create new tissue prior probability images from 1457 subjects in HD dataset<br />
In progress:<br />
# Clean and fix prior images (cerebellum WM vs. cerebral WM, etc.)<br />
<br />
<br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify) '''YES, atlas and label files'''<br />
<br />
==References==</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:Enhance_and_update_SPL_atlas&diff=827052013 Summer Project Week:Enhance and update SPL atlas2013-06-21T14:02:55Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
'''TODO: add images'''<br />
<br />
==Key Investigators==<br />
* UIowa: Hans Johnson, Dave Welch<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Add spatial and tissue class priors, AC-PC alignment, all images and labels at same resolution (0.75 mm isotropic) <br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
# Register latest SPL atlas to AC-PC aligned space<br />
# Resample label image to 0.75mm resolution<br />
# Create new tissue prior probability images from 1457 subjects in HD dataset<br />
# Clean and fix prior images (cerebellum WM vs. cerebral WM, etc.)<br />
# Register and resample prior images to 0.75mm<br />
# Create basal ganglia region<br />
# Reconcile overlapping prior maps to normalized probability<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Completed:<br />
# Register latest SPL atlas to AC-PC aligned space<br />
# Resample label image to 0.75mm resolution<br />
# Create new tissue prior probability images from 1457 subjects in HD dataset<br />
In progress:<br />
# Clean and fix prior images (cerebellum WM vs. cerebral WM, etc.)<br />
<br />
<br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify) '''YES, atlas and label files'''<br />
<br />
==References==</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:DWIConvert&diff=826492013 Summer Project Week:DWIConvert2013-06-21T13:34:47Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]<br />
==Key Investigators==<br />
* UIowa: Kent Williams, esqr.<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Improve the DICOM - DWI conversion mechanism in Slicer to support more scanners and file output formats.<br />
<br />
<h6> Specific goals </h6><br />
#Working with the PREDICT and HDNI longitudinal data sets as sample multi-site, multi-scanner test data corpus, add support for more scanning protocols and software versions.<br />
#General code clean-up -- DicomToNrrd had been repeatedly modified over the past few years by multiple authors, to the point where there is many instances of 'dead' code (never executed) and confusing paths of execution.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
#Approach<br />
##Begin with original DicomToNrrd code.<br />
##Analyze source code to capture the implicit knowledge about DWI DICOM data sets.<br />
##Refactor code to straighten out program logic and remove obsolete and incorrect code.<br />
#Plan<br />
##Incrementally refactor and improve C++ code<br />
##Use regression tests, and tests against large collections of DICOM data sets to validate code<br />
##Incorporate program into BRAINSTools suite (hosted at github) to facilitate inclusion in Slicer.<br />
##Work with Slicer community to come up with new 'problem' datasets for testing.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Refactored original monolithic code into a collection of classes, one per scanner manufacturer, with common code isolated from scanner-specific code.<br />
* More modular structure makes it easier to add new scanner models.<br />
</div><br />
</div><br />
<div style="width: 85%; float: center;"><br />
{| class="wikitable" | width = 100%<br />
! Scanner <br />
Manufacturer<br />
! Software version<br />
|-<br />
| Seimans<br />
| Avanto<br/>Espree<br/>Sonata<br/>Symphony<br/>SymphonyTim<br/>TrioTim<br/>Verio<br />
|-<br />
| GE <br />
| GENESIS_SIGNA<br/>SIGNA<br/>SIGNA EXCITE<br/>SIGNA HDx<br/>Signa HDxt<br />
|-<br />
| Philips<br />
| Achieva<br/>Intera<br />
|-<br />
| Hitachi<br />
| style="font-style: italic; color: red;" | In Progress<br />
|}<br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
# Part of BRAINSTools suite https://github.com/BRAINSia/BRAINSTools<br />
#Slicer Module<br />
##Built-in YES<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
<br />
==References==</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:Dynamically_Configurable_Quality_Assurance_Module_for_Large_Huntington%27s_Disease_Database_Frontend&diff=826302013 Summer Project Week:Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend2013-06-21T13:19:39Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2012.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
Image:QAEvaluationScreenShot.png| Original GUI<br />
Image:QualityAssurance_initial.png| Configurable GUI<br />
Image:QualityAssurance_0.png| Example 1<br />
Image:QualityAssurance_1.png| Example 2<br />
Image:QualityAssurance_2.png| Example 3<br />
</gallery><br />
[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]<br />
==Key Investigators==<br />
* UIowa: Dave Welch, Hans Johnson<br />
* Kitware: JC Fillion-Robin<br />
* Isomics: Steve Pieper<br />
* BWH: Andrey Fedorov<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
QA evaluation of derived images for large population studies is vital to ensure study results are accurate and relevant. We will create a Slicer module capable of querying a database of associated derived volumes and label maps from our AutoWorkup pipeline for interactive QA evaluation. <br />
<br />
We will also minimize duplication of QA efforts through database management within the module, allowing multiple Slicer instances on a network to evaluate our results by subject without repetition or conflict. In addition, we will optimize the evaluator's time through process schemes like pre-loading of batched data.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
We will use the Python scripting capabilities to create a loadable module for Slicer that is able to query a database. We will take advantage of QT Designer to streamline our UI development and test on a copied version of our network hierarchy. In order to normalize our QA across evaluators, we will control the slice views from the module and expose only the necessary volumes and label nodes to the users.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
We have successfully generated a robust GUI via configuration files ONLY. In addition, we have laid out the configuration file to describe a database to the GUI backend. <br />
<br />
Our module requires at least three configuration files (INI-compliant): <br />
<br />
1) <strong>qualityassurance.cfg</strong>: describes the available modules within this module<br />
<br />
For each defined module:<br />
<br />
2) <strong>GUI configuration file</strong>: describes the GUI layout and logic<br />
<br />
3) <strong>database configuration file</strong>: describes the database schema<br />
<br />
We currently support Postgres SQL and the design is intended for easy extension to other SQL flavors. <br />
Excel interaction would be desirable, but we don't support it currently.<br />
<br />
TODO: <br />
# dynamic definition of logic functions<br />
# more integration of CompareVolumes<br />
# support for QButtonGroup?<br />
<br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module ('''Yes''')<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify)</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:SinglePrecisionRegistrationITK&diff=826292013 Summer Project Week:SinglePrecisionRegistrationITK2013-06-21T13:19:20Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]<br />
[[Image:GreenDashboardForSinglePrecision.png|900px]]<br />
<br />
==Key Investigators==<br />
* UIowa: Ali Ghayoor, Hans, Dave<br />
* NLM: Brad Lowekamp<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
<br />
The current registration framework of ITK just can process data using double precision. However, in some cases using 'float' type is enough for the precision of computations.<br />
<br />
This feature allows CPU to process more data in its cache in a limited period of time, so it can increase the computations speed. Also, writing outputs to the disk using single precision needs much less memory rather than we save them by values in double precision.<br />
Saving the memory space is specially important when our outputs are huge files that need hundreds of giga bytes of memory disk. An example of such outputs is transforms files that contain several deformation fields.<br />
<br />
To make ANTS capable to do its computations in single point precision, first, we need improve ITK for this purpose. <br />
Currently registration framework of ITK, just can use 'double' precision for its internal computations, so we should add single precision (float Type) as another possible option.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
This project will be considered successfully executed when the following deliverables are accepted:<br />
<br />
1- A new flag is added to antsRegistration to run it on single precision mode. For now, it can be called "--float".<br />
<br />
2- A template parameters of "T", that defines the precision type, is added to all classes needed by antsRegistration if it cannot be extracted inside the class.<br />
<br />
3- Currently ITK cannot be used in single precision. Necessary changes should be taken to make ITK be able to do its processing in single precision. (It is defined as a Sub-Task to this ticket).<br />
<br />
4- Make sure that the ITK-Standalone is built based on new changes.<br />
<br />
5- Build ANTS using the new local version of ITK when float mode is on.<br />
<br />
6- Fix all possible compiler errors in ANTS codes or ITK new version codes when ANTS is compiling using the new ITK, and the float mode is on.<br />
<br />
7- We can make sure that the ANTS and ITK are now compatible with single precision mode if the build process is done successfully (all compiler and linker errors are fixed).<br />
<br />
8- Design a simple experiment to catch the running time errors (you may need to use GDB).<br />
<br />
9- If antsRegistration can be run successfully, it is time to start evaluation steps. Evaluate the efficiency of new feature using the following criteria:<br />
I) Compare the running time of antsRegistration on the float mode with the case that it is run on double precision mode. Experiments should be run on the same system.<br />
II) Compare the precision of registration task between the single and double precision modes. We can run antsRegistration using the "print-similarity-measure-interval" flag that prints out the CC similarity metric measure on iterations intervals.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
# ITK is built successfully, and all test pass, and no compiler warnings on Windows, Mac, Linux. [http://review.source.kitware.com/#/c/11396/ Gerrit Review process] (BIG THANKS TO BRAD LOWEKAMP!)<br />
# ANTS tool build against this version successfully,<br />
# BRAINSTools built agains this successfully,<br />
# Slicer Built against this successfully<br />
# Small regression in SimpleITK resolved with small patch to SimpleITK [http://review.source.kitware.com/#/c/11696/ Gerrit Fix for SimpleITK]<br />
The last patch is sent to gerrit and it is under review.<br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as an improvement to the underlying ITK library. It provides opportutinity for CLI modules to take advantage of single precision registration and transformations where appropriate to provide potential significant speed increases. At least 1 test case showed 30% speed improvement.</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:Investigate_Potential_Tensor_Computation_Improvement_via_Positive_Semi-Definite_(PSD)_Tensor_Estimation&diff=826282013 Summer Project Week:Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation2013-06-21T13:19:00Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]<br />
<gallery><br />
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
Image:PSD_NewOption.png|How the CLI needs to expose a new feature for PSD.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* BWH: Raul San Jose, Carl-Fredrik Westin, Demian Wassermann<br />
* UNC: Marc Niethammer<br />
* UIowa: Hans Johnson, Joy Matsui<br />
<br />
==Background==<br />
Tensor estimation in Slicer4 is done by vtkTeemEstimateDiffusionTensor. In the inner loop of this class, the tensor fitting is actually computed by _tenEstimate1TensorSingle (teem/src/ten/estimate.c). The solution that teem takes to deal with negative eigenvalues is to add an isotropic part corresponding to the smallest eigenvalue if the eigenvalue is negative and the flag negEvalShift is On. This flag is part of the tenContext structure that controls the estimation options and, in turn, can be set in the vtk class by means of ShiftNegativeEigenvalues. By default, ShiftNegativeEigenvalues is Off in the constructor.<br />
<br />
Long story short, teems shifts the value of the eigenvalues so the most negative eigenvalue becomes zero that it is not what it is exactly done in the PSD constrained paper. I've (Raul) been digging through the old slicer2 repository but I did not find that implementation. I'm sure that we played with it but it never made it to any of the CSV branches !!! (old stuff, as you can see). I recalled that we used to do the correction when computing the scalar quantities rather than at tensor estimation. But, surprise, surprise, I found the code in Slicer4. It is funny how you forget things that you have done. I believe this code has traveled through the time machine of Slicer2, to Slicer3 and now to Slicer4. <br />
<br />
If you check vtkDiffusionTensorMathematics you will find the magic in FixNegativeEigenvaluesMethod<br />
[https://github.com/Slicer/Slicer/blob/master/Libs/vtkTeem/vtkDiffusionTensorMathematics.cxx#L922]<br />
<br />
However, if you go to the ExecuteData, this method is commented in favor of applying the same approach that teem applies. I'm sure that this was, at the time, an unconscious decision to be consistent.<br />
<br />
I have to say that this might be a good time to revisit this issue and add some consistency across the code about where to apply this kind of tricks. The PSD trick is only valid under the least-square solution, so it would be the most sense to apply it as an option in vtkTeemEstimationDiffusionTensor when the LS method is selected. I don't know if this can be generalized to the WLS but my experience is that WLS deals with many of this negative eigenvalues oddities when it weights down the noise DWIs.<br />
<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
<br />
Discuss approach and schedule making this change after project week.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
# Modify the CLI code to expose the alternate analysis processing schemes at runtime rather than at compile time<br />
# Modify XML to expose option in the Slicer GUI <br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
Discussions occured, and it was determined that this work is best done after project week.<br />
<br />
[[File:DWItoDTI_with_PSD_EmailConversation.pdf]] E-mail conversation<br />
<br />
<br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as an improvement to the existing DWItoDTI module<br />
<br />
==References==<br />
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/niethammerEMBS06.pdf On Diffusion Tensor Estimation]</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=Learn_and_Apply_FiberBundleLabelSelect_for_Huntington%27s_Disease_Data&diff=82627Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data2013-06-21T13:18:29Z<p>Dmwelch: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]<br />
==Key Investigators==<br />
* UIowa: Hans Johnson<br />
* BWH: Demian Wasserman<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Integrate processing Freesurfer, BRAINSTools, and Slicer's FiberBundleLabelSelect<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
1) Label based tractography modules <br />
<br />
2) Auto run paint updates training <br />
<br />
3) Request "dictionary" of regional include/excludes <br />
<br />
4) Need filter bundle as input <br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
After Discussion with Demian, we determined that the the tract querier ([http://www.na-mic.org/Wiki/index.php/2013_Summer_Project_Week:WMQL_Integration_in_Slicer See WMQL project page ] and [ http://ww4.aievolution.com/hbm1201/index.cfm?do=abs.viewAbs&abs=6409 Poster ] ) was a better fit for the HD processing needs. <br />
<br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify)<br />
<br />
==References==<br />
'''TODO'''</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=2013_Summer_Project_Week:Dynamically_Configurable_Quality_Assurance_Module_for_Large_Huntington%27s_Disease_Database_Frontend&diff=826262013 Summer Project Week:Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend2013-06-21T13:16:46Z<p>Dmwelch: /* Project Description */ Update of project week status and image loading</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2012.png|[[2013_Summer_Project_Week#Projects|Projects List]]<br />
Image:QAEvaluationScreenShot.png| Original GUI<br />
Image:QualityAssurance_initial.png| Configurable GUI<br />
Image:QualityAssurance_0.png| Example 1<br />
Image:QualityAssurance_1.png| Example 2<br />
Image:QualityAssurance_2.png| Example 3<br />
<br />
</gallery><br />
<br />
==Key Investigators==<br />
* UIowa: Dave Welch, Hans Johnson<br />
* Kitware: JC Fillion-Robin<br />
* Isomics: Steve Pieper<br />
* BWH: Andrey Fedorov<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
QA evaluation of derived images for large population studies is vital to ensure study results are accurate and relevant. We will create a Slicer module capable of querying a database of associated derived volumes and label maps from our AutoWorkup pipeline for interactive QA evaluation. <br />
<br />
We will also minimize duplication of QA efforts through database management within the module, allowing multiple Slicer instances on a network to evaluate our results by subject without repetition or conflict. In addition, we will optimize the evaluator's time through process schemes like pre-loading of batched data.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
We will use the Python scripting capabilities to create a loadable module for Slicer that is able to query a database. We will take advantage of QT Designer to streamline our UI development and test on a copied version of our network hierarchy. In order to normalize our QA across evaluators, we will control the slice views from the module and expose only the necessary volumes and label nodes to the users.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
We have successfully generated a robust GUI via configuration files ONLY. In addition, we have laid out the configuration file to describe a database to the GUI backend. <br />
<br />
Our module requires at least three configuration files (INI-compliant): <br />
<br />
1) <strong>qualityassurance.cfg</strong>: describes the available modules within this module<br />
<br />
For each defined module:<br />
<br />
2) <strong>GUI configuration file</strong>: describes the GUI layout and logic<br />
<br />
3) <strong>database configuration file</strong>: describes the database schema<br />
<br />
We currently support Postgres SQL and the design is intended for easy extension to other SQL flavors. <br />
Excel interaction would be desirable, but we don't support it currently.<br />
<br />
TODO: <br />
# dynamic definition of logic functions<br />
# more integration of CompareVolumes<br />
# support for QButtonGroup?<br />
<br />
</div><br />
</div><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module ('''Yes''')<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify)</div>Dmwelchhttps://www.na-mic.org/w/index.php?title=File:QualityAssurance_2.png&diff=82609File:QualityAssurance 2.png2013-06-21T12:55:59Z<p>Dmwelch: </p>
<hr />
<div></div>Dmwelch