NAMIC Wiki - User contributions [en]

2014 Project Week:CardiacStemCellMonitoring

2014-01-10T15:50:10Z

Ktdiedrich: /* Key Personnel */

==Project Description==
Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI

== Key Personnel ==
<ul>
<li>Karl Diedrich, AZE Technology, Inc.</li>
<li>Nicholas Herlambang, AZE Technology, Inc.</li>
<li>Yuka Matsuura, Stanford University School of Medicine</li>
<li>Rajesh Dash, Stanford University School of Medicine</li>
<li>Phillip Yang, Stanford University School of Medicine</li>
</ul>

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
<ul>
<li> The goal of the entire project is to restore cardiac function after a heart attack by injecting cardiac stem cells in the infarcted tissue.</li>
<li> This part of the project seeks to monitor injected stem cells over time. </li>
</ul>
</div>
<div style="width: 54%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
<ul>
<li> Pigs (and soon mice) are given a heart attack by inflating a balloon in an artery</li>
<li> Transgenic stem cells over expressing manganese importer are injected into the infarcted cardiac tissue</li>

<li>Images are taken of the hearts at stem cell engraftment day 0, 7, and 45</li>
<li> The images taken are </li>
<ul>
<li> PET-CT: PET signal is expected to be reduced in the infarcted tissue ROI on day 0 and increase over day 7 and day 45 as stem cells grow.</li>
<li>Post GD: Gadolinium Enhanced MRI signal is expected to be high in the infarcted tissue ROI on day 0 and decrease over day 7 and day 45 as stem cells grow and replace the dead tissue. </li>
<li>Post MN: Manganese is added a contrast agent, the signal is expected to be low in the infarcted tissue ROI on day 0 and increase over day 7 and day 45 as stem cells grow. </li>
</ul>
<li> The pigs are growing over the time points by as much as 30% over day 0 to 45. </li>
<li> Register the locator MRIs of the 3 time points together and apply the transformations to to Post MN images. The Post MN images are too narrow to register directly but were taken in the same frame of reference with low resolution locator or scout images. The registration needs to scale based on the change in heart volume. The change in heart volume may be less than the change in total volume of the pigs. </li>
<li> Register The time points by CT and then apply the transformations to the PET. </li>

<li> Copy an ROI across the time points to measure the change in Post MN MRI, Post GD MRI, and PET signal over day 0, 7, 45</li>
</ul>

</div>
</div>

<h3>Progress</h3>
<ul>
<li>Split 3 plane MRI locator images for 3 time-points into separate planes. Only the axial slices are used for image registration</li>
<li>Registered the previous 1 (green) and previous 2 locator images to the current fixed (red) locator image. </li>
<ul>
<li>A rigid 6-degree freedom registration does not handle the growth of the juvenile pig. Current fixed locator in red, previous 1 moving image in green. <br>[[File:MovedLinear1fusion.png]]</li>
<li>A 7-degree freedom scaling registration fits the size of the smaller previous 1 and previous 2 images to the current fixed image. Current fixed locator in red, previous 1 moving image in blue. <br>[[File:MovedScaled1fusion.png]]</li>
<li>The Post MN (manganese) MRI images of the stem cell area are transformed into the frame of reference of the current stem cell area image.(Top left) The Post MN (manganese) image of the stem cells (green) is oriented inside the fixed locator (red). (Top right) Previous 1 Post MN slice transformed (Bottom left) Previous 2 post MN image (Bottom right) Previous 2 post MN image. <br>[[File:StemCellfusions.png]]</li>
<li>Place an ROI around the potential stem cells on the current Post MN image and found intensity 67.64+/-5.932 <br>[[File:StemCellROICurrent.png]]</li>
</ul>
</ul>

<h3>Next steps</h3>
<ul>
<li>Transfer the ROI to the images from the previous 1 and previous 2 time points and measure the MN MRI signal</li>
<li>Repeat the measurement from PET-CT images of the same pigs to correlate PET signal to MN MRI signal.</li>
</ul>

2014 Project Week:CardiacStemCellMonitoring

2014-01-10T15:39:14Z

Ktdiedrich: /* Key Personnel */

==Project Description==
Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI

== Key Personnel ==
<ul>
<li>Karl Diedrich, AZE Technology, Inc.</li>
<li>Yuka Matsuura, Stanford University School of Medicine</li>
<li>Rajesh Dash, Stanford University School of Medicine</li>
<li>Phillip Yang, Stanford University School of Medicine</li>
</ul>

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
<ul>
<li> The goal of the entire project is to restore cardiac function after a heart attack by injecting cardiac stem cells in the infarcted tissue.</li>
<li> This part of the project seeks to monitor injected stem cells over time. </li>
</ul>
</div>
<div style="width: 54%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
<ul>
<li> Pigs (and soon mice) are given a heart attack by inflating a balloon in an artery</li>
<li> Transgenic stem cells over expressing manganese importer are injected into the infarcted cardiac tissue</li>

<li>Images are taken of the hearts at stem cell engraftment day 0, 7, and 45</li>
<li> The images taken are </li>
<ul>
<li> PET-CT: PET signal is expected to be reduced in the infarcted tissue ROI on day 0 and increase over day 7 and day 45 as stem cells grow.</li>
<li>Post GD: Gadolinium Enhanced MRI signal is expected to be high in the infarcted tissue ROI on day 0 and decrease over day 7 and day 45 as stem cells grow and replace the dead tissue. </li>
<li>Post MN: Manganese is added a contrast agent, the signal is expected to be low in the infarcted tissue ROI on day 0 and increase over day 7 and day 45 as stem cells grow. </li>
</ul>
<li> The pigs are growing over the time points by as much as 30% over day 0 to 45. </li>
<li> Register the locator MRIs of the 3 time points together and apply the transformations to to Post MN images. The Post MN images are too narrow to register directly but were taken in the same frame of reference with low resolution locator or scout images. The registration needs to scale based on the change in heart volume. The change in heart volume may be less than the change in total volume of the pigs. </li>
<li> Register The time points by CT and then apply the transformations to the PET. </li>

<li> Copy an ROI across the time points to measure the change in Post MN MRI, Post GD MRI, and PET signal over day 0, 7, 45</li>
</ul>

</div>
</div>

<h3>Progress</h3>
<ul>
<li>Split 3 plane MRI locator images for 3 time-points into separate planes. Only the axial slices are used for image registration</li>
<li>Registered the previous 1 (green) and previous 2 locator images to the current fixed (red) locator image. </li>
<ul>
<li>A rigid 6-degree freedom registration does not handle the growth of the juvenile pig. Current fixed locator in red, previous 1 moving image in green. <br>[[File:MovedLinear1fusion.png]]</li>
<li>A 7-degree freedom scaling registration fits the size of the smaller previous 1 and previous 2 images to the current fixed image. Current fixed locator in red, previous 1 moving image in blue. <br>[[File:MovedScaled1fusion.png]]</li>
<li>The Post MN (manganese) MRI images of the stem cell area are transformed into the frame of reference of the current stem cell area image.(Top left) The Post MN (manganese) image of the stem cells (green) is oriented inside the fixed locator (red). (Top right) Previous 1 Post MN slice transformed (Bottom left) Previous 2 post MN image (Bottom right) Previous 2 post MN image. <br>[[File:StemCellfusions.png]]</li>
<li>Place an ROI around the potential stem cells on the current Post MN image and found intensity 67.64+/-5.932 <br>[[File:StemCellROICurrent.png]]</li>
</ul>
</ul>

<h3>Next steps</h3>
<ul>
<li>Transfer the ROI to the images from the previous 1 and previous 2 time points and measure the MN MRI signal</li>
<li>Repeat the measurement from PET-CT images of the same pigs to correlate PET signal to MN MRI signal.</li>
</ul>

File:StemCellfusions.png

2014-01-10T15:33:48Z

Ktdiedrich: uploaded a new version of "File:StemCellfusions.png"

File:MovedScaled1fusion.png

2014-01-10T15:31:18Z

Ktdiedrich: uploaded a new version of "File:MovedScaled1fusion.png"

File:MovedLinear1fusion.png

2014-01-10T15:29:34Z

Ktdiedrich: uploaded a new version of "File:MovedLinear1fusion.png"

File:StemCellROICurrent.png

2014-01-10T15:26:55Z

Ktdiedrich: uploaded a new version of "File:StemCellROICurrent.png"

2014 Project Week:CardiacStemCellMonitoring

2014-01-10T15:23:48Z

Ktdiedrich: /* Project Description */

==Project Description==
Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI

== Key Personnel ==
<ul>
<li>Karl Diedrich, AZE Technology, Inc.</li>
<li>Yuka Matsuura, Stanford University School of Medicine</li>
<li>Rajesh Dash, Stanford University School of Medicine</li>
<li>Phillip Yang, Stanford University School of Medicine</li>
</ul>

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
<ul>
<li> The goal of the entire project is to restore cardiac function after a heart attack by injecting cardiac stem cells in the infarcted tissue.</li>
<li> This part of the project seeks to monitor injected stem cells over time. </li>
</ul>
</div>
<div style="width: 54%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
<ul>
<li> Pigs (and soon mice) are given a heart attack by inflating a balloon in an artery</li>
<li> Transgenic stem cells over expressing manganese importer are injected into the infarcted cardiac tissue</li>

<li>Images are taken of the hearts at stem cell engraftment day 0, 7, and 45</li>
<li> The images taken are </li>
<ul>
<li> PET-CT: PET signal is expected to be reduced in the infarcted tissue ROI on day 0 and increase over day 7 and day 45 as stem cells grow.</li>
<li>Post GD: Gadolinium Enhanced MRI signal is expected to be high in the infarcted tissue ROI on day 0 and decrease over day 7 and day 45 as stem cells grow and replace the dead tissue. </li>
<li>Post MN: Manganese is added a contrast agent, the signal is expected to be low in the infarcted tissue ROI on day 0 and increase over day 7 and day 45 as stem cells grow. </li>
</ul>
<li> The pigs are growing over the time points by as much as 30% over day 0 to 45. </li>
<li> Register the locator MRIs of the 3 time points together and apply the transformations to to Post MN images. The Post MN images are too narrow to register directly but were taken in the same frame of reference with low resolution locator or scout images. The registration needs to scale based on the change in heart volume. The change in heart volume may be less than the change in total volume of the pigs. </li>
<li> Register The time points by CT and then apply the transformations to the PET. </li>

<li> Copy an ROI across the time points to measure the change in Post MN MRI, Post GD MRI, and PET signal over day 0, 7, 45</li>
</ul>

</div>
</div>

<h3>Progress</h3>
<ul>
<li>Split 3 plane MRI locator images for 3 time-points into separate planes. Only the axial slices are used for image registration</li>
<li>Registered the previous 1 (green) and previous 2 locator images to the current fixed (red) locator image. </li>
<ul>
<li>A rigid 6-degree freedom registration does not handle the growth of the juvenile pig. Current fixed locator in red, previous 1 moving image in green. [[File:MovedLinear1fusion.png]]</li>
<li>A 7-degree freedom scaling registration fits the size of the smaller previous 1 and previous 2 images to the current fixed image. Current fixed locator in red, previous 1 moving image in blue.[[File:MovedScaled1fusion.png]]</li>
<li>The Post MN (manganese) MRI images of the stem cell area are transformed into the frame of reference of the current stem cell area image.(Top left) The Post MN (manganese) image of the stem cells (green) is oriented inside the fixed locator (red). (Top right) Previous 1 Post MN slice transformed (Bottom left) Previous 2 post MN image (Bottom right) Previous 2 post MN image. [[File:StemCellfusions.png]]</li>
<li>Place an ROI around the potential stem cells on the current Post MN image and found intensity 67.64+/-5.932[[File:StemCellROICurrent.png]]</li>
</ul>
</ul>

<h3>Next steps</h3>
<ul>
<li>Transfer the ROI to the images from the previous 1 and previous 2 time points and measure the MN MRI signal</li>
<li>Repeat the measurement from PET-CT images of the same pigs to correlate PET signal to MN MRI signal.</li>
</ul>

2014 Project Week:CardiacStemCellMonitoring

2014-01-09T18:43:38Z

Ktdiedrich: /* Project Description */

==Project Description==
Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
<ul>
<li> The goal of the entire project is to restore cardiac function after a heart attack by injecting cardiac stem cells in the infarcted tissue.</li>
<li> This part of the project seeks to monitor injected stem cells over time. </li>
</ul>
</div>
<div style="width: 54%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
<ul>
<li> Pigs (and soon mice) are given a heart attack by inflating a balloon in an artery</li>
<li> Transgenic stem cells over expressing manganese importer are injected into the infarcted cardiac tissue</li>

<li>Images are taken of the hearts at stem cell engraftment day 0, 7, and 45</li>
<li> The images taken are </li>
<ul>
<li> PET-CT: PET signal is expected to be reduced in the infarcted tissue ROI on day 0 and increase over day 7 and day 45 as stem cells grow.</li>
<li>Post GD: Gadolinium Enhanced MRI signal is expected to be high in the infarcted tissue ROI on day 0 and decrease over day 7 and day 45 as stem cells grow and replace the dead tissue. </li>
<li>Post MN: Manganese is added a contrast agent, the signal is expected to be low in the infarcted tissue ROI on day 0 and increase over day 7 and day 45 as stem cells grow. </li>
</ul>
<li> The pigs are growing over the time points by as much as 30% over day 0 to 45. </li>
<li> Register the locator MRIs of the 3 time points together and apply the transformations to to Post MN images. The Post MN images are too narrow to register directly but were taken in the same frame of reference with low resolution locator or scout images. The registration needs to scale based on the change in heart volume. The change in heart volume may be less than the change in total volume of the pigs. </li>
<li> Register The time points by CT and then apply the transformations to the PET. </li>

<li> Copy an ROI across the time points to measure the change in Post MN MRI, Post GD MRI, and PET signal over day 0, 7, 45</li>
</ul>

</div>
</div>

<h3>Progress</h3>
<ul>
<li>Split 3 plane MRI locator images for 3 time-points into separate planes. Only the axial slices are used for image registration</li>
<li>Registered the previous 1 (green) and previous 2 locator images to the current fixed (red) locator image. </li>
<ul>
<li>A rigid 6-degree freedom registration does not handle the growth of the juvenile pig. Current fixed locator in red, previous 1 moving image in green. [[File:MovedLinear1fusion.png]]</li>
<li>A 7-degree freedom scaling registration fits the size of the smaller previous 1 and previous 2 images to the current fixed image. Current fixed locator in red, previous 1 moving image in blue.[[File:MovedScaled1fusion.png]]</li>
<li>The Post MN (manganese) MRI images of the stem cell area are transformed into the frame of reference of the current stem cell area image.(Top left) The Post MN (manganese) image of the stem cells (green) is oriented inside the fixed locator (red). (Top right) Previous 1 Post MN slice transformed (Bottom left) Previous 2 post MN image (Bottom right) Previous 2 post MN image. [[File:StemCellfusions.png]]</li>
<li>Place an ROI around the potential stem cells on the current Post MN image and found intensity 67.64+/-5.932[[File:StemCellROICurrent.png]]</li>
</ul>
</ul>

<h3>Next steps</h3>
<ul>
<li>Transfer the ROI to the images from the previous 1 and previous 2 time points and measure the MN MRI signal</li>
<li>Repeat the measurement from PET-CT images of the same pigs to correlate PET signal to MN MRI signal.</li>
</ul>

File:StemCellROICurrent.png

2014-01-09T18:35:50Z

Ktdiedrich:

2014 Project Week:CardiacStemCellMonitoring

2014-01-09T00:13:25Z

Ktdiedrich: /* Project Description */

2014 Project Week:CardiacStemCellMonitoring

2014-01-08T23:58:31Z

Ktdiedrich: /* Project Description */

File:StemCellfusions.png

2014-01-08T23:52:46Z

Ktdiedrich:

2014 Project Week:CardiacStemCellMonitoring

2014-01-08T21:41:54Z

Ktdiedrich: /* Project Description */

File:MovedScaled1fusion.png

2014-01-08T21:36:53Z

Ktdiedrich:

File:MovedLinear1fusion.png

2014-01-08T21:36:35Z

Ktdiedrich:

2014 Project Week:CardiacStemCellMonitoring

2014-01-08T16:33:27Z

Ktdiedrich: /* Project Description */

2014 Project Week:CardiacStemCellMonitoring

2014-01-08T16:29:33Z

Ktdiedrich: /* Project Description */

2014 Project Week:CardiacStemCellMonitoring

2014-01-03T21:27:40Z

Ktdiedrich: Created page with '==Project Description== Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI <div style="margin: 20px;"> <div style="width: 27%; float: le…'

2014 Winter Project Week

2014-01-03T20:59:48Z

Ktdiedrich:

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

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

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

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

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

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

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

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

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

=Background and Preparation=

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

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

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

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

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

==Cardiac==
*[[2014_Project_Week:CardiacStemCellMonitoring|Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI]] (Karl Diedrich)

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

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

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

==Stroke==

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

==Brain Segmentation==
*[[2014_Project_Week:MultiAtlas_MultiImage_Segmentation|Multi-Atlas based Multi-Image Segmentation]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

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

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

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

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

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

==Chronic Obstructive Pulmonary Disease ==
* [[2014_Winter_Project_Week:CIP Core|Chest Imaging Platform (CIP) - Core Infrastructure]] (Raul San Jose, Rola Harmouche, Pietro Nardelli, James Ross)
* [[2014_Winter_Project_Week:CIP Infrastructure Testing and SuperBuild|CIP Testing and SuperBuild]] (James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Slicer MRML| Slicer CIP- MRML consolidation]] (Pietro Nardelli, Rola Harmouche, James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Modules| Slicer CIP- Modules]] (Rola Harmouche, Pietro Nardelli, James Ross, Raul San Jose)

==Infrastructure==
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*CLI - Resources? Conditionals? Autonaming? Provenance? CTK unification? (Jim Miller)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonlinearTransforms|Integration nonlinear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Nicole Aucoin, Steve Pieper, Jc, Andras Lasso, Csaba Pinter, ???)
* [[2014_Winter_Project_Week:XNATSlicerLink| 3DSlicer annotations in XNAT]] (Erwin Vast, Nicole Aucoin, Andrey Fedorov)
* [[2014_Winter_Project_Week:ParameterSerialization | JSON Parameter Serialization]] (Matt McCormick, ???)

2012 Summer Project Week

2012-06-22T03:00:43Z

Ktdiedrich: /* Neurosurgery, Brain and Spine, Traumatic Brain Injury */

Back to [[Events]]

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

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

==Agenda==

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

==Projects==

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

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

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

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

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

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

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

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

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

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

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

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

==Background==

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

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

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

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

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

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

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

==Registrants==

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

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

2012 Summer Project Week

2012-06-15T15:13:21Z

Ktdiedrich: /* Neurosurgery, Brain and Spine, Traumatic Brain Injury */

Back to [[Events]]

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

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

==Agenda==

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

==Projects==

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

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

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

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

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

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

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Needle Tip Tracking | Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda)

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

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

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

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

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

==Background==

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

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

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

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

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

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

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

==Registrants==

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

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

2012 Summer Project Week

2012-06-15T15:12:49Z

Ktdiedrich: /* Radiation Therapy */

Back to [[Events]]

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

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

==Agenda==

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

==Projects==

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

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

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

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

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

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

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Needle Tip Tracking | Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda)

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

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

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

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

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

==Background==

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

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

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

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

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

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

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

==Registrants==

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

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

2012 Summer Project Week

2012-06-15T15:12:26Z

Ktdiedrich: /* Neurosurgery, Brain and Spine, Traumatic Brain Injury */

Back to [[Events]]

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

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

==Agenda==

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

==Projects==

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

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

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

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, James Shackleford, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck| Atlas-based segmentation for head and neck]] (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch integration]] (James Shackleford, Greg Sharp)
#[[2012_Summer_Project_Week:TimeSeriesMonitoringIntracranialBones| Monitoring time series images of intracranial bone ]] (Karl Diedrich)

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

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

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Needle Tip Tracking | Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda)

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

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

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

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

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

==Background==

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

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

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

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

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

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

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

==Registrants==

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

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

2012 Summer Project Week:TimeSeriesMonitoringIntracranialBones

2012-06-15T15:10:25Z

Ktdiedrich: Time series monitoring of intracranial bones for watchful waiting of meningioma.

__NOTOC__
<gallery>

</gallery>

==Key Investigators==
* AZE Research and Development, Cambridge, MA: Karl Diedrich

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

<h3>Objective</h3>
* The goal of this project is to increase the performance (sensitivity and specificity) of detection of bone involvement in meningioma. Meningiomas are the most common form of intracranial tumor [1]. Meningiomas are either managed by watchful waiting or treated by resection and optional radiation therapy [2]. Bone involvement signals a more dangerous form of disease with increased death rates and recurrence after treatment warranting more aggressiveness treatment [2], [3]. Bone involvement is detected by radiographic evidence of hyperostosis, bone sclerosis or osteolytic lesions [2]. Watchful waiting involves repeated time series imaging of patients by magnetic resonance imaging (MRI) following initial discovery often by computed tomography (CT).

* Learn to develop Slicer commandline extensions
* Learn to develop Slicer modules

</div>

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

<h3>Approach, Plan</h3>
*Segment the intracranial bones by thresholding the intensity by histogram and keeping the largest connected component
*Rigid register the time series bone tissue. The sparse data from the segmentation will be converted into a filled out distance map for gradient descent optimization using the mutual information cost function for intermodality CT MRI registration.

</div>

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

<h3>Progress</h3>
* Segmented part of intracranial bone by intensity threshold.
* Turned the bone into a distance map and registered bone on the distance map.

</div>
</div>

==Delivery Mechanism==

Distance map module.
* Slicer Module
* Extension -- commandline

==References==
# J. Wiemels, M. Wrensch, and E. B. Claus, “Epidemiology and etiology of meningioma,” J. Neurooncol., vol. 99, no. 3, pp. 307–314, Sep. 2010.
# D. Gabeau-Lacet, M. Aghi, R. A. Betensky, F. G. Barker, J. S. Loeffler, and D. N. Louis, “Bone Involvement Predicts Poor Outcome in Atypical Meningioma,” J Neurosurg, vol. 111, no. 3, pp. 464–471, Sep. 2009.
# R. Graf, M. Plotkin, I. G. Steffen, R. Wurm, P. Wust, W. Brenner, V. Budach, and H. Badakhshi, “Magnetic resonance imaging, computed tomography, and 68Ga-DOTATOC positron emission tomography for imaging skull base meningiomas with infracranial extension treated with stereotactic radiotherapy--a case series,” Head Face Med, vol. 8, p. 1, 2012.

2012 Summer Project Week

2012-06-15T14:53:56Z

Ktdiedrich: /* Time series monitoring of intracranial bones */

Back to [[Events]]

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

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

==Agenda==

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

==Projects==

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

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

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

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, James Shackleford, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck| Atlas-based segmentation for head and neck]] (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch integration]] (James Shackleford, Greg Sharp)
#[[2012_Summer_Project_Week:TimeSeriesMonitoringIntracranialBones| Monitoring time series images of intracranial bone ]] (Karl Diedrich)

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

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

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Needle Tip Tracking | Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda)

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

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

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

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

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

==Background==

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

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

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

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

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

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

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

==Registrants==

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

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

2012 Winter Project Week:CTLiverRegistration

2012-01-21T04:54:24Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire unregistered 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. Look into using vtkITKDistanceTransform for distance map. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional unregistered 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47.
<ul>
<li> Rotationally different data. [[File:LiverFullA_B_unreg.png]]</li>
<li>Different point in respiration to test non-rigid registration. [[File:Stanford2LiverPatient0_0_90saggital.png]]</li>
</ul>
</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Look into using vtkITKDistanceTransform for distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]
[[File:LiverFullTransformedFixed.png]]
[[File:Liver1_2coronal.png]]
</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

File:Liver1 2coronal.png

2012-01-21T04:52:45Z

Ktdiedrich: Liver data set transformed from bone registration.

Liver data set transformed from bone registration.

2012 Winter Project Week:CTLiverRegistration

2012-01-15T15:09:01Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire unregistered 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. Look into using vtkITKDistanceTransform for distance map. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional unregistered 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47.
<ul>
<li> Rotationally different data. [[File:LiverFullA_B_unreg.png]]</li>
<li>Different point in respiration to test non-rigid registration. [[File:Stanford2LiverPatient0_0_90saggital.png]]</li>
</ul>
</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Look into using vtkITKDistanceTransform for distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]
[[File:LiverFullTransformedFixed.png]]
</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

File:Stanford2LiverPatient0 0 90saggital.png

2012-01-15T15:04:54Z

Ktdiedrich: Time series at different points in respiration for optimizing and testing non-rigid registration algorithms and parameters.

Time series at different points in respiration for optimizing and testing non-rigid registration algorithms and parameters.

2012 Winter Project Week:CTLiverRegistration

2012-01-13T17:04:51Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire unregistered 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. Look into using vtkITKDistanceTransform for distance map. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional unregistered 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. [[File:LiverFullA_B_unreg.png]]</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Look into using vtkITKDistanceTransform for distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]
[[File:LiverFullTransformedFixed.png]]
</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-13T16:57:29Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire unregistered 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. Look into using vtkITKDistanceTransform for distance map. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional unregistered 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. [[File:LiverFullA_B_unreg.png]]</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]
[[File:LiverFullTransformedFixed.png]]
</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T16:13:54Z

Ktdiedrich:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is to design a cost function that could effectively work on real data including left atrium and its surrounding wall.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
* A model using image profile has been designed and cost functions based on that have been induced to optimally segment the left atrium and its surrounding wall.
<ul>
<li>[[File:multilineblurnoise_scimg.png]]</li>
<li>[[File:multilineblur_scimgop.png]]</li>
<li>[[File:Slice20_seg.png]]</li>
<li>[[File:Slice20_segzoom.png]]</li>
</ul>

</div>
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T16:09:47Z

Ktdiedrich: /* Key Partners */

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[MLBN_S|Computer generated image]]
Image:multilineblur_scimgop.png|[[MLBN_S|Output]]
Image:Slice20_seg.png|[[left_atrium_slice| segmentation of a Left atrium slice]]
Image:Slice20_segzoom.png|[[left_atrium_slice_zoom| zoomed version]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is to design a cost function that could effectively work on real data including left atrium and its surrounding wall.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
* A model using image profile has been designed and cost functions based on that have been induced to optimally segment the left atrium and its surrounding wall.
<ul>
<li>[[File:]]</li>
<li>[[File:]]</li>
<li>[[File:]]</li>
<li>[[File:]]</li>
</ul>

</div>
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-13T00:22:44Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire unregistered 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional unregistered 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. [[File:LiverFullA_B_unreg.png]]</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]
[[File:LiverFullTransformedFixed.png]]
</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-13T00:21:42Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire unregistered 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional unregistered 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. [[File:LiverFullA_B_unreg.png|200px|left|Full liver data sets with transformed moving time point image on the fixed time point image. ]]</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]
[[File:LiverFullTransformedFixed.png]]
</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-13T00:18:25Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire unregistered 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional unregistered 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. [[File:LiverFullA_B_unreg.png]]</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]
[[File:LiverFullTransformedFixed.png]]
</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-13T00:17:43Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. [[File:LiverFullA_B_unreg.png]]</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]
[[File:LiverFullTransformedFixed.png]]
</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

File:LiverFullTransformedFixed.png

2012-01-13T00:12:22Z

Ktdiedrich: Full liver data sets with transformed moving time point image on the fixed time point image.

Full liver data sets with transformed moving time point image on the fixed time point image.

2012 Winter Project Week:CTLiverRegistration

2012-01-13T00:03:17Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. [[File:LiverFullA_B_unreg.png]]</li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. See upper left images below.</li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). See lower left images below.</li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. See lower right images below.</li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]

</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

File:LiverFullA B unreg.png

2012-01-13T00:00:44Z

Ktdiedrich: Unregistered 4D liver CT data taken at two time points.

Unregistered 4D liver CT data taken at two time points.

2012 Winter Project Week:CTLiverRegistration

2012-01-12T23:58:48Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. </li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. </li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). </li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. </li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]

</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
Develop a Slicer CLI module using the ITK distance map itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html. Then chain the steps together in Python.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-12T23:56:11Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. </li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. </li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). </li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. </li>
</ol>

[[File:LiverSceneViewAxial.png]]
[[File:LiverSceneViewSaggital.png]]

</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
This work will be delivered to the NA-MIC Kit as a Slicer extension.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

File:LiverSceneViewAxial.png

2012-01-12T23:54:58Z

Ktdiedrich: Liver registration steps.

Liver registration steps.

2012 Winter Project Week:CTLiverRegistration

2012-01-12T23:52:56Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. </li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. </li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). </li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. </li>
</ol>

[[File:LiverSceneViewSaggital.png]]

</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
This work will be delivered to the NA-MIC Kit as a Slicer extension.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

File:LiverSceneViewSaggital.png

2012-01-12T23:50:27Z

Ktdiedrich: Bones near liver are segmented for two time point images of a liver. Time point A is red and B is green. The moving green image is registered on the red fixed image. The green image is transformed to the cyan image. The same transformation matrix on the c

Bones near liver are segmented for two time point images of a liver. Time point A is red and B is green. The moving green image is registered on the red fixed image. The green image is transformed to the cyan image. The same transformation matrix on the cyan bone image is used to transformed the moving liver data set B.

2012 Winter Project Week:CTLiverRegistration

2012-01-12T23:38:48Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>Acquire 4D liver data sets. </li>
<li>Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>Acquired additional 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. </li>
<li>Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. </li>
<li>ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). </li>
<li>Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. </li>
</ol>

</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
This work will be delivered to the NA-MIC Kit as a Slicer extension.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-12T23:37:47Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of detecting changes in liver tumors.
</div>

<div style="width: 97%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
<ol>
<li>1. Acquire 4D liver data sets. </li>
<li>2. Segment bone using upper and lower Hounsfield unit threshold. </li>
<li>3. Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects. </li>
<li>4. Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer. </li>
<li>5. Apply the resulting transform to the full moving liver data set. </li>
</ol>
</div>

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

<h3>Progress</h3>
<ol>
<li>1. Acquired additional 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47. </li>
<li>2. Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring. </li>
<li>3. ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images. </li>
<li>4. Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF). </li>
<li>5. Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name. </li>
</ol>

</div>

<div style="width: 97%; float: left;">
<h3>Delivery mechanism</h3>
This work will be delivered to the NA-MIC Kit as a Slicer extension.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-12T23:32:34Z

Ktdiedrich: /* Key Investigators */

==Key Investigators==
* AZE Research and Development, Karl Diedrich
* Brigham and Women's Hospital, Nobuhiko Hata
* Brigham and Women's Hospital, Atsushi Yamada

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

<h3>Objective</h3>
Register CT images of livers taken at different time points for the purpose of
detecting changes in liver tumors.

</div>

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

<h3>Approach, Plan</h3>
1. Acquire 4D liver data sets.
2. Segment bone using upper and lower Hounsfield unit threshold.
3. Create a distance map from the threshold segmented bones. The bones are very sparse making poor registration subjects.
4. Conduct a fixed registration of the fixed and moving bones near the liver using BRAINSfit in slicer.
5. Apply the resulting transform to the full moving liver data set.

</div>

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

<h3>Progress</h3>
1. Acquired additional 4D liver time series data sets for development and testing from http://midas.kitware.com/community/view/47.
2. Used Slicer to segment the bones using a lower threshold of 252. Segmented the bones with a label of 255 to allow blurring.
3. ITK contains a filter class, itkSignedDanielssonDistanceMapImageFilter, http://www.itk.org/Doxygen/html/classitk_1_1SignedDanielssonDistanceMapImageFilter.html for creating a distance map. Need to develop a Slicer CLI module for generating distance maps of the fixed and moving bone images.
4. Registered two time points of the same patient as fixed and moving images in BRAINSfit using Initialize Transform Mode: useGeometryAlign Registration Phase: Rigid (6 DOF) AND Rigid+Scale (7DOF) AND Rigid+Scale+Skew (10 DOF).
5. Applied the resulting transform to the full moving liver data set in the Slicer Data module Nodes panel by dragging the moving liver data set onto the output transform name.

</div>

<div style="width: 40%; float: left;">
<h3>Delivery mechanism</h3>
This work will be delivered to the NA-MIC Kit as a Slicer extension.
</div>

<div style="width: 97%; float: left;">
<h3>References</h3>
Hans Johnson, Greg Harris, Kent Williams. BRAINSFit: Mutual Information Rigid Registrations of Whole-Brain 3D Images, Using the Insight Toolkit. The Insight Journal. 2009.
</div>

2012 Winter Project Week:CTLiverRegistration

2012-01-08T14:05:24Z

Ktdiedrich: /* Key Investigators */

2012 Winter Project Week

2012-01-08T14:04:36Z

Ktdiedrich: /* Registration */

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

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

== Dates.Venue.Registration ==

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

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

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

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

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

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

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

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
*[[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]
* [[2012_Winter_Project_Week:CTLiverRegistration|Register liver CT images for tumor progress monitoring]] (Karl Diedrich, Nobuhiko Hata, Atsushi Yamada)

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

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