NAMIC Wiki - User contributions [en]

2013 Winter Project Week

2012-12-06T20:28:37Z

Caok: /* NA-MIC Kit Internals */

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

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

= Dates.Venue.Registration =

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

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

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

=Background and Preparation=

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

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

=Projects=

==TBI==

==Atrial Fibrillation==
* Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)

==Huntington's Disease==
* [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson)
* [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch)
* [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch)

==Head and Neck Cancer==

==Prostate Interventions==
* BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)
* PkModeling for prostate DCE MRI (Jim, Andrey)

==Neurosurgery==

==General Image Guided Therapy==

==General Image Segmentation==

==General Image Registration==

==NA-MIC Kit Internals==
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and [http://slicer-devel.65872.n3.nabble.com/ANN-Oldies-But-Goodies-Volume-Data-tt4026821.html Sample Data Refactor]]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Nicole Aucoin?, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Jim Miller, Steve Pieper, Kunlin Cao)

Engineering:TCON 2012

2012-12-06T20:07:33Z

Caok: /* 2012-12-06 */

Back to [[TCON:Main|TCON:Main]], [[Events]]

__TOC__

==2012-12-06==
Attendees: Jim, Steve, Ron, Tina, Sunil Kumar (WashU), Dave, Kunlin

Agenda:
*review project week projects: http://wiki.na-mic.org/Wiki/index.php/2013_Winter_Project_Week

==2012-11-27==
Attendees: Steve, Jim, Tina, JC, Isaiah

Agenda:
*Are there any Slicer lung tumor segmentation (from CT) automated algorithms? suggested workflows? (Hugo Aerts, BWH Radiation Oncology)
**Talk to Raul San Jose and James Ross at 1249 Boylston
**Is there a lung lesion size tool at Kitware that will be incoporrated into Slicer (contact Rick Avila)?
**ePad tool may be applicable? (http://epad.stanford.edu/)
*MRML code refactoring needed to improve response time (view this: https://www.youtube.com/watch?v=pf5cssbVALg where on the right is slicer with pnl/spl brain atlas loaded, and left is xtk with the same) (Tina Kapur, Isaiah Norton)

==2012-11-15==

Attendees: Steve, Tina, Sonia, Nicole, JC, Sunil, Kunlin

Agenda: Project Week Kick off call

*NCBC Meeting Update
*AHM+Project Week: http://wiki.na-mic.org/Wiki/index.php/AHM_2013
**review/edit agenda esp. breakouts and extensions presentations
**add engr projects
*RSNA prep

==2012-11-07==

No call. NCBC Showcase at NIH.

==2012-11-01==

Attendees: Jim, Ron, Nicole, Steve, Tina, Jc, ...

Agenda:
*NCBC Showcase mtg
* 4.2.1 development
** crashes
** MRB files + restoring scene views
** annotations in lightboxes

==2012-10-18==

Attendees: Jim, Steve, Tina, Nicole, JC, Kunlin

Agenda:
* Discussion of [http://www.youtube.com/watch?v=YwApMSbNJoo&feature=plcp SlicerHands experiments (movie)] using the Microsoft Kinect and http://www.threegear.com threegear software. Sample slicer code is in [https://github.com/pieper/SlicerHands the SlicerHands github repository].
* Discussion of recent changes to annotations and crosshairs ([http://na-mic.org/Bug/view.php?id=2663 #2663] and [http://na-mic.org/Bug/view.php?id=2664 #2664])
* RSNA Planning http://www.na-mic.org/Wiki/index.php/RSNA2012_Planning

==2012-10-11==

Attendees:

Agenda:
* RSNA Planning http://www.na-mic.org/Wiki/index.php/RSNA2012_Planning

==2012-10-04==

Attendees: Nicole, jc, guillaume, tina, dave, xiaojun

Agenda:
* RSNA Planning http://www.na-mic.org/Wiki/index.php/RSNA2012_Planning
* https://plus.google.com/hangouts/_/d1f84c048ebf04a7940139e16041015b45826b09?authuser=0&hl=en -- iGyne in Slicer 4

==2012-09-27==

Attendees: Jim, Steve, Nicole, JC, Tina, Kunlin, Dave

Agenda:

* Factory machine discussion
* RSNA Planning http://www.na-mic.org/Wiki/index.php/RSNA2012_Planning
* Bremen trip update

==2012-09-20==

Attendees:

Agenda:
* RSNA Planning http://www.na-mic.org/Wiki/index.php/RSNA2012_Planning

==2012-09-13==

Attendees: Steve, Ron, Tina, Stephen, Jim, Nicole, Kunlin, Jc

Agenda:
* Factory machine
* Annotations
* Extensions
* RSNA Planning http://www.na-mic.org/Wiki/index.php/RSNA2012_Planning

==2012-09-06==

Attendees: Steve, Sunil, Kunlin, Tina, Dave, Jim

Agenda:
* Discussion of XNAT module for slicer4 (Sunil)
** General status and goals
** [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/009792.html Discussion of need for storage node for data transfer.]
** [http://xnatslicer.wikispaces.com/home Project wiki.]
** [https://bitbucket.org/skumar_wustl/xnatslicerbeta Code repository (svn).]

==2012-08-30==

Attendees: Jim, Steve, Nicole, J2, Ron

* Discussion of models hierarchy behavior

==2012-08-23==

Attendees: Tina, Jim, Steve, Rui, Andriy. nicole, dave, hans

* ITKv4 project discussion
** Agreed to Start Slicer43 Project as a staging point while 4.2 is frozen

==2012-08-16==

Attendees: Tina, Andrey, Demian, Steve, Nicole, Sunil, Dave, Hans, Chen, Ron, Jim

*Including Pyxnat in Slicer build (Sunil Kumar from WUSTL will be calling in)
* Andrey would like to ask Jim if we can finalize linking modifier for slice / composite slice nodes https://github.com/fedorov/Slicer/tree/1772-linking-modifier

Discussion:
* http://na-mic.org/Bug/view.php?id=2352
* Other python requested:
** pg8000 (pure python postgres interface) (can be done with pip) http://html.pg8000.googlecode.com/hg/index.html

PyXNAT users potential
* Hans, Jayashree, Murat, Andrey, Isaiah
NiPype
* Hans, Demian

==2012-08-09==

Attendees: Steve, Tina, Nicole

* Discussion of NAMIC impact

==2012-08-02==

Attendees:Steve, Nicole, Jim, Ron

* Jim and Steve talk about CTK & DICOM
** clean build should fix it
* Nicole and Jim talk about PARSE_ARGS
** Jim will take a look at emailed command line
* Ron and Nicole talk about model hierarchies
** feature request to have a template hierarchy to fill in when running model maker (and more)

==2012-07-26==

Attendees:Steve, Nicole, Tina

* Reminder: Please put the NA-MIC logo on MICCAI slides and posters
* Image Guided Therapy Workshop in Boston, Sept 21: http://www.ncigt.org/pages/IGT_Workshop_2012

==2012-07-19==
Attendees: Jim, Dave, Nicole, Hans

Agenda:
* Please put the NA-MIC logo on MICCAI slides and posters
* Feature request to have mutually exclusive "sets" of parameters (radio button control that would enable/disable complete blocks of parameters)

==2012-07-12==
Attendees: Jim, Dave, Nicole

Agenda:
* Strategies for Qt widget development (CTK, Slicer, Python)
* CTK Hackfest

==2012-07-05==
Attendees: Jim, Steve, Dave, Nicole, JC, Julien

Agenda:
* volume loading
** discussing refactor of AddArchetypeVolume
** best way to read vector volumes?
** Gordon wants us on the newest version of ITK first to update the NRRD readers
** Julien wants to support mapping one extension to different types of extensions

==2012-06-14==
Attendees: Tina, Pete Anderson, Nicole Aucoin, Simrin, Guillaume, JC, Tyler, Nabgha, Yan, Steve Pieper, Jim

Agenda:
* Project Week last minute planning

==2012-06-07==
Attendees: Tina, Jim, Dave, Pete, Tomas, Andrash, Simrin, Samira, Saman, Nicole, Hans, Steven, Rui, Ron

Agenda:
* NIH Progress report comments
** DBP comments and follow-up revisions
* Project week
** Registration (currently ~50)
*** Hotel costs have been prohibitive this year
*** Suggestion - new location for Summer Project Week, earlier time of the year?
*** Airport hub
*** TODO: Discuss during Project Week
** [http://www.cars-int.org/ CARS] & Project Week
*** Avoiding conflict may not be advantageous
*** TODO: Discuss during Project Week
** AMIGO session: Saturday
** Discussion of projects

==2012-05-31==
Attendees: Jim, Steve, Sonja, Nicole, Tamas, Hans, Anthony, Jerome, Peter, Tina, Rui, Tobias, Dave, Ron

Agenda:
* Project Week discussion http://wiki.na-mic.org/Wiki/index.php/2012_Summer_Project_Week
** IGT Day
*** Tracker breakout session for Thursday?
*** Ultrasound moved to Thursday
** Tutorial contest submissions
** Discussion of projects

==2012-05-24==

Attendees: Jim, Steve, Emma, Peter Anderson, Markus, Rui, Adita, Tamas, Francios, Simrin, Peitro, Stephen

Agenda:

*Project Week Agenda review http://wiki.na-mic.org/Wiki/index.php/2012_Summer_Project_Week
**put topics for different slicer talks and breakouts: Developer (extensions, editor extensions) Ultrasound, ITKv4, SimpleITK...
**review list of registered attendees

==2012-05-17==

Attendees: Jim, Tina, Emma, Nicole, Simrin, Rui, Dave, Tamas, Pete Anderson,

Highlights:
*review project week projects and add/edit

==2012-05-10==
Attendees: Marcel, Steve, Tina, Nicole, Jim, Jack van Horn, Andriy I, JC, Emma, Rui, Yi, Simrin (queens), Guillaume, Stephen, Allen, Danny, Greg (CARMA, Utah), Dave

Highlights
*TBI DBP
**Intro from Jack Van Horn
**Update from Marcel - work has focused on morphological analysis. Code in matlab right now.
**visit from Guido to UCLA in two weeks
**Stephen updated on publications - geometric metamorphosis
*Afib DBP
**Intro from Allen
**two slicer extensions will get integrated into nightly build this week - 1) inhomogeneity correction 2) auto scar segmentation

==2012-05-03==

Attendees: Steve, Tina, Jim, Dan Marcus, Sunil, Nicole, Xiaojun, J2, Emma

Agenda:
*Project Week Planning [[2012_Summer_Project_Week#Projects]]
**Slicer RT Projects
**

==2012-04-26==

Attendees: Steve, Jim, Nicole, Emma, Dave

Agenda:
*Project Week Kickoff w/ discussion of engineering core lead projects: http://wiki.na-mic.org/Wiki/index.php/2012_Summer_Project_Week#Projects
http://boggs.bwh.harvard.edu:8070/remote.html

==2012-04-19==

Attendees: Steve, Tina, Jan, Nicole, Dave, Hans, Rui, Ron

Agenda:

*Better Integration of ITK4.0/SimpleITK with Slicer

==2012-04-12==

Attendees: Steve, Jim, Tina, Jan, Guillame, Harini, Dave, Hans, Nicole, Greg, Stephen, J2, Andriy

Agenda:
* Discuss 3D Slicer version 4.1 release
** Developer documentation: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/HowTo (to update this documentation: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1)
** Announcement page: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Announcements
** Where shall announcement email be sent:
*** slicer-devel, slicer-user, namic-all, nitrc, ncigt, namic-projectweek... (who else?)
*what is a good way to share iGyne code
** For example, https://github.com/pieper/iGyne
*Project Week Kick off TCON on Thursday, April 26, 3pm ET

==2012-04-05==

Attendees: Jim, Steve, Ron, Jc, J2, Emma, Dave, Mike

Agenda:
*Extensions (see the Extensions/Template directory for the best examples to start from)
*Web Services api for stats

==2012-03-29==

Attendees: Jim, Steve, Tina, Nicole

Agenda:
*You will hear soon from Ann Adams about the progress report (due at NIH at the end of May)

==2012-03-22==

Attendees: Jim, Steve, Tina, JC

Agenda:
*DICOM transfer in AMIGO works with Slicer 4
*General discussion of python, extensions, memory handling...

==2012-03-15==

Attendees: Jim, Steve, Tina, Emma, Jan, Dave, Nicole

Agenda:
*Iowa workshop (Dave)
*Feedback from Using Slicer 4 in AMIGO (Tina, Jan, Xiaojun)
* [http://www.na-mic.org/Wiki/index.php/Slicer-4.1#Features_and_Responsibilities Slicer 4.1 release]

==2012-03-08==

Attendees: Steve, Jim, Tina, Dave, Nicole, Emma, J2

Agenda:
* [[User:Millerjv/ProvenanceWorkflow | Provenance]]
*Progress Report

==2012-03-01==

Attendees: Nicole, Steve, Jim, Dave, Tina, Emma

Agenda:
*Snow day!
*Initial planning for Chennai Slicer workshop. Deadline for funding application is in June. Interested presenters to contact Steve.
*Slicer Webinar update: 100 attendees (capacity reached for line)! Video is here: http://player.vimeo.com/video/37671358. Full recording including questions/answers coming soon.

==2012-02-23==

Attendees: Tina, Stephen, Nicole, Steve, Emma, Dave

Agenda:
* [http://www.na-mic.org/Wiki/index.php/Slicer-4.1#Features_and_Responsibilities Slicer 4.1 release]

==2012-02-16==

Attendees: Jim, Nicole, Dave, Ron, Emma, Rui, Julien, and more

Agenda:
* [http://www.na-mic.org/Wiki/index.php/Slicer-4.1#Features_and_Responsibilities Slicer 4.1 release]

==2012-02-09==

Attendees: Steve, Hans, Tina, Nicole, Dave (Iowa), Greg, J2, Emma

Agenda:
*Iowa Diffusion workshop

==2012-02-02==

Attendees: jim, steve, nicole, tina, j2, dave (the new Mark)

Agenda:

* Finalize the project pages so Tina can submit to NIH.
* Chart futures, Object::disconnect on exit() issues
* DICOM, DWI. Steve is creating DICOM plugin. Plugins will read volumes, RT, Structured Reports, Slicer Data Bundles, DCE, Transforms.

==2012-01-26==

Attendees: Jim, Steve, Nicole, Mark, Dave, Tina

Agenda:
* Visual Studio 2010 numpy issue
* Qt + Python question

==2012-01-19==

Attendees: Jim, Steve, Nicole, Tina, Emma,

Agenda:
* Project Week review
* Discussion of web view and chart view

==2012-01-12==

All Hands Meeting in Progress in Salt Lake City. No call today.

==2012-01-05==

Attendees: Jim, Steve, Nicole, Mark, Mehdi, Julien, Tina

Agenda:
* Project week preparation: [[2012_Winter_Project_Week#Projects | Project List]]
* Python demo: http://vimeo.com/33236047

2012 Summer Project Week:SteeredRegistration

2012-06-22T14:26:03Z

Caok:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
*Technical University of Munich: Guillaume Pernelle
* BWH: Guillaume Pernelle, Jan Egger, Tina Kapur
* Isomics: Steve Pieper
* GRC: Kunlin Cao, Jim Miller

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide user an interface to interact with the registration program during the matching progress, in case the result from automatic registration is not satisfactory.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow user to pause the progress if the intermediate results are visually unsatisfactory. User inputs such as translation and rotation by dragging the mouse will be fed into the registration, and be used to correct the current transformation. Registration will continue to run starting from the corrected transform.

</div>

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

<h3>Progress</h3>
At the end of this week, we have a better understanding of the problems we are facing. We accomplished to have the first step of the steered registration which is the translation (illustrated above: "Interaction: Translate").

</div>
</div>

==Delivery Mechanism==

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

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

==References==

File:Translate-after.png

2012-06-22T14:23:27Z

Caok:

File:Translate-before.png

2012-06-22T14:23:10Z

Caok:

2012 Summer Project Week Breakout Session: Ultrasound: Denoising

2012-06-21T16:57:29Z

Caok:

===Module Name===
US Speckle Parameter Estimate

{|
|[[Image:USSpeckleParameterEstimate-input1.png|thumb|280px|Input Image-Case1]]
|[[Image:USSpeckleParameterEstimate-output1.png|thumb|280px|Output Parameter Estimate Image-Case1]]
|[[Image:USSpeckleParameterEstimate-input2.png|thumb|280px|Input Image-Case2]]
|[[Image:USSpeckleParameterEstimate-output2.png|thumb|280px|Output Parameter Estimate Image-Case2]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering.Denoising

===Authors, Collaborators & Contact===
* Author: Kunlin Cao and Kedar Patwardhan (GE Research)
* Contact: cao@ge.com

===Module Description===
The USSpeckleParameterEstimate filter performs an information-theoretic based probabilistic modeling of speckles in Ultrasound images. Intensities of speckles in Ultrasound images are modeled using Rayleigh distribution or normalized Fisher-Tippett distribution.

Speckles are formed from coherent accumulation of random scattering in a cell of ultrasound beam. The pixel intensity of the speckle in the inphase/quadrature image follows a zero-mean Gaussian distribution. Then envelope detection of the inphase/quadrature image is performed to produce a real image/magnitude image, whose intensity corresponds to a Rayleigh distribution. Due to the large dynamic range of the magnitude image, log-compress is usually performed to produce an image suitable for display. A pixel’s intensity in the resulting image follows the normalized Fisher-Tippett distribution. The maximum likelihood estimate (MLE) of the distribution parameters in a neighborhood are calculated to describe the image information and with less speckle effects.

A complete description of the algorithm may be found in:

G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is used to reduce speckles in an ultrasound image. Usually the normalized Fisher-Tippett distribtuion is used to model the statistical parameter.

* A command line example of running this module is

USSpeckleParameterEstimate
--neighborhood 1,1,1
inputUltrasoundImage.nhdr outputSmoothedImage.nhdr

The screenshots on the top illustrate how to use the filter and the expected results in two cases. The inputs are ultrasound images, and outputs are MLE estimate of normalized Fisher-Tippett distribution parameters (smoothed image).

===Quick Tour of Features and Use===
* '''Input/output panel:'''
[[Image:USSpeckleParameterEstimate-IO.png|thumb|right|280px|Input/Output panels]]
User selects an ultrasound image as input upon which the estimate filter will apply. User creates an output image to store the result. Upon completion, the output image will be displayed in the viewing panel.

* '''Parameters panel:'''
[[Image:USSpeckleParameterEstimate-parameters.png|thumb|right|280px|Input/Output panels]]
User specifies the neighborhood radius in three dimensions (comma separated without spaces).
User chooses the distribution type for modeling (Rayleigh or Fisher-Tippett).

* '''Viewing panel:'''
[[Image:USSpeckleParameterEstimate-display.png|thumb|right|280px|Input/Output panels]]
Upon completion, the estimate filter result is displayed in the viewing panel.

== Development ==

===Dependencies===

None other than the core Slicer3 modules for image IO and display.

===Known bugs===

===Usability issues===

===References===
* G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.
* Z. Wang, G. Slabaugh, G. Unal, and T. Fang. Information-Theoretic Feature Detection and Its Application to Registration of Ultrasound Images. International Journal of Intelligent Control and Systems, 13(2):136–145, 2008.

2012 Summer Project Week Breakout Session: Ultrasound: Denoising

2012-06-20T19:07:49Z

Caok:

===Module Name===
US Speckle Parameter Estimate

{|
|[[Image:USSpeckleParameterEstimate-input1.png|thumb|280px|Input Image-Case1]]
|[[Image:USSpeckleParameterEstimate-output1.png|thumb|280px|Output Parameter Estimate Image-Case1]]
|[[Image:USSpeckleParameterEstimate-input2.png|thumb|280px|Input Image-Case2]]
|[[Image:USSpeckleParameterEstimate-output2.png|thumb|280px|Output Parameter Estimate Image-Case2]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering.Denoising

===Authors, Collaborators & Contact===
* Author: Kunlin Cao and Kedar Patwardhan (GE Research)
* Contact: cao@ge.com

===Module Description===
The USSpeckleParameterEstimate filter performs an information-theoretic based probabilistic modeling of speckles in Ultrasound images. Intensities of speckles in Ultrasound images are modeled using Rayleigh distribution or normalized Fisher-Tippett distribution.

Speckles are formed from coherent accumulation of random scattering in a cell of ultrasound beam. The pixel intensity of the speckle in the inphase/quadrature image follows a zero-mean Gaussian distribution. Then envelope detection of the inphase/quadrature image is performed to produce a real image/magnitude image, whose intensity corresponds to a Rayleigh distribution. Due to the large dynamic range of the magnitude image, log-compress is usually performed to produce an image suitable for display. A pixel’s intensity in the resulting image follows the normalized Fisher-Tippett distribution. The maximum likelihood estimate (MLE) of the distribution parameters in a neighborhood are calculated to describe the image information and with less speckle effects.

A complete description of the algorithm may be found in:

G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is used to reduce speckles in an ultrasound image. Usually the normalized Fisher-Tippett distribtuion is used to model the statistical parameter.

* A command line example of running this module is

USSpeckleParameterEstimate
--neighborhood 1,1,1
inputUltrasoundImage.nhdr outputSmoothedImage.nhdr

The screenshots on the top illustrate how to use the filter and the expected results in two cases. The inputs are ultrasound images, and outputs are MLE estimate of normalized Fisher-Tippett distribution parameters (smoothed image).

===Quick Tour of Features and Use===
* '''Input/output panel:'''
[[Image:USSpeckleParameterEstimate-IO.png|thumb|right|280px|Input/Output panels]]
User selects an ultrasound image as input upon which the estimate filter will apply. User creates an output image to store the result. Upon completion, the output image will be displayed in the viewing panel.

* '''Parameters panel:'''
[[Image:USSpeckleParameterEstimate-parameters.png|thumb|right|280px|Input/Output panels]]
User specifies the neighborhood radius in three dimensions (comma separated without spaces).

* '''Viewing panel:'''
[[Image:USSpeckleParameterEstimate-display.png|thumb|right|280px|Input/Output panels]]
Upon completion, the estimate filter result is displayed in the viewing panel.

== Development ==

===Dependencies===

None other than the core Slicer3 modules for image IO and display.

===Known bugs===

===Usability issues===

===References===
* G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.
* Z. Wang, G. Slabaugh, G. Unal, and T. Fang. Information-Theoretic Feature Detection and Its Application to Registration of Ultrasound Images. International Journal of Intelligent Control and Systems, 13(2):136–145, 2008.

2012 Summer Project Week Breakout Session: Ultrasound: Denoising

2012-06-20T18:45:51Z

Caok:

===Module Name===
US Speckle Parameter Estimate

{|
|[[Image:USSpeckleParameterEstimate-input1.png|thumb|280px|Input Image-Case1]]
|[[Image:USSpeckleParameterEstimate-output1.png|thumb|280px|Output Parameter Estimate Image-Case1]]
|[[Image:USSpeckleParameterEstimate-input2.png|thumb|280px|Input Image-Case2]]
|[[Image:USSpeckleParameterEstimate-output2.png|thumb|280px|Output Parameter Estimate Image-Case2]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering.Denoising

===Authors, Collaborators & Contact===
* Author: Kunlin Cao (GE Research)
* Contact: cao@ge.com

===Module Description===
The USSpeckleParameterEstimate filter performs an information-theoretic based probabilistic modeling of speckles in Ultrasound images. Intensities of speckles in Ultrasound images are modeled using Rayleigh distribution or normalized Fisher-Tippett distribution.

Speckles are formed from coherent accumulation of random scattering in a cell of ultrasound beam. The pixel intensity of the speckle in the inphase/quadrature image follows a zero-mean Gaussian distribution. Then envelope detection of the inphase/quadrature image is performed to produce a real image/magnitude image, whose intensity corresponds to a Rayleigh distribution. Due to the large dynamic range of the magnitude image, log-compress is usually performed to produce an image suitable for display. A pixel’s intensity in the resulting image follows the normalized Fisher-Tippett distribution. The maximum likelihood estimate (MLE) of the distribution parameters in a neighborhood are calculated to describe the image information and with less speckle effects.

A complete description of the algorithm may be found in:

G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is used to reduce speckles in an ultrasound image. Usually the normalized Fisher-Tippett distribtuion is used to model the statistical parameter.

* A command line example of running this module is

USSpeckleParameterEstimate
--neighborhood 1,1,1
inputUltrasoundImage.nhdr outputSmoothedImage.nhdr

The screenshots on the top illustrate how to use the filter and the expected results in two cases. The inputs are ultrasound images, and outputs are MLE estimate of normalized Fisher-Tippett distribution parameters (smoothed image).

===Quick Tour of Features and Use===
* '''Input/output panel:'''
[[Image:USSpeckleParameterEstimate-IO.png|thumb|right|280px|Input/Output panels]]
User selects an ultrasound image as input upon which the estimate filter will apply. User creates an output image to store the result. Upon completion, the output image will be displayed in the viewing panel.

* '''Parameters panel:'''
[[Image:USSpeckleParameterEstimate-parameters.png|thumb|right|280px|Input/Output panels]]
User specifies the neighborhood radius in three dimensions (comma separated without spaces).

* '''Viewing panel:'''
[[Image:USSpeckleParameterEstimate-display.png|thumb|right|280px|Input/Output panels]]
Upon completion, the estimate filter result is displayed in the viewing panel.

== Development ==

===Dependencies===

None other than the core Slicer3 modules for image IO and display.

===Known bugs===

===Usability issues===

===References===
* G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.
* Z. Wang, G. Slabaugh, G. Unal, and T. Fang. Information-Theoretic Feature Detection and Its Application to Registration of Ultrasound Images. International Journal of Intelligent Control and Systems, 13(2):136–145, 2008.

2012 Summer Project Week Breakout Session: Ultrasound: Denoising

2012-06-20T18:40:24Z

Caok:

===Module Name===
US Speckle Parameter Estimate

{|
|[[Image:USSpeckleParameterEstimate-input1.png|thumb|280px|Input Image-1]]
|[[Image:USSpeckleParameterEstimate-output1.png|thumb|280px|Output Parameter Estimate Image-1]]
|[[Image:USSpeckleParameterEstimate-input2.png|thumb|280px|Input Image-2]]
|[[Image:USSpeckleParameterEstimate-output2.png|thumb|280px|Output Parameter Estimate Image-2]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering.Denoising

===Authors, Collaborators & Contact===
* Author: Kunlin Cao (GE Research)
* Contact: cao@ge.com

===Module Description===
The USSpeckleParameterEstimate filter performs an information-theoretic based probabilistic modeling of speckles in Ultrasound images. Intensities of speckles in Ultrasound images are modeled using Rayleigh distribution or normalized Fisher-Tippett distribution.

Speckles are formed from coherent accumulation of random scattering in a cell of ultrasound beam. The pixel intensity of the speckle in the inphase/quadrature image follows a zero-mean Gaussian distribution. Then envelope detection of the inphase/quadrature image is performed to produce a real image/magnitude image, whose intensity corresponds to a Rayleigh distribution. Due to the large dynamic range of the magnitude image, log-compress is usually performed to produce an image suitable for display. A pixel’s intensity in the resulting image follows the normalized Fisher-Tippett distribution. The maximum likelihood estimate (MLE) of the distribution parameters in a neighborhood are calculated to describe the ultrasound image information.

A complete description of the algorithm may be found in:

G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is used to reduce speckles in an ultrasound image. Usually the normalized Fisher-Tippett distribtuion is used to model the statistical parameter.

* A command line example of running this module is

USSpeckleParameterEstimate
--neighborhood 1,1,1
inputUltrasoundImage.nhdr outputSmoothedImage.nhdr

The screenshots on the top illustrate how to use the filter and the expected results in two cases. The inputs are ultrasound images, and outputs are MLE estimate of normalized Fisher-Tippett distribution parameters (smoothed image).

===Quick Tour of Features and Use===
* '''Input/output panel:'''
[[Image:USSpeckleParameterEstimate-IO.png|thumb|right|280px|Input/Output panels]]
User selects an ultrasound image as input upon which the estimate filter will apply. User creates an output image to store the result. Upon completion, the output image will be displayed in the viewing panel.

* '''Parameters panel:'''
[[Image:USSpeckleParameterEstimate-parameters.png|thumb|right|280px|Input/Output panels]]
User specifies the neighborhood radius in three dimensions (comma separated without spaces).

* '''Viewing panel:'''
[[Image:USSpeckleParameterEstimate-display.png|thumb|right|280px|Input/Output panels]]
Upon completion, the estimate filter result is displayed in the viewing panel.

== Development ==

===Dependencies===

None other than the core Slicer3 modules for image IO and display.

===Known bugs===

===Usability issues===

===References===
* G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.
* Z. Wang, G. Slabaugh, G. Unal, and T. Fang. Information-Theoretic Feature Detection and Its Application to Registration of Ultrasound Images. International Journal of Intelligent Control and Systems, 13(2):136–145, 2008.

2012 Summer Project Week Breakout Session: Ultrasound: Denoising

2012-06-20T18:38:48Z

Caok:

===Module Name===
US Speckle Parameter Estimate

{|
|[[Image:USSpeckleParameterEstimate-input1.png|thumb|280px|Input Image-1]]
|[[Image:USSpeckleParameterEstimate-output1.png|thumb|280px|Parameter Estimate Image-1]]
|[[Image:USSpeckleParameterEstimate-input2.png|thumb|280px|Input Image-2]]
|[[Image:USSpeckleParameterEstimate-output2.png|thumb|280px|Parameter Estimate Image-2]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering.Denoising

===Authors, Collaborators & Contact===
* Author: Kunlin Cao
* Contact: cao@ge.com

===Module Description===
The USSpeckleParameterEstimate filter performs an information-theoretic based probabilistic modeling of speckles in Ultrasound images. Intensities of speckles in Ultrasound images are modeled using Rayleigh distribution or normalized Fisher-Tippett distribution.

Speckles are formed from coherent accumulation of random scattering in a cell of ultrasound beam. The pixel intensity of the speckle in the inphase/quadrature image follows a zero-mean Gaussian distribution. Then envelope detection of the inphase/quadrature image is performed to produce a real image/magnitude image, whose intensity corresponds to a Rayleigh distribution. Due to the large dynamic range of the magnitude image, log-compress is usually performed to produce an image suitable for display. A pixel’s intensity in the resulting image follows the normalized Fisher-Tippett distribution. The maximum likelihood estimate (MLE) of the distribution parameters in a neighborhood are calculated to describe the ultrasound image information.

A complete description of the algorithm may be found in:

G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is used to reduce speckles in an ultrasound image. Usually the normalized Fisher-Tippett distribtuion is used to model the statistical parameter.

* A command line example of running this module is

USSpeckleParameterEstimate
--neighborhood 1,1,1
inputUltrasoundImage.nhdr outputSmoothedImage.nhdr

The screenshots on the top illustrate how to use the filter and the expected results in two cases. The inputs are ultrasound images, and outputs are MLE estimate of normalized Fisher-Tippett distribution parameters (smoothed image).

===Quick Tour of Features and Use===
* '''Input/output panel:'''
[[Image:USSpeckleParameterEstimate-IO.png|thumb|right|280px|Input/Output panels]]
User selects an ultrasound image as input upon which the estimate filter will apply. User creates an output image to store the result. Upon completion, the output image will be displayed in the viewing panel.

* '''Parameters panel:'''
[[Image:USSpeckleParameterEstimate-parameters.png|thumb|right|280px|Input/Output panels]]
User specifies the neighborhood radius in three dimensions (comma separated without spaces).

* '''Viewing panel:'''
[[Image:USSpeckleParameterEstimate-display.png|thumb|right|280px|Input/Output panels]]
Upon completion, the estimate filter result is displayed in the viewing panel.

== Development ==

===Dependencies===

None other than the core Slicer3 modules for image IO and display.

===Known bugs===

===Usability issues===

===References===
* G. Slabaugh, G. Unal, M. Wels, T. Fang, and B. Rao. Statistical Region-based Segmentation of Ultrasound Images. Ultrasound in Medicine and Biology, 35(5):781 – 795, 2009.
* Z. Wang, G. Slabaugh, G. Unal, and T. Fang. Information-Theoretic Feature Detection and Its Application to Registration of Ultrasound Images. International Journal of Intelligent Control and Systems, 13(2):136–145, 2008.

File:USSpeckleParameterEstimate-display.png

2012-06-20T18:01:17Z

Caok:

File:USSpeckleParameterEstimate-parameters.png

2012-06-20T18:01:02Z

Caok:

File:USSpeckleParameterEstimate-IO.png

2012-06-20T18:00:50Z

Caok:

2012 Summer Project Week Breakout Session: Ultrasound: Denoising

2012-06-20T06:44:27Z

Caok: Created page with '===Module Name=== US Speckle Parameter Estimate {| |Input Image-1 |[[Image:USSpeckleParameterEstimate-output1.png|thu…'

File:USSpeckleParameterEstimate-output2.png

2012-06-20T06:41:32Z

Caok:

File:USSpeckleParameterEstimate-output1.png

2012-06-20T06:41:18Z

Caok:

File:USSpeckleParameterEstimate-input2.png

2012-06-20T06:40:57Z

Caok:

File:USSpeckleParameterEstimate-input1.png

2012-06-20T06:40:32Z

Caok:

File:InteractiveReg-lmk.png

2012-06-18T15:31:42Z

Caok: uploaded a new version of "File:InteractiveReg-lmk.png"

File:InteractiveReg-rotation.png

2012-06-18T15:31:10Z

Caok: uploaded a new version of "File:InteractiveReg-rotation.png": Reverted to version as of 15:30, 18 June 2012

File:InteractiveReg-rotation.png

2012-06-18T15:31:01Z

Caok: uploaded a new version of "File:InteractiveReg-rotation.png": Reverted to version as of 15:30, 18 June 2012

File:InteractiveReg-rotation.png

2012-06-18T15:30:21Z

Caok: uploaded a new version of "File:InteractiveReg-rotation.png": Reverted to version as of 15:29, 18 June 2012

File:InteractiveReg-rotation.png

2012-06-18T15:30:14Z

Caok: uploaded a new version of "File:InteractiveReg-rotation.png"

File:InteractiveReg-rotation.png

2012-06-18T15:29:36Z

Caok: uploaded a new version of "File:InteractiveReg-rotation.png"

File:InteractiveReg-translation.png

2012-06-18T15:29:10Z

Caok: uploaded a new version of "File:InteractiveReg-translation.png": Reverted to version as of 15:27, 18 June 2012

File:InteractiveReg-translation.png

2012-06-18T15:28:48Z

Caok: uploaded a new version of "File:InteractiveReg-translation.png"

File:InteractiveReg-translation.png

2012-06-18T15:27:52Z

Caok: uploaded a new version of "File:InteractiveReg-translation.png"

2012 Summer Project Week:SteeredRegistration

2012-06-16T23:07:44Z

Caok:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
</gallery>

==Key Investigators==
* BWH: Guillaume Pernelle (visiting from Technical University Munich), Jan Egger, Tina Kapur
* Isomics: Steve Pieper
* GRC: Kunlin Cao, Jim Miller

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide user an interface to interact with the registration program during the matching progress, in case the result from automatic registration is not satisfactory.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow user to pause the progress while the results is visually unsatisfactory. User inputs such as translation and rotation by dragging the mouse will be fed into the registration, and be used to correct the current transformation. Registration will continue to run starting from the corrected transform.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

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

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

==References==

File:InteractiveReg-lmk.png

2012-06-16T23:01:26Z

Caok:

File:InteractiveReg-rotation.png

2012-06-16T23:01:15Z

Caok:

File:InteractiveReg-translation.png

2012-06-16T23:00:52Z

Caok:

2012 Summer Project Week Breakout Session:Ultrasound

2012-06-14T20:54:49Z

Caok: /* Topic suggestions */

[[2012_Summer_Project_Week#Agenda|Back to agenda]]

=Topic suggestions=

* Improving Ultrasound imaging. This involves acquiring RF level or other data from the mid-processor stage of the imager (see http://www.ti.com/lit/wp/sprab12/sprab12.pdf, Figure 2) with the intent to provide a more suitable image for a particular application.
* Ultrasound post-processing, in which the image is processed to better enable, for example, registration to a CT data set.
** [[2012 Summer Project Week Breakout Session: Ultrasound: Denoising|Denoising with Ultrasound specific statistical filters]]
* Calibration, registration and display of ultrasound in 3D Slicer
* Real time (lag free) display of high quality US in Slicer for procedure guidance and lag free registered display in 3D models.
* The combination of 3 and 4 on low cost commodity hardware.
* The capture of all data to enable post procedure replay of a experimental or clinical session, so that the various processing steps can be debugged and optimized.

=Tentative list of presentations=

* Temporal and spatial calibration of US using PLUS (Andras/Csaba)
* Registration and real time display of US in Slicer for procedure guidance (Tamas)
* Perk Tutor: A configurable, Slicer-based training platform for ultrasound-guided needle insertions (Tamas)
* Low cost hardware. Capture and replay of experimental or clinical sessions (Kirby)
* Slicer CaseHub - Plans for capturing, organizing, and accessing multi-track procedure data (Steve)

2012 Summer Project Week:InteractiveReg

2012-06-13T18:06:39Z

Caok: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List </gallery> ==Key Investigators== * GRC: Kunlin Cao * BWH: Guillaume Pernelle * Qu…'

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

==Key Investigators==
* GRC: Kunlin Cao
* BWH: Guillaume Pernelle
* Queens: Simrin Nagpal

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide user an interface to interact with the registration program during the matching progress, in case the result from automatic registration is not satisfactory.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow user to pause the progress while the results is visually unsatisfactory. User inputs such as translation and rotation by dragging the mouse will be fed into the registration, and be used to correct the current transformation. Registration will continue to run starting from the corrected transform.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

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

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

==References==

2012 Summer Project Week

2012-06-13T16:53:58Z

Caok: /* General Registration */

Back to [[Events]]

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

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

==Agenda==

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

==Projects==

This is where the list of projects goes...

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

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

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

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

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

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

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

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

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

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

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

==Background==

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

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

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

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

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

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

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

==Registrants==

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

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blevins, Scott, BWH, stblevins@gmail.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#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
#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
#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
#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