NAMIC Wiki - User contributions [en]

BRAINSFit prostate registration

2015-05-13T15:52:50Z

Blowekamp: /* Standing SimpleITK issues */

=Goal=

We are developing registration module in Slicer version 4 (which is using ITKv4) for deformable registration of prostate MRI.

We want to develop a prostate registration tool in Slicer4/ITKv4. This Slicer4/ITKv4 registration tool should be functional, accurate and fast (i.e., comparable with the functionality we had in Slicer3/ITKv3, which has been evaluated previously [1]). We worked on implementing BRAINSFit registration in SimpleITK but due to several issues (see [http://www.na-mic.org/Wiki/index.php/BRAINSFit_prostate_registration#Standing_SimpleITK_issues here]) we are considering a C++ implementation that uses ITKv3 libraries and can be integrated in the latest Slicer versions.

=Details on the registration approach=
Registration is applied to align preprocedural and intraoperational MR T2 image volumes. We are using masks the prostate for both image data sets. Registration is done using MMI metric with rigid, affine and B-spline stages applied in sequence. In Slicer3/BRAINSFit we use gradient descent for rigid/affine, and LBFGS for B-spline.

=Parameters we are using to call BRAINSFit in Slicer 3.6 and Slicer 4.4=

{| class="wikitable"
|-
! Parameter !! Slicer 3.6 !! Slicer 4.4
|-
| --fixedVolume || dir || dir
|-
| --movingVolume || dir || dir
|-
| --outputVolume || dir || dir
|-
| --bsplineTransform || dir || dir
|-
| --movingBinaryVolume || dir || dir

|-
| --fixedBinaryVolume || dir || dir

|-
| --useCenterOfROIAlign || True || style="background:#cef2e0;"|   not an option

|-
| --initializeTransformMode || style="background:#cef2e0;"|   not an option || useCenterOfROIAlign

|-
| --samplingPercentage || style="background:#cef2e0;"|   not an option || 0.002

|-
| --useRigid || True || True

|-
| --useAffine || True || True

|-
| --useROIBSpline || True || True

|-
| --useScaleVersor3D || True || True

|-
| --useScaleSkewVersor3D || True || True

|-
| --useBSpline || style="background:#cef2e0;"|   not an option || True

|-
| --splineGridSize || 3,3,3 || 3,3,3

|-
| --numberOfIterations || 1500 || 1500

|-
| --maskProcessing || ROI || ROI

|-
| --outputVolumePixelType || float || float

|-
| --backgroundFillValue || 0 || 0

|-
| --maskInferiorCutOffFromCenter || 1000 || 1000

|-
| --interpolationMode || Linear || Linear

|-
| --minimumStepSize || 0.005 || style="background:#cef2e0;"|   not an option

|-
| --minimumStepLength || style="background:#cef2e0;"|   not an option || 0.005

|-
| --translationScale || 1000 || 1000

|-
| --reproportionScale || 1 || 1

|-
| --skewScale || 1 || 1

|-
| --numberOfHistogramBins || 50 || 50

|-
| --numberOfMatchPoints || 10 || 10

|-
| --numberOfSamples || 100000 || style="background:#cef2e0;"|   not an option

|-
| --fixedVolumeTimeIndex || 0 || 0

|-
| --movingVolumeTimeIndex || 0 || 0

|-
| --medianFilterSize || 0,0,0 || 0,0,0

|-
| --ROIAutoDilateSize || 0 || 0

|-
| --relaxationFactor || 0.5 || 0.5

|-
| --maximumStepSize || 0.2 || style="background:#cef2e0;"|   not an option

|-
| --maximumStepLength || style="background:#cef2e0;"|   not an option || 0.2

|-
| --failureExitCode || -1 || -1

|-
| --debugNumberOfThreads || -1 || style="background:#cef2e0;"|   not an option

|-
| --numberOfThreads || style="background:#cef2e0;"|   not an option || -1

|-
| --debugLevel || 0 || 0

|-
| --costFunctionConvergenceFactor || 1.00E+09 || 1.00E+09

|-
| --projectedGradientTolerance || 1.00E-05 || 1.00E-05

|-
| --maxBSplineDisplacement || 0 || 0

|-
| --maximumNumberOfEvaluations || style="background:#cef2e0;"|   not an option || 900

|-
| --maximumNumberOfCorrections || style="background:#cef2e0;"|   not an option || 25

|-
| --metricSamplingStrategy || style="background:#cef2e0;"|   not an option || Random

|-
| --costMetric || style="background:#cef2e0;"|   not an option || MMI

|-
| --removeIntensityOutliers || style="background:#cef2e0;"|   not an option || 0

|-
| --ROIAutoClosingSize || style="background:#cef2e0;"|   not an option || 9

|-
| --useExplicitPDFDerivativesMode || AUTO || style="background:#cef2e0;"|   not an option

|-
| --useCachingOfBSplineWeightsMode || ON || style="background:#cef2e0;"|   not an option

|}

=Results using the above parameters=
We used [http://www.slicer.org/publications/item/view/2147 this sample data] with Reader 1 segmentations to visually evaluate differences in the registration results.
All three results of BRAINSFit with ITKv3 in Slicer 3.6 look reasonable. Using BRAINSFit with ITKv4 in Slicer 4.4 creates a reasonable result for Case 7, but look strongly distorted towards the edges of the bounding box in Case 8 and 9.

{|
| Case 7
|[[Image:pat7-ref.png‎ |thumb|300px|Reference intraop volume]]
|[[Image:pat7-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]]
|[[Image:pat7-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]]
|}

{|
| Case 8
|[[Image:pat8-ref.png‎ |thumb|300px|Reference intraop volume]]
|[[Image:pat8-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]]
|[[Image:pat8-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]]
|}

{|
| Case 9
|[[Image:pat9-ref.png‎ |thumb|300px|Reference intraop volume]]
|[[Image:pat9-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]]
|[[Image:pat9-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]]
|}

=Current status=

SimpleITK registration code on github: [https://github.com/PeterBehringer/SimpleITKtraining/blob/master/BRAINSFit_to_sitk_MMI.py here]

'''Latest update: Mai 9, 2015'''

==Things that are working==
* exhaustive search based initialization procedure implemented and produces good results (cross-correlation metric) in SimpleITK

==Things that are implemented, but are not working==
* SimpleITK code for rigid registration
** the voxel sampling exception can be avoided by cropping the images sharply around the masks.
{|
|
|[[Image:FixedVolume.png|thumb|300px|Fixed Volume as Reference]]
|[[Image:AfterInit.png|thumb|300px|SimpleITK result after Initialization]]
|[[Image:AfterRigid.png|thumb|300px|SimpleITK result after rigid registration]]
|[[Image:BRAINSFitOut.png|thumb|300px|BRAINSFit result after rigid without using masks and --useCenterOfGeometryAlign]]
|}
** The rigid registration result is too much rotated and translated. Also the number of iteration steps varies with every computation. Reason might be that seed is set randomized and not set as done in BRAINSFit [https://github.com/BRAINSia/BRAINSTools/blob/af0ff12b8b751f9423061d42178268acab5f85f4/BRAINSCommonLib/BRAINSFitHelper.h#L375 here]. There is no option at the [http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html SimpleITK::ImageRegistrationMethod] to set a metric seed.

==Things that are not implemented, but need to be implemented==
* SimpleITK code for affine registration
** setting affineOptimizer [https://github.com/BRAINSia/BRAINSTools/blob/19fa37dfbdee37deff4ccee412bb601f7a787bda/BRAINSCommonLib/genericRegistrationHelper.hxx#L158-L187 here]
** setting RegistrationMethod [https://github.com/BRAINSia/BRAINSTools/blob/19fa37dfbdee37deff4ccee412bb601f7a787bda/BRAINSCommonLib/genericRegistrationHelper.hxx#L289-L353 here]
* SimpleITK code for BSpline registration (started [https://github.com/PeterBehringer/SimpleITKtraining/blob/master/simpleITK_to_sitk_BSpline.py here])

=Unresolved issues out of our direct control=
==Standing SimpleITK issues==
* no API for consistent initialization of the metric seed
** The ITKv4 ImageRegistrationMethod random sampling utilizes a fixed seed ([https://github.com/InsightSoftwareConsortium/ITK/blob/03f28bb2e0c4b3d00f1ceeb772b342746c89e148/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx#L903-L967 here])
*

==Standing ITKv4 issues==
* capability to sample voxels only within the mask (see topic under review on Gerrit: http://review.source.kitware.com/#/c/19684/)
*

==Standing Slicer4 issues==
=References=
[1] Fedorov A, Tuncali K, Fennessy FM, Tokuda J, Hata N, et al. (2012) Image registration for targeted MRI-guided transperineal prostate biopsy. J Magn Reson Imaging 36: 987–992. Available: http://dx.doi.org/10.1002/jmri.23688.

BRAINSFit prostate registration

2015-05-13T15:52:22Z

Blowekamp: /* Standing SimpleITK issues */

=Goal=

We are developing registration module in Slicer version 4 (which is using ITKv4) for deformable registration of prostate MRI.

We want to develop a prostate registration tool in Slicer4/ITKv4. This Slicer4/ITKv4 registration tool should be functional, accurate and fast (i.e., comparable with the functionality we had in Slicer3/ITKv3, which has been evaluated previously [1]). We worked on implementing BRAINSFit registration in SimpleITK but due to several issues (see [http://www.na-mic.org/Wiki/index.php/BRAINSFit_prostate_registration#Standing_SimpleITK_issues here]) we are considering a C++ implementation that uses ITKv3 libraries and can be integrated in the latest Slicer versions.

=Details on the registration approach=
Registration is applied to align preprocedural and intraoperational MR T2 image volumes. We are using masks the prostate for both image data sets. Registration is done using MMI metric with rigid, affine and B-spline stages applied in sequence. In Slicer3/BRAINSFit we use gradient descent for rigid/affine, and LBFGS for B-spline.

=Parameters we are using to call BRAINSFit in Slicer 3.6 and Slicer 4.4=

{| class="wikitable"
|-
! Parameter !! Slicer 3.6 !! Slicer 4.4
|-
| --fixedVolume || dir || dir
|-
| --movingVolume || dir || dir
|-
| --outputVolume || dir || dir
|-
| --bsplineTransform || dir || dir
|-
| --movingBinaryVolume || dir || dir

|-
| --fixedBinaryVolume || dir || dir

|-
| --useCenterOfROIAlign || True || style="background:#cef2e0;"|   not an option

|-
| --initializeTransformMode || style="background:#cef2e0;"|   not an option || useCenterOfROIAlign

|-
| --samplingPercentage || style="background:#cef2e0;"|   not an option || 0.002

|-
| --useRigid || True || True

|-
| --useAffine || True || True

|-
| --useROIBSpline || True || True

|-
| --useScaleVersor3D || True || True

|-
| --useScaleSkewVersor3D || True || True

|-
| --useBSpline || style="background:#cef2e0;"|   not an option || True

|-
| --splineGridSize || 3,3,3 || 3,3,3

|-
| --numberOfIterations || 1500 || 1500

|-
| --maskProcessing || ROI || ROI

|-
| --outputVolumePixelType || float || float

|-
| --backgroundFillValue || 0 || 0

|-
| --maskInferiorCutOffFromCenter || 1000 || 1000

|-
| --interpolationMode || Linear || Linear

|-
| --minimumStepSize || 0.005 || style="background:#cef2e0;"|   not an option

|-
| --minimumStepLength || style="background:#cef2e0;"|   not an option || 0.005

|-
| --translationScale || 1000 || 1000

|-
| --reproportionScale || 1 || 1

|-
| --skewScale || 1 || 1

|-
| --numberOfHistogramBins || 50 || 50

|-
| --numberOfMatchPoints || 10 || 10

|-
| --numberOfSamples || 100000 || style="background:#cef2e0;"|   not an option

|-
| --fixedVolumeTimeIndex || 0 || 0

|-
| --movingVolumeTimeIndex || 0 || 0

|-
| --medianFilterSize || 0,0,0 || 0,0,0

|-
| --ROIAutoDilateSize || 0 || 0

|-
| --relaxationFactor || 0.5 || 0.5

|-
| --maximumStepSize || 0.2 || style="background:#cef2e0;"|   not an option

|-
| --maximumStepLength || style="background:#cef2e0;"|   not an option || 0.2

|-
| --failureExitCode || -1 || -1

|-
| --debugNumberOfThreads || -1 || style="background:#cef2e0;"|   not an option

|-
| --numberOfThreads || style="background:#cef2e0;"|   not an option || -1

|-
| --debugLevel || 0 || 0

|-
| --costFunctionConvergenceFactor || 1.00E+09 || 1.00E+09

|-
| --projectedGradientTolerance || 1.00E-05 || 1.00E-05

|-
| --maxBSplineDisplacement || 0 || 0

|-
| --maximumNumberOfEvaluations || style="background:#cef2e0;"|   not an option || 900

|-
| --maximumNumberOfCorrections || style="background:#cef2e0;"|   not an option || 25

|-
| --metricSamplingStrategy || style="background:#cef2e0;"|   not an option || Random

|-
| --costMetric || style="background:#cef2e0;"|   not an option || MMI

|-
| --removeIntensityOutliers || style="background:#cef2e0;"|   not an option || 0

|-
| --ROIAutoClosingSize || style="background:#cef2e0;"|   not an option || 9

|-
| --useExplicitPDFDerivativesMode || AUTO || style="background:#cef2e0;"|   not an option

|-
| --useCachingOfBSplineWeightsMode || ON || style="background:#cef2e0;"|   not an option

|}

=Results using the above parameters=
We used [http://www.slicer.org/publications/item/view/2147 this sample data] with Reader 1 segmentations to visually evaluate differences in the registration results.
All three results of BRAINSFit with ITKv3 in Slicer 3.6 look reasonable. Using BRAINSFit with ITKv4 in Slicer 4.4 creates a reasonable result for Case 7, but look strongly distorted towards the edges of the bounding box in Case 8 and 9.

{|
| Case 7
|[[Image:pat7-ref.png‎ |thumb|300px|Reference intraop volume]]
|[[Image:pat7-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]]
|[[Image:pat7-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]]
|}

{|
| Case 8
|[[Image:pat8-ref.png‎ |thumb|300px|Reference intraop volume]]
|[[Image:pat8-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]]
|[[Image:pat8-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]]
|}

{|
| Case 9
|[[Image:pat9-ref.png‎ |thumb|300px|Reference intraop volume]]
|[[Image:pat9-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]]
|[[Image:pat9-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]]
|}

=Current status=

SimpleITK registration code on github: [https://github.com/PeterBehringer/SimpleITKtraining/blob/master/BRAINSFit_to_sitk_MMI.py here]

'''Latest update: Mai 9, 2015'''

==Things that are working==
* exhaustive search based initialization procedure implemented and produces good results (cross-correlation metric) in SimpleITK

==Things that are implemented, but are not working==
* SimpleITK code for rigid registration
** the voxel sampling exception can be avoided by cropping the images sharply around the masks.
{|
|
|[[Image:FixedVolume.png|thumb|300px|Fixed Volume as Reference]]
|[[Image:AfterInit.png|thumb|300px|SimpleITK result after Initialization]]
|[[Image:AfterRigid.png|thumb|300px|SimpleITK result after rigid registration]]
|[[Image:BRAINSFitOut.png|thumb|300px|BRAINSFit result after rigid without using masks and --useCenterOfGeometryAlign]]
|}
** The rigid registration result is too much rotated and translated. Also the number of iteration steps varies with every computation. Reason might be that seed is set randomized and not set as done in BRAINSFit [https://github.com/BRAINSia/BRAINSTools/blob/af0ff12b8b751f9423061d42178268acab5f85f4/BRAINSCommonLib/BRAINSFitHelper.h#L375 here]. There is no option at the [http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html SimpleITK::ImageRegistrationMethod] to set a metric seed.

==Things that are not implemented, but need to be implemented==
* SimpleITK code for affine registration
** setting affineOptimizer [https://github.com/BRAINSia/BRAINSTools/blob/19fa37dfbdee37deff4ccee412bb601f7a787bda/BRAINSCommonLib/genericRegistrationHelper.hxx#L158-L187 here]
** setting RegistrationMethod [https://github.com/BRAINSia/BRAINSTools/blob/19fa37dfbdee37deff4ccee412bb601f7a787bda/BRAINSCommonLib/genericRegistrationHelper.hxx#L289-L353 here]
* SimpleITK code for BSpline registration (started [https://github.com/PeterBehringer/SimpleITKtraining/blob/master/simpleITK_to_sitk_BSpline.py here])

=Unresolved issues out of our direct control=
==Standing SimpleITK issues==
* no API for consistent initialization of the metric seed
** The ITKv4 ImageRegistrationMethod random sampling utilizes a fixed seed
*

==Standing ITKv4 issues==
* capability to sample voxels only within the mask (see topic under review on Gerrit: http://review.source.kitware.com/#/c/19684/)
*

==Standing Slicer4 issues==
=References=
[1] Fedorov A, Tuncali K, Fennessy FM, Tokuda J, Hata N, et al. (2012) Image registration for targeted MRI-guided transperineal prostate biopsy. J Magn Reson Imaging 36: 987–992. Available: http://dx.doi.org/10.1002/jmri.23688.

2015 Winter Project Week

2015-01-12T15:08:51Z

Blowekamp: /* Infrastructure */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

== Note of Remembrance ==

[[file:ferenc.jpg|right]]
This project week is dedicated to Ferenc Jolesz, leader and mentor to many in the image guided therapy community. There is a [http://ferenc.jolesz.muchloved.com/ tribute page to Ferenc] for people who want to share their thoughts.

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session: CIP]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
| Neurosurgical Ultrasound Breakout
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| 3:15-4pm: [[2015_Winter_Project_Week_Infrastructure_Breakout|Breakout Session: Infrastructure (JC, Steve, Alex, Hans, Raul)]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[New Distance|A modified distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* [[2015_Winter_Project_Week:SlicerModelGlyphs | Display of point data vectors on Slicer models]] (Francois Budin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Jim Miller, Bradley Lowekamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)

* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson, Bill Lorensen, JC)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson, Jim Miller)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2015 Winter Project Week:SlicerMicroMacroScale

2015-01-12T15:08:19Z

Blowekamp: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:CtkVTKSeedsScaling.jpg|CTK example showing seed widget scaling between slice view and three dimensional view.
Image:SlicerSeedScaling.jpg|Slicer example with 2d fiducial manager scaling set to 1.0 instead of 0.003
</gallery>

==Key Investigators==

* Nicole Aucoin (BWH)
* Bradley Lowekamp (Medical Science Computing)
* Jim Miller (GE)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix bugs exposed by using small and large scale images

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* List of related bugs:
** [http://na-mic.org/Mantis/view.php?id=3547 Fiducials disappear with large image spacing]
** [http://na-mic.org/Mantis/view.php?id=3657 Setting the unit to microns doesn't help]
** [http://na-mic.org/Mantis/view.php?id=3713 landmark size in 3D view not consistant with 2D views]
* Sample data sets
** [https://www.dropbox.com/s/a8ie3eww7ssis2u/E12.5-3747-r7__rec.7z Small] - link out of date, need new sample from Murat
** [http://placid.nlm.nih.gov/folder/286 Large] - 1005x1004x296 with spacing of 3x3x3.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Investigating the base scaling assumptions for vtkSeedWidgets in 3d ctkVTKRenderView vs 2d ctkVTKSliceView
** writing a pure CTK test case - it shows that in the default set up for the two kinds of views and mirrored seed widgets the seeds are the same size (large)
** in Slicer, the camera in the 2d view is looking at the 2d scene from a camera distance of 1.0 while the default 3D distance is 600.0
** in the pure CTK test case, resetting the 3D camera to a position (0,0,600) the same issues can be seen as are visible in Slicer (tiny seed in 3D, large in 2D)
** talking with Jim:
*** when background volume changes, reset the camera position for each slice view to take into account the bounding box of the data
*** use a distance calculation formula that takes the viewing angle into account (default 30): (max_data_dim/2.0) / sin(view_angle / 2.0)
** once have a new setting:
*** reset the scale factor 2d on the 2d fid disp manager to 1.0
*** reset the Z distance of the camera position in the slice view
**** make sure set the camera on the correct renderer
***** there is an overlay renderer on the slice viewers so using the first renderer from the collection in my ctk example didn't work
***** get the renderer from the light box manager at all times, a light box index of 0 is always fine
***** turns out that when creating a new seed, you need to explictly reset the renderer on the new handle
***** lost ability to manipulate seeds, need more debugging
*** trigger rerendering of the seeds (in tests, we needed to remove all and readd them to see the new size)
*** double check placing rulers and ROIs in 2d
*** double check display to world coordinate calculation in the 2d disp managers
</div>
</div>

2015 Winter Project Week:RemoveITKv3Compatibility

2015-01-09T14:52:23Z

Blowekamp: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Bradley Lowekamp (MSC/NLM)
* Han Johnson (University of Iowa)
* Bill Lorensen (Noware)
* JC

==Project Description==

To enable support of large images ( >4GB ) on MS Windows the ITKv3 compatibility flag needs to be removed.

This flag can now be disabled by default after announcing on the mailing list, and allowing extensions maintainer time to update the extensions.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Evaluate the number of number of modules that are dependent on the ITKv3 Compatibility flag.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Look into the difference between the ITK's v3 Compatibility module and the deprecated, to determine if one can be enabled.
* Build Slicer with Slicer_ITKV3_COMPATIBILITY OFF, and compile extensions against.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Successfully compiles Slicer core with the Slicer_ITKV3_COMPATIBILITY flag set to off.
* Built the entire ExtensionsIndex against Slicer without compatibility.
* Searched for the extensions with ITK related compilation errors:
** ABC
** DTIAtlasBuilder
** ErodeDilateLabel
** houghTransformCLI
** LASegmenter
** MABMIS
** PkModeling
** SegmentationAidedRegistration
** SkullStripper
** EMSegmenter
* All extensions have been notified of the changes needed to be make
** Patches were generated for many extensions and pull requests place in Github.
** Some maintainers were directly contacted to update

</div>
</div>

2015 Winter Project Week:RemoveITKv3Compatibility

2015-01-09T14:44:31Z

Blowekamp: /* Key Investigators */

2015 Winter Project Week

2015-01-09T14:43:52Z

Blowekamp: /* Infrastructure */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

== Note of Remembrance ==

[[file:ferenc.jpg|right]]
This project week is dedicated to Ferenc Jolesz, leader and mentor to many in the image guided therapy community. There is a [http://ferenc.jolesz.muchloved.com/ tribute page to Ferenc] for people who want to share their thoughts.

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session: CIP]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
| Neurosurgical Ultrasound Breakout
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| 3:15-4pm: [[2015_Winter_Project_Week_Infrastructure_Breakout|Breakout Session: Infrastructure (JC, Steve, Alex, Hans, Raul)]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Quantitative Evaluation of Digitally Registered Pre and Post op DTI by 3D ROI Segmentation]] (Li Ye, Sonia Pujol, Steve Pieper, Alireza Mehrtash)
* [[New Distance|A modified distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* [[2015_Winter_Project_Week:SlicerModelGlyphs | Display of point data vectors on Slicer models]] (Francois Budin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson, Bill Lorensen, JC)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson, Jim Miller)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2015 Winter Project Week:VersorTransforms

2015-01-05T13:48:46Z

Blowekamp:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Bradley Lowekamp (MSC/NLM)
* Han Johnson (University of Iowa)?

==Project Description==

The ITK transforms ScaleSkewVersor3D, and Simularity3D surprisinging use addition to compose the matrix components instead of matrix multiplication.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Determine if this is expected and known behavior, and determine if the expected transforms are needed.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Winter Project Week:RemoveITKv3Compatibility

2015-01-05T13:37:55Z

Blowekamp:

2015 Winter Project Week:RemoveITKv3Compatibility

2015-01-05T13:37:38Z

Blowekamp:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Bradley Lowekamp (MSC/NLM)
* Han Johnson (University of Iowa)?

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

To enable support of large images ( >4GB ) on MS Windows the ITKv3 compatibility flag needs to be removed.

<h3>Objective</h3>
* Evaluate the number of number of modules that are dependent on the ITKv3 Compatibility flag.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Look into the difference between the ITK's v3 Compatibility module and the deprecated, to determine if one can be enabled.
* Build Slicer with Slicer_ITKV3_COMPATIBILITY OFF, and compile extensions against.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Winter Project Week:VersorTransforms

2015-01-05T13:33:38Z

Blowekamp:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Bradley Lowekamp (MSC/NLM)
* Han Johnson (University of Iowa)?

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Winter Project Week:RemoveITKv3Compatibility

2015-01-05T13:33:23Z

Blowekamp:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Bradley Lowekamp (MSC/NLM)
* Han Johnson (University of Iowa)?

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Winter Project Week:VersorTransforms

2015-01-05T13:30:50Z

Blowekamp:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

Bradley Lowekamp (MSC/NLM)
Han Johnson (University of Iowa)?

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Winter Project Week

2015-01-05T13:29:45Z

Blowekamp: /* Infrastructure */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis]] (Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson?, ?)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson?, ?)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2015 Winter Project Week:VersorTransforms

2015-01-05T13:28:47Z

Blowekamp: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Winter Project Week:RemoveITKv3Compatibility

2015-01-05T13:28:38Z

Blowekamp: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'

2015 Winter Project Week

2015-01-05T13:28:08Z

Blowekamp: /* Infrastructure */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis]] (Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson?, ?)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transform]] (Bradley Lowekamp, Hans Johnson?, ?)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2014 Project Week Breakout Session: Slicer for users

2014-06-25T12:56:11Z

Blowekamp:

[[2014_Summer_Project_Week|Back to project week]]

Wednesday, 11-12

This will be an informal discussion of new features in 3D Slicer. Some of the extensions will be mentioned as well.

*Improved handling of transforms including non-rigid (Alex Yarmakovic)
*Patient hierarchies and multi-objects (Csaba Pinter)
*Data Store
**Registration library (Dominik Meier)
***<small>brief overview over the Data Store access to the Registration Library
***example case, link to tutorial pages, screencasts, FAQ
***new support for nonlinear transforms and transform visualization</small>
**Tutorial data sets
*Extensions:
**Slicer RT - Csaba Pinter
**IASEM ( Ion-Abrasion Scanning Electron Microscopy ) - Bradley Lowekamp
*** Data: http://placid.nlm.nih.gov/folder/286
**Carrera - Ivan Kolesov
**TCIABrowser - Alireza Mehrtash

2014 Project Week Breakout Session: Slicer for users

2014-06-24T14:20:52Z

Blowekamp:

[[2014_Summer_Project_Week|Back to project week]]

Wednesday, 11-12

This will be an informal discussion of new features in 3D Slicer. Some of the extensions will be mentioned as well.

*Data Store
**Registration library

*Extensions:
**Slicer RT
**IASEM - Bradley Lowekamp
**Carrera - Ivan Kolesov
**TCIA - Andrey Fedorov

2014 Summer Project Week

2014-06-17T18:11:24Z

Blowekamp: /* Infrastructure */

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
<br>----------------------------------------<br>
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Background''' ==

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

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

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

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

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

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

==TBI==

==Atrial Fibrillation==

==Huntington's Disease==

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg, Ivan)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg, Ivan)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg, Paolo)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp)

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Nobuhiko Hata)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer(WPI), Nirav Patel(WPI), Nobuhiko Hata (BWH) )
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

==Radiation Therapy==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg, Maxime Desplanques, ?)

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Ethan, Andras, Steve, Jim, ...)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*Pluggable Label Statistics (Andrey , Ethan, Steve, Brad, Jim? Dirk?)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras?, ?)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc, ?)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba, ?)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

==Feature Extraction==
*Breast Tumor Segmentation and Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Sandy Wells)

==Other==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp, Danielle Pace?)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, University College Cork (UCC), Ireland)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Saskia Camps, SPL, saskiacamps@gmail.com
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Yangming Li, University of Washington, ymli81@uw.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Project Week:Modules scripting

2014-01-08T20:27:34Z

Blowekamp: /* Project Description */

==Key Investigators==
* Iowa: David Welch
* NLM: Brad Lowekamp
* Iowa: Hans Johnson

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Enhance the integration of SimpleITK with Slicer and expand the documentation for building modules from SimpleITK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Enhance the interface for the existing "SimpleFilters" module to allow for label maps and image types to be better handled.
** [BRAD] Explain how the SimpleFilters module works
** [DAVE] Make outputs default to NOT overwriting the inputs
** [Brad] For binary image outputs, set them as labelmaps

* Convert SimpleITK functions to user interface modules
** [DAVE] Create a SimpleITK function that histogram equalizes one image to another. "outimage=histEQ(refImage,inputImage,numberOfBins)"
** [DAVE] Convert that simple function to a Slicer GUI interface

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2014 Winter Project Week

2014-01-08T13:50:10Z

Blowekamp: /* Huntington's Disease */

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

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

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

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

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

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

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

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

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

=Background and Preparation=

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

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

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

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

==Atrial Fibrillation==
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Salma, Josh, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Salma, Josh, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Salma, Josh)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)
*[[2014_Project_Week:AblationSuccessRatePredictionUsingJointImageAndShapeAnalysis|Ablation Success Rate Prediction Using Joint Image And Shape Analysis]](Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
*[[2014_Project_Week:GrowCutLevelSetLA|Grow cut, level set integration for interactive LA segmentation]] ( Liangjia Zhu, Ivan Kolesov, Yi Gao, Allen Tannenbaum)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion & Compressed Sensing Conversions]] (Hans, CF, Peter Savadjiev, Kent, David)
*[[2014_Project_Week:Modules scripting|Slicer module scripting]] (David, Bradley Lowekamp)
*[[2014_Project_Week:DWIConverter|DWIConverter]] (Hans, Kent)
*[[2014_Project_Week:Slicer_Based_Surface_Template_Estimation|Slicer Based Surface Template Estimation]] (Saurabh Jain, 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)
*[[2014_Project_Week:WMQLExtension|WMQL implementation as a Slicer extension]] (Lichen Liang, Peter Savadjiev, Lauren O'Donnell, Steve Pieper)

==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)

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

==Cardiac==
*[[2014_Project_Week:CardiacStemCellMonitoring|Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI]] (Karl Diedrich)
*[[2014_Project_Week:CardiacCongenitalSegmentation|Whole-heart segmentation of cardiac MR images in congenital heart defect cases]] (Danielle Pace, Polina Golland)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Polina Binder, Ramesh Sridharan, Polina Golland)
*[[2014_Project_Week:Processing_Pipelines|Processing Pipelines]] (Ramesh Sridharan, Polina Golland)

==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:OpenIGTLink| OpenIGTLink Interface: New data types and structures]] (Junichi Tokuda, Andras Lasso, Steve Piper, ???)
*[[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:PercutaneousApproachAnalysis| Percutaneous Approach Analysis]] (Atsushi Yamada, Junichi Tokuda, Koichiro Murakami)
*[[2014_Project_Week:EndoscopeConsole| Endoscope Console]] (Atsushi Yamada, Junichi Tokuda)
*[[2014_Project_Week:Statistical Shape Model for robotic spine surgery| Statistical Shape Model for robotic spine surgery]] (Marine Clogenson, ???)
*[[2014_Project_Week:ImmersiveVR| Immersive VR devices]] (Franklin King, Andras Lasso)

==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, Steve Pieper, Greg Sharp)
*[[2014_Project_Week:External_Beam_Planning|External Beam Planning Visualization]] (Kevin Wang, Greg Sharp, Csaba Pinter)

==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]] (Vinicius Boen, Beatriz Paniagua, Nicole Aucoin, Steve Pieper, Francois Budin)
* [[2014_Winter_Project_Week:4DShape Analysis of mandibular changes|4DShape Analysis of mandibular changes]] (Vinicius Boen, James Fishbaugh, Guido Gerig)

==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)

==[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: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, Rick Herrick)
*[[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)
*[[2014_Project_Week:Slicer DICOM Module Interface Redesign|Slicer DICOM Module Interface Redesign]] (Alireza, Andrey, Steve, Ron, Rick Herrick)

==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, Rick Herrick)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin, Rick Herrick)
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Andras Lasso, Nicole Aucoin, Steve Pieper, Jc, Csaba Pinter, ???, Rick Herrick)
*[[2014_Project_Week:CLI|CLI]] (Jim Miller, Matt McCormick, Nicole Aucoin, Steve Pieper, Jc)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration (LandmarkRegistration module)]] (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:ParameterSerialization | JSON Parameter Serialization]] (Matt McCormick, Steve Pieper, Jim Miller)
* [[2014_Winter_Project_Week:XNATSlicerLink| 3DSlicer annotations in XNAT]] (Erwin Vast, Nicole Aucoin, Andrey Fedorov, Rick Herrick)
* [[2014_Winter_Project_Week:PlanarImage|Planar Images]] (Franklin King, Csaba Pinter, Andras Lasso)

AHM2014-Simple-ITK

2014-01-07T21:09:11Z

Blowekamp:

[[AHM_2013#Agenda|Back to AHM_2013 Agenda]]
* Time 4-5pm
** Solve your problems with SimpleITK
*** Q&A Help session
*** How do I do this?
** Design Review of Proposed Commands and Image Registration Interfaces for SimpleITK
*** Do these proposals meet your needs?
*** What other features do you need?
*** Review proposed Command call-back interference in IPython Notebook.
**** Get the notebook: [http://nbviewer.ipython.org/github/SimpleITK/SimpleITK-Notebooks/blob/STRAW/STRAW_Progress.ipynb viewer] [http://raw.github.com/SimpleITK/SimpleITK-Notebooks/STRAW/STRAW_Progress.ipynb github]
*** Review proposed image registration with the ImageRegistrationMethod in SimpleITK
**** Get the notebook: [http://nbviewer.ipython.org/github/SimpleITK/SimpleITK-Notebooks/blob/STRAW/STRAW_Registration.ipynb viewer] [http://raw.github.com/SimpleITK/SimpleITK-Notebooks/STRAW/STRAW_Registration.ipynb github]

AHM2014-Simple-ITK

2014-01-07T21:06:29Z

Blowekamp:

[[AHM_2013#Agenda|Back to AHM_2013 Agenda]]
* Time 4-5pm
** Solve your problems with SimpleITK
*** Q&A Help session
*** How do I do this?
** Design Review of Commands and Image Registration for SimpleITK
*** Do these proposals meet your needs?
*** What other features do you need?
*** Review proposed Command call-back interference in IPython Notebook.
**** Get the notebook: [http://nbviewer.ipython.org/github/SimpleITK/SimpleITK-Notebooks/blob/STRAW/STRAW_Progress.ipynb viewer] [http://raw.github.com/SimpleITK/SimpleITK-Notebooks/STRAW/STRAW_Progress.ipynb github]
*** Review proposed image registration with the ImageRegistrationMethod in SimpleITK
**** Get the notebook: [http://nbviewer.ipython.org/github/SimpleITK/SimpleITK-Notebooks/blob/STRAW/STRAW_Registration.ipynb viewer] [http://raw.github.com/SimpleITK/SimpleITK-Notebooks/STRAW/STRAW_Registration.ipynb github]

AHM2014-Simple-ITK

2014-01-07T18:44:22Z

Blowekamp:

AHM2014-Simple-ITK

2013-12-06T18:55:44Z

Blowekamp: Created page with ' Back to AHM_2013 Agenda *Time 4-5pm * Overview In IPython Notebooks * What's New in SimpleITK ** ?Progress reporting ** ?PDE Registation ** ?Using SimpleITK …'

[[AHM_2013#Agenda|Back to AHM_2013 Agenda]]
*Time 4-5pm
* Overview In IPython Notebooks
* What's New in SimpleITK
** ?Progress reporting
** ?PDE Registation
** ?Using SimpleITK in Slicer3D
* How do I do this?
** Solve your problems with SimpleITK
* What are important Feature to add to SimpleITK for Slicer3D?
** Wrap your own classes?
** What would you want to do with Registration from SimpleITK?
*** Specifics to drive interface design.

AHM 2014

2013-12-06T18:51:02Z

Blowekamp: /* Agenda */

Back to [[Events]]
[[image:PW-SLC2014.png|300px]]

Dates: January 6-10, 2014.

Location: Salt Lake City, UT.

== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2014 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2014 project week, see below.

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2014 AHM, EAB and Project Week will be held <br>'''January 6-10, 2014''', in '''Salt Lake City''', Utah.
|}
== Dates, Venue, Registration ==
{|
|align="left" style="width:60%"|
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 9th'''.
* Project Activities will be held rest of the week between '''Monday, January 6th and Friday, January 10th'''.

'''Registration:''' Please click [http://www.sci.utah.edu/namic2014.html '''here'''] to register online before '''January 2'''. All participants must pay a registration fee ('''$250''' for AHM only, and '''$550''' for AHM+Project Week), which covers our catering and facilities costs.
After December 25 registration prices will increase by $100. Last call registrations after January 1st will be increased by $200.

'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. The room rate for the meeting is 149 USD per night, and the code is "NA-MIC 2014 Conference." You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=NA-MIC%202014%20Conference^SLCCC%60NACNACA%60149%60USD%60false%601/5/14%601/10/14%6012/06/13&app=resvlink&stop_mobi=yes here.] PLEASE NOTE THAT THE DEADLINE FOR BOOKING ROOMS AT THESE RATES IS DECEMBER 13th.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:15%" | '''Monday, January 6'''
| style="width:15%" | '''Tuesday, January 7'''
| style="width:15%" | '''Wednesday, January 8'''
| style="width:35%" | '''Thursday, January 9 '''
| style="width:15%" | '''Friday, January 10'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#ffffff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Capitol BC)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Capitol BC)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Capitol BC)''</font>
| style="background:#F2E5D3; color:#522200"| '''AHM''' <br><font color="#44AA88">''(Capitol ABC)''</font>, '''[http://wiki.na-mic.org/Wiki/index.php/2014_EAB EAB]'''<br>[[2014_Winter_Project_Week|Project Activities]]
| style="background:#dbf3ff; color:#522200"|'''[[2014_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Capitol BC)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#F2E5D3; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2014 Winter Project Week DICOM Breakout|Breakout Session:DICOM]] (Steve Pieper) <br><font color="#44AA88">''(Capitol B)''</font> <br> <font color="#44AA88">''(Amethyst)''</font>
|
| '''8-8:05am:''' Welcome (Ron Kikinis) <br>
'''8:05-8:15am:''' [[2014 How about the Future|How about the future?]] (Ron Kikinis) <br>
'''8:15-9:15am:''' [[AHM_2014_alg_core_presentations | Algorithms Core: Update and Future Plans]] <br> '''9:20-9:55am:''' Invited Speaker: Prof. Wiro Niessen, Erasmus MC. "Quantitative Imaging Biomarkers and Imaging Genetics in Neurodegenerative Disease"<br>
| style="background:#dbf3ff; color:#522200"|[[2014_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Capitol BC)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#F2E5D3; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
| <font color="#9966cc">Breakout Session: [[AHM2014-IGT|Image Guided Therapy]] <br> ''(Amethyst)''</font> <br> [[AHM2014-Robotics|Robotics]]<br> <font color="#44AA88">''(Capitol A)''</font>
| [[2014 Winter Project Week DTI Tools Breakout|Breakout Session: DTI Tools]] (Martin Styner) <br><font color="#44AA88">''(Capitol B)''</font> <br> <font color="#44AA88">''(Amethyst)''</font>
| DBP Update and Future Plans<br> '''10:30-10:55am:''' TBI (Jack Van Horn, [[Media:NAMIC_AHM_2014_van_horn.pdf‎|Slides]]) <br> '''10:55-11:20am:''' Huntington's Disease (Hans Johnson, [[Media:20140110_IowaDBPProgress.pdf|Slides]]) <br> '''11:20-11:45am:''' Head and Neck Cancer (Greg Sharp, [[Media:NAMIC-AHM-2014-01-Sharp.pdf|Slides]]) <br> '''11:45-12:10pm:''' Atrial Fibrillation (Rob MacLeod, [[Media:DBP-AF-AHM2014.pdf|Slides]]) <br> '''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#F2E5D3; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"|[[2014_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Capitol BC)''</font>
| <font color="#44AA88">''(Amethyst)''</font>
|'''DBP Team Meetings''' <br><font color="#44AA88">''(Capitol A)''</font> <br> '''1-2pm:''' [[DBP MGH Head and Neck Cancer]] <br>'''2-3pm:''' [[DBP Utah Atrial Fibrillation]]
|
'''1:15-1:30pm:''' Collaboration R01: Quantification Of 3d Bony Changes In Temporomandibular Joint Osteoarthritis (Lucia Cevidanes, University of Michigan) <br>
'''1:30-2:15pm:''' [[AHM2014-Engineering_Updates | Engineering Core: Updates and Future Plans]] <br> '''2:15-2:45pm:''' [[Media:AHM2014_TrainingCore_SoniaPujol.pdf | Outreach ]] (Sonia Pujol, Steve Pieper) <br>
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#F2E5D3; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|Breakout: TBD <br> <font color="#44AA88">''(Capitol BC)''</font> <br>Breakout: TBD <br><font color="#44AA88">''(Capitol A)''</font> <br> <br> <font color="#44AA88">''(Amethyst)''</font>
|3:15-4pm: Breakout Session: [[AHM2014-SubjectHierarchy|Subject Hierarchy]] <br><font color="#44AA88">''(Amethyst)'' <br> 4:15-5pm: [[AHM2014-Simple-ITK|SimpleITK Breakout Session]]</font> <br> Amethyst <br> <br> <font color="#44AA88">''(Capitol A)''</font>
|'''DBP Team Meetings''' <br><font color="#44AA88">''(Capitol A)''</font> <br> '''3-4pm:''' [[DBP UCLA Traumatic Brain Injury]] <br>'''4-5pm:''' [[DBP Iowa Huntington's Disease]]
|'''3-4pm''': [[2014_EAB|EAB meeting]] (Core, Site, and DBP PIs to join) <br><font color="#9966cc">''(Olympus A)''</font><br> '''4-5pm:''' EAB closed session <br><font color="#9966cc">''(Olympus A)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

'''General Announcements:'''

**Will be added here

==Registered Attendees==

<big>'''NOTE:'''</big> <font color="maroon">The registered attendee list will be posted here by the organizers. '''DO NOT''' add your name to this list yourself.</font> To register, please click [http://www.sci.utah.edu/namic2014-registration.html here].

2013 Summer Project Week

2013-06-21T13:36:15Z

Blowekamp: /* Infrastructure */

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

<gallery widths="800px" heights="300px" perrow="1" caption="Lunch in the Amphitheater at Stata, June 20 2013">
Image:Lunch at Project week IMG 0367.JPG|Shade was a popular commodity
</gallery>

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|
'''9:30-10:30am''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|[http://www.na-mic.org/Wiki/index.php/File:NamicToAmphi.png Lunch in Outdoor Amphitheather!]
|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''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-262]]
|
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|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 wiki pages for your project. Then link the page here with a list of key personnel.

==Some Stats==
73 Projects, 104 Attendees. First time attendees 25.

===Huntington's Disease===
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Josh, Hans, Ross)


7 projects

===Traumatic Brain Injury===
* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)


5 projects

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)


8 projects

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Creating DICOM series from ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Karl Fritscher, Christian Wachinger, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, Alireza Mehrtash)


8 projects

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Ultrasound_Needle_Detection| Ultrasound Needle Detection]] (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:ProstateBRP| MRI-guided robotic prostate interventinos]] (Junichi Tokuda, Greg Fischer, Nirav Patel, Nobuhiko Hata, Clare Tempnay)


12 projects

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)


3 projects

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:VicomTech| VicomTech visit: Imaging solutions and Slicer use]] (Ivan Macia)
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Francois Budin, Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Lilla Zollei, Nathaniel Reynolds, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Kayhan Batmanghelich, Polina Golland)
* [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)
* [[2013_Summer_Project_Week:Documentation for Slicer 4.2 Data Loading and 3D Visualization|Documentation for Slicer 4.2 Data Loading and 3D Visualization]] (Parth Amin WIT, Matt Flynn WIT, Dr. Pujol HMS)
* [[2013_Summer_Project_Week:WM Geometry Tools|Integration in Slicer of white matter geometry tools]] (Peter Savadjiev, Carl-Fredrik Westin)


16 projects

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[ITK -VTK wrapper]] (Paolo Zaffino, Greg Sharp, Steve Pieper)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Dave Welch, Brad Lowekamp, Hans Johnson, Steve)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter (time) Hierarchy]] (Adam Rankin)
* [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Jim,Brad Lowekamp, Jc)
* [[2013_Summer_Project_Week:Python_Embedding| Python Embedding Library]] (Rui, Jim, Jc, Steve)

14 projects

== '''Background''' ==

We are pleased to announce the 17th 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 25th 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 17-21, 2013.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''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 projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. 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 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, 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 13: 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=1233699 Please click here to register.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Kayhan Batmanghelich, MIT, kayhan@csail.mit.edu
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Taylor Braun-Jones, GE Healthcare, taylor.braun-jones@ge.com
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Alexandra Golby, BWH, agolby@partners.org
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Dan Groszmann, GE Healthcare, daniel.groszmann@ge.com
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Sylvain Jaume, WIT, jaumes@wit.edu
#Daniel Jimenez, daniel.jimenez@gmail.com
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#William Plishker, IGI Technologies, will@igitechnologies.com
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Tobias Schroeder, GE Healthcare, tobias.schroeder@ge.com
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2013 Summer Project Week:ITK Shared IO Libraries

2013-06-21T13:35:29Z

Blowekamp: /* Key Investigators */

==Key Investigators==
* Jim Miller, GE
* Bradley Lowekamp, MSC/NLM
* Jean-Christophe Fillion-Robin, Kitware

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

<h3>Objective</h3>

We are looking at converting ITK's IO libraries to be shared on Windows systems. This should address the problems of ITK's ImageIO factories being registered multiple time during static initialization.

</div>

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

<h3>Approach, Plan</h3>

We want to create a patch for ITK which adds a modular option for shared libraries, then turn this option on for all ITK modules which contain ObjectFactories. Then we will disable complication added to Slicer3D to deal with the current complication.

</div>

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

<h3>Progress</h3>

We have successfully created an improvement patch to the ITK library which enables this option. Evaluating this impact this change has on Slicer is still pending.

</div>
</div>

==Delivery Mechanism==

This goal of this work is to push it in to ITK upstream for the 4.5 development cycle.

==References==

* http://review.source.kitware.com/#/c/11567/

2013 Summer Project Week:SimpleITK GUI

2013-06-21T12:38:51Z

Blowekamp: /* References */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnected
Image:SimpleFilters-GridImageSource.png|GridImage
</gallery>

==Key Investigators==
* MSC/NLM: Bradley Lowekamp
* UIowa: Hans Johnson, Dave Welch
* Isomics: Steve Pieper

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

<h3>Objective</h3>

A Slicer module that provides some 'common usage' of SimpleITK within Slicer to facilitate learning and adoption of the Python scripting in Slicer with SimpleITK.

</div>

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

<h3>Approach, Plan</h3>

We will create a Scripted Module with four sections:

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</div>

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

<h3>Progress</h3>

Created a scripted python modules in a extension framework for access to 241 ITK filters through SimpleITK. Parameters are generated from SimpleITK JSON and include annotation fiducials. Basic background processing can be enabled with SimpleITK threads enabled. The current extension is available on github.

</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 YES
##Built-in - MAYBE?
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* https://www.icts.uiowa.edu/jira/secure/attachment/22053/SlicerSimpleITKUserGUI.pdf
* https://github.com/blowekamp/Slicer-SimpleFilters

2013 Summer Project Week:SimpleITK GUI

2013-06-21T12:38:18Z

Blowekamp: /* Key Investigators */

2013 Summer Project Week:SimpleITK GUI

2013-06-21T12:37:25Z

Blowekamp: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnected
Image:SimpleFilters-GridImageSource.png|GridImage
</gallery>

==Key Investigators==
* MSC/NLM: Bradley Lowekamp
* UIowa: Hans Johnson, Dave Welch
* Isomics: Steve Pieper

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

<h3>Objective</h3>

A Slicer module that provides some 'common usage' of SimpleITK within Slicer to facilitate learning and adoption of the Python scripting in Slicer with SimpleITK.

</div>

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

<h3>Approach, Plan</h3>

We will create a Scripted Module with four sections:

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</div>

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

<h3>Progress</h3>

Created a scripted python modules in a extension framework for access to 241 ITK filters through SimpleITK. Parameters are generated from SimpleITK JSON and include annotation fiducials. Basic background processing can be enabled with SimpleITK threads enabled.

</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 YES
##Built-in - MAYBE?
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* https://www.icts.uiowa.edu/jira/secure/attachment/22053/SlicerSimpleITKUserGUI.pdf

2013 Summer Project Week:SimpleITK GUI

2013-06-21T02:24:49Z

Blowekamp:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnected
Image:SimpleFilters-GridImageSource.png|GridImage
</gallery>

==Key Investigators==
* MSC/NLM: Bradley Lowekamp
* UIowa: Hans Johnson, Dave Welch
* Isomics: Steve Pieper

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

<h3>Objective</h3>

A Slicer module that provides some 'common usage' of SimpleITK within Slicer to facilitate learning and adoption of the Python scripting in Slicer with SimpleITK.

</div>

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

<h3>Approach, Plan</h3>

We will create a Scripted Module with four sections:

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</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 YES
##Built-in - MAYBE?
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* https://www.icts.uiowa.edu/jira/secure/attachment/22053/SlicerSimpleITKUserGUI.pdf

File:SimpleFilters-GridImageSource.png

2013-06-21T02:24:15Z

Blowekamp: SimpleFilter module to generate GridImageSource

SimpleFilter module to generate GridImageSource

2013 Summer Project Week:SimpleITK GUI

2013-06-21T02:07:47Z

Blowekamp: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnectedImageFilter
</gallery>

==Key Investigators==
* MSC/NLM: Bradley Lowekamp
* UIowa: Hans Johnson, Dave Welch
* Isomics: Steve Pieper

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

<h3>Objective</h3>

A Slicer module that provides some 'common usage' of SimpleITK within Slicer to facilitate learning and adoption of the Python scripting in Slicer with SimpleITK.

</div>

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

<h3>Approach, Plan</h3>

We will create a Scripted Module with four sections:

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</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 YES
##Built-in - MAYBE?
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* https://www.icts.uiowa.edu/jira/secure/attachment/22053/SlicerSimpleITKUserGUI.pdf

2013 Summer Project Week:SimpleITK GUI

2013-06-21T02:07:31Z

Blowekamp:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnectedImageFilter
</gallery>

==Key Investigators==
* MSC/NLM: Bradley Lowekamp
* UIowa: Hans Johnson, Dave Welch
* Isomics: Steve Pieper

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

<h3>Objective</h3>

A Slicer module that provides some 'common usage' of SimpleITK within Slicer to facilitate learning and adoption of the Python scripting in Slicer with SimpleITK.

</div>

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

<h3>Approach, Plan</h3>

We will create a Scripted Module with four sections:

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</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 YES
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* https://www.icts.uiowa.edu/jira/secure/attachment/22053/SlicerSimpleITKUserGUI.pdf

File:SimpleFilters-ConfidenceConnected.png

2013-06-21T02:04:08Z

Blowekamp: SimpleFilters module with Confidence Connected filter.

SimpleFilters module with Confidence Connected filter.

2013 Summer Project Week:ITK Shared IO Libraries

2013-06-21T01:44:52Z

Blowekamp: /* Key Investigators */

==Key Investigators==
* Bradley Lowekamp, MSC/NLM
* Jean-Christophe Fillion-Robin, Kitware
* Jim Miller, GE

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

<h3>Objective</h3>

We are looking at converting ITK's IO libraries to be shared on Windows systems. This should address the problems of ITK's ImageIO factories being registered multiple time during static initialization.

</div>

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

<h3>Approach, Plan</h3>

We want to create a patch for ITK which adds a modular option for shared libraries, then turn this option on for all ITK modules which contain ObjectFactories. Then we will disable complication added to Slicer3D to deal with the current complication.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This goal of this work is to push it in to ITK upstream for the 4.5 development cycle.

==References==

* http://review.source.kitware.com/#/c/11567/

2013 Summer Project Week:SimpleITK GUI

2013-06-21T01:43:05Z

Blowekamp: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MSC/NLM: Bradley Lowekamp
* UIowa: Hans Johnson, Dave Welch
* Isomics: Steve Pieper

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

<h3>Objective</h3>

A Slicer module that provides some 'common usage' of SimpleITK within Slicer to facilitate learning and adoption of the Python scripting in Slicer with SimpleITK.

</div>

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

<h3>Approach, Plan</h3>

We will create a Scripted Module with four sections:

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</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 YES
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* https://www.icts.uiowa.edu/jira/secure/attachment/22053/SlicerSimpleITKUserGUI.pdf

2013 Summer Project Week

2013-06-21T01:42:07Z

Blowekamp: /* Infrastructure */

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

<gallery widths="800px" heights="300px" perrow="1" caption="Lunch in the Amphitheater at Stata, June 20 2013">
Image:Lunch at Project week IMG 0367.JPG|Shade was a popular commodity
</gallery>

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|
'''9:30-10:30am''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|[http://www.na-mic.org/Wiki/index.php/File:NamicToAmphi.png Lunch in Outdoor Amphitheather!]
|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''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-262]]
|
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|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 wiki pages for your project. Then link the page here with a list of key personnel.

==Some Stats==
73 Projects, 97 Attendees. First time attendees 25.

===Huntington's Disease===
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Josh, Hans, Ross)


7 projects

===Traumatic Brain Injury===
* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)


5 projects

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)


8 projects

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Creating DICOM series from ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, Alireza Mehrtash)


8 projects

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Ultrasound_Needle_Detection| Ultrasound Needle Detection]] (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:ProstateBRP| MRI-guided robotic prostate interventinos]] (Junichi Tokuda, Greg Fischer, Nirav Patel, Nobuhiko Hata, Clare Tempnay)


12 projects

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)


3 projects

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:VicomTech| VicomTech visit: Imaging solutions and Slicer use]] (Ivan Macia)
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Lilla Zollei, Nathaniel Reynolds, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Kayhan Batmanghelich, Polina Golland)
* [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)
* [[2013_Summer_Project_Week:Documentation for Slicer 4.2 Data Loading and 3D Visualization|Documentation for Slicer 4.2 Data Loading and 3D Visualization]] (Parth Amin WIT, Matt Flynn WIT, Dr. Pujol HMS)
* [[2013_Summer_Project_Week:WM Geometry Tools|Integration in Slicer of white matter geometry tools]] (Peter Savadjiev, Carl-Fredrik Westin)


16 projects

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[ITK -VTK wrapper]] (Paolo Zaffino, Greg Sharp, Steve Pieper)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Brad Lowekamp, Hans Johnson, Dave Welch, Steve)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter (time) Hierarchy]] (Adam Rankin)
* [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Brad Lowekamp, Jc, Jim)
* [[2013_Summer_Project_Week:Python_Embedding| Python Embedding Library]] (Rui, Jim, Jc, Steve)

14 projects

== '''Background''' ==

We are pleased to announce the 17th 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 25th 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 17-21, 2013.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''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 projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. 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 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, 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 13: 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=1233699 Please click here to register.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Kayhan Batmanghelich, MIT, kayhan@csail.mit.edu
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Taylor Braun-Jones, GE Healthcare, taylor.braun-jones@ge.com
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Alexandra Golby, BWH, agolby@partners.org
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Dan Groszmann, GE Healthcare, daniel.groszmann@ge.com
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Sylvain Jaume, WIT, jaumes@wit.edu
#Daniel Jimenez, daniel.jimenez@gmail.com
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#William Plishker, IGI Technologies, will@igitechnologies.com
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Tobias Schroeder, GE Healthcare, tobias.schroeder@ge.com
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2013 Summer Project Week:ITK Shared IO Libraries

2013-06-17T15:53:01Z

Blowekamp:

==Key Investigators==
* MSC/NLM: Bradley Lowekamp

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

<h3>Objective</h3>

We are looking at converting ITK's IO libraries to be shared on Windows systems. This should address the problems of ITK's ImageIO factories being registered multiple time during static initialization.

</div>

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

<h3>Approach, Plan</h3>

We want to create a patch for ITK which adds a modular option for shared libraries, then turn this option on for all ITK modules which contain ObjectFactories. Then we will disable complication added to Slicer3D to deal with the current complication.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This goal of this work is to push it in to ITK upstream for the 4.5 development cycle.

==References==

* http://review.source.kitware.com/#/c/11567/

2013 Summer Project Week:SimpleITK GUI

2013-06-17T15:52:40Z

Blowekamp:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* MSC/NLM: Bradley Lowekamp
* UIowa: Hans Johnson, Dave Welch

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

<h3>Objective</h3>

A Slicer module that provides some 'common usage' of SimpleITK within Slicer to facilitate learning and adoption of the Python scripting in Slicer with SimpleITK.

</div>

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

<h3>Approach, Plan</h3>

We will create a Scripted Module with four sections:

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</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 YES
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* https://www.icts.uiowa.edu/jira/secure/attachment/22053/SlicerSimpleITKUserGUI.pdf

2013 Summer Project Week

2013-06-17T15:52:11Z

Blowekamp: /* Infrastructure */

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''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''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|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 wiki pages for your project. Then link the page here with a list of key personnel.

==Some Stats==
69 Projects, 95 Attendees. First time attendees? 5+ time attendees?

===Huntington's Disease===
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Dave, Manasi, Hans, Ross)

===Traumatic Brain Injury===
* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Using ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, Alireza Mehrtash)

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Nathaniel Reynolds, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar, Lilla Zollei)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
* [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[ITK -VTK wrapper]] (Paolo, Dave, Hans)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Brad Lowekamp, Hans Johnson, Dave Welch)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter Hierarchy]] (Adam Rankin)
* [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Brad Lowekamp)

== '''Background''' ==

We are pleased to announce the 17th 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 25th 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 17-21, 2013.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''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 projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. 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 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, 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 13: 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=1233699 Please click here to register.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2013 Summer Project Week:ITK Shared IO Libraries

2013-06-17T15:51:44Z

Blowekamp:

==Key Investigators==
* Bradley Lowekamp

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

<h3>Objective</h3>

We are looking at converting ITK's IO libraries to be shared on Windows systems. This should address the problems of ITK's ImageIO factories being registered multiple time during static initialization.

</div>

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

<h3>Approach, Plan</h3>

We want to create a patch for ITK which adds a modular option for shared libraries, then turn this option on for all ITK modules which contain ObjectFactories. Then we will disable complication added to Slicer3D to deal with the current complication.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This goal of this work is to push it in to ITK upstream for the 4.5 development cycle.

==References==

* http://review.source.kitware.com/#/c/11567/

2013 Summer Project Week:ITK Shared IO Libraries

2013-06-17T15:50:26Z

Blowekamp: Created page with '==Key Investigators== * Bradley Lowekamp <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Objective</h3> We are looking at converting …'

==Key Investigators==
* Bradley Lowekamp

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

<h3>Objective</h3>
We are looking at converting ITK's IO libraries to be shared on Windows systems. This should address the problems of ITK's ImageIO factories being registered multiple time during static initialization.

</div>

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

<h3>Approach, Plan</h3>

We want to create a patch for ITK which adds a modular option for shared libraries, then turn this option on for all ITK modules which contain ObjectFactories.

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This goal of this work is to push it in to ITK upstream for the 4.5 development cycle.

==References==

* http://review.source.kitware.com/#/c/11567/

2013 Project Week:Threaded SimpleITK Modules

2013-01-11T16:33:07Z

Blowekamp: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:yourimagehere.png| Image description
</gallery>

==Key Investigators==

* Brad Lowekamp, NLM
* Steve Pieper, Isomics

==Project Description==

For some filters and segmentation algorithms written using SimpleITK in slicer it would be nice to let them run in the background while letting slicer's main thread continue to process events. But the python byte code interpreter only allows a single path of python code to run at a time (see the discussion in the Preliminary Work section below). However since SimpleITK's implementation is in C++, it could release the GIL to allow the rest of the application to run while it processes. Care must be taken when processing progress events or modifying variables that are shared with the main thread.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Support multi-threaded execution of SimpleITK filters.
* Try releasing the GIL when calling into SimpleITK
* Look at what's required for synchronization and progress reporting
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Review other threading implementations in slicer, vtk, and itk to look for best practices
** Processing tasks (for CLIs) [https://github.com/Slicer/Slicer/blob/master/Base/Logic/vtkSlicerApplicationLogic.cxx#L312 in vtkSlicerApplicationLogic]
** ITK MultiThreader
** VTK MultiThreader
** [http://docs.python.org/2/library/threading.html Python threading]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Able to patch SimpleITK to enable threading in all SimpleITK methods
* Compiled patch into Slicer and confirmed able to run ITK filters in background
**https://github.com/blowekamp/Slicer/tree/EnableSimpleITKThreads
* Designed some threading methodologies for modules and Editor Effects
</div>
</div>

== Preliminary Work ==

The example code below calls two different python functions from inside threads. One function calls the 'time.sleep' method, and one uses VTK to do some processing. As you can see from the output printed below, the VTK threads block, and a new thread is not started until the last one completes. On the other hand, the sleep based thread does return right away. The behavior is based on the [http://docs.python.org/2/glossary.html#term-global-interpreter-lock CPython global interpreter lock]. The topic was [http://web.archiveorange.com/archive/v/aysypJwvM9H8MY8BtpyP discussed in detail] on the vtk developers list back in 2005.

<pre>
import vtk
import threading
import Queue
import time, datetime
import os

class ThreadClass(threading.Thread):
def __init__(self, queue, work):
threading.Thread.__init__(self)
self.queue = queue
self.work = work

def run(self):
now = datetime.datetime.now()
self.queue.put( "start %s, time: %s" % (self.getName(), now) )
self.work()
now = datetime.datetime.now()
self.queue.put( "end %s, time: %s" % (self.getName(), now) )

def process():
e = vtk.vtkImageEllipsoidSource()
e.SetWholeExtent(0,300,0,300,0,300)
s = vtk.vtkImageGaussianSmooth()
s.SetInputConnection(e.GetOutputPort())
s.Update()

def sleep():
time.sleep(1)

for work,message in ((process,'vtk'), (sleep,'sleep')):
print ('threading test with %s:' % message)
threads = 3
queue = Queue.Queue()
for i in range(threads):
t = ThreadClass(queue,work)
t.start()
print('started:')

for i in range(2*threads):
print(queue.get())
print('finished\n')
</pre>

<pre>
#8 Slicer-superbuild $ ./VTK-build/bin/vtkpython /Users/pieper/Dropbox/hacks/threadVTK.py
threading test with vtk:
started:
start Thread-1, time: 2012-12-18 17:13:17.047282
end Thread-1, time: 2012-12-18 17:13:18.006989
start Thread-2, time: 2012-12-18 17:13:18.007318
end Thread-2, time: 2012-12-18 17:13:18.953446
start Thread-3, time: 2012-12-18 17:13:18.953762
end Thread-3, time: 2012-12-18 17:13:19.897673
finished

threading test with sleep:
started:
start Thread-4, time: 2012-12-18 17:13:19.898124
start Thread-5, time: 2012-12-18 17:13:19.898346
start Thread-6, time: 2012-12-18 17:13:19.898506
end Thread-4, time: 2012-12-18 17:13:20.899137
end Thread-6, time: 2012-12-18 17:13:20.899378
end Thread-5, time: 2012-12-18 17:13:20.899469
finished
</pre>

== Update ==

Multi-threading proof of concept:

<pre>
import SimpleITK as sitk
import threading
import Queue
import time, datetime
import os

class ThreadClass(threading.Thread):
def __init__(self, queue, work):
threading.Thread.__init__(self)
self.queue = queue
self.work = work

def run(self):
now = datetime.datetime.now()
self.work()
self.queue.put( "start %s, time: %s" % (self.getName(), now) )
now = datetime.datetime.now()
self.queue.put( "end %s, time: %s" % (self.getName(), now) )

def process():
img = sitk.GaussianSource(sitk.sitkFloat32, [256]*3)
simg = sitk.SmoothingRecursiveGaussian(img)

def sleep():
time.sleep(1)

for work,message in ((process,'sitk'), (sleep,'sleep')):
print ('threading test with %s:' % message)
threads = 5
queue = Queue.Queue()
for i in range(threads):
t = ThreadClass(queue,work)
t.start()

print(queue.qsize())
while queue.empty():
print('empty')
sleep()

for i in range(2*threads):
print(queue.get())
print('finished\n')
</pre>

Results:

<pre>
threading test with sitk:
0
empty
empty
empty
empty
empty
empty
start Thread-2, time: 2013-01-11 11:03:27.098504
end Thread-2, time: 2013-01-11 11:03:32.171759
start Thread-4, time: 2013-01-11 11:03:27.099969
end Thread-4, time: 2013-01-11 11:03:32.563888
start Thread-1, time: 2013-01-11 11:03:27.097554
end Thread-1, time: 2013-01-11 11:03:33.151524
start Thread-5, time: 2013-01-11 11:03:27.103264
end Thread-5, time: 2013-01-11 11:03:33.333674
start Thread-3, time: 2013-01-11 11:03:27.099090
end Thread-3, time: 2013-01-11 11:03:33.586790
finished

threading test with sleep:
0
empty
start Thread-6, time: 2013-01-11 11:03:33.587261
end Thread-6, time: 2013-01-11 11:03:34.589810
start Thread-7, time: 2013-01-11 11:03:33.587563
end Thread-7, time: 2013-01-11 11:03:34.590058
start Thread-8, time: 2013-01-11 11:03:33.587745
end Thread-8, time: 2013-01-11 11:03:34.590183
start Thread-9, time: 2013-01-11 11:03:33.587997
end Thread-9, time: 2013-01-11 11:03:34.590300
start Thread-10, time: 2013-01-11 11:03:33.588265
end Thread-10, time: 2013-01-11 11:03:34.590451
finished
</pre>

2013 Project Week:Threaded SimpleITK Modules

2013-01-11T16:31:57Z

Blowekamp: /* Preliminary Work */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:yourimagehere.png| Image description
</gallery>

==Key Investigators==

* Brad Lowekamp, NLM
* Steve Pieper, Isomics

==Project Description==

For some filters and segmentation algorithms written using SimpleITK in slicer it would be nice to let them run in the background while letting slicer's main thread continue to process events. But the python byte code interpreter only allows a single path of python code to run at a time (see the discussion in the Preliminary Work section below). However since SimpleITK's implementation is in C++, it could release the GIL to allow the rest of the application to run while it processes. Care must be taken when processing progress events or modifying variables that are shared with the main thread.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Support multi-threaded execution of SimpleITK filters.
* Try releasing the GIL when calling into SimpleITK
* Look at what's required for synchronization and progress reporting
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Review other threading implementations in slicer, vtk, and itk to look for best practices
** Processing tasks (for CLIs) [https://github.com/Slicer/Slicer/blob/master/Base/Logic/vtkSlicerApplicationLogic.cxx#L312 in vtkSlicerApplicationLogic]
** ITK MultiThreader
** VTK MultiThreader
** [http://docs.python.org/2/library/threading.html Python threading]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Able to patch SimpleITK to enable threading in all SimpleITK methods
* Compiled patch into Slice and confirmed able to run ITK filters in background
**https://github.com/blowekamp/Slicer/tree/EnableSimpleITKThreads
</div>
</div>

== Preliminary Work ==

The example code below calls two different python functions from inside threads. One function calls the 'time.sleep' method, and one uses VTK to do some processing. As you can see from the output printed below, the VTK threads block, and a new thread is not started until the last one completes. On the other hand, the sleep based thread does return right away. The behavior is based on the [http://docs.python.org/2/glossary.html#term-global-interpreter-lock CPython global interpreter lock]. The topic was [http://web.archiveorange.com/archive/v/aysypJwvM9H8MY8BtpyP discussed in detail] on the vtk developers list back in 2005.

<pre>
import vtk
import threading
import Queue
import time, datetime
import os

class ThreadClass(threading.Thread):
def __init__(self, queue, work):
threading.Thread.__init__(self)
self.queue = queue
self.work = work

def run(self):
now = datetime.datetime.now()
self.queue.put( "start %s, time: %s" % (self.getName(), now) )
self.work()
now = datetime.datetime.now()
self.queue.put( "end %s, time: %s" % (self.getName(), now) )

def process():
e = vtk.vtkImageEllipsoidSource()
e.SetWholeExtent(0,300,0,300,0,300)
s = vtk.vtkImageGaussianSmooth()
s.SetInputConnection(e.GetOutputPort())
s.Update()

def sleep():
time.sleep(1)

for work,message in ((process,'vtk'), (sleep,'sleep')):
print ('threading test with %s:' % message)
threads = 3
queue = Queue.Queue()
for i in range(threads):
t = ThreadClass(queue,work)
t.start()
print('started:')

for i in range(2*threads):
print(queue.get())
print('finished\n')
</pre>

<pre>
#8 Slicer-superbuild $ ./VTK-build/bin/vtkpython /Users/pieper/Dropbox/hacks/threadVTK.py
threading test with vtk:
started:
start Thread-1, time: 2012-12-18 17:13:17.047282
end Thread-1, time: 2012-12-18 17:13:18.006989
start Thread-2, time: 2012-12-18 17:13:18.007318
end Thread-2, time: 2012-12-18 17:13:18.953446
start Thread-3, time: 2012-12-18 17:13:18.953762
end Thread-3, time: 2012-12-18 17:13:19.897673
finished

threading test with sleep:
started:
start Thread-4, time: 2012-12-18 17:13:19.898124
start Thread-5, time: 2012-12-18 17:13:19.898346
start Thread-6, time: 2012-12-18 17:13:19.898506
end Thread-4, time: 2012-12-18 17:13:20.899137
end Thread-6, time: 2012-12-18 17:13:20.899378
end Thread-5, time: 2012-12-18 17:13:20.899469
finished
</pre>

== Update ==

Multi-threading proof of concept:

<pre>
import SimpleITK as sitk
import threading
import Queue
import time, datetime
import os

class ThreadClass(threading.Thread):
def __init__(self, queue, work):
threading.Thread.__init__(self)
self.queue = queue
self.work = work

def run(self):
now = datetime.datetime.now()
self.work()
self.queue.put( "start %s, time: %s" % (self.getName(), now) )
now = datetime.datetime.now()
self.queue.put( "end %s, time: %s" % (self.getName(), now) )

def process():
img = sitk.GaussianSource(sitk.sitkFloat32, [256]*3)
simg = sitk.SmoothingRecursiveGaussian(img)

def sleep():
time.sleep(1)

for work,message in ((process,'sitk'), (sleep,'sleep')):
print ('threading test with %s:' % message)
threads = 5
queue = Queue.Queue()
for i in range(threads):
t = ThreadClass(queue,work)
t.start()

print(queue.qsize())
while queue.empty():
print('empty')
sleep()

for i in range(2*threads):
print(queue.get())
print('finished\n')
</pre>

Results:

<pre>
threading test with sitk:
0
empty
empty
empty
empty
empty
empty
start Thread-2, time: 2013-01-11 11:03:27.098504
end Thread-2, time: 2013-01-11 11:03:32.171759
start Thread-4, time: 2013-01-11 11:03:27.099969
end Thread-4, time: 2013-01-11 11:03:32.563888
start Thread-1, time: 2013-01-11 11:03:27.097554
end Thread-1, time: 2013-01-11 11:03:33.151524
start Thread-5, time: 2013-01-11 11:03:27.103264
end Thread-5, time: 2013-01-11 11:03:33.333674
start Thread-3, time: 2013-01-11 11:03:27.099090
end Thread-3, time: 2013-01-11 11:03:33.586790
finished

threading test with sleep:
0
empty
start Thread-6, time: 2013-01-11 11:03:33.587261
end Thread-6, time: 2013-01-11 11:03:34.589810
start Thread-7, time: 2013-01-11 11:03:33.587563
end Thread-7, time: 2013-01-11 11:03:34.590058
start Thread-8, time: 2013-01-11 11:03:33.587745
end Thread-8, time: 2013-01-11 11:03:34.590183
start Thread-9, time: 2013-01-11 11:03:33.587997
end Thread-9, time: 2013-01-11 11:03:34.590300
start Thread-10, time: 2013-01-11 11:03:33.588265
end Thread-10, time: 2013-01-11 11:03:34.590451
finished
</pre>

2013 Project Week:Threaded SimpleITK Modules

2013-01-11T15:24:57Z

Blowekamp: /* Project Description */

AHM2013-Simple-ITK

2013-01-08T21:59:42Z

Blowekamp: /* Run the environment */

[[AHM_2013#Agenda|Back to AHM_2013 Agenda]]

Presenters: Bradley Lowekamp

== Background ==

SimpleITK is an abstraction layer on top of ITK which provides Python bindings for many of the algorithms in ITK. The tool is under active development and recent additions have focus on providing a more Pythonic interface to the Image class, numerous additional algorithms, along with the addition of transforms and interpolators.

SimpleITK is currently a build option in Slicer3D when using ITKv4. It can provide access to many powerful algorithms in Slicer as python modules or SimpleITK can be used in the Python Interactor for image manipulation and segmentation.

Version 0.6.0rc01 is currently available as a binary download.

== Summary ==

This session will consists of interactive demonstrations of the fundamental concepts and style of SimpleITK along with showing the latest features in the 0.6 release. The presentation will make use of matplotlib and the Scientific Python environment to illustrate a Pythonic workflow to perform common image tasks and segmentation.

== Attendee Preparation ==

Attendees are encouraged to setup a python environment to follow along during this session.

Under the best of circumstances (tested on OSX 10.8 and 10.7.5) this environment can be setup with the following:

sudo pip install virtualenv
virtualenv ~/sitkpy --no-site-packages
~/sitkpy/bin/pip install ipython
~/sitkpy/bin/pip install ipython[zmq]
~/sitkpy/bin/pip install tornado
~/sitkpy/bin/pip install numpy
~/sitkpy/bin/pip install matplotlib

===Install SimpleITK 0.6rc1===

Download the built egg for your system from Source Forge:
http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.6.rc1/Python/

Use easy_install to install or upgrade:

~/sitkpy/bin/easy_install -U SimpleITK-0.6.0.rc1_gc9d89-py$(python version)-$(OS)-$(arch).egg

If there is not a built distribution for your system you will need to build SimpleITK:
http://www.itk.org/Wiki/ITK_Release_4/SimpleITK/GettingStarted#Build_It_Yourself

===Download the course material===

The "notebooks" are available for download as a git repository:

git clone git@github.com:SimpleITK/SimpleITK-Notebooks.git

Additionally the SPL's "Multi-modality MRI-based Atlas of the Brain" should be downloaded and extracted into the SimpleITK-Notebooks/Data directory.

http://www.spl.harvard.edu/publications/item/view/2037

===Run the environment===

To launch:
cd SimpleITK-Notebooks
~/sitkpy/bin/ipython notebook --pylab=inline

Note: On Linux platforms you may be able to obtain many of these packages as system packages which may suffice ( Ubuntu 12+).
Note: On Window platforms some of these packages should be obtained as binary downloads and installed.

AHM2013-Simple-ITK

2013-01-08T03:55:18Z

Blowekamp: /* Install SimpleITK 0.6rc1 */

[[AHM_2013#Agenda|Back to AHM_2013 Agenda]]

Presenters: Bradley Lowekamp

== Background ==

SimpleITK is an abstraction layer on top of ITK which provides Python bindings for many of the algorithms in ITK. The tool is under active development and recent additions have focus on providing a more Pythonic interface to the Image class, numerous additional algorithms, along with the addition of transforms and interpolators.

SimpleITK is currently a build option in Slicer3D when using ITKv4. It can provide access to many powerful algorithms in Slicer as python modules or SimpleITK can be used in the Python Interactor for image manipulation and segmentation.

Version 0.6.0rc01 is currently available as a binary download.

== Summary ==

This session will consists of interactive demonstrations of the fundamental concepts and style of SimpleITK along with showing the latest features in the 0.6 release. The presentation will make use of matplotlib and the Scientific Python environment to illustrate a Pythonic workflow to perform common image tasks and segmentation.

== Attendee Preparation ==

Attendees are encouraged to setup a python environment to follow along during this session.

Under the best of circumstances (tested on OSX 10.8) this environment can be setup with the following:

sudo pip install virutalenv
virtualenv ~/sitkpy --no-site-packages
~/sitkpy/bin/pip install ipython
~/sitkpy/bin/pip install ipython[zmq]
~/sitkpy/bin/pip install Tornado
~/sitkpy/bin/pip install numpy
~/sitkpy/bin/pip install matplotlib

===Install SimpleITK 0.6rc1===

Download the built egg for your system from Source Forge:
http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.6.rc1/Python/

Use easy_install to install or upgrade:

~/sitkpy/bin/easy_install -U SimpleITK-0.6.0.rc1_gc9d89-py$(python version)-$(OS)-$(arch).egg

If there is not a built distribution for your system you will need to build SimpleITK:
http://www.itk.org/Wiki/ITK_Release_4/SimpleITK/GettingStarted#Build_It_Yourself

===Download the course material===

The "notebooks" are available for download as a git repository:

git clone git@github.com:SimpleITK/SimpleITK-Notebooks.git

Additionally the SPL's "Multi-modality MRI-based Atlas of the Brain" should be downloaded and extracted into the SimpleITK-Notebooks/Data directory.

http://www.spl.harvard.edu/publications/item/view/2037

===Run the environment===

To launch:

~/sitkpy/bin/ipython notebook --pylab=inline

Note: On Linux platforms you may be able to obtain many of these packages as system packages which may suffice ( Ubuntu 12+).
Note: On Window platforms some of these packages should be obtained as binary downloads and installed.