NAMIC Wiki - User contributions [en]

File:Dicom2NrrdUIPanel2.png

2011-06-23T18:27:23Z

Taox:

Engineering:TCON 2011

2011-06-16T19:38:19Z

Taox: /* 2011-06-16 */

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

__TOC__

==2011-06-16==
Attendees: Xiadong, Tina, Marc, Nicole, Daniel (UPenn), Mohasen, Lupin (SPL)

*Working meeting to do documentation: http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers

==2011-06-09==
Attendees: Jim, Xiadong, Sonia, Dominik, Dominique, Andreas, Ron, Tina, Nicole, Stephen, Mohasen, Mark Scully, Drew Rotham, Steve Pieper

Agenda:
*[http://www.na-mic.org/Wiki/index.php/Summer_2011_Tutorial_Contest 2011 Summer 2011 Tutorial contest ]dead-line extended until June 13
*DICOM projects at summer project week:
** Networking: putting ctk/dcmtk into slicer4; use case scenarios (Nicole, Steve, Noby, +?)
** ITKv4 DICOM Support: what features will be available? (Drew, Steve, Dan, Bill, +?)
** DICOMRT: mapping between RT/ITK/Slicer datastructures (Greg, Steve, Luis)
** DWI DICOM: what will we do without Xiaodong?!? (Xiaodong, Jim, Hans, Demian)
** other topics?
*Discuss the structure of Slicer 4 documentation in preparation for next week [http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0 Slicer 4 documentation placeholder]
*Agenda for next week will be to have a working meeting where appropriate people join the call and spend the hour on Slicer 4 documentation in preparation for project week http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers

==2011-06-02==

Attendees: Jim, Tina, Steve, Stephen, Demian, Szymon, Anthony Blumsfield, Xiaodong, Nicole, Julien, Suarez, Hans Johnson, Mohasen (VA Hospital), Lauren O'Donnell

Agenda:
*DTI projects at summer project week:
**Tractography Projects: http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Diffusion#Features_to_be_addressed_before_the_Summer_NA-MIC_meeting
**http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week#Projects
*Szymon (EPFL)
**OpenIGT interface Slicer and lab robot
*Anthony
**Spine segmentation project
*Mohasen
**

== 2011-05-26==

Attendees: Junichi, Tina, Tamas, Tamas, Stephen, Jim, Noby, Peter Kazanzies, Ehsan Azimi, Greg Fischer, Hao, Suarez, Csaba

* OpenIGTLink at Project Week

==2011-05-19==
Attendee: Jim, Steve, Dominik, Nicole, Xiaodong, Ross, Marc, Tina, Chiara Carminati (Milan), Adrian(MIT), Ramesh(MIT), Clement (UNC), Nadya (MGH)

Agenda:

*http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week
*openIGTLink discussion next week.

==2011-05-12==

Attendees: Tina, Steve, Allen, Clement, Yi, Ivan, Yi Fi Lou, Jim, Stephen, Mark, Nicole,

Algorithm core participants discuss project week.
* RSS as Editor module
* Mass Spect for Brain Tumors (GaTech, NCIGT, BWH collaboration)
* Head and Neck cancer bone registration
* Multi-modality image registration

==2011-05-05==

No t-con.

==2011-04-28==

Agenda:

*Summer Project Week Kickoff -- Engineering Projects
**http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week

==2011-04-21==
Attendees: Steve, Tina, Julien, Xiaodong, Dominik, Marc, Nicole, Dan, Danielle

Agenda:
*Slicer4 windows build question (Steve)
*MGH DBP discussion with Greg Sharp about multilayer treatment plans (Steve).
*visualizing deformation fields via RGB or vector fields via tensor image (Dominik, Steve)
*Since we had some time today, we did a pre-kickoff discussion of engineering projects: [[2011_Summer_Project_Week#Projects]]

==2011-04-14==
Attendees:

Agenda:

* Continue Slicer4 discussion
** Can schedule another call with Extension developers once the Factory is up and running with example extensions - http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Breakout_Slicer#Extensions
** Any objection to removing all KWWidget code from slicer4 svn?
*** Jc: Option Slicer_BUILD_KWWIDGETS is not supported anymore (it means the build system has been cleaned already) Module and GUI folder code are still here though
** Wrapping Module code (MRML and Logic) in python
*** Jc: Already functional. Need to make wrapping works when module are build as extension
*** VTK classes associated with module should be properly exposed in python.
** Check out "what changed?" and "multivolume containers" in the [http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers#Projects list of Slicer 4 projects].
** Speed, Speed, Speed
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:VisualBlog

==2011-04-07==
Attendees: Jim, Steve, Tina, Dominik, Daniel, Nicole, JC, Suares, Demian, Kilian, Stephen, Andras, Tamas, Marc, Julien Finet, Danielle P.

Agenda:

* Slicer4
** Progress on Modules? Review and update of: http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Breakout_Slicer
*** See comments associated with each modules on 2011_Winter_Project_Week:Breakout_Slicer page
** Any objection to removing all KWWidget code from slicer4 svn?
*** Jc: Option Slicer_BUILD_KWWIDGETS is not supported anymore (it means the build system has been cleaned already) Module and GUI folder code are still here though
** Wrapping Module code (MRML and Logic) in python
*** Jc: Already functional. Need to make wrapping works when module are build as extension
*** VTK classes associated with module should be properly exposed in python.
** Check out "what changed?" and "multivolume containers" in the [http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers#Projects list of Slicer 4 projects].
** Speed, Speed, Speed

==2011-03-24==
Attendees: Steve, Jim, Ann, Tina, Daniel, Suares, Marc, Jack, Nicole, Dominique, Ron

Agenda:

*Scientific Progress Report Discussion (Ann Adams will join at 3pm for 20 minutes)
* http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

==2011-03-24==
Attendees: Jim, Ron, Tina, Dominik, Dominique, Marc, Hans, Daniel, Nicole, Curt, Julien

* Slicer4 layouts - [[Media:FirstCompareViewInSlicer4.png|Hey a CompareView]]
* http://wiki.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:LinkedControls
* http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer
* Licensing Question: CMTK/Brainsfit/

==2011-03-17==
Attendees: Jim, Ron, Marc, Tina, Nicole, Xiaodong, Greg, Dave Partika, Julien Finet

Agenda:
*Slicer 3.6.3: 64 bit versions, extensions
*the default location for a lot of slicer things is the user home directory. This should be changed. It causes problems in the SPL.
**where to put it, how to initiate?
*saving Slicer 4 mrml scenes as secondary capture (Ron)
**I would like to be able to save an entire scene as a [http://www.medicalconnections.co.uk/wiki/Creating_Secondary_Capture_Images dicom secondary capture]. This would allow to use accessible pacs systems as repositories for slicer scenes
**is there a way to incorporate thumbnails and descriptions from the new sceneviews?
*Slicer3 linked controls
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:LinkedControls#cite_note-0 Jim's notes]
** [http://www.na-mic.org/Bug/view.php?id=1117 bug 117]

Notes:
* Dave P will build Windows builds of Slicer and extensions (a version without numpy, make a release note) and Steve will upload. Also the darwin, need to match svn version
* Default location: ask user for not home dir directory if default is not set
** related bugs: [http://www.na-mic.org/Bug/view.php?id=598 598]
* Secondary capture to interact with PACS
** tcon before project week with Jim, Nicole, Wendy, Steve to talk about infrastructure
* Linked controls
** Scroll wheel and arrows after Steve/Nicole's implementation of the link/orientation flag only scroll the current slice viewer and the other viewers with the same orientation, need more feedback from users/Andrey
** use cases between move all slices by copying this slices's RAS matrix to the other slice nodes, and linked increment slice that moves the other slices by an incremental distance
** reformat mode and linking. If in compare view mode and change one of multiple reformat slices, the other reformatted slice views will jump to that
** proposal: link some mode, so have more granularity than all or none (currently do have a one slice link toggle key)
*** reserve some link states so can by default link certain slices
* Ron to Xiaodong: use HAMMER on new brain atlas? not tried yet

==2011-03-10==

Attendees: Jim, Steve, Mark S., Nicole, Tina

Agenda:
* 3.6.4 release planning discussion [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues]
** In particular, fix for the linked slice views [http://www.na-mic.org/Bug/view.php?id=1115] (see also [http://www.na-mic.org/Bug/view.php?id=1003 1003])
** pan mode resets slice orientation ([http://www.na-mic.org/Bug/view.php?id=1117 bug #1117])
** What steps should be used for testing fixes for these bugs?
*** Are all use cases covered in currently [http://www.slicer.org/slicerWiki/index.php/Modules:MainApplicationGUI-Documentation-3.6#Linking_Control_of_Slice_Viewers documented behavior]?
***Show hide reformat widget behavior should incorporate the Michal Depa/Steve Pieper modifcations for linked views with reformat widget.
*** What optimizations (delayed updates) are we expected in for situations like compare view?
**when linked views are in the same location and visible, there are artifacts in the 3d viewer.
* More flexibility in the names of the results of CLI's. It would be good to have the ability to incorporate:
**Source volume name
**Module name
**some important parameters

Notes:
* linked slice views: Jim will write up a wiki page describing the expected behaviour, Steve and Nicole will debug
* CLI names: Jim says "yes"
* CLI compilation with separated header files: Jim, Steve, Mark to look into this via webex

==2011-03-03==

Attendees: Steve, Nicole, Jim, Andrey, Suarez, Ron, Stephen A., Daniel H, Dominique B., Xioadong, Greg Sharp, Mark S, Dominik, Hans

Agenda:
* C++/C wrapping of modules
** Hans and Greg figured out what was going wrong. In BRAINS tools they did a trick to get around Bill's trick. It takes 8 minutes to build BRAINSfit, to break it down into smaller compilation units and test it using ITK testing framework. It has a thin wrapper around program to add comparator functions. BRAINSfit is a small 3 line wrapper around BRAINS fit primary that takes argc and argv and includes generated header file. You can't include CLP header file in both compilation units since functions are defined in header file. See error at link time. If you put the right ifdef compiling for slicer and module description is defined you can make it work. Hans would like to see the CLP broken apart into a compile until and a header unit. Jim: harder to build and link - but is done through macros. Could have a test before include CLP.h. Hans: wants to be able to include the .h file in every file. Change: now would have to write a programCLP.h and programCLP.cxx.
** definitely needs to be done in Slicer4, tbd in Slicer3 (Hans using Slicer3 in his class).
*** the add executable, add library lines macros would need to be touched, need to link new object file
*** before when build both a shared and a command line module it would have to rebuild all the itk stuff twice, Casey made the change to not require it
*** Steve: came up wrt diffusion modules because they're using vtk nrrd readers that don't know about shared memory pointers
*** Hans: was building itk files three times for exec, lib, testing
** Jim will take a look at what breaks when try to split it out, code generation is easy, the add_executable will be a bit tricky
** Hans: suggests adding the .cxx to the GenerateCLP macro that defines the .h, to use in the CMakeLists. Hans will do the changes to all the execution modules that need to be changed once the infrastructure is changed (or not).
** One BRAINSfit test failing: any multi threaded mutual information code is suspect to the bug that they found. Quick fix: restrict to one thread, huge slow down (2-4x). Bug is in the Mattes mutual information optimize metric (?) in the registration framework for certain number of threads (4,7, etc). Stephen A will look at it after March 9.
* Annotation module widget priority for ROI nodes
** Ron, Daniel agrees to put it as higher than the bidimensional widget
** ROI widget is in the critical path for the volume rendering module, as well as others
** Reformat widget to priority list? will require taking something out. Will is working on a new widget, wait on that. Andrey says the reformat widget will be useful in crop volume as well. General Slicer4 widget (was integrated in the 3d viewer in Slicer3). Nicole is taking on the integration of the vtk widgets.
* Contributing modules to Slicer4 (policy review)
** by default new modules should got to an external repository (NITRC, external module) and remain there for a while until whole module goes into Slicer4 if it's determined to be core functionality
** Slicer4 core to remail lean, but external modules to be first class citizens.
** Documentation requirements, building and testing on the factory machine every night.
** If a new module fails it shouldn't break Slicer4 building or running
** Timeline on extension mechanism in Slicer4?
*** Steve wanted to get the base nightly builds working first, but need to get the extensions built nightly asap
*** new feature in next release of cdash and cmake, ctest upload command to upload binaries, can get a list of uploads from dashboard
*** harvest the information from the cdash dashboard and make it available to the extension manager rather than have the extension manager communicate directly with the (sometimes slow) dashboards. Only let uploads come from factory machines. Use VMs to run test code.
*** Steve will be the gatekeeper to allow code to be built and tested on the factory for now
**** flag for if it gets redistributed, critical/non critical build
**** allow to build locally but submit to main slicer dashboard (no code upload), already supported via Experimental
** Greg: wants to be able to build a bug fixed version of an extension for an old release (limited support for it)

==2011-02-10==

Attendees: Jim, Mark, Tina, Nicole, Dan

Agenda:
*Updates from ITK meeting
*http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
**Heads up given to everyone that progress report is due on wiki by mid April

==2011-02-03==
Attendees: Suares, Dominik, Kilian, Dominique, Nicole, Daniel, Stephen, Tina, Xiaodong

Agenda:
*ITK meeting in progress in Boston. Steve and Jim attending it.
*http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0
**Automatic documentation generation options are being explored at Kitware. Stephen will report as progress is made.
*http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
**Heads up given to everyone that progress report is due on wiki by mid April

==2011-01-27==

No tcon today.

==2011-01-20==

Attendees: Xiaodong, Wendy, Tina, Mark, Nicole, Dominik, Daniel,

Agenda

* [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues Slicer 3.6.3]
* http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week
* http://wiki.na-mic.org/Wiki/index.php/Resources#Active_Job_Openings

==2011-01-06==

Attendees: Steve, Stephen, Jim, Ron, Tina, Dan Marcus, Xiaodong

Agenda:

*News: DCMTK 3.6 was released today
* http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week#Projects
* Command line module logic, supporting multiple argument for images in Slicer3/4
* Discussion of ITK support for large (greater than 4Gig) image volumes on win64. This will be further investigated at project week. It is only one of several issues to be researched as part of porting slicer3 and slicer4 to win64. Dave Partyka has a [[2011_Winter_Project_Week:64bit_Windows_Builds|project to work on this]] at project week.

2011 Summer Project Week Dicom2Nrrd

2011-06-16T19:05:43Z

Taox:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Dicom2NrrdUIPanel.png|UI Panel
</gallery>

'''Dicom To NRRD Converter'''

==Key Investigators==
* GE Research: Xiaodong Tao
* UIowa: Mark Scully

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

<h3>Objective</h3>


*Refactoring the DWI DicomToNrrdConverter using GDCM 2.x.

By separating the big (and only) .cxx file into multiple small classes that handle one type of data each, the maintainability of the entire code will be greatly improved. And the program can easily be extended into new vendor's format and new data types (for example, time series).

</div>

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

<h3>Approach, Plan</h3>


*Separate code for supporting different DICOM format from various vendors into individual classes.
*As a project week activity, we will code up the base class and implementation for one vendor format.
*The interface visible to the users (the driver program) will be keep unchanged.
</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

*[[http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:DicomToNrrdRefactoring 2011 winter Utah project week]]
*[[NAMIC_Wiki:DTI:Nrrd_format | DTI:Nrrd_Format]]
*[[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI|DICOM_for_DWI_and_DTI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a command line module.

File:Dicom2NrrdUIPanel.png

2011-06-16T19:04:31Z

Taox:

2011 Summer Project Week Dicom2Nrrd

2011-06-16T19:03:25Z

Taox:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:PW-MIT2011.png|UI Panel
</gallery>

'''Dicom To NRRD Converter'''

==Key Investigators==
* GE Research: Xiaodong Tao
* UIowa: Mark Scully

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

<h3>Objective</h3>


*Refactoring the DWI DicomToNrrdConverter using GDCM 2.x.

By separating the big (and only) .cxx file into multiple small classes that handle one type of data each, the maintainability of the entire code will be greatly improved. And the program can easily be extended into new vendor's format and new data types (for example, time series).

</div>

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

<h3>Approach, Plan</h3>


*Separate code for supporting different DICOM format from various vendors into individual classes.
*As a project week activity, we will code up the base class and implementation for one vendor format.
*The interface visible to the users (the driver program) will be keep unchanged.
</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

*[[http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:DicomToNrrdRefactoring 2011 winter Utah project week]]
*[[NAMIC_Wiki:DTI:Nrrd_format | DTI:Nrrd_Format]]
*[[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI|DICOM_for_DWI_and_DTI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a command line module.

2011 Summer Project Week Dicom2Nrrd

2011-06-16T18:56:32Z

Taox: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:DicomToNrrdUIPanel.jpg
</gallery>

'''Dicom To NRRD Converter'''

==Key Investigators==
* GE Research: Xiaodong Tao
* UIowa: Mark Scully

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

<h3>Objective</h3>


*Refactoring the DWI DicomToNrrdConverter using GDCM 2.x.

By separating the big (and only) .cxx file into multiple small classes that handle one type of data each, the maintainability of the entire code will be greatly improved. And the program can easily be extended into new vendor's format and new data types (for example, time series).

</div>

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

<h3>Approach, Plan</h3>


*Separate code for supporting different DICOM format from various vendors into individual classes.
*As a project week activity, we will code up the base class and implementation for one vendor format.
*The interface visible to the users (the driver program) will be keep unchanged.
</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

*[[http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:DicomToNrrdRefactoring 2011 winter Utah project week]]
*[[NAMIC_Wiki:DTI:Nrrd_format | DTI:Nrrd_Format]]
*[[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI|DICOM_for_DWI_and_DTI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a command line module.

2011 Summer Project Week Dicom2Nrrd

2011-06-16T18:55:50Z

Taox: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:DicomToNrrdUIPanel.jpg
</gallery>

'''Dicom To NRRD Converter'''

==Key Investigators==
* GE Research: Xiaodong Tao
* UIowa: Mark Scully

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

<h3>Objective</h3>


*Refactoring the DWI DicomToNrrdConverter using GDCM 2.x.
*Clean up current code.
*Better documentation.

By separating the big (and only) .cxx file into multiple small classes that handle one type of data each, the maintainability of the entire code will be greatly improved. And the program can easily be extended into new vendor's format and new data types (for example, time series).

</div>

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

<h3>Approach, Plan</h3>


*Separate code for supporting different DICOM format from various vendors into individual classes.
*As a project week activity, we will code up the base class and implementation for one vendor format.
*The interface visible to the users (the driver program) will be keep unchanged.
</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

*[[http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:DicomToNrrdRefactoring 2011 winter Utah project week]]
*[[NAMIC_Wiki:DTI:Nrrd_format | DTI:Nrrd_Format]]
*[[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI|DICOM_for_DWI_and_DTI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a command line module.

2011 Summer Project Week Dicom2Nrrd

2011-06-16T18:54:26Z

Taox: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:DicomToNrrdUIPanel.jpg
</gallery>

'''Dicom To NRRD Converter'''

==Key Investigators==
* GE Research: Xiaodong Tao
* UIowa: Mark Scully

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

<h3>Objective</h3>


Refactoring the DWI DicomToNrrdConverter using GDCM 2.x. Clean up current code and better documentation. By separating the big (and only) .cxx file into multiple small classes that handle one type of data each, the maintainability of the entire code will be greatly improved. And the program can easily be extended into new vendor's format and new data types (for example, time series).

</div>

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

<h3>Approach, Plan</h3>


Separate code for supporting different DICOM format from various vendors into individual classes. As a project week activity, we will code up the base class and implementation for one vendor format. The interface visible to the users (the driver program) will be keep unchanged.
</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

*[[http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:DicomToNrrdRefactoring 2011 winter Utah project week]]
*[[NAMIC_Wiki:DTI:Nrrd_format | DTI:Nrrd_Format]]
*[[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI|DICOM_for_DWI_and_DTI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a command line module.

2011 Summer Project Week Dicom2Nrrd

2011-06-16T15:08:05Z

Taox: /* References */

2011 Summer Project Week Dicom2Nrrd

2011-06-16T15:06:38Z

Taox: /* Delivery Mechanism */

2011 Summer Project Week Dicom2Nrrd

2011-06-16T15:05:42Z

Taox:

2011 Summer Project Week Dicom2Nrrd

2011-06-16T15:04:58Z

Taox: Created page with '__NOTOC__ <gallery> Image:PW-MIT2011.png|Projects List Image:Slicer4-AnnotationGUI.jpg </gallery> '''Dicom To NRRD Converter''' ==Key Inve…'

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-AnnotationGUI.jpg
</gallery>

'''Dicom To NRRD Converter'''

==Key Investigators==
* GE Research: Xiaodong Tao
* UIowa: Mark Scully

<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: 40%; float: left;">

<h3>Progress</h3>



</div>
</div>

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

==References==

[[http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:DicomToNrrdRefactoring 2011 winter Utah project week]]

==Delivery Mechanism==

2011 Summer Project Week

2011-06-16T15:01:52Z

Taox: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[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)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

#[[2011_Summer_Project_Week_Slicer_DICOM_RT_Brachytherapy|Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer]](Tina Kapur, Greg Sharp, Jan Egger, Firdaus Janoos)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#[[2011_Summer_Project_Week_Dicom2Nrrd|DicomToNrrdConverter refactoring]] ( Xiaodong Tao, Mark Scully)
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#[[Multimodality Image Registration for TBI]] (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
#Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
#Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Mark Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#[[2011_Summer_Project__Week_Live_Tracked_Ultrasound|Live Tracked Ultrasound with Slicer4 (Tamas Heffter)]]
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#[[2011_Summer_Project_Week_DTIPrep|DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation]] - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
#Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Mark Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
#Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
#Refactoring of the tractography display widget (Isaiah)
#Laterality (Lauren)
#Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
#[[Summer_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions]] (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#Slicer module for building an average population HARDI Atlas (Ryan Eckbo)
#4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)
#EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)
#[[2011_Summer_Project_Week_ODF_though_Fiber_Counting | ODF computation through fiber counting]] (Yinpeng Li, Ipek Oguz, Martin Styner)
#[[2011_Summer_Project_Week_Intraoperative_Brain_Shift_Monitor|Intraoperative Brain Shift Monitor]] (Jason White, Alex Golby, Steve Pieper)
#[[2011_Summer_Project_Week_DTI_Volumetric_Segmentation_for_Group_studies | DTI Volumetric Segmentation for Group studies]] (Gopal Veni, Ross Whitaker)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, 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 28th 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], and [http://www.cimit.org CIMIT]. 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 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, 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 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)
# Nicole Aucoin , Brigham and Women's Hospital
# Dominique Belhachemi , University of Pennsylvania
# Anthony Blumfiled , Radnostics
# Lucile Bompard , UNC NIRAL
# Sylvain Bouix , Brigham and Women's Hospital
# Francois Budin , UNC NIRAL
# Steve Callahan , University of Utah
# Joshua Cates , University of Utah
# Laurent Chauvin , Brigham and Women's Hospital
# Adrian Dalca , MIT CSAIL
# Manasi Datar , University of Utah
# Colin Davey ,
# Ryan Eckbo , Brigham and Women's Hospital
# Jan Egger , University Hospital of Marburg
# Luping Fang , Zhejiang University of Technology, China
# mahshid farzinfar , UNC
# Andriy Fedorov , Brigham and Women's Hospital
# Julien Finet , Kitware Inc.
# James Fishbaugh , University of Utah
# Greg Gardner , University of Utah
# Ronen Globinsky , Yale University
# Maged Goubran , Robarts Research Institute
# Daniel Haehn , University of Pennsylvania
# Mike Halle , Brigham and Women's Hospital
# Noby Hata , Brigham and Women's Hospital
# Tamas Heffter , Queen's University
# Andrei Irimia , University of California, Los Angeles
# Hans Johnson , University of Iowa
# Ilknur Kabul , Kitware
# Tina Kapur , Brigham and Women's Hospital
# Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School
# Regina Kim , University of Iowa
# Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee , University of Utah
# Yinpeng Li , UNC-NIRAL
# Yifei Lou , Georgia Institute of Technology
# mohsen mahvash , Harvard Medical School (BWH and VA)
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University of Iowa
# Dominik Meier , BWH
# Mikhail Milchenko , Washington University in St. Louis
# James Miller , GE Research
# Isaiah Norton , Brigham and Women's Hospital
# Danielle Pace , Kitware
# Beatriz Paniagua , University of North Carolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Kedar Patwardhan , GE Global Research
# Steve Pieper , Isomics, Inc.
# Csaba Pinter , Queen's University
# Wendy Plesniak , Brigham and Women's Hospital
# Kilian Pohl , UPenn
# Marcel Prastawa , University of Utah
# Sonia Pujol , Brigham and Women's Hospital
# Martin Rajchl , Robarts Research Institute
# Petter Risholm , Brigham and Women's Hospital
# Peter Savadjiev , Brigham and Women's Hospital
# Andreas Schuh , University of Pennsylvania
# Mark Scully , University of Iowa
# Gregory Sharp , MGH
# Yundi Shi , UNC-Chapel Hill
# Nadya Shusharina , MGH
# Ramesh Sridharan , MIT CSAIL
# Hao Su , WPI
# Suarez Tamekue , Brigham and Women's Hospital
# Xiaodong Tao , GE Research
# Clement Vachet , UNC Chapel Hill
# Antonio Vega , Brigham and Women's Hospital
# Gopal Veni , University of Utah
# Bo Wang , University of Utah
# Demian Wasserman , Brigham and Women's Hospital
# Sandy Wells , Brigham and Women's Hospital
# Jason White , Brigham and Women's Hospital
# Atsushi Yamada , Brigham and Women's Hospital
# Alexander Yarmarkovich , Isomics
# Alexander Zaitsev , Brigham and Women's Hospital

Engineering:TCON 2011

2011-06-09T19:29:31Z

Taox: /* 2011-06-09 */

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

__TOC__

==2011-06-16==

*Working meeting to do documentation: http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers

==2011-06-09==

Agenda:
*[http://www.na-mic.org/Wiki/index.php/Summer_2011_Tutorial_Contest 2011 Summer 2011 Tutorial contest ]dead-line extended until June 13
*DICOM projects at summer project week:
** Networking: putting ctk/dcmtk into slicer4; use case scenarios (Nicole, Steve, Noby, +?)
** ITKv4 DICOM Support: what features will be available? (Drew, Steve, Dan, Bill, +?)
** DICOMRT: mapping between RT/ITK/Slicer datastructures (Greg, Steve, Luis)
** DWI DICOM: what will we do without Xiaodong?!? (Xiaodong, Jim, Hans, Demian)
** other topics?
*Discuss the structure of Slicer 4 documentation in preparation for next week [http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0 Slicer 4 documentation placeholder]
*Agenda for next week will be to have a working meeting where appropriate people join the call and spend the hour on Slicer 4 documentation in preparation for project week http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers

==2011-06-02==

Attendees: Jim, Tina, Steve, Stephen, Demian, Szymon, Anthony Blumsfield, Xiaodong, Nicole, Julien, Suarez, Hans Johnson, Mohasen (VA Hospital), Lauren O'Donnell

Agenda:
*DTI projects at summer project week:
**Tractography Projects: http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Diffusion#Features_to_be_addressed_before_the_Summer_NA-MIC_meeting
**http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week#Projects
*Szymon (EPFL)
**OpenIGT interface Slicer and lab robot
*Anthony
**Spine segmentation project
*Mohasen
**

== 2011-05-26==

Attendees: Junichi, Tina, Tamas, Tamas, Stephen, Jim, Noby, Peter Kazanzies, Ehsan Azimi, Greg Fischer, Hao, Suarez, Csaba

* OpenIGTLink at Project Week

==2011-05-19==
Attendee: Jim, Steve, Dominik, Nicole, Xiaodong, Ross, Marc, Tina, Chiara Carminati (Milan), Adrian(MIT), Ramesh(MIT), Clement (UNC), Nadya (MGH)

Agenda:

*http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week
*openIGTLink discussion next week.

==2011-05-12==

Attendees: Tina, Steve, Allen, Clement, Yi, Ivan, Yi Fi Lou, Jim, Stephen, Mark, Nicole,

Algorithm core participants discuss project week.
* RSS as Editor module
* Mass Spect for Brain Tumors (GaTech, NCIGT, BWH collaboration)
* Head and Neck cancer bone registration
* Multi-modality image registration

==2011-05-05==

No t-con.

==2011-04-28==

Agenda:

*Summer Project Week Kickoff -- Engineering Projects
**http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week

==2011-04-21==
Attendees: Steve, Tina, Julien, Xiaodong, Dominik, Marc, Nicole, Dan, Danielle

Agenda:
*Slicer4 windows build question (Steve)
*MGH DBP discussion with Greg Sharp about multilayer treatment plans (Steve).
*visualizing deformation fields via RGB or vector fields via tensor image (Dominik, Steve)
*Since we had some time today, we did a pre-kickoff discussion of engineering projects: [[2011_Summer_Project_Week#Projects]]

==2011-04-14==
Attendees:

Agenda:

* Continue Slicer4 discussion
** Can schedule another call with Extension developers once the Factory is up and running with example extensions - http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Breakout_Slicer#Extensions
** Any objection to removing all KWWidget code from slicer4 svn?
*** Jc: Option Slicer_BUILD_KWWIDGETS is not supported anymore (it means the build system has been cleaned already) Module and GUI folder code are still here though
** Wrapping Module code (MRML and Logic) in python
*** Jc: Already functional. Need to make wrapping works when module are build as extension
*** VTK classes associated with module should be properly exposed in python.
** Check out "what changed?" and "multivolume containers" in the [http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers#Projects list of Slicer 4 projects].
** Speed, Speed, Speed
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:VisualBlog

==2011-04-07==
Attendees: Jim, Steve, Tina, Dominik, Daniel, Nicole, JC, Suares, Demian, Kilian, Stephen, Andras, Tamas, Marc, Julien Finet, Danielle P.

Agenda:

* Slicer4
** Progress on Modules? Review and update of: http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Breakout_Slicer
*** See comments associated with each modules on 2011_Winter_Project_Week:Breakout_Slicer page
** Any objection to removing all KWWidget code from slicer4 svn?
*** Jc: Option Slicer_BUILD_KWWIDGETS is not supported anymore (it means the build system has been cleaned already) Module and GUI folder code are still here though
** Wrapping Module code (MRML and Logic) in python
*** Jc: Already functional. Need to make wrapping works when module are build as extension
*** VTK classes associated with module should be properly exposed in python.
** Check out "what changed?" and "multivolume containers" in the [http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers#Projects list of Slicer 4 projects].
** Speed, Speed, Speed

==2011-03-24==
Attendees: Steve, Jim, Ann, Tina, Daniel, Suares, Marc, Jack, Nicole, Dominique, Ron

Agenda:

*Scientific Progress Report Discussion (Ann Adams will join at 3pm for 20 minutes)
* http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

==2011-03-24==
Attendees: Jim, Ron, Tina, Dominik, Dominique, Marc, Hans, Daniel, Nicole, Curt, Julien

* Slicer4 layouts - [[Media:FirstCompareViewInSlicer4.png|Hey a CompareView]]
* http://wiki.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:LinkedControls
* http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer
* Licensing Question: CMTK/Brainsfit/

==2011-03-17==
Attendees: Jim, Ron, Marc, Tina, Nicole, Xiaodong, Greg, Dave Partika, Julien Finet

Agenda:
*Slicer 3.6.3: 64 bit versions, extensions
*the default location for a lot of slicer things is the user home directory. This should be changed. It causes problems in the SPL.
**where to put it, how to initiate?
*saving Slicer 4 mrml scenes as secondary capture (Ron)
**I would like to be able to save an entire scene as a [http://www.medicalconnections.co.uk/wiki/Creating_Secondary_Capture_Images dicom secondary capture]. This would allow to use accessible pacs systems as repositories for slicer scenes
**is there a way to incorporate thumbnails and descriptions from the new sceneviews?
*Slicer3 linked controls
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:LinkedControls#cite_note-0 Jim's notes]
** [http://www.na-mic.org/Bug/view.php?id=1117 bug 117]

Notes:
* Dave P will build Windows builds of Slicer and extensions (a version without numpy, make a release note) and Steve will upload. Also the darwin, need to match svn version
* Default location: ask user for not home dir directory if default is not set
** related bugs: [http://www.na-mic.org/Bug/view.php?id=598 598]
* Secondary capture to interact with PACS
** tcon before project week with Jim, Nicole, Wendy, Steve to talk about infrastructure
* Linked controls
** Scroll wheel and arrows after Steve/Nicole's implementation of the link/orientation flag only scroll the current slice viewer and the other viewers with the same orientation, need more feedback from users/Andrey
** use cases between move all slices by copying this slices's RAS matrix to the other slice nodes, and linked increment slice that moves the other slices by an incremental distance
** reformat mode and linking. If in compare view mode and change one of multiple reformat slices, the other reformatted slice views will jump to that
** proposal: link some mode, so have more granularity than all or none (currently do have a one slice link toggle key)
*** reserve some link states so can by default link certain slices
* Ron to Xiaodong: use HAMMER on new brain atlas? not tried yet

==2011-03-10==

Attendees: Jim, Steve, Mark S., Nicole, Tina

Agenda:
* 3.6.4 release planning discussion [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues]
** In particular, fix for the linked slice views [http://www.na-mic.org/Bug/view.php?id=1115] (see also [http://www.na-mic.org/Bug/view.php?id=1003 1003])
** pan mode resets slice orientation ([http://www.na-mic.org/Bug/view.php?id=1117 bug #1117])
** What steps should be used for testing fixes for these bugs?
*** Are all use cases covered in currently [http://www.slicer.org/slicerWiki/index.php/Modules:MainApplicationGUI-Documentation-3.6#Linking_Control_of_Slice_Viewers documented behavior]?
***Show hide reformat widget behavior should incorporate the Michal Depa/Steve Pieper modifcations for linked views with reformat widget.
*** What optimizations (delayed updates) are we expected in for situations like compare view?
**when linked views are in the same location and visible, there are artifacts in the 3d viewer.
* More flexibility in the names of the results of CLI's. It would be good to have the ability to incorporate:
**Source volume name
**Module name
**some important parameters

Notes:
* linked slice views: Jim will write up a wiki page describing the expected behaviour, Steve and Nicole will debug
* CLI names: Jim says "yes"
* CLI compilation with separated header files: Jim, Steve, Mark to look into this via webex

==2011-03-03==

Attendees: Steve, Nicole, Jim, Andrey, Suarez, Ron, Stephen A., Daniel H, Dominique B., Xioadong, Greg Sharp, Mark S, Dominik, Hans

Agenda:
* C++/C wrapping of modules
** Hans and Greg figured out what was going wrong. In BRAINS tools they did a trick to get around Bill's trick. It takes 8 minutes to build BRAINSfit, to break it down into smaller compilation units and test it using ITK testing framework. It has a thin wrapper around program to add comparator functions. BRAINSfit is a small 3 line wrapper around BRAINS fit primary that takes argc and argv and includes generated header file. You can't include CLP header file in both compilation units since functions are defined in header file. See error at link time. If you put the right ifdef compiling for slicer and module description is defined you can make it work. Hans would like to see the CLP broken apart into a compile until and a header unit. Jim: harder to build and link - but is done through macros. Could have a test before include CLP.h. Hans: wants to be able to include the .h file in every file. Change: now would have to write a programCLP.h and programCLP.cxx.
** definitely needs to be done in Slicer4, tbd in Slicer3 (Hans using Slicer3 in his class).
*** the add executable, add library lines macros would need to be touched, need to link new object file
*** before when build both a shared and a command line module it would have to rebuild all the itk stuff twice, Casey made the change to not require it
*** Steve: came up wrt diffusion modules because they're using vtk nrrd readers that don't know about shared memory pointers
*** Hans: was building itk files three times for exec, lib, testing
** Jim will take a look at what breaks when try to split it out, code generation is easy, the add_executable will be a bit tricky
** Hans: suggests adding the .cxx to the GenerateCLP macro that defines the .h, to use in the CMakeLists. Hans will do the changes to all the execution modules that need to be changed once the infrastructure is changed (or not).
** One BRAINSfit test failing: any multi threaded mutual information code is suspect to the bug that they found. Quick fix: restrict to one thread, huge slow down (2-4x). Bug is in the Mattes mutual information optimize metric (?) in the registration framework for certain number of threads (4,7, etc). Stephen A will look at it after March 9.
* Annotation module widget priority for ROI nodes
** Ron, Daniel agrees to put it as higher than the bidimensional widget
** ROI widget is in the critical path for the volume rendering module, as well as others
** Reformat widget to priority list? will require taking something out. Will is working on a new widget, wait on that. Andrey says the reformat widget will be useful in crop volume as well. General Slicer4 widget (was integrated in the 3d viewer in Slicer3). Nicole is taking on the integration of the vtk widgets.
* Contributing modules to Slicer4 (policy review)
** by default new modules should got to an external repository (NITRC, external module) and remain there for a while until whole module goes into Slicer4 if it's determined to be core functionality
** Slicer4 core to remail lean, but external modules to be first class citizens.
** Documentation requirements, building and testing on the factory machine every night.
** If a new module fails it shouldn't break Slicer4 building or running
** Timeline on extension mechanism in Slicer4?
*** Steve wanted to get the base nightly builds working first, but need to get the extensions built nightly asap
*** new feature in next release of cdash and cmake, ctest upload command to upload binaries, can get a list of uploads from dashboard
*** harvest the information from the cdash dashboard and make it available to the extension manager rather than have the extension manager communicate directly with the (sometimes slow) dashboards. Only let uploads come from factory machines. Use VMs to run test code.
*** Steve will be the gatekeeper to allow code to be built and tested on the factory for now
**** flag for if it gets redistributed, critical/non critical build
**** allow to build locally but submit to main slicer dashboard (no code upload), already supported via Experimental
** Greg: wants to be able to build a bug fixed version of an extension for an old release (limited support for it)

==2011-02-10==

Attendees: Jim, Mark, Tina, Nicole, Dan

Agenda:
*Updates from ITK meeting
*http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
**Heads up given to everyone that progress report is due on wiki by mid April

==2011-02-03==
Attendees: Suares, Dominik, Kilian, Dominique, Nicole, Daniel, Stephen, Tina, Xiaodong

Agenda:
*ITK meeting in progress in Boston. Steve and Jim attending it.
*http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0
**Automatic documentation generation options are being explored at Kitware. Stephen will report as progress is made.
*http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
**Heads up given to everyone that progress report is due on wiki by mid April

==2011-01-27==

No tcon today.

==2011-01-20==

Attendees: Xiaodong, Wendy, Tina, Mark, Nicole, Dominik, Daniel,

Agenda

* [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues Slicer 3.6.3]
* http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week
* http://wiki.na-mic.org/Wiki/index.php/Resources#Active_Job_Openings

==2011-01-06==

Attendees: Steve, Stephen, Jim, Ron, Tina, Dan Marcus, Xiaodong

Agenda:

*News: DCMTK 3.6 was released today
* http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week#Projects
* Command line module logic, supporting multiple argument for images in Slicer3/4
* Discussion of ITK support for large (greater than 4Gig) image volumes on win64. This will be further investigated at project week. It is only one of several issues to be researched as part of porting slicer3 and slicer4 to win64. Dave Partyka has a [[2011_Winter_Project_Week:64bit_Windows_Builds|project to work on this]] at project week.

2011 Summer Project Week

2011-04-28T19:24:05Z

Taox: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 20
!width="250px"|Tuesday, June 21
!width="250px"|Wednesday, June 22
!width="250px"|Thursday, June 23
!width="250px"|Friday, June 24
|-
|
|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'''
|
|'''Updates on NA-MIC Kit'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10:15am:''' Break
<br>----------------------------------------<br>
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[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)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font>
<br> Breakout Session TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] TO BE CONFIRMED (Sean Megason)
<br>[[MIT_Project_Week_Rooms#Kiva|Kiva Room]]
<br>----------------------------------------<br>
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[2011 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms|Room TBD]]
<br>----------------------------------------<br>
<br>'''5pm: <font color="#4020ff">Reception'''</font><br>
<br>[[MIT_Project_Week_Rooms#R&D Pub|R&D Pub]]
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>----------------------------------------<br>
'''2-3pm:'''Breakout Session:TBD'''
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session: TBD'''</font><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
|
|}

==Projects==
*Evaluate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
*Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
*Annotation Module in Slicer4 (Nicole Aucoin, Daniel Haehn)
*Slicer4 Multivolume Containers (Ron Kikinis, Nicole Aucoin, Steve Pieper, ... )
**RECIST Slicer4 module (Nicole Aucoin)
*DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, 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 28th 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], and [http://www.cimit.org CIMIT]. 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 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Check back for a link to online registration, which will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, 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 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

2011 Winter Project Week:Breakout Pathology and Longitudinal Followup

2011-01-11T20:25:37Z

Taox: /* Expected Participants */

Back to [[AHM 2011#Agenda| Project Week Agenda]]

'''Session Leader:Guido Gerig'''

Informal discussion on development and implementation of:
*a) methods towards segmentation and visualization of pathology
*b) methodology required to assess follow-up data with and without pathology

The session was mainly motivated by questions in regard to the UCLA DBP project on TBI, but the discussion might be relevant to all other clinical subject-specific analysis involving pathology and/or serial or longitudinal data.

== Expected Participants ==

*Guido Gerig, Utah
*Stephen Aylward, Kitware
*Marcel Prastawa, Utah
*Martin Styner, UNC
*Micah Chambers, UCLA
*Andrei Irmia, UCLA
*Bo Wang, Utah
*Anuja Sharma, Utah
*Hans Johnson, Iowa
*Mark Scully, Iowa
*Joy Matsui, Iowa
*Xiaodong Tao, GE Research
*also invited: John Van Horn, UCLA
*etc., everyone interested in this topic is welcome to attend

2011 Winter Project Week:DicomToNrrdRefactoring

2011-01-11T18:45:06Z

Taox: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Mark Scully, Joy Matsui
* GE: Xiaodong Tao

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

<h3>Objective</h3>
Gather requirements in support of refactoring the DWI DicomToNrrdConverter.

</div>

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

<h3>Approach, Plan</h3>
Meet with anyone interested and establish a list of known requirements for DicomToNrrdConverter.
Collectively brainstorm approaches to the refactoring, such as the use of GDCM 1.2 vs. GDCM 2.x vs. DCMTK.
References:
*[[NAMIC_Wiki:DTI:Nrrd_format | DTI:Nrrd_Format]]
*[[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI|DICOM_for_DWI_and_DTI]]

</div>

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

<h3>Progress</h3>
Current DWI variations list:
* slice ordering (S->I vs I->S),
* transfer syntax endianness (big, little, and unknown),
* slice arrangement (mosaic vs split, slice interleaving vs volume interleaving),
* #B-Values (single vs multiple),
* gradient vector reference frame (Scanner vs patient),
* slice orientation (orthogonal vs oblique),
* multiple B0s (all at beginning, all at end, interspersed)
* vendor (different ways of storing diffusion information),
* software versions (changes in how diffusion information is stored and interpreted).

</div>
</div>



==Activities at SLC meeting==

'''Objectives'''

* Redesign DicomToNrrdConverter so that it is more maintainable.
* Design a general base class to support most of the medical images in dicom format.
* Supports for vendor/version/datatype combinations are implemented as derived classes and are independent from each other.
* (Possibly) define APIs and derived classes for functional MRI.

'''Designs'''

*Target for Slicer4. First working version (passing current tests) in April.
* Define API's for GDCM 2.x. Integrate with GDCM 2.x at summer programming week.
* Separate functionalities for extracting essential spacial information from those for extracting non-essential information.
*Essential information (all in public tags): space location, resolution, image orientation (IJK->xyz), and how the ordering of dicom files corresponds to the organization of the slices. This information is essential for putting measurements in the correct physical locations.
*Non-essential information (some are in private tags, vendor dependent): diffusion related information -- b-values, gradient weighting direction, B-matrix.

2011 Winter Project Week:DicomToNrrdRefactoring

2011-01-11T17:25:54Z

Taox:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Mark Scully, Joy Matsui
* GE: Xiaodong Tao

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

<h3>Objective</h3>
Gather requirements in support of refactoring the DWI DicomToNrrdConverter.

* Redesign DicomToNrrdConverter so that it is more maintainable.
* Design a general base class to support most of the medical images in dicom format.
* Supports for vendor/version/datatype combinations are implemented as derived classes and are independent from each other.
* (Possibly) define APIs and derived classes for functional MRI.

</div>

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

<h3>Approach, Plan</h3>
Meet with anyone interested and establish a list of known requirements for DicomToNrrdConverter.
Collectively brainstorm approaches to the refactoring, such as the use of GDCM 1.2 vs. GDCM 2.x vs. DCMTK.
References:
*[[NAMIC_Wiki:DTI:Nrrd_format | DTI:Nrrd_Format]]
*[[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI|DICOM_for_DWI_and_DTI]]

'''Refactoring of Dicom to NRRD converter:

*Target for Slicer4. First working version (passing current tests) in April.
* Define API's for GDCM 2.x. Integrate with GDCM 2.x at summer programming week.
* Separate functionalities for extracting essential spacial information from those for extracting non-essential information.
*Essential information (all in public tags): space location, resolution, image orientation (IJK->xyz), and how the ordering of dicom files corresponds to the organization of the slices. This information is essential for putting measurements in the correct physical locations.
*Non-essential information (some are in private tags, vendor dependent): diffusion related information -- b-values, gradient weighting direction, B-matrix.

</div>

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

<h3>Progress</h3>
Current DWI variations list:
* slice ordering (S->I vs I->S),
* transfer syntax endianness (big, little, and unknown),
* slice arrangement (mosaic vs split, slice interleaving vs volume interleaving),
* #B-Values (single vs multiple),
* gradient vector reference frame (Scanner vs patient),
* slice orientation (orthogonal vs oblique),
* multiple B0s (all at beginning, all at end, interspersed)
* vendor (different ways of storing diffusion information),
* software versions (changes in how diffusion information is stored and interpreted).

</div>
</div>

2011 Winter Project Week

2009-09-10T19:05:39Z

Taox: /* 2009-09-10 */

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

==2009-09-10==
* Attendees: Katie, Jim, Nicole, Steve, Sebastian, Casey, Xiaodong, Andriy, Tina, Ron, Dan

* Discussion of [[Sept-2009-SlicerWidgetsBrainstorm | Slicer Widget Brainstorming meeting]]
* Registration useability effort (Casey, Dominik)
* Multiple camera support in Slicer (Seb)

==2009-09-03==
* Attendees: Jim, Vince, Tina, Wendy, Nicole, Katie, Xiaodong
* Nicole bugged Jim about the test he said he would fix last week

==2009-08-27==
* Attendees: Jim, Steve, Wendy, Katie, Sebastian, Nicole, Dan, and somebody on mute
* fixing slicer's dashboard [http://www.cdash.org/CDash/index.php?project=Slicer3]
** Leaks (FourD)
** Failing Tests (Multiply)
*** Needs to regression image since the method now enforces that we do not wrap around the dynamic range of the pixel type. Jim will look into that. Maybe with a new data.
** would be nice to have a few continuous builds
** can subprojects be used to test the Slicer extensions?
* Linked and compare view bug. Steve to dig into whether the slider/entry causes anything strange when a SliceNode is told to go to a particular RAS (not from the slider/entry)
* Defer population of color swatches?
* Collapsible frame collapse issue?
* Volume rendering colormaps: Lung, Lung + 1000
* FA values greater 1.0. Expose the option for negevalshift?

==2009-08-20==
* Wendy, Casey, Stephen, Katie, Nicole, Steve
* Plans for [[Events:Registration_Summit_August_2009|registration meeting]]
* Update on Nokia/Qt meeting
* Update on MAF

==2009-08-13==

*Review and add to : http://www.ncbcs.org/cal.html
* Discuss Attila's discovery of conflicting compiler settings for VTK and ITK for the Sun compiler http://massmail.spl.harvard.edu/pipermail/slicer-devel/2009/003393.html
** related discussion on tryng to compile VTK on Solaris: http://www.vtk.org/pipermail/vtkusers/2009-August/102171.html
** failing dashboard for VTK 5.4 with SunOS 5.8 and cc/CC: http://www.cdash.org/CDash/viewBuildError.php?buildid=401331. Andriy will (try to) set up that platform to send nightly builds with oth gcc and cc for ITK and VTK
* Update on Steve Pieper's trip to Yale to work with Xenios. Basically all of [http://www.bioimagesuite.org/ BioImageSuite]'s modules are available in slicer. We tested image filtering, model-to-model registration and they worked nicely. Outstanding to do items:
**Add biomimagesuite Logo (what is the format for the --logo flag exactly?) Partial success shown [http://www.slicer.org/slicerWiki/index.php/Slicer3:VisualBlog here]
**Transfomations output format (where is document for ITK transform files?)
**Output format for filenames (nii) – hacked in code (need to use fileFormat attribute from XML)
**Point format as opposed to –seed –seed –seed (is this supported yet?)
**Xenios to test intensity based registration … for output of resliced image
* Discuss Qt progress http://my-trac.assembla.com/protoctk/wiki/WidgetPlans
* W&M Solaris platform for Slicer dashboard testing

==2009-08-06==

Attendees: Katie, Tina, Steve (Jim is off the grid this week. Good luck!),

* playing with Dropbox (http://getdropbox.com)

==2009-07-30==
Attendees: Jim, Xiaodong, Wendy, Steve, Nicole, Stephen, Dan

* Nokia/Qt update
** PythonQt is working nicely for Stephen - Qt wrapped slicer command line modules are auto-exported via signals and slots, making them callable from python
* Wendy debriefing about meeting with Curt about XNAT and FetchMI
** planned an extension for FetchMI that will work with XNE
** content type tags to identify data types (like multi-file volumes)
** possible use of Resources to handle multi-file volumes
* Dan says XNAT 1.4 is just "weeks away" (conservatively by end of August).
* XND discussion
** XND is not being released at the same time as XNE 1.4 (official XND is 0.8).
** XNE 1.4 API will eventually become the unified API for both XNE and XND
* XNAT DICOMGateway http://nrg.wustl.edu/xnd/download/gw/
** Dan says it works well, for example with scanners and osirix
** only handles dicom, not other research data types and metadata
* MICCAI Best Biomedical Image Visualization Contest - enter early and often!!! $750 first prize!
* After-tcon discussion of DYLD_LIBRARY_ISSUES on mac.
** from: http://lists.apple.com/archives/cocoa-dev/2005/Apr//msg01620.html
>
> One idea I (probably stupid) idea is to set
>
> DYLD_LIBRARY_PATH at runtime. Is this possible?

You cannot do this as the dynamic linker reads these variables at the time the application launches, and not each time a new framework is loaded.

==2009-07-23==
Attendees: Katie, Wendy, Nicole, Xiaodong, Steve, Jim, Tina

*Jim built numpy for windows
*QT retreat to be planned in August
*opencv support to be considered?

==2009-07-16==

Attendees: Tina, Katie, Vince
*[[2009_Summer_Project_Week]] - check out google map of participant sites (thanks to marianna)

==2009-07-09==

Attendees: Jim, Steve, Tina, Ron, Stephen, Will
Agenda:

*http://www.washingtonpost.com/wp-dyn/content/article/2009/07/08/AR2009070802769.html
*update from Steve's WUSTL visit
*[[NA-MIC_External_Collaborations#Projects_funded_by_.22Collaborations_with_NCBC_PAR.22 |updated list of collaboration grants]]
** [[NA-MIC_External_Collaborations#Broader_Community_Involvement_of_NA-MIC_Investigators | placeholder for broader community grants]] - possibly for OpenMAF, IGSTK, SBIRs, etc...
* Steve's South America photos:
**Galapagos - http://www.facebook.com/album.php?aid=28255&id=1185661914&l=01b60d0091
**Amazon I - http://www.facebook.com/album.php?aid=28259&id=1185661914&l=c6cce28f96
**Amazon II - http://www.facebook.com/album.php?aid=28264&id=1185661914&l=c4a68b718b

==2009-07-02==

Attendees: Steve, Katie, Stephen, Tina, Luis, Andinet, Sebastien, Julien Finet, Will, Noby

* Report from Steve and Stephen about the recent [[Events:CTK-Workshop-June-2009|Common Toolkit Workshop]]
**QT has been used extensively by others presenting in the group. Great reinforcement that QT work planning for NA-MIC is heading in the right direction.
**Maverick discussion. (See link above for slides on it).

==2009-06-18==
Attendees: Curt, Katie, Jim, Dan, Xiaodong, Tina

==2009-06-11==
Attendees (partial list): Randy Gollub, Steve Pieper, Nobi Hata, Snehashis Roy, Kenneth Hisley, Tina Kapur, Wendy, Nicole, Andras Lasso

Agenda:
*DBP tutorials/tutorial contest: [[Events:TutorialContestJune2009]]. To be reviewed by Randy. Randy can be contacted any time by email and at the NAMIC week on Wednesday if there were any questions about how to create the tutorials. The tutorials will be presented on the NAMIC week on Thursday.
*Snehashis Roy (JHU) about Skull Stripping project: algorithm is based on deformable registration and segmentation; it is a Java software that will be ported into Slicer.
*Kenneth Hisley from Iowa (invited by Noby) was introduced to the concept of project week. He plans to do radiation treatment planning / longitudinal tracking with Slicer. Many interesting connection points with other projects, such as XNAT.

==2009-06-04==
Agenda:
*CUDA intro by Joe Stam
*Snehashis Roy (Jerry Prince student) will join next week to discuss Skull stripping project at project week
Attendees (partial list): Joe Stam, Andrewy, danielle, Diego Cantor, Greg Sharp, Jack Blevins, James Balter, Jay, Jim Miller, Keith Gunderson, Kim Powell, Leiquin, Luis (+8 from kitware), Matthew lauer, Mike Halle, M. Hasak, Michel Audette, Nicole A, Petar S, Petter, Sandy, Seb, Shalini (NVIDIA), Sharon peled, Sylvain J, Torsten, Xenios (+10 from yale)

Highlights: 50+ people attended the webex presentation on CUDA. Projects for project week will be outlined in the next week.

==2009-05-28==
Attendees: wendy, nicole, katie, jim, tina, dan

*next Thursday - CUDA intro
*vtk3d widgets project meeting is being organized by Nicole
*Katie will cmake project
*Jim will contact Ran and Sam G about project pages
*dan will complete project pages
*Only slicer3.4 bug fixes should go into the 3.4 branch (no new features)

==2009-05-21==
Attendees: Will, Ron, Xiadong, Nicole, Vince
*A day of rest,

==2009-05-14==
Attendees: Will, Steve, Tina, Katie, Wendy, Seb, Jim, Xiaodong, Dan M, Ron
*Progress Report - due tomorrow
*When can we invite Utah student to discuss B-spline registration project? High priority for project week.
*Review Project week list and pages
*[http://tinyurl.com/cu9bzp remaining 3.4 release bugs]

==2009-05-07==
Xiadong, Tina, Katie, Nicole, Saikat, Harish, Wen, James, Steve, Vince, Dan M,

Agenda
*Stanford Simbios collaboration (Haikat, Saikat, need help on registration)
** http://slicer.spl.harvard.edu/slicerWiki/index.php/Stanford_Simbios_group

*NA-MIC engineering projects

==2009-04-30==

Agenda
Jim Balter, Vince, John M., Nicole A, Bjorn, Jim, Steve, Jim, Xiaodong, Alex G., Sandy, Eric, Katie, Will
* Project: MRSI (3pm)
** Bjorn has MRSI code that is slicer-compatible for reconstruction and registration.
** Vince had MRSI phantom data (specially prepared phantom) so he can provide data.
** (See http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_MRSI)
* Project 2d-3d registration (3:30)
** Jim Balter, Sandy Wells, and probably Greg Sharp,
** GPGPU image registration
** Targets:
*** Back projection
*** 2D/3D Registration
*** Jimmy and Yogesh have some GPGPU affine registration code
*** NVIDIA field engineer may attend
*** Look at CUDA Volume rendering to see if it can emulate radiographs
*** There is an nvidia ray casting framework that may be available soon
*** There will be cuda-enabled workstations available (Apple from SPL, Microway demo unit?)

==2009-04-23==

Agenda

* [[2009_Summer_Project_Week]] - IGT projects
* projects for upcoming TCONS: MRSI, 2d-3d registration

==2009-04-16==
Agenda

* [[2009_Summer_Project_Week]]

Notes: discussion during this tcon was about projects, and these were added to the above link.

==2009-04-09==
Attendees: Katie, Ron, Tina, Steve, Jim, Wendy, Kevin Archie, Nicole, Xiaodong, Randy
*http://www.slicer.org/pages/Special:SlicerDownloads - can the OS and the last stable release be filled in automatically on this page?
** forwarded request to Zack
* Slicer 3.4 release
* 3.4 bugs to be fixed: http://tinyurl.com/cu9bzp
** Documentation still outstanding
* 3.4 tutorials
*Progress Report: please update project pages by April 15
*Project Week Prep
**next thursday, april 16th is kickoff tcon
**april 23 - igt tcon?
**Breakout/Tutorial candidate topics:
***Slicer-Python candidate tutorials/breakouts (Demian and maybe Luca and/or Daniel?)
****Introduction to Python/scipy developement
****Exploratory image processing in Slicer through the python console
****Slicer Modules in Python
***4D+t microscopy cell dataset segmentation (alex g.) What is the relation for FourDAnalysis? http://wiki.na-mic.org/Wiki/index.php/Slicer3:FourDAnalysis
***ITK by Luis
***Data Clinic (already on agenda)
***Tutorial Contest (already on agenda)

==2009-04-02==

* Discussion of dicom handling (follow up on questions from Queen's DBP prostate MR) (Steve)
**Issue with DICOM handling using gdcm with malformed DICOM
**Read image data with wrong geometric information
**Deprecate older DICOM parsers in ITK
**Unregister older DICOM1 and DICOM2 versions of DICOM reading in ITK

* Luca's question about how to avoid accidental program execution during module discovery (Steve)
**Have CMake generate a manifest when building?
**Possibly have subdirectories for support files

* FYI http://wiki.na-mic.org/Wiki/index.php/2009_Summer_Project_Week#Preparation
* FYI http://wiki.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009

Attendees: Steve, Jim, Nicole, Katie, Tina, Ron, Vince, Sebastien

==03-26-2009==

* Making build/install compatible with LSB (Linux Standard Base) and FHS (File Hierarchy Standard) to support effort to put slicer into the debian repository. (Steve) http://www.na-mic.org/Bug/view.php?id=511 A few of the questions to discuss with the engineering core:
** rpaths in GenerateCLP/GenerateLM (should we be using the GenerateCLPLauncher instead)
** version numbers on all .so files
** Dominique's patches: http://svn.debian.org/wsvn/debian-science/packages/slicer/trunk/debian/patches/50_all_changes.dpatch?op=file&rev=0&sc=0
** Problems finding the tk.tcl file (build is looking in /usr/lib/tk8.5 but on debian it is in /usr/share/tcltk/tk8.5/tk.tcl
*Tutorials at/before Project Week?
*FYI: starting this year, the project week is a joint activity between NA-MIC, NAC, and NCIGT. April 16th is the kickoff TCON.

Attendees:
Steve, Jim, Will, Bill H., Nicole, Katie

Notes:
* Tina will Ron Steve talking about tutorials, will we hold them during the project week? proposed and nixed the idea of holding anything the week before project week. Hold it online (shared desktop)? Get them out of PW and into own spot, out of week before PW.
** during PW they don't get the attention they deserve?
** will concerned about travel time/costs
** Tina not expanding the span of project week beyond the week, suggests keeping some tutorials in there, but not make them 5 hours long
** ask potential attendees if they have specific things they want to learn about
** try not to shuffle the tutorials as people plan to attend them on specific days
** make electronic versions available ahead of time
* PW is a join project week now with NAC and NCIGT, Apr 16th is kickoff TCON, Tina thinks 10-20 people more might attend
* debian style Slicer compilation
** GenerateCLP/GenerateLM, not using the launchers in general. Will fwd this to Sebastien and bill hoffman
** GenerateCLP/LM lib and bin in different dirs, generated during compile time, not found
** Bill H: not familiar with LSB and FHS
** Jim: we could change how GenerateCLP is built so change how the rpaths are set?
** Bill H: cmake can be set up with rpaths when building when install clear them out? skip rpaths, check with Brad King, check version of cmake
** Steve: rpaths are off everywhere but 64 bit linux. May not be necessary any more. They don't want them at all in debian.
** shared library version number, symlinks. Work on windows? in dll header, ignored. Is there a cmake command? set target properties, it'll set the name and set up the sym link.
** #3 in bug tracker, use Slicer3-real in /usr/bin? two assumptions in launcher, in build or install dirs, if it's in /usr/bin that's different again. current cpack slicer3, top level has Slicer3 and then sub dirs bin and lib, launcher should be in the bin dir? makes sense for install, but not for a zipped up dev build where have to look in bin for what to run. If bypass the launcher and run the core exec, it should be able to find all the shared libs in a properly installed debian. Module libs don't' make sense in /usr/lib as they don't stand on their own. Jim: build two launchers? one in bin dir and one outside, and in debian package the outside one doesn't. Reliance on SLICER_HOME - is it where started, installed, where Slicer3-real is? Bill: depend on the launcher to get paths right, as opposed to ld paths. Worry about installing the vtk libs in places where others can find them. We treat them as our own private versions. Debian: system vtk, etc, and the package manager deals with the library versions.
** #5 Bill: reason stick libraries in bin is due to Windows
** #6, 7: fine to fix if it doesn't break modules/libs that depend on each other
* Jim: Manaz want to do picking, fibre clustering into Slicer way.
** look at the Base/GUI/vtkSlicerViewerWidget.cxx for the CellPicker, it is called from an observer on the vtkSlicerViewerInteractorStyle when that reports a mouse mode event (see the vtkSlicerFiducialListWidget for example of how to set up the observer and respond to PickEvent)

==03-19-2009==
Attendees: Katie, Tina, Nicole, Steve, Vince, Jim, Xiaodong, Ron, Will

*During Project Week: full integration of the roadmap projects into the NA-MIC kit
** Tools developed under DBPs to be integrated to NA-MIC kit. Need to check progress and understand where we are. 1. MIND, 2. Harvard, 3. Queens, and 4. UNC.

*Core 2 Renewal meeting
** Mid-May in Georgia, Will to coordinate.

*Modules in slicer release
** Steve and Alex identified a list of bugs in Slicer 3.4 pre-release.

==03-12-2009==

Agenda:
*Registration in Slicer 3.4 (Ron)
**Which modules to list
**What guidance to give to potential end-users
*Check out http://www.ncbcs.org/cal.html

Attendees: Ron, Tina, Will, Nicole, Vince, Bill, +1

Notes:
* Registration
** bspline registration is a deliverable for the project week
** leaving registration as it is, Ron will reorder them:
***linear then affine then deformable then register images
** Ron will draft a note and send it around for comments
** documentation needs to be updated, Bill Lorensen can do bspline?
* Bill fixed the command line module loader to use an html to go to the web pages, use the documentation-url tag in your CLI xml file (See the Checkerboard filter help), update the CLIs to put them in
* there may be some supplement money from the stimulus package for our grant
* no release dates yet
* working on a welcome module Slicer3 UI design wiki page has some details
** http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:WelcomeModule:Draft
* Bill signing off to shoot off a pvc pipe model rocket, also found an open source project, put your GPS location in and it shows you the annotated night sky, Stellarium.
* Will: are cheques being received, Tina hasn't heard yet, they're out and people should be receiving them.
* Tina: one of the NIH people working with Joy the dissemination person at Stanford (?), put together a calendar.
** Steve, Jim and Will are going to Georgia Tech in May, should show up on the calendar.
** when events page on the wiki gets updated, it will show up on the calendar

==03-05-2009==
Attendees: Ron, Jim, Tina, Xiaodong, Marco, Dan

Agenda:
*Documentation for Slicer 3.4
*New GWE released and tutorial added: [[Slicer3.2:Training]]
*Xnat central has been updated so it doesn't require login (default is to login as guest).

==02-26-2009==

Attendees: Katie, Curt, Tina, Steve, Jim, Nicole, Xiaodong, Ron

* Check out the NA-MIC Events Calendar (WIP) on google: http://www.google.com/calendar/embed?src=r8bddigidepgvog24cpfk1bjgs%40group.calendar.google.com&ctz=America/New_York
* Time to start thinking about the [[2009_Annual_Scientific_Report]], deadline May 15.
* NCI update
* Slicer release
** File format for sending/receiving displacement fields. Hans suggested MATLAB.
** Release notes for command line modules. Keep module name the same as the cxx/xml filename.

==02-19-2009==
* Attendees: Katie, Wendy, Nicole, Will, Jim, Xiaodong, Vince, plus lurkers
* VTK cvs repository frozen in preparation of a 5.4 release. Perhaps mid-March.
* Teem can now build with CMake though no one can use it yet can because it is not checked in.
* EM Segment bug wrt to signed data (i.e. CT data in Hounsfield numbers).
* Slicer release tentative for first week in March

==02-12-2009==
*Agenda:
**Topic #1: NA-MIC data repository
**Topic #2: Python wrapping of ITK in Slicer: adding vtk-itk glue pipeline connection filters to Slicer build, so Python scripts can use ITK filters.
* Attendees: Jim Miller, Tina Kapur, Nicole Aucoin, Kurt Lisle, Ron Kikinis, Clement, Dan Marcus, Katie Hayes, Wendy Plesniak, Xiodong, Vincent Magnotta, Steve Pieper, Will Schroeder

* NAMIC data rep:
* there is namic data, test data and tutorial data floating around in various places (including in Slicer download, different data bases), Ron suggests that we think about how we should organise it into one place for nightly builds, tutorials etc.
* Wendy: we have an instance of XND web services running on xnd.slicer.org, we could use it
** Steve: it's on an Amazon cloud, fine for testing, but not good for a high availability server. Should be where BWH sysadmins can monitor it. Shouldn't be hidden by a firewall. Need something hardened.
** also using central.xnat.org, Midas
** Dan: says right long term place for it is XNAT central, but right now Slicer is programmed against the desk top API. He suggests putting everything in a desktop and then porting it to central. WJP: could put .xcat files on central, Slicer3 can read them automatically.
** Ron: manual upload is okay for now, need reliable downloads
** Steve: for some tutorial and sample data put links in the GUI, ie file menu, sample data. Dan: start with XNAT Central, then.
** Ron: Two areas: tutorial data sets, compiled test data sets. For read, completely open.
** Use cases: Slicer 101 training page, link to data could point directly into xnat central. Nightly build: been using SVN, but the data is being packaged up for distribution right now, would like to avoid depending on another server, make it clear as to if need to install testing data (assume for now stay in source tree, but do need to test installed version - dl data in that case).
** Clean up: take out extra data files, .h files, if not needing to build extra stuff against an installed Slicer (has been abandoned due to different compilers?). Need guidelines for the developers as to what should be installed.
*** If someone wants to write a CLI or loadable module, they have to have a built version of Slicer to do that
** Action items: Create a Slicer tutorial data project on xnat central and upload to it, make it open. Make xnat central so can access open projects w/o having to log in at all. Can it be done within 2 days? Dan says: Monday. He'll send an email when it's set up, make a wiki page on how to upload it.
** For the test data sets, keep using SVN, but encourage developers to make the smallest possible test data set
*** Add an upper limit for test data size, over it it should go in central.xnat.org
*** Add documentation for the test data sets somewhere. In directory as a ReadMe.txt file?
*** Make sure fill in doxygen style comments for auto generated documentation
** There will be a new Slicer 3.4 tutorial page, everything will be on the central xnat repository

* Topic 2 : Curt: wrap ITK in python.
** To be able to move Slicers python console and ITK filters en mass for experimental prototyping.
** Historic vtkITK project, hand wrappers for indiv filters want to us, and CLI mechanism so can put in ITK filters directly.
** If we do auto wrapping, the wrapping is there, but there's no vtkITK pipeline connection available.
** Steve: You can go into ITK build and turn on the wrapping, Vince says builds take really long on Windows, so hesitant to turn it on by default in Slicer build.
** in python console can instantiate an ITK filter, but getting things into and out of it is a problem. Curt envisions loading a data set into Slicer and trying out different filters to see what you want to put in a CLI. Can try using the numpy? get a numpy array of slicer image data and manipulate it w/numpy or use as a vtk array? Something else needed? Checking Luca's old emails... the Slicer way of wrapping for python is different than the native VTK way of wrapping python. Luca would like some examples from Curt, use cases. There is a way to go from Slicer mrml to numpy array to ITK. Jim could embed this into a helper.
** Jim: want to grab a mrml node and say get the ITK representation of the data in that node (have the orientations come across, and meta data in mrml node that ITK can represent, LPS/RAS conversion).
** no action items just yet, Curt will explore and report what is needed to make wrappers
** Luca: need to be clear when working with VTK wrapped things versus Slicer wrapped things, can't go from one to the other, but each one individually should be able to do .
** Will: some email on the ParaView list about wrapping, he'll send stuff to Curt and Steve.
** building python problems on Dash18: connection problems with the scipy svn server. Mirror?

* Dave Cole has been working with Gordon, has teem building with CMake, working on a "proper" Mac release (new feature?)
* Jim updating a couple of builds today, errors building from getbuildtest.tcl, source tree is checked out of someplace else (teem, igt link), need to remove the directory and rebuild.
* Steve: latest windows build installer can bring up the python console. Katie reports seg faults on Darwin (unrelated?).
** there are python versions 2.6 and 3.0, but consensus here has been to stick with 2.5 for numpy and other packages.
* Been going through the bug tracker and clean up things for the release of Slicer 3.4
* Was there a recent workshop that Randy Gollub was involved in Puerto Rico? mBIRN spring last year

==02-05-2009==
Agenda:

*Attendees: Jim, Wendy, Tina, Ron, Nicole, Steve, Curt, Vince

*Topic #1 - Feature Freeze
*http://www.slicer.org/slicerWiki/index.php/Documentation-3.4#List_of_Modules_in_need_of_documentation

Feature freeze occurred on 2/4/09 - we should be only cleaning up, fixing bugs, and writing documentation for existing Slicer modules.

Target for code freeze will be at the end of February. Please get bug fixes in during February, if possible. We will start making release candidate builds on or around March 1st.

Everyone please check the module documentation pages and make sure to fill out the documentation. Ron has added candidate names for individuals responsible for the modules. Please use the template and go along with the naming scheme. Some reorganization of the list may occur. Email will go out for everyone to finish their module in the next week or so.

*Topic #2 NA-MIC-related Research
*http://wiki.na-mic.org/Wiki/index.php/NA-MIC:Site_PI_Other_Research
Compile a list of grants that have benefitted from NA-MIC. Both active and expired grants which have benefitted should be entered. Collaborations with other groups is good. Joint publications are preferred to demonstrate effective collaboration. We are also trying to show that NA-MIC people are involved in other productive activities, as well.

Core 2 NAC and BIRN activity should be listed.

Collaboration grants should be added to be listed. We are looking to list solid grants or efforts that should be listed. Send to Tina or add to this list.

*New Tools
New tools for registration and atlas development have been recently released. UCLA NCBC effort or related grant may have assisted with this (James Gee). Jim Miller evaluating to decide if these could make useful Slicer plug-ins. They are currently command line tools which could be adapted for use with Slicer. Is this a benefit to show that this NCBC's tool products are compatible with Slicer.

*Python building in Windows
Steve is experiencing some Python build problems under Windows related to GenerateCLP. Jim and Steve discussed how to resolve.

iPython is now available for use with Slicer. There is a small installation script to run after Slicer is built. WrapITK is the newest way to wrap ITK in Python. vtkITK is the older way. All of ITK can be wrapped automatically, but this option is turned off by default, since it slows down the build.

==01-29-2009==
Attendees: Jim, Steve, Tina, Dan, Nicole

* Discussion of [http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:SlicerInformatics:Draft1 XNAT Integration Timeline]

==01-22-2009==
Attendees: Jim, Steve, Tina, Wendy, Xiadong, Nicole

*collaboration grants - doesn't look like anything is going in feb

==01-15-2009==

Attendees: Jim, Steve, Katie, Tina, Wendy, Nicole, Vince, Xiaodong, Sebastien

Agenda:
*LGPL QT - should we consider this going forward?
*Slicer code freeze on Feb 4th. [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Events Slicer3 Events] for requirements for modules to be included.

2009 Summer Project Week Skull Stripping

2009-06-26T13:22:08Z

Taox:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:SkullStrippingInSlicer.png | Deformble surface modle for skull stripping as part of Slicer.
Image:JHUSkullStripper.png | Work in progress. Joint segmentation/registration for skull stripping.
</gallery>

<gallery>
Image:GESkullStripping.png | Deformble surface modle for skull stripping.
Image:JHUSkullStripping.png | Skull stripping using joint registration and segmentation.
</gallery>

==Key Investigators==
* JHU: Snehashis Roy
* GE : Xiaodong Tao
* BWH: Nicole Aucoin

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

<h3>Objective</h3>
We will discuss the possibility of combining the skull stripping algorithm developed at JHU (a joint registration and segmentation approach) and the one developed at GE (a deformable surface model) into a single skull stripping algorithm to be included in NA-MIC kit.

</div>

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

<h3>Approach, Plan</h3>
To understand each approach and discuss the best way to combining the effort. Develop a plan for implementation as a Slicer module.

</div>

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

<h3>Progress</h3>
The deformable surface based approach is similar to Brain Extraction Tool (BET). The algorithm has been tested on 300+ T1 weighted images from OASIS database and shows a DICE score of 0.94 with the brain masks provided in the OASIS database. This algorithm may be modified to work on images with other contrast mechanisms. The joint registration and segmentation algorithm also works on T1 weighted images, and has been tested on a few hundreds of images with good accuracy.

* '''Update #1''': We have successfully compiled the skull stripping algorithm, Simple Paradigm for Extra-Cranial Tissue Removal (SPECTRE) as a Slicer3.4 plugin. The following images show an OASIS brain skull-stripped with the plugin. The method requires a registration. The Affine Registration module of Slicer3.4 does not provide desired result. So we will include Deformable BSpline registration and provide a plugin.
</div>
</div>
<h2>OASIS brain with skull</h2>
[[Image:Skull.png |500px]]

<h2>OASIS brain skull-stripped</h2>
[[Image:Ss_volume.png |500px]]

==References==
* Aaron Carass, M. Bryan Wheeler, Jennifer Cuzzocreo, Pierre-Louis Bazin, Susan S. Bassett and Jerry L. Prince, A JOINT REGISTRATION AND SEGMENTATION APPROACH TO SKULL STRIPPING, ISBI 2007.

File:JHUSkullStripper.png

2009-06-26T13:18:49Z

Taox:

File:SkullStrippingInSlicer.png

2009-06-26T13:15:22Z

Taox:

2009 Summer Project Week Skull Stripping

2009-06-26T13:14:07Z

Taox:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:GESkullStripping.png | Deformble surface modle for skull stripping.
Image:JHUSkullStripping.png | Skull stripping using joint registration and segmentation.
Image:SkullStrippingInSlicer.png | Deformble surface modle for skull stripping as part of Slicer.
</gallery>

==Key Investigators==
* JHU: Snehashis Roy
* GE : Xiaodong Tao
* BWH: Nicole Aucoin

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

<h3>Objective</h3>
We will discuss the possibility of combining the skull stripping algorithm developed at JHU (a joint registration and segmentation approach) and the one developed at GE (a deformable surface model) into a single skull stripping algorithm to be included in NA-MIC kit.

</div>

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

<h3>Approach, Plan</h3>
To understand each approach and discuss the best way to combining the effort. Develop a plan for implementation as a Slicer module.

</div>

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

<h3>Progress</h3>
The deformable surface based approach is similar to Brain Extraction Tool (BET). The algorithm has been tested on 300+ T1 weighted images from OASIS database and shows a DICE score of 0.94 with the brain masks provided in the OASIS database. This algorithm may be modified to work on images with other contrast mechanisms. The joint registration and segmentation algorithm also works on T1 weighted images, and has been tested on a few hundreds of images with good accuracy.

* '''Update #1''': We have successfully compiled the skull stripping algorithm, Simple Paradigm for Extra-Cranial Tissue Removal (SPECTRE) as a Slicer3.4 plugin. The following images show an OASIS brain skull-stripped with the plugin. The method requires a registration. The Affine Registration module of Slicer3.4 does not provide desired result. So we will include Deformable BSpline registration and provide a plugin.
</div>
</div>
<h2>OASIS brain with skull</h2>
[[Image:Skull.png |500px]]

<h2>OASIS brain skull-stripped</h2>
[[Image:Ss_volume.png |500px]]

==References==
* Aaron Carass, M. Bryan Wheeler, Jennifer Cuzzocreo, Pierre-Louis Bazin, Susan S. Bassett and Jerry L. Prince, A JOINT REGISTRATION AND SEGMENTATION APPROACH TO SKULL STRIPPING, ISBI 2007.

2009 Summer Project Week HAMMER Registration

2009-06-14T11:56:34Z

Taox: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png | .
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
</gallery>

==Key Investigators==
* UNC: Guorong Wu, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

2009 Summer Project Week WML SEgmentation

2009-06-14T11:56:00Z

Taox: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png | .
Image:UNCWMLSegmentation.png|One training dataset (T1, T2, PD, FLAIR images and wml segmentation.
</gallery>

==Key Investigators==
* UNC: Minjeong Kim, Dinggang Shen
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing the white matter lesion segmentation algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the white matter lesion segmentation algorithm. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented WML segmentation algorithm using ITK classes. Subtasks implemented includes: 1. a skull stripping algorithm working on T1 weighted images; 2. a fuzzy clustering algorithm for tissue segmentation; 3. a parametric modle for gain field correction. All these are implemented using ITK. The training step uses AdaBoost and the segmenation step uses a support vector machine.

</div>
</div>

==References==
* Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/WMlesionSegmentation.pdf Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition], Academic Radiology, 15(3):300-313, March 2008.

2009 Summer Project Week

2009-06-11T13:58:58Z

Taox: /* Projects */

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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.

Active preparation will begin on''' Thursday, April 16th 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 30-50 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], and [http://www.cimit.org CIMIT]. 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
# Need Lupus Project here
# Need VCSF Project here
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal Stanford)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
# [[EMSegment|EM Segment]] (Sylvain Jaume BWH)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_Slicer3_registration| Slicer 3 registration ]] (Andrew Rausch)

===CUDA Projects===

This is a list of candidate cuda projects that will be discussed with Joe Stam shortly:

#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins Acousticmed)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)
#acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[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 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC) (Attending Tuesday-Friday)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc (Attending: Monday/Tuesday/Wednesday)
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (1st day only)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)
#Dana Peters, Beth Israel Deaconess
#Sun Woo Lee, BWH
# Melanie Grebe, Siemens Corporate Research
# Megumi Nakao, BWH/NAIST
# Moti Freiman, The Hebrew Univ. of Jerusalem
#Jack Blevins, Acoustic Med Systems
#Michael Halle, BWH
#Amanda Peters, Harvard SEAS
#Joe Stam, NVIDIA (Wednesday, Thursday)
#Petter Risholm, BWH (NCIGT)
#Kimberly Powell, NVIDIA (Wednesday)
#Padma Akella, BWH (NCIGT)
#Clif Burdette, Acousticmed (Mon, Tue, Wed)

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

File:UNCWMLSegmentation.png

2009-06-09T19:55:23Z

Taox:

2009 Summer Project Week WML SEgmentation

2009-06-09T19:54:34Z

Taox: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png | . Image:UNCWMLSegmentation.png|One training dataset (T1, T2, PD, FLAIR images and wml segmentation. </gallery> ==Key Investigators== * ...'

__NOTOC__
<gallery>
Image:PW2009-v3.png | .
Image:UNCWMLSegmentation.png|One training dataset (T1, T2, PD, FLAIR images and wml segmentation.
</gallery>

==Key Investigators==
* UNC: Minjeong Kim
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing the white matter lesion segmentation algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the white matter lesion segmentation algorithm. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented WML segmentation algorithm using ITK classes. Subtasks implemented includes: 1. a skull stripping algorithm working on T1 weighted images; 2. a fuzzy clustering algorithm for tissue segmentation; 3. a parametric modle for gain field correction. All these are implemented using ITK. The training step uses AdaBoost and the segmenation step uses a support vector machine.

</div>
</div>

==References==
* Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/WMlesionSegmentation.pdf Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition], Academic Radiology, 15(3):300-313, March 2008.

2009 Summer Project Week HAMMER Registration

2009-06-09T19:28:34Z

Taox: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png | . Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors. Image:HammerSimilarity.png|Similarity map (middle column) computed o...'

__NOTOC__
<gallery>
Image:PW2009-v3.png | .
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
</gallery>

==Key Investigators==
* UNC: Guorong Wu
* GE : Xiaodong Tao, Jim Miller

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

<h3>Objective</h3>
We will continue developping and testing HAMMER registration algorithm implemented using ITK. The goal is to have an initial version ready by the end of the week that can be distributed within NA-MIC community for more extensive testing.

</div>

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

<h3>Approach, Plan</h3>
We will develop a Slicer module for the current implementation of the Hammer registration algorithm and test on images from multiple sources to make the algorithm robust and easy to use. Base line results and test will be generated.

</div>

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

<h3>Progress</h3>
Since winter project week in Utah, we have developed/implemented HAMMER registration algorithm using ITK classes. New ITK classes have been created for tasks of HAMMER. Each component has been tested. The source code is version controlled at NITRC site. The current development corresponds to the original Hammer algorithm that is based on tissue classification of T1 weighted images (as outlined on the first HAMMER paper).

</div>
</div>

==References==
* Dinggang Shen, Christos Davatzikos, [http://www.med.unc.edu/~dgshen/papers/Hammer_VersionInTMI.pdf HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration], IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002.

File:GESkullStripping.png

2009-06-04T02:41:00Z

Taox: