NAMIC Wiki - User contributions [en]

2008 Winter Project Week

2007-12-06T20:59:00Z

Wbsmith: /* NA-MIC Kit - Slicer 3 */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#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]]

Please note that we would like to have four clinical application focused parallel tracks at the meeting, each corresponding to a DBP problem.

#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)

===Structural Analysis===
#DBP Analysis of Brain Lesions in Lupus: [[2008_Winter_Project_Week:Lesions|Lesions]], Towards an end to end lesion analysis feature in Slicer3 (Mark Scully, Jeremy, Brad, others)
#Groupwise Registration and Atlas Building (Brad, Serdar?, Casey) [[2008_Winter_Project_Week_GroupwiseReg|'''Template''']]
# Cortical thickness analysis of pediatric brains (Clement Vachet, Martin Styner), [[DBP2:UNC:Cortical_Thickness_Roadmap | Roadmap]]

===Diffusion Image Analysis===
#Incorporating DTI data into entropy-based particle system for cortical correspondence (Ipek Oguz, Josh Cates, Tom Fletcher)
#Integrating population based DTI tools into NAMIC Kit (Casey Goodlett) [[2008_Winter_Project_Week:Population_DTI|'''Template''']]

===Image Guided Therapy===
#IGSTK-Slicer (Liu, w. Georgetown team, Hata, Tokuda) '''NA-MIC supplement''' [[NA-MIC_NCBC_Collaboration:An_Integrated_System_for_Image-Guided_Radiofrequency_Ablation_of_Liver_Tumors || Description]]
#Japanese Intelligent Surgical Instrument Project (Hata, Chinzei, Hong)

===NA-MIC Kit - Slicer 3===

#MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Nicole, Alex, Steve, Will, Vince, Bob O'Bara)
#Python Support in Slicer 3 (Luca, Bryan Smith)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#Drafting Human Interface and Slicer Style Guidelines (Wendy,Sebastien)
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)
#Revisit - ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)
#Volume rendering (Andy Freudling, Steve Pieper, Grauer)
#Stereo Displays (Katharina, Curt)
#3D W Widgets and Picking (Will, Nicole, Curt, Kiran, Nicole)
#MRML support for out of core processing with fMRI and DTI as use cases (Steve, Jim, Wendy, Alex, Will)
#[http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake] Integration (Dan Marcus, Steve, Stephen, Jeff, Julien)
#KWWidgets Roadmap (Sebastien, Wendy, Katie)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)

===External Collaborations===
#Finite Element Meshing into NA-MIC [Univ. of Iowa] (Nicole, Vince, Kiran, Steve, Curt)
#Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt)
#Rewriting GoFigure to be cross-plateform: GUI from MFC to KWWidget (+vtkINRIA3D) ( Alex. G, Sean Megason, Arnaud Gelas?)
#microSlicer3:Doing microscopy image analysis with Slicer3[Ohio State U](Kishore M., Raghu M.), NAMIC(Brad D.,Stephen A., Steve P.)
#fmri image analysis with Slicer 3[Ohio State U](Firdaus J.,Raghu M.), NAMIC [Luis I.,Steve P., Wendy P.]

===Non-Medical Collaborations===

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. 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)
# By 3pm ET on Jan 3, 2008: [[2008_Winter_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.
# 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...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].

2008 Winter Project Week

2007-12-06T18:48:41Z

Wbsmith: /* NA-MIC Kit - Slicer 3 */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]

Please note that we would like to have four clinical application focused parallel tracks at the meeting, each corresponding to a DBP problem.

#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)

===Structural Analysis===
#DBP Analysis of Brain Lesions in Lupus: [[2008_Winter_Project_Week:Lesions|Lesions]], Towards an end to end lesion analysis feature in Slicer3 (Mark Scully, Jeremy, Brad, others)
#Groupwise Registration and Atlas Building (Brad, Serdar?)
# Cortical thickness analysis of pediatric brains (Clement Vachet, Martin Styner), [[DBP2:UNC:Cortical_Thickness_Roadmap | Roadmap]]

===Diffusion Image Analysis===
#Incorporating DTI data into entropy-based particle system for cortical correspondence (Ipek Oguz, Josh Cates, Tom Fletcher)

===Image Guided Therapy===
#IGSTK-Slicer (Hata, w. Georgetown team, Liu, Tokuda)
#Japanese Intelligent Surgical Instrument Project (Hata, Chinzei, Hong)
#Fast volume rendering in Slicer for 4d IGT(Hata, Grauer, Freudling, Mori)

===NA-MIC Kit - Slicer 3===

#MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Nicole, Alex, Steve, Will, Vince, Bob O'Bara)
#Python Support in Slicer 3 (Luca, Bryan Smith)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#Drafting Human Interface and Slicer Style Guidelines (Wendy,Sebastien)
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith)
#Revisit - ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)
#Volume rendering (Andy Freudling, Steve Pieper, +)
#Stereo Displays (Katharina, Curt)
#3D W Widgets (Will, Nicole, Curt, Kiran, Nicole)
#MRML support for out of core processing with fMRI and DTI as use cases (Steve, Jim, Wendy, Alex, Will)
#[http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake] Integration (Dan Marcus, Steve, Stephen, Jeff, Julien)
#KWWidgets Roadmap (Sebastien, Wendy, Katie)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)

===External Collaborations===
#Finite Element Meshing into NA-MIC [Univ. of Iowa] (Nicole, Vince, Kiran, Steve, Curt)
#Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt)

===Non-Medical Collaborations===

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#3 to discuss outstanding projects and teams]]
# December 6, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. 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)
# By 3pm ET on Jan 3, 2008: [[2008_Winter_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.
# 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...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].

Projects/Slicer3/2007 Project Week Support for electron microscopy

2007-06-29T07:53:36Z

Wbsmith: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Spines01.jpg|thumb|320px|A small fragment of a dendrite (gray) with segmented spines (color).]]
|[[Image:SpineSample.jpg|thumb|520px|A sample of spines plotted into individual axes.]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

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

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

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

<h1>Progress</h1>
* Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]), but it creates planes rather than lines in parts of some spines.

* Obtained code from Martin Styner (via Stephen Aylward). Will implement and see if works.

* Suggestion to try CorCTA module in Slicer2; Crashes

</div>

<br style="clear: both;" />

</div>

===References===
* Insert some refs here

Projects/Slicer3/2007 Project Week Support for electron microscopy

2007-06-29T07:53:13Z

Wbsmith: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Spines01.jpg|thumb|320px|A small fragment of a dendrite (gray) with segmented spines (color).]]
|[[Image:SpineSample.jpg|thumb|520px|A sample of spines plotted into individual axes.]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

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

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

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

<h1>Progress</h1>
* Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]),
but it creates planes rather than lines in parts of some spines.

* Obtained code from Martin Styner (via Stephen Aylward). Will implement and see if works.

* Suggestion to try CorCTA module in Slicer2; Crashes

</div>

<br style="clear: both;" />

</div>

===References===
* Insert some refs here

Projects/Slicer3/2007 Project Week Support for electron microscopy

2007-06-29T07:52:21Z

Wbsmith: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Spines01.jpg|thumb|320px|A small fragment of a dendrite (gray) with segmented spines (color).]]
|[[Image:SpineSample.jpg|thumb|520px|A sample of spines plotted into individual axes.]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

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

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

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

<h1>Progress</h1>
Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]),
but it creates planes rather than lines in parts of some spines.

Obtained code from Martin Styner (via Stephen Aylward). Will implement and see if works.

Suggestion to try CorCTA module in Slicer2; Crashes

</div>

<br style="clear: both;" />

</div>

===References===
* Insert some refs here

Projects/Slicer3/2007 Project Week Support for electron microscopy

2007-06-29T07:45:52Z

Wbsmith: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Spines01.jpg|thumb|320px|A small fragment of a dendrite (gray) with segmented spines (color).]]
|[[Image:SpineSample.jpg|thumb|520px|A sample of spines plotted into individual axes.]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

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

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

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

<h1>Progress</h1>
Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]),
but it creates planes rather than lines in parts of some spines.

</div>

<br style="clear: both;" />

</div>

===References===
* Insert some refs here

Projects/Slicer3/2007 Project Week Support for electron microscopy

2007-06-08T21:46:57Z

Wbsmith:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Spines01.jpg|thumb|320px|A small fragment of a dendrite (gray) with segmented spines (color).]]
|[[Image:SpineSample.jpg|thumb|520px|A sample of spines plotted into individual axes.]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

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

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Insert some refs here

Projects/Slicer3/2007 Project Week Support for electron microscopy

2007-06-08T21:42:49Z

Wbsmith:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Spines01.jpg|thumb|320px]]
|[[Image:SpineSample.jpg|thumb|520px]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

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

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Insert some refs here

Projects/Slicer3/2007 Project Week Support for electron microscopy

2007-06-08T21:40:20Z

Wbsmith:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Spines01.jpg|thumb|320px]]
|[[Image:SpineSample.jpg|thumb|320px]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

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

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Insert some refs here

File:SpineSample.jpg

2007-06-08T21:39:05Z

Wbsmith: A sample population of segmented spines in their own axes.

A sample population of segmented spines in their own axes.

File:Spines01.jpg

2007-06-08T21:30:13Z

Wbsmith: Segmented reconstruction of dendritic spines from a Purkinje neuron. The main dendritic shaft is shown in gray, and the manually segmented spines are shown in various colors.

Segmented reconstruction of dendritic spines from a Purkinje neuron. The main dendritic shaft is shown in gray, and the manually segmented spines are shown in various colors.

Projects/Slicer3/2007 Project Week Support for electron microscopy

2007-06-08T21:23:07Z

Wbsmith:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

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

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Insert some refs here

2007 Programming/Project Week MIT

2007-06-08T21:14:11Z

Wbsmith: /* NA-MIC Kit */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) 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.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]]and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
Please note that this agenda is a draft and will be finalized by June 15th.

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman)
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/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.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# 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...

== Projects ==

=== Template ===

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please use this template intead of the 4-block ppts.

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
#[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
#[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
#[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|vtkITK wrapper for rule based segmentation]] (John Melonakos GATech, Tauseef Rehman GATech, Brad Davis Kitware, Marek Kubicki BWH)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)

===NA-MIC Kit===
#Slicer3
##[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
##[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt)
## [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Luca, Steve, Dan)
## [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
## [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
## [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Scalars and Tensors]] (Katharina, Sylvain, Steve)
## [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# Slicer2

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# Image-Guided Therapy
## [[Collaboration/BWH/Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
## [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
## [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
## [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* [[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jim Miller, GE Core 2, Booked at the Hotel At MIT
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2, Booked at the Hotel At MIT
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2
#Zack Galbreath, Kitware, Core 4
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator (Hotel at MIT request)
#Alex Kogan, Northwestern University, Collaborator (Hotel at MIT request)
#Vladimir Kleper, Northwestern University, Collaborator (Hotel at MIT request)
#Pat Mongkolwat, Northwestern University, Collaborator (Hotel at MIT request)
#Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
#Mark Scully, The MIND Institute, DBP2:MIND software engineer
#Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
#Greg Sharp, MGH, Collaborator
#Lauren O'Donnell, BWH
#Raul San Jose, BWH
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Kevin Teich, MGH
#Michael Halle, BWH/IIC
#James Ross, GE
#Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
#Douglas Alan, Harvard IIC
#Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
#Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
#Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)
#Ran Tao, Utah, Core 1
#Alex. Gouaillard, CEGS caltech Software Engineer, QuadEdgeMesh project Lead (ITK)
#Sean Megason, CEGS caltech PI, (not full week)
#Clif Burdette (Acousticmed, Collaborator)
#Jack Blevins (Acousticmed, Collaborator)
#Lilla Zollei (MGH)
#Serdar K Balci (MIT)

2007 Programming/Project Week MIT

2007-05-31T18:56:29Z

Wbsmith: /* NA-MIC Kit */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) 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.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]]and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
Please note that this agenda is a draft and will be finalized by June 15th.

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman)
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/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.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# 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...

== Projects ==

=== Template ===

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please use this template intead of the 4-block ppts.

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
#[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
#[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
#[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|vtkITK wrapper for rule based segmentation]] (John Melonakos GATech, Tauseef Rehman GATech, Brad Davis Kitware, Marek Kubicki BWH)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)

===NA-MIC Kit===
#Slicer3
##[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
##[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt)
## [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Luca, Steve, Dan)
## [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
## [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
## [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Scalars and Tensors]] (Katharina, Sylvain, Steve)
## [[Slicer3:Fluorescence and Electron Microscopy Support | Dendritic Spine Morphometrics]] (Bryan Smith)
# Slicer2

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# Image-Guided Therapy
## [[Collaboration/BWH/Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
## [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
## [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
## [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* [[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jim Miller, GE Core 2, Booked at the Hotel At MIT
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2, Booked at the Hotel At MIT
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator (Hotel at MIT request)
#Alex Kogan, Northwestern University, Collaborator (Hotel at MIT request)
#Vladimir Kleper, Northwestern University, Collaborator (Hotel at MIT request)
#Pat Mongkolwat, Northwestern University, Collaborator (Hotel at MIT request)
#Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
#Mark Scully, The MIND Institute, DBP2:MIND software engineer
#Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
#Greg Sharp, MGH, Collaborator
#Lauren O'Donnell, BWH
#Raul San Jose, BWH
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Kevin Teich, MGH
#Michael Halle, BWH/IIC
#James Ross, GE
#Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
#Douglas Alan, Harvard IIC
#Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
#Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
#Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)
#Ran Tao, Utah, Core 1
#Alex. Gouaillard, CEGS caltech Software Engineer, QuadEdgeMesh project Lead (ITK)
#Sean Megason, CEGS caltech PI, (not full week)
#Clif Burdette (Acousticmed, Collaborator)
#Jack Blevins (Acousticmed, Collaborator)
#Lilla Zollei (MGH)
#Serdar K Balci (MIT)

Slicer3:Fluorescence and Electron Microscopy Support

2007-05-31T18:39:44Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective (Electron Microscopy):''' Analyze dendritic spine morphologies from electron tomographic reconstructions.

'''Background Info:''' Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region.

'''Links:'''
*[http://ncmir.ucsd.edu/~bryan/spines01.jpg A segmented spiny dendrite from cerebellum]
*[http://ncmir.ucsd.edu/~bryan/spineSample.jpg An example set of segmented spines]

'''Objective (Light Microscopy):''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* A [[Media:NCMIR example dataset.zip | sample dataset]] is available.

'''Screenshot:'''

[[Image:SlicerAstrocyte.jpg | NCMIR image processing pipeline]]

Slicer3:Fluorescence and Electron Microscopy Support

2007-05-31T18:33:56Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective (Electron Microscopy):''' Analyze dendritic spine morphologies from electron tomographic reconstructions.

'''Background Info:''' Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region.

'''Objective (Light Microscopy):''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* A [[Media:NCMIR example dataset.zip | sample dataset]] is available.

'''Screenshot:'''

[[Image:SlicerAstrocyte.jpg | NCMIR image processing pipeline]]

2007 Programming/Project Week MIT

2007-05-31T18:22:28Z

Wbsmith: /* NA-MIC Kit */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) 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.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]]and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Agenda===
Please note that this agenda is a draft and will be finalized by June 15th.

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman)
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# By 3pm ET on June 21, 2007: [[NA-MIC/Projects/Theme/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.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# 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...

== Projects ==

=== Template ===

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please use this template intead of the 4-block ppts.

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
#[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
#[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
#[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis, Sylvain Bouix)
#[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|vtkITK wrapper for rule based segmentation]] (John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett, Jim Miller, Marek Kubicki)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos, Marc Niethammer, Marek Kubicki)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Y.)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Y.)

===NA-MIC Kit===
#Slicer3
##[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
##[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt)
## [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Luca, Steve, Dan)
## [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
## [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
## [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Scalars and Tensors]] (Katharina, Sylvain, Steve)
## [[Slicer3:Fluorescence and Electron Microscopy Support | Fluorescence and Electron Microscopy Support]] Dendritic Spine Morphometrics (Bryan Smith)
# Slicer2

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# Image-Guided Therapy
## [[Collaboration/BWH/Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
## [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
## [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
## [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* [[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jim Miller, GE Core 2, Booked at the Hotel At MIT
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2, Booked at the Hotel At MIT
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator (Hotel at MIT request)
#Alex Kogan, Northwestern University, Collaborator (Hotel at MIT request)
#Vladimir Kleper, Northwestern University, Collaborator (Hotel at MIT request)
#Pat Mongkolwat, Northwestern University, Collaborator (Hotel at MIT request)
#Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
#Mark Scully, The MIND Institute, DBP2:MIND software engineer
#Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
#Greg Sharp, MGH, Collaborator
#Lauren O'Donnell, BWH
#Raul San Jose, BWH
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Kevin Teich, MGH
#Michael Halle, BWH/IIC
#James Ross, GE
#Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
#Douglas Alan, Harvard IIC
#Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
#Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
#Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)
#Ran Tao, Utah, Core 1
#Alex. Gouaillard, CEGS caltech Software Engineer, QuadEdgeMesh project Lead (ITK)
#Sean Megason, CEGS caltech PI, (not full week)
#Clif Burdette (Acousticmed, Collaborator)
#Jack Blevins (Acousticmed, Collaborator)
#Lilla Zollei (MGH)
#Serdar K Balci (MIT)

2007 Programming/Project Week MIT

2007-05-24T14:52:35Z

Wbsmith: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast and lunch for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' There is no official hotel for the meeting. Here is some information about 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.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Draft Agenda===
Please note that this agenda is a draft and will be finalized by June 15th.

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce Projects using templated wiki pages (all Project Leads)
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9-945am: NA-MIC Software Process (Bill Hoffman - TBC)
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using the templated wiki pages
** noon lunch boxes and adjourn

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# By 3pm ET on June 21, 2007: Complete the templated wiki page for your project. THe final version of this template will be circulated by May 25th.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# 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...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
*[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
*[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
*[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
*[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (John Melonakos, Brad Davis, Marek Kubicki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===
* [[Algorithm:UNC:DTI#Population_Analysis | DTI population analysis]] (Casey Goodlett)
* Slicer3 Whole brain Seeding platform: data representation and pipeline execution (Raul San Jose, Lauren O'Donnell, Alex Y.)
* Slicer3 Tractography editor (Lauren O'Donnell, Raul San Jose, Alex Y.)

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** [[2007_Project_Week_MIT_Display_Optimization | Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
** [[2007_Project_Week_MIT_MRML_Scenes_for_the_Execution_Model]], including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (Luca, Steve, Dan)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
** Drafting Human Interface and Slicer Style Guidelines (Wendy)
** Slicer Matlab Pipeline for scalars and tensors (Katharina, Sylvain, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT
** [[Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
** [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
** [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
* Registration
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
** [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe)
** [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
* [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek(GE))
* [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
* [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
* [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* AstroMed (Michael Halle, Douglas Alan)

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1, (Hotel at MIT request)
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jim Miller, GE Core 2, Booked at the Hotel At MIT
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2, Booked at the Hotel At MIT
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator (Hotel at MIT request)
#Alex Kogan, Northwestern University, Collaborator (Hotel at MIT request)
#Vladimir Kleper, Northwestern University, Collaborator (Hotel at MIT request)
#Pat Mongkolwat, Northwestern University, Collaborator (Hotel at MIT request)
#Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
#Mark Scully, The MIND Institute, DBP2:MIND software engineer
#Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
#Greg Sharp, MGH, Collaborator
#Lauren O'Donnell, BWH
#Raul San Jose, BWH
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Kevin Teich, MGH
#Michael Halle, BWH/IIC
#James Ross, GE
#Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
#Douglas Alan, Harvard IIC
#Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
#Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
#Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)

Slicer3:Fluorescence and Electron Microscopy Support

2007-05-03T21:21:37Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective:''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* A [[Media:NCMIR example dataset.zip | sample dataset]] is available.

'''Screenshot:'''

[[Image:SlicerAstrocyte.jpg | NCMIR image processing pipeline]]

Slicer3:Fluorescence and Electron Microscopy Support

2007-05-03T21:11:26Z

Wbsmith:

Slicer3:Fluorescence and Electron Microscopy Support

2007-05-03T21:04:14Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective:''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* Some sample data are available here: [[Image:NCMIR example dataset.zip]]

'''Screenshot:'''

[[Image:SlicerAstrocyte.jpg]]

Slicer3:Fluorescence and Electron Microscopy Support

2007-05-03T21:00:59Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective:''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* Some sample data are available here: [[Image:NCMIR example dataset.zip|NCMIR dataset]]

'''Screenshot:'''

[[Image:SlicerAstrocyte.jpg]]

File:NCMIR example dataset.zip

2007-05-03T20:55:26Z

Wbsmith: Representative image volumes and associated text file describing images and the sort of analysis we wish to perform.

Representative image volumes and associated text file describing images and the sort of analysis we wish to perform.

Engineering:TCON 2007

2007-04-29T20:04:35Z

Wbsmith: /* 2007-04-26 */

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

==2007-05-17 ==
Agenda:
*Summer Project Week Contd.

==2007-05-10 ==
Agenda:
*Summer Project Week discussions Contd.

==2007-05-03 ==
Agenda:
*Summer Project Week Kickoff with the Engineering Core.

==2007-04-26 ==
Attendees: Nicole Aucoin, Brad Davis, Tina Kapur, Jim Miller, Madelaine Miller, Skip and Pat from Nothwestern, Vince, Katie Hayes, Bryan Smith, Steve Pieper, Jeff Grethe

Agenda:
*Report from Bryan Smith (UCSD NCMIR) on his visit to BWH to develop ITK-based command line modules for connected component and math morphology analysis of microscopy data.
**Update on progress
**Reading data into Slicer
**Slice through surfaces, generate models
*Review progress report progress
**Voxel statistics from image data
**Otsu contains connected components...problems on OS X

**Reworking the wiki page hierarchy for progress report
**Final pass on NA-MIC kit projects
**How to handle projects which use GPLed code in Slicer extensions
**Review the publications page to make sure all of your pubs are there

*Slicer bugs
**Problems reading 3-D TIFFs with RGB colormaps

==2007-04-19 ==
Agenda:
* http://www.na-mic.org/Bug/view.php?id=38 A bug in TIFF IO. Given a high-priority rating by Ron. Volunteer needed.
* There is an emerging slate of bioinformatics platforms for research: BIRN, XNAT, CaBig, I2B2 etc. Slicer3 will need to work with these environments.
** We are already working with BIRN on [http://www.xnat.org XNAT], [http://www.nbirn.net/downloads/index.shtm HID], and [http://www.nbirn.net/downloads/xcede/index.shtm XCEDE]
** What kind of additional interactions should we attempt for the near term?
** What kind of functional behaviour is realistic, given resources available?
** Does [[media:Slicer3-Architecture.jpg | this diagram]] accurately reflect our approach?
* NITRC Administrative Supplements available (Steve)
** See announcement [http://grants.nih.gov/grants/guide/notice-files/NOT-EB-07-002.html]
** Dave Kennedy plays a major role in the program
** Applications are accepted any time, but there's a review coming up so getting proposals in by May 15th is a good idea
** These supplements can support documentation and integration of tools into the NITRC (Neuroimaging Informatics Tools and Resources Clearinghouse)
** NITRC is based to some extent on [http://gforge.org/ gforge].
** Goal is for "modifying, documenting, and otherwise making more adoptable, interoperable, and usable existing neuroimaging informatics tools and resources."
* Patching vtkImageReslice in Slicer-2-6 VTK, also do we want a Slicer-2-7 branch of VTK/ITK?

Attendees: Jim, Steve, Ron, Jeff, Nicole, Will, Stephen, Neil

* TIFF Bug: Jim will ask one of his people to look into the TIFF bug.
*

==2007-04-12 ==
Agenda:
*Slicer2 RuleBasedSegmentation Module (for the DLPFC semi-automatic segmentation)
*Further discussion of large scale experiment control (Dan, Steve, Sebastien)
*Process for annual report (Tina, Jim)
*Collaboration grant updates
*fBIRN / BIRN informatics update (Steve)

Attendees: Jim, Dan, Sebastien, Brad, Tina, Vince, John, Ramsey, Nicole, Stephen, Jeff
Notes:
* (Pre meeting discussion of sunspots)
* Rule-Based Segmentation Module
** Marek would like to use it for his data
** GATech provided info on work so far, Brad has reviewed
** VTK/ITK implementation issues that can be easily resolved
** Slicer2 module needs to be integrated with actual filter
** Delphine and Ramsey wrote the interface and filters based on Jim Fallon's rules
** Slicer2 implementation relies on subvolume and draw capabilities (discussion of slicer3 implementation).
*** possible new subvolume selector to add to slicer3
*** could use new editor in slicer3 for ROI
*** also need some kind of wizard or detailed instructions to help guide
*** then the rule based code could be a command line module
** GATech is planning to do a project with Jim Fallon using the Slicer
** At project week we can look at getting Marek up to speed on Slicer2 and the engineering group can work on a slicer3 implementation.
* Issue with NAMICSandBox ability to commit? John may be specific to John.
* Update on Neil's work on the GWiz (Grid Wizard) and discussions with Jeff and Steve at fBIRN meeting
* Stephen update
** Starting to do 'batchboard' tests on bspline registration
** planning public face for registration optimized methods
** integration of BatchMake and CMake for running tests on multiple platforms
* Sebastien is doing timing tests on various machines at BWH
** ITK timer class does the clocking (wall clock timing) but could look at performance timers at the processor API (build in the CPU).
** Process priority is set high to get best guess of fastest behavior
** may need an administrative approach to avoid multiple jobs running during night performance tests
** new features being added to cmake/ctest/batchmake to help determine machine environment, could be extended
* Progress report mechanics
** The report describes just the current year (not the cumulative sum of all the years).
** Tina is going to send email about the themes for the progress report
** Need to be sure the pdf has clickable URLs for wiki page entries
** Discussion of Impact for the highlights section
*** non-na-mic people at the programmer events and AHM
* Update on XCEDE work at fBIRN AHM

==2007-04-05 ==
Agenda:
*Collaboration proposal Peter Y.

Minutes:

* Attendees: Peter, Dan, Jim, Katie, Steve, Wendy, Nicole, Vince, Tina, Will, Sebastien, Stephen, Brad

Discussion of Peter Yim's plans for disseminating algorithms through the NA-MIC Kit.
* Biomedical Engineering, UNC, NIH
* Algorithms for MRA, vessel reconstruction
** Segmentation, skeletonization
** University of Medicine and Dentistry of NJ
** Vascular diagnostics, quantifying angiogenesis, stroke...
* Algorithms could be valuable, but aren't written in a way that can be disseminated (written in C for IRIS Explorer)
** Peter needs to have collaborators to re-write the code
** Peter can provide the clinical background and potential user community
* Could be good candidates for integration into ITK
** Need to review what it means for the NIH patented technology to be deployed
** Some of the algorithms require close interaction and others are more automated
* Discussion of the possible allocations of effort and collaboration

* Discussion of [[Slicer3:Large scale experiment control brainstorming]]

==2007-03-29 ==

Agenda:
* DBPII: Marek (harvard), Csaba (JHU)
* [[2007_Annual_Scientific_Report|Progress Report]]:the folks who lead the sections last time are invited to do the same again this year
* [[Slicer3:MiniRetreat March 29, 30, 2007 | Slicer Mini-retreat (ongoing)]] - Jim and Dan at 1249

Highlights:

Attendees: Will, Jim, Wendy, Csaba, Marek, Nicole, Katie, Dan, Steve, Sebastien, Brad, Ron, Tina
*Marek - vcsf data on 5 patients. familiar with software and algorithms available in na-mic. segmentation and fine tuning of algorithms is needed in slicer. Would like to use GeorgiaTech algorithm for automated segmentation of DLPFC.
*Csaba putting details of JHU project on wiki. Will schedule himself into the tcon in about 4 weeks.

==2007-03-22 ==

Agenda:

*Progress Reports - the folks who lead the sections last time will be invited to do the same again this year, or to nominate someone else who they will help.
*DBP-II - algorithms contacts added by Ross. (UNC: Guido, Harvard: Polina, MIND: Bruce Fischl, JHU: Allen)
*Invitation sent to [[DBP2]] for this call, with the following agenda suggestion:
**Notes: Marek has conflict on 3/22 and will attend 3/29 tcon.
**reminder that he would like your pages to be updated in March. Example of an updated page is: http://www.na-mic.org/Wiki/index.php/DBP2:MIND
**introducing you to your namic engineering contact points and the role they will be playing. (we expect to introduce you to your namic algorithms core contact points at a later point as well).
**summer project week at MIT (June 25-29). Ron's expectation is that by then (1) you will have identified a problem that can be solved with the na-mic kit in a 6-month timeframe and the results for which you will use in your work, (2) you will send an engineer and data to this project week, and the engineer will be able to articulate to the larger group what the problem is, and use that week to work on it with the na-mic team.

Jim has notes and attendees to add.

==2007-03-15 ==

Agenda:

* Heads up: [[2007_Annual_Scientific_Report|2007 Progress Report]]. Recommendations needed from Ron on section/theme leads.
* Dissemination and Outreach for the rest of us (Will, Tina)
* [[DBP2]] Points of Contact (DBP, Engineering, Algorithm). Need contact information for DBP2s. Algorithm contact points still need to be added. (Update: email sent to Ross 3/1 and 3/15 with request to provide names in march.)
* Performance analysis tools and strategies: [[ITK_Registration_Optimization]], [[Slicer3:Performance_Analysis]] (Steve Pieper, Sebastian Barre, Stephen Aylward, Katie Hayes)
* Slicer release schedule (Steve)

*'''Question''' from Douglas Alan: At the January NA-MIC All Hands meeting in SLC, Mike Halle and I met with Bill Lorensen and Jim Miller to discuss how in Slicer we might pass a FITS world coordinate system transform (and its inverse) from an ITK FITS image reader to the resulting Slicer VTK image so that Slicer can then be enhanced to use the transform to properly display the world coordinates. The proposed solution was for me to define a subclass of itk::Transform (i.e., FITSWCSTransform) that would handle the WCS transform, and once I had completed this (which I have) for me to then modify my FITSImageIO reader so as to include a pointer to a FITSWCSTransform object in the FITSImageIO's MetaDataDictionary. As it turns out, there seems to be a snafu with this plan: the MetaDataDictionary of an ITK image appears to be stripped from the image whenever it passes through an ITK filter. Or so it is the case, at least, for the filters that I have tried. Any ideas on how we should proceed, in light of this?

Notes:

Attendees: Jim, Steve, Will, Katie, Nicole, Raymundo, Stephen, Sebastien, Wendy, Tina, Jeff

* Schedule for the progress report in on the wiki. Last year's report is also available. Assignments are imminent.
* Need to update the NA-MIC web presence. ''Wiki to web'' will be used to author and publish the content. Ron will set the vision for the web presence statement (DBP focus? Theme focus? Core focus?). Everyone is responsible ensuring all NA-MIC activities and contributions are advertised.
* Tina will get the contact info for the DBP2's
* Stephen is pulling together a test application to run across systems to evaluate registration performance.
** Note that only one optimizer is relevent to B-Spline registration (LBFGS-B?)
** Torsten has a hierarchical B-Spline algorithm that Killian uses as the yardstick.
** Brad developing proposal to evaluate EM pipeline soup-to-nuts for sources of errors.
* Steve and Katie looking at Callgrind and Callgrind Control to track the overhead of observers and potentially the over-calling of callbacks.
* Tracker performance okay but the images update slowly
* Slicer3 release at the end of March
** DTI tools availability gated by MICCAI deadline
** Launchers work with getbuildtest but may have impacted CPack installations.
** ModelMaker needs MRML read/write (Jim!)
** Filebrowser will be available
** Any features to suppress?
** Any additional documentation needed?
* Slicer 2.7 release at the end of March
** Mostly bug fixes but a few new features
* Jim will talk to Mike about the FITS needs for the MetaDataDictionary and the pipeline.

==2007-03-08 ==

Agenda:

* Question from Steve: best way to handle "neurological" analyze files (where right-is-right unlike radiological files where "left -is-right"). The [http://www.oasis-brains.org oaisis brains] data collection from mBIRN stores their data this way and the ITK IO factory doesn't have a way to know which kind of file these are.
* [[Slicer3::Python | Python in Slicer]] - project overview: Dan
* Google Summer of Code - are there any project takers?

Notes:
* Update - it turns out oasis-brains.org analyze files are stored in radiological convention but displayed in neurological convention, so everything is as 'correct' as it can be for this file format. But the ambiguity remains about the real meaning of analyze files, so in the future oasis will supply nifti formated files.

==2007-03-01 ==

Agenda:
* Adding Engr+Algorithms core representatives to each DBP-II team: [[DBP2:MIND]]
* [http://code.google.com/soc/ Google Summer of Code]
* [http://nifti.nimh.nih.gov/dfwg/internal/wiki/sifti_home/ SIfTI] effort to standardize spatial transform files. (login info will be given on the phone)
* Technical Slicer3 item: command line executables

Notes:
* Eng contacts for DBP-II:
** Katie Hayes for the JHU project
** Jim Miller for UNC
** Brad Davis for Harvard (Confirmed)
** Steve Pieper for MIND
* Summer of Code
** Generally agreed to be a good idea if there's time
** Check with Luis
* SIfTI
* Command Line Interface to EMSegmenter
** Jim will work on making MRML scenes come as arguments to command line modules and give an example that can be used for EMSegmenter and other projects like the ModelMaker.

==2007-02-22 ==

Attendees: Wendy, Jim, Nicole, Dan, Andy, Katie, Tina, Ron

Highlights:
* match dbp-IIs to engineering core members (Jim and Tina to do offline)
* contact dpbs regarding participation in project week (Tina)

== 2007-02-15 ==

Agenda:

Attendees: Jim, Nicole, Tina, Katie, Jags

== 2007-02-08 ==

Agenda:
*Please note that we now use a new TCON#. If you don't have it, please send an email to namic-eng@na-mic.org.
*Review remaining [[2007_Project_Half_Week#Projects|Project Half-Week Updates]]

== 2007-02-01 ==

Agenda:
*First call with Jim's tcon # (was emailed to participants)
*Review [[2007_Project_Half_Week#Projects|Project Half-Week Updates]]

== 2007-01-25 ==

Attendees: Bill, Jim, Steve, Wendy, Nicole, Katie, Brad, Andy & Jags

Agenda:
*Last call with Bill as the PI...
*Next TCON (Feb 1) to review 4-block from project half week. Will use Jim's tcon #.

Highlights:
*New phone number for TCON next week; email Jim for the number
*Problem with region growing?
*Bye, Bill! We'll see you in three weeks when you get bored with retirement.

== 2007-01-18 ==
Attendees: Bill, Tina, Steve, Katie, Sebastien, Zack, Jags

* Slicer3 release schedule discussion
* Which teem are we on?
* Status of filebrowser?
** Current unix browser does not allow for making a new directory
** Does the new one support specifying a list of file types? (Yes)
* Feb 1/8 for project half-week results 4-blocks review?

Highlights:
*Feb 1 and 8 for project half-week results 4-blocks review
*12 days till Bill's retirement...
*OHMB workshop agenda info by Steve: DTI tutorial for Slicer3 is a candidate topic.

== 2007-01-11 ==

No tcon this week. [[AHM_2007]] in progress.

== 2007-01-04 ==

Agenda and Highlights:
* [[2007_Project_Half_Week|Project Half-Week Activities]] - Focus on Slicer3 Projects. And any others that need resolution of title/team. 4-blocks should appear asap. Each project lead will use these to introduce their project on Wednesday, Jan 10th.
* There are pages in google cache that are not yet on the namic-wiki. What is the process for pulling those in? Should each person who finds a page just cut and paste the text as best as they can? How should we use the "wanted pages" list on the wiki?

Highlights:
*Slicer3 Projects have been added to the wiki.
*Wanted page list is being pared down as a high priority item,.
*Jim and Bill will be on Daniel Goldberg's project half week project.

Attendees: Bill, Will, Ron, Steve, Jim, Stephen, Neil, Andy, Luis, Nicole, Katie, Wendy, Jags, Tina

Slicer3:Fluorescence and Electron Microscopy Support

2007-04-29T04:38:26Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective:''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* Some sample data are available here: http://ncmir.ucsd.edu/~bryan/testData/

'''Screenshot:'''

[[Image:SlicerAstrocyte.jpg]]

Slicer3:Fluorescence and Electron Microscopy Support

2007-04-29T04:32:12Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective:''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* Some sample data are available here: [[http://ncmir.ucsd.edu/~bryan/testData/]]

'''Screenshot:'''

[[Image:SlicerAstrocyte.jpg]]

Slicer3:Fluorescence and Electron Microscopy Support

2007-04-26T19:09:21Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective:''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* Some sample data are available here: [[NCMIR|http://ncmir.ucsd.edu/~bryan/testData/]]

'''Screenshot:'''

[[Image:SlicerAstrocyte.jpg]]

File:SlicerAstrocyte.jpg

2007-04-26T19:06:58Z

Wbsmith: Screenshot of astrocyte image in Slicer, and proposed processing and analysis project.

Screenshot of astrocyte image in Slicer, and proposed processing and analysis project.

File:Slide1.jpg

2007-04-26T19:01:45Z

Wbsmith: Screenshot of astrocyte image in Slicer, and proposed processing and analysis project.

Screenshot of astrocyte image in Slicer, and proposed processing and analysis project.

Slicer3:Fluorescence and Electron Microscopy Support

2007-04-26T18:55:56Z

Wbsmith:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective:''' Incorporate into Slicer our existing microscopy processing and analysis routines, currently being done in Matlab.

'''Progress:'''
Reading 3-D TIFF images and generating surface models has been easily accomplished.

* 2007-04-26: Modifying Otsu Segmentation CLM to make use of Connected Components Image Filter.
** Works in Linux, not OS X.
* 2007-04-25: Discussion of relevant steps to accomplish initial astrocyte parsing project.
** Using EM Segmentation or 2-D histogram normalization approach to segment immunostaining data.
** Need 3-D erosion functionality for 'shrinking' astrocyte image volume to separate into two domains: an outer, "hull", and an inner, "core" domain in which differential protein distributions will be assessed.
** Can ParaView be used as visualization tool for surface rendering? Is it faster?

'''Key Investigators:'''
* NCMIR/UCSD: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

'''Links:'''

* Some sample data are available here: [[NCMIR|http://ncmir.ucsd.edu/~bryan/testData/]]

2007 Programming/Project Week MIT

2007-04-02T20:08:56Z

Wbsmith: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

June 25-29, 2007, MIT

==Please Note==

Programming/Project week is one of the major events in the NA-MIC calendar. This will be our third annual Summer Programmming/Project Week.

* Core 1 - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* Core 2 - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* Core 3 - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Results ==
Results of this event will be summarized here after it is completed.

== Projects ==

Projects will be added here...

===Structural Analysis===

===Diffusion Image Analysis===

===NA-MIC Kit===
===External Collaborations===
== Logistics ==

'''Dates:''' June 25-29, 2007
'''Registration Fee:''' Registration fee is TBD. It will be payable by check onsite.

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#|TBD: Kickoff TCON]]
# TBD: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_2007#|TBD: TCON#2 to discuss projects and verify teams]]
# TBD: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# [[Engineering:TCON_2007#|TBD: TCON#3 last preparation tcon]]
# By June 24, 2007: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# 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...

==Attendee List==

#Jim Miller, GE Core 2
#Steve Pieper, Isomics, Core 2
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, collaborator
#Katie Hayes, BWH, Core 2
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#Dan Blezek, GE Core 2 (Tentative)
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)

AHM 2007 Attendee List

2007-03-16T18:10:44Z

Wbsmith:

# Mohan Vandana Georgia Institute of Technology Core 1 (attended PHW)
# Nain Delphine Georgia Institute of Technology Core 1 (attended PHW)
# Gao Yi Georgia Institute of Technology Core 1 (attended PHW)
# Melonakos John Georgia Institute of Technology Core 1 (attended PHW)
# Tannenbaum Allen Georgia Institute of Technology Core 1
# Jen Dennis Harvard University MGH Core 1 (attended PHW)
# Fischl Bruce Harvard University MGH Core 1
# Balci Serdar Kemal MIT Core 1 (attended PHW)
# Kim Bryce MIT Core 1
# Maddah Mahnaz MIT Core 1
# Ngo Tri MIT Core 1
# Ou Wanmei MIT Core 1
# Pohl Kilian MIT Core 1 (attended PHW)
# Sabuncu Mert MIT Core 1
# Yeo Boon Thye MIT Core 1
# Ziyan Ulas MIT Core 1
# Davis McKay SCI Institute Core 1
# Fletcher Tom SCI Institute Core 1
# Whitaker Ross SCI Institute Core 1
# Styner Martin UNC CH Core 1
# Gerig Guido UNC Chapel Hill Core 1
# Goodlett Casey UNC Chapel Hill Core 1
# Oguz Ipek UNC Chapel Hill Core 1
# Tao Ran University of Utah Core 1
# Yarmarkovich Alexander Brigham and Women's Hospital Core 2 (attended PHW)
# Blezek Daniel GE Research Core 2 (attended PHW)
# Lorensen William GE Research Core 2 (attended PHW)
# Miller James GE Research Core 2 (attended PHW)
# Aylward Stephen Kitware, Inc. Core 2 (attended PHW)
# Barre Sebastien Kitware, Inc. Core 2 (attended PHW)
# Davis Bradley Kitware, Inc. Core 2 (attended PHW)
# Ibanez Luis Kitware, Inc. Core 2 (attended PHW)
# Schroeder Will Kitware, Inc. Core 2 (attended PHW)
# Rajendiran Jagadeeswaran UCLA Core 2 (attended PHW)
# Ellisman Mark UCSD Core 2
# Smith W. Bryan UCSD/NCMIR Core 2 (attended PHW)
# Jones Neil UCSD Core 2
# Markant Doug Brigham and Women's Hospital Core 3
# Niethammer Marc Brigham and Women's Hospital Core 3
# Quintus Katharina Brigham and Women's Hospital Core 3
# Roth Robert Dartmouth Medical School Core 3
# Saykin Andrew Dartmouth Medical School Core 3
# West John IUPUI Core 3
# Voineskos Aristotle Neurogenetics/University of Toronto Core 3
# Shenton Martha Harvard/BWH Core 3
# Potkin Steve UC Irvine Core 3
# Preda Adrian UC Irvine Core 3
# Kennedy James University of Toronto Core 3
# Kubicki Marek Brigham and Women's Hospital Core 3-II
# Fichtinger Gabor Johns Hopkins University Core 3-II
# Grosland Nicole The University of Iowa Core 3-II
# Hazlett Heather Cody UNC Chapel Hill Core 3-II
# Cedilnik Andy Kitware, Inc. Core 4 (attended PHW)
# Pujol Sonia Brigham and Women's Hospital Core 5
# Pieper Steve Isomics, Inc. Core 6 (attended PHW)
# Kikinis Ron Brigham and Women's Hospital Core 7
# Johnson Chris Chair, External Advisory Board EAB
# Ackerman Michael External Advisory Board EAB
# Napel Sandy External Advisory Board EAB
# Pearlson Godfrey External Advisory Board EAB
# Pierpaoli Carlo External Advisory Board EAB
# Prior Fred External Advisory Board EAB
# Cohen Zohara National Institutes of Health NIH
# Peng Grace National Institutes of Health NIH
# Burdette E. Clif Acoustic MedSystems /Johns Hopkins Collaborator
# Aucoin Nicole Brigham and Women's Hospital Collaborator (attended PHW)
# Bouix Sylvain Brigham and Women's Hospital Collaborator
# DiMaio Simon Brigham and Women's Hospital Collaborator (attended PHW)
# Goldberg-Zimring Daniel Brigham and Women's Hospital Collaborator (attended PHW)
# Halle Michael Brigham and Women's Hospital Collaborator (attended PHW)
# Hata Nobuhiko Brigham and Women's Hospital Collaborator (attended PHW)
# Hayes Kathryn Brigham and Women's Hospital Collaborator (attended PHW)
# Liu Haiying Brigham and Women's Hospital Collaborator (attended PHW)
# ODonnell Lauren Brigham and Women's Hospital Collaborator (attended PHW)
# Plesniak Wendy Brigham and Women's Hospital Collaborator (attended PHW)
# Sierra Raimundo Brigham and Women's Hospital Collaborator (attended PHW)
# San Jose Estepar Raul Brigham and Women's Hospital Collaborator (attended PHW)
# Megason Sean Cal Tech Collaborator
# Zhao Zheen Duke University Collaborator
# Alan Douglas Harvard University IIC Collaborator (attended PHW)
# Lisle Curtis KnowledgeVis Collaborator
# Antiga Luca Mario Negri Institute Collaborator (attended PHW)
# Wells William MIT Collaborator (attended PHW)
# Zollei Lilla MIT Collaborator (attended PHW)
# Talbot Skip Northwestern Dept. of Radiology Collaborator
# Kogan Alex Northwestern University Collaborator
# Mongkolwat Pattanasak Northwestern University Collaborator (attended PHW)
# Wilson Nathan Stanford University Collaborator
# Bockholt H Jeremy The MIND Institute Collaborator
# Bafna Ritesh The University of Iowa Collaborator
# DeVries Nicole The University of Iowa Collaborator
# Kallemeyn Nicole The University of Iowa Collaborator
# Magnotta Vincent The University of Iowa Collaborator (attended PHW)
# Shivanna Kiran The University of Iowa Collaborator (attended PHW)
# Tadepalli Srinivas The University of Iowa Collaborator
# Wyatt Chris Virginia Tech Collaborator (attended PHW)