NAMIC Wiki - User contributions [en]

NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine

2008-06-26T17:58:00Z

Nessus: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to see if we can add support for World Coordinate System grid images to Slicer3 in order to allow astronomical coordinate readout from slice planes.
</div>

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

<h1>Progress</h1>
We have implemented software that has allowed Slicer to be used as a platform for doing cutting-edge radio astronomy. Peer-reviewed publications are pending, including one in <i>Nature</i>.

<h3>At 2008 Summer Project Week</h3>
<ul>
<li>Learned how we can use the new Loadable Modules feature to help solve our problem.</li>
<li>Worked with Luis to make itk::Transform<>::GetInverse() virtual.
<li>Learned that another group is working on adding support for grid transform MRML storage and transform nodes. Assuming that this pans out, we only need to add support for using these from the SliceSWidget.</li>
<li>Devised with Steve and Jim several different plans for getting the coordinate transforms into SliceSWidget.</li>
<li>Learned from Luca how to make Loadable Modules in Python.</li>
</ul>

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
* [http://astromed.iic.harvard.edu/DendroStar DendroStar] applet for visualization of dendrogram representations of spectral line data cubes.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine

2008-06-26T15:56:45Z

Nessus: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to see if we can add support for World Coordinate System grid images to Slicer3 in order to allow astronomical coordinate readout from slice planes.
</div>

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

<h1>Progress</h1>
We have implemented software that has allowed Slicer to be used as a platform for doing cutting-edge radio astronomy. Peer-reviewed publications are pending, including one in <i>Nature</i>.

<h3>At 2008 Summer Project Week</h3>
<ul>
<li>Learned how we can use the new Loadable Modules feature to help solve our problem.</li>
<li>Worked with Luis to make itk::Transform<>::GetInverse() virtual.
<li>Learned that another group is working on adding support for grid transform MRML storage and transform nodes. Assuming that this pans out, we only need to add support for using these from the SliceSWidget.</li>
<li>Devised with Steve and Jim several different plans for getting the coordinate transforms into SliceSWidget.</li>
</ul>

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
* [http://astromed.iic.harvard.edu/DendroStar DendroStar] applet for visualization of dendrogram representations of spectral line data cubes.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine

2008-06-26T15:41:04Z

Nessus: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to see if we can add support for World Coordinate System grid images to Slicer3 in order to allow astronomical coordinate readout from slice planes.
</div>

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

<h1>Progress</h1>
We have implemented software that has allowed Slicer to be used as a platform for doing cutting-edge radio astronomy. Peer-reviewed publications are pending, including one in <i>Nature</i>.

<h3>At 2008 Summer Project Week</h3>
<ul>
<li>Learned about how we can use the new Loadable Modules feature to help solve our problem.</li>
<li>Worked with Luis to make itk::Transform<>::GetInverse() virtual.
<li>Learned that another group is working on adding support for grid transform MRML storage and transform nodes, so assuming that this pans out, we need to figure out how to add support for using these from the SliceSWidget.</li>
</ul>

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
* [http://astromed.iic.harvard.edu/DendroStar DendroStar] applet for visualization of dendrogram representations of spectral line data cubes.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine

2008-06-05T23:04:41Z

Nessus: /* Key Investigators */

NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine

2008-06-05T22:49:31Z

Nessus: New page: {| |Project Week Main Page ]] |[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future vers...

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to make further progress in integrating our ITK FITS reader into Slicer as a plug-in, and to begin work on Slicer GUI enhancements to support our FITS plug-in and to allow the display of astronomical coordinates in slice viewers.
</div>

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

<h1>Progress</h1>
====January 2008 Project Week====

* Created vtkCoordinateSpaceManager, a container that manages multiple named coordinate spaces and the transforms between them. A reader can populate a coordinate space manager with all the coordinate spaces it knows about. Registration tools can link otherwise unrelated coordinate spaces, and the manager can hand back a (possibly composite) transform between any two related spaces. This module hasn't been incorporated into Slicer3 yet.
* With Wendy Plesniak's help, we now have the ability to recenter on data not located at the origin in Slicer. She's incorporating similar changes into the "look from" Slicer control. We'll need to look at autozooming as well for very small volumes.
* Slicer3 volume rendering works reasonably well with astronomical data, but the world size of model seems to influence rendering appearance. Solved some performance issues on the Mac.
* Experimental linearized celestial coordinate system implementation being tested now.
* Prototyped Slicer3 plugin module adapter for fits2itk.
** Debugged performance issues with the Slicer3 implementation of plugin modules for OS X and submitted bug report.
* Prototyped ITK-based NaN masking filter.
** Still need standard way to deal with NaNs in ITK/VTK/Slicer3.

====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released a subsequent version as an open-source FITS-to-NRRD file converter, which is available [http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008 Summer Project Week

2008-06-05T22:45:03Z

Nessus: /* Non-Medical Collaborations */

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

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

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

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

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

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.]This rate is good only through June 1.

Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

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

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a 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. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
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]] capabilities, integrate Core 1 algorithms, and refine workflows 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 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==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm 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
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[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.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##Work Flow Tool for regional cortical thickness pipeline (Clement Vachet UNC)
##NITRC registration of cortical thickness modules (Clement Vachet UNC)
##DTI tools for a) DWI preparation and b) DTI atlas building (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[DBP2:JHU:Roadmap|Trans-Rectal Prostate Biopsy module (David Gobbi, Gabor Fichtinger, Queens/JHU)]]
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)]]
##Hardware/software overlay for percutaneous intervention (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#NIREP: Non-rigid Image Registration Evaluation (Gary Christensen Group)
#Lung Atlas (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 2
# David Gobbi, Queen's, Core 2
# Purang Abolmaesumi, Queen's, Core 2
# Siddharth Vikal, Queen's, Core 2
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 2
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University
# Tim Olsen, Washington University
# Kevin Archie, Washington University
# Misha Milchenko, Washington University
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT

==Pictures==

2008 Summer Project Week

2008-06-05T21:38:50Z

Nessus: /* Attendee List */

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

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

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

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

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

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.]This rate is good only through June 1.

Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

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

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a 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. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
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]] capabilities, integrate Core 1 algorithms, and refine workflows 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 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==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm 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
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[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.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##Work Flow Tool for regional cortical thickness pipeline (Clement Vachet UNC)
##NITRC registration of cortical thickness modules (Clement Vachet UNC)
##DTI tools for a) DWI preparation and b) DTI atlas building (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[DBP2:JHU:Roadmap|Trans-Rectal Prostate Biopsy module (David Gobbi, Gabor Fichtinger, Queens/JHU)]]
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)]]
##Hardware/software overlay for percutaneous intervention (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#NIREP: Non-rigid Image Registration Evaluation (Gary Christensen Group)
#Lung Atlas (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)

===Non-Medical Collaborations===

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 2
# David Gobbi, Queen's, Core 2
# Purang Abolmaesumi, Queen's, Core 2
# Siddharth Vikal, Queen's, Core 2
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 2
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University
# Tim Olsen, Washington University
# Kevin Archie, Washington University
# Misha Milchenko, Washington University
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator

==Pictures==

2008 Winter Project Week:Astronomical Medicine

2008-06-05T21:34:33Z

Nessus: /* January 2008 Project Week */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to make further progress in integrating our ITK FITS reader into Slicer as a plug-in, and to begin work on Slicer GUI enhancements to support our FITS plug-in and to allow the display of astronomical coordinates in slice viewers.
</div>

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

<h1>Progress</h1>
====January 2008 Project Week====

* Created vtkCoordinateSpaceManager, a container that manages multiple named coordinate spaces and the transforms between them. A reader can populate a coordinate space manager with all the coordinate spaces it knows about. Registration tools can link otherwise unrelated coordinate spaces, and the manager can hand back a (possibly composite) transform between any two related spaces. This module hasn't been incorporated into Slicer3 yet.
* With Wendy Plesniak's help, we now have the ability to recenter on data not located at the origin in Slicer. She's incorporating similar changes into the "look from" Slicer control. We'll need to look at autozooming as well for very small volumes.
* Slicer3 volume rendering works reasonably well with astronomical data, but the world size of model seems to influence rendering appearance. Solved some performance issues on the Mac.
* Experimental linearized celestial coordinate system implementation being tested now.
* Prototyped Slicer3 plugin module adapter for fits2itk.
** Debugged performance issues with the Slicer3 implementation of plugin modules for OS X and submitted bug report.
* Prototyped ITK-based NaN masking filter.
** Still need standard way to deal with NaNs in ITK/VTK/Slicer3.

====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released a subsequent version as an open-source FITS-to-NRRD file converter, which is available [http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008 Winter Project Week:Astronomical Medicine

2008-01-08T01:00:49Z

Nessus: /* June 2006 Project Week */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to make further progress in integrating our ITK FITS reader into Slicer as a plug-in, and to begin work on Slicer GUI enhancements to support our FITS plug-in and to allow the display of astronomical coordinates in slice viewers.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released a subsequent version as an open-source FITS-to-NRRD file converter, which is available [http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008-SCI-tour

2008-01-08T00:57:15Z

Nessus: /* List of Participants */

__NOTOC__

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

=Tour of the Scientific Computing and Imaging (SCI) Institute=

The SCI Institute (http://www.sci.utah.edu) recently moved into the new Warnock Engineering Building at the University of Utah.

Here is information about our new space:

http://www.sci.utah.edu/stories/2007/Warnock.html

http://www.sci.utah.edu/stories/2007/sci_moving.html

Please join us for a short tour of the SCI Institute.

=Logistics=
We have rented a van/bus that will hold 20 people and take people from the Marriott Hotel to the SCI Institute and then back again to the Hotel.

The van/bus will leave the Marriott Hotel at '''5:00 p.m. on Wednesday, January 9''' and return to the Hotel around 6:15 p.m.

The first 20 people to sign up will be able to ride on the van/bus. Others who would like to join us can car pool.

Here is a map and directions to the SCI Institute (Warnock Engineering Building). It is about a 10 minute drive from the Hotel to the SCI Institute.

http://www.sci.utah.edu/map.html

=List of Participants=
Please add your name to the bottom of the list, if you intend to participate in the tour.
#Ron Kikinis
#Zohara Cohen
#Curtis Lisle
#Martin Styner
#Vincent Magnotta
#Nicole Grosland
#Carl-Fredrik Westin
#Nikos Chrisochoides
#Marek Kubicki
#Sonia Pujol
#Csaba Csoma
#Steve Pieper
#Randy Gollub
#Terry Yoo
#Michael Halle
#Luis Ibanez
#Carlo Pierpaoli
#Sylvain Bouix
#Katie Hayes
#Douglas Alan

2008 Winter Project Week

2008-01-02T21:21:44Z

Nessus: /* External Collaborations */

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]]
*Next Project Week is at MIT -- June 23-27, 2008

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

Please read an introduction about these events [[Project_Events#Introduction|here]].

===NA-MIC DBP Roadmap Projects===
Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

#[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant) [[DBP2:Harvard:Brain_Segmentation_Roadmap|[Harvard Roadmap Project: Stochastic Tractography for VCFS]]]
#[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller) [[DBP2:UNC:Cortical_Thickness_Roadmap|[UNC Roadmap Project: Cortical Thickness Measurement for Autism]]]
#[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)[[DBP2:MIND:Roadmap|[MIND Roadmap Project: Brain Lesion Analysis in Lupus]]]
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions |Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)[[DBP2:JHU:Roadmap|[JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]]
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)[[DBP2:JHU:Roadmap|[JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]]

===Other NA-MIC Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu,Luis Ibanez,Brad Davis)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett, Alex Yarmakovich)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Alex Yarmakovich, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Luis Ibanez, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman,Alex Yarmakovich, Jim Miller)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#[[2008_Winter_Project_Week:UnstructuredGrids | Unstructured Grids and Mesh Support]] (Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim Miller, Steve Pieper, Alex Yarmakovich, Luca Antiga, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie Hayes, Steve Pieper, Bill Hoffman, Sebastien Barre)
#[[2008_Winter_ProjectWeek:SlicerCookbook | Slicer GUI Style Guide and Cookbook]] (Wendy Plesniak, Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics and Colon Polyps (Bryan Smith, Padma Sundaram, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Benjamin Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Benjamin Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier, Kevin Archie, Misha Milchenko)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)

===External Collaborations===
#[[2008_Winter_Project_Week:Astronomical_Medicine|Astronomical coordinate system support]] [Harvard IIC] (Mike Halle, Douglas Alan, Steve Pieper)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?, Stephen Aylward)
#[[2008_Winter_Project_Week:microslicer_3 | Doing microscopy image analysis with Slicer3]] [The Ohio State University](Kishore Mosaliganti, Raghu Machiraju, Brad Davis,Stephen Aylward, Steve Pieper)
#[[2008_Winter_Project_Week:fmri_image_analysis | fMRI Analysis with Slicer 3]] [The Ohio State University](Firdaus Janoos,Raghu Machiraju, Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix, Xiaodong Tao)
#[[2008_Winter_Project_Week:fmri_eeg_analysis | Analyzing fMRI and concurrent EEG with Slicer and SCIRun]] [BWH] (Padma Sundaram)
#[[2008_Winter_Project_Week:fmri_var | Bayesian hierarchical models for fMRI variance components analysis]] (Kinh Tieu, Sandy Wells, Jim Miller)

== 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]])

=== 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]]
# By December 20, 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.
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# 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)
# 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:Astronomical Medicine

2008-01-02T21:15:21Z

Nessus:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to make further progress in integrating our ITK FITS reader into Slicer as a plug-in, and to begin work on Slicer GUI enhancements to support our FITS plug-in and to allow the display of astronomical coordinates in slice viewers.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this as an open-source FITS-to-NRRD file converter, which is available [http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T21:14:07Z

Nessus:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to make further progress in integrating our ITK FITS reader into Slicer as a plug-in, and to begin work on Slicer GUI enhancements to support our FITS plug-in and to allow the display of astronomical coordinates in slicer viewers.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this as an open-source FITS-to-NRRD file converter, which is available [http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T21:13:34Z

Nessus:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to make further progress in integrating our ITK FITS reader into Slicer as a plug-in, and to begin work on Slicer GUI enhancements to support our FITS plug-in and to allow the display of astronomical coordinates in slicer viewers.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this as an open-source FITS-to-NRRD file converter, which is available [http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T21:02:27Z

Nessus: /* June 2007 Project Week */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this as an open-source FITS-to-NRRD file converter, which is available [http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T21:00:21Z

Nessus: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata
dictionary through the Slicer pipeline, worked with Luis Ibanez to
help implement ITK streaming file I/O, set up more robust dependency
rules in our CMake config, and debugged a problem with our use of ITK
filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's
"extended filename syntax", identified compatibility issues present in
the most recent version of Slicer 3, and devised a plan for passing
FITS WCS transforms around in Slicer by encapsulating them in
itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this
as an open-source FITS-to-NRRD file converter, which is available
[http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* The [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:59:46Z

Nessus: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata
dictionary through the Slicer pipeline, worked with Luis Ibanez to
help implement ITK streaming file I/O, set up more robust dependency
rules in our CMake config, and debugged a problem with our use of ITK
filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's
"extended filename syntax", identified compatibility issues present in
the most recent version of Slicer 3, and devised a plan for passing
FITS WCS transforms around in Slicer by encapsulating them in
itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this
as an open-source FITS-to-NRRD file converter, which is available
[http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====
* [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:56:06Z

Nessus: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata
dictionary through the Slicer pipeline, worked with Luis Ibanez to
help implement ITK streaming file I/O, set up more robust dependency
rules in our CMake config, and debugged a problem with our use of ITK
filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's
"extended filename syntax", identified compatibility issues present in
the most recent version of Slicer 3, and devised a plan for passing
FITS WCS transforms around in Slicer by encapsulating them in
itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this
as an open-source FITS-to-NRRD file converter, which is available
[http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

* [http://am.iic.harvard.edu Astronomical Medicine web site]
* [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:54:50Z

Nessus: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata
dictionary through the Slicer pipeline, worked with Luis Ibanez to
help implement ITK streaming file I/O, set up more robust dependency
rules in our CMake config, and debugged a problem with our use of ITK
filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's
"extended filename syntax", identified compatibility issues present in
the most recent version of Slicer 3, and devised a plan for passing
FITS WCS transforms around in Slicer by encapsulating them in
itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this
as an open-source FITS-to-NRRD file converter, which is available
[http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:53:42Z

Nessus:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata
dictionary through the Slicer pipeline, worked with Luis Ibanez to
help implement ITK streaming file I/O, set up more robust dependency
rules in our CMake config, and debugged a problem with our use of ITK
filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's
"extended filename syntax", identified compatibility issues present in
the most recent version of Slicer 3, and devised a plan for passing
FITS WCS transforms around in Slicer by encapsulating them in
itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this
as an open-source FITS-to-NRRD file converter, which is available
[http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1><br>
====References====

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

====Additional Information====

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:51:06Z

Nessus:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata
dictionary through the Slicer pipeline, worked with Luis Ibanez to
help implement ITK streaming file I/O, set up more robust dependency
rules in our CMake config, and debugged a problem with our use of ITK
filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's
"extended filename syntax", identified compatibility issues present in
the most recent version of Slicer 3, and devised a plan for passing
FITS WCS transforms around in Slicer by encapsulating them in
itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this
as an open-source FITS-to-NRRD file converter, which is available
[http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1></h1>
====References====

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:49:20Z

Nessus: /* June 2007 Project Week */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>
====June 2007 Project Week====

Worked with Jim Miller to implement preservation of the ITK metadata
dictionary through the Slicer pipeline, worked with Luis Ibanez to
help implement ITK streaming file I/O, set up more robust dependency
rules in our CMake config, and debugged a problem with our use of ITK
filters.

====Jan 2007 Project Half Week====

Solved problem of itk::ImageIOBase being incompatible with CFITSIO's
"extended filename syntax", identified compatibility issues present in
the most recent version of Slicer 3, and devised a plan for passing
FITS WCS transforms around in Slicer by encapsulating them in
itk::Transform objects held in an image's metadata dictionary.

====June 2006 Project Week====

Implemented a prototype FITS reader for ITK. We later released this
as an open-source FITS-to-NRRD file converter, which is available
[http://astromed.iic.harvard.edu/FITS-reader here].

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

<h1>References</h1>

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:48:01Z

Nessus: /* June 2007 Project Week */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With some help from Luis, set up more robust dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Luis helped us track down a problem with our use of ITK filters. (The filters were being GC'ed due to no smart pointers pointing to them anymore.)

====Pior====
We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

</div>

<h1>References</h1>

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:16:18Z

Nessus: /* Pior= */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With some help from Luis, set up more robust dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Luis helped us track down a problem with our use of ITK filters. (The filters were being GC'ed due to no smart pointers pointing to them anymore.)

====Pior====
We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:16:01Z

Nessus: /* Progress During Programming Week */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With some help from Luis, set up more robust dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Luis helped us track down a problem with our use of ITK filters. (The filters were being GC'ed due to no smart pointers pointing to them anymore.)

====Pior=====
We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

2008 Winter Project Week:Astronomical Medicine

2008-01-02T20:07:38Z

Nessus: New page: {| |Return to [[2008_Winter_Project_Week ]] |[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features de...

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Havard IIC: Douglas Alan
* BWH/Harvard IIC: Mike Halle
* Isomics: Steve Pieper

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
** Debugged alpha version of the code.
** Modified FITS reader to work with new streaming interface.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
** Will require wrapping our transform object into a subclass of vtkSlicerLogic.
** Will require loading our FITS reader into Slicer as a DLL.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With some help from Luis, set up more robust dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Talked with Curtis Lisle who might implement a volume renderer for Slicer. (This is something that we need.)
* Luis helped us track down a problem with our use of ITK filters. (The filters were being GC'ed due to no smart pointers pointing to them anymore.)
* Luis showed us how to use Source Navigator, which turns out to be a very useful tool for fathoming large C++ code bases.

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-07-02T21:07:06Z

Nessus: /* Progress During Programming Week */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Douglas Alan: Havard IIC
* Mike Halle: BWH/Harvard IIC
* Jim Miller: GE
* Luis Ibanez: Kitware
<div style="margin: 20px;">

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
** Debugged alpha version of the code.
** Modified FITS reader to work with new streaming interface.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
** Will require wrapping our transform object into a subclass of vtkSlicerLogic.
** Will require loading our FITS reader into Slicer as a DLL.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With some help from Luis, set up more robust dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Talked with Curtis Lisle who might implement a volume renderer for Slicer. (This is something that we need.)
* Luis helped us track down a problem with our use of ITK filters. (The filters were being GC'ed due to no smart pointers pointing to them anymore.)
* Luis showed us how to use Source Navigator, which turns out to be a very useful tool for fathoming large C++ code bases.

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-06-29T20:29:40Z

Nessus: /* Progress During Programming Week */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Douglas Alan: Havard IIC
* Mike Halle: BWH/Harvard IIC
* Jim Miller: GE
* Luis Ibanez: Kitware
<div style="margin: 20px;">

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
** Debugged alpha version of the code.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
** Will require wrapping our transform object into a subclass of vtkSlicerLogic.
** Will require loading our FITS reader into Slicer as a DLL.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With some help from Luis, set up more robust dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Talked with Curtis Lisle who might implement a volume renderer for Slicer. (This is something that we need.)
* Luis helped us track down a problem with our use of ITK filters.

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-06-29T13:19:47Z

Nessus: /* Progress During Programming Week */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Douglas Alan: Havard IIC
* Mike Halle: BWH/Harvard IIC
* Jim Miller: GE
* Luis Ibanez: Kitware
<div style="margin: 20px;">

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
** Will require wrapping our transform object into a subclass of vtkSlicerLogic.
** Will require loading our FITS reader into Slicer as a DLL.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With some help from Luis, set up more robust dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Talked with Curtis Lisle who might implement a volume renderer for Slicer. (This is something that we need.)
* Luis helped us track down a problem with our use of ITK filters.

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-06-29T03:53:40Z

Nessus: /* Progress During Programming Week */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Douglas Alan: Havard IIC
* Mike Halle: BWH/Harvard IIC
* Jim Miller: GE
* Luis Ibanez: Kitware
<div style="margin: 20px;">

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
** Will require wrapping our transform object into a subclass of vtkSlicerLogic.
** Will require loading our FITS reader into Slicer as a DLL.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With some help from Luis, set up more robust dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Talked with Curtis Lisle who might implement a volume renderer for Slicer. (This is something that we need.)

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-06-29T01:24:29Z

Nessus: /* Progress During Programming Week */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Douglas Alan: Havard IIC
* Mike Halle: BWH/Harvard IIC
* Jim Miller: GE
* Luis Ibanez: Kitware
<div style="margin: 20px;">

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
** Will require wrapping xxxx into an xxxx Logic object.
** Will require loading our FITS reader into Slider as a DLL.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With help from Luis, set up proper dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Talked with xxxx who might implement a volume renderer for Slicer. (This is something that we need.)

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-06-29T01:23:22Z

Nessus: /* Key Investigators */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Douglas Alan: Havard IIC
* Mike Halle: BWH/Harvard IIC
* Jim Miller: GE
* Luis Ibanez: Kitware
<div style="margin: 20px;">

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
** Will require wrapping xxxx into an xxxx Logic object.
** Will require loading our FITS reader into Slider as a DLL.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With help from Luis, set up proper dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Talked with xxxx who might implement a volume renderer for Slicer. (This is something that we need.)

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-06-29T01:20:36Z

Nessus: /* Progress During Programming Week */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Mike Halle: BWH/Harvard IIC
* Douglas Alan: Havard IIC
* Jim Miller: GE

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.
** Will require wrapping xxxx into an xxxx Logic object.
** Will require loading our FITS reader into Slider as a DLL.
* Learned from Luis how to turn our FITS reader into a DLL that can be autoloaded by any ITK application.
* With help from Luis, set up proper dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our particular use case.
* Talked with xxxx who might implement a volume renderer for Slicer. (This is something that we need.)

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-06-29T01:13:24Z

Nessus: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Mike Halle: BWH/Harvard IIC
* Douglas Alan: Havard IIC
* Jim Miller: GE

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===Progress During Programming Week===

* Worked with Jim to implement preservation of the ITK metadata dictionary through the Slicer pipeline.
* Worked with Luis to implement interface for streaming file I/O.
* Learned from Luis how to turn our FITS reader into a DLL that will be autoloaded by any ITK application.
* With help from Luis, set up proper dependency rules in our CMake config.
* Talked with Wendy Plesniak about a couple Slicer 3 interface tweaks that will help out our use case.
* Talked with Steve Pieper to plan out next step to achieve our goal of being able to display astronomical coordinates in Slicer.

{|
! '''Before''' !! '''After'''
|-
|     [[Image:caffeine-free.jpg]]     ||     [[Image:jolt.jpg]]    
|}

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

File:Jolt.jpg

2007-06-29T01:03:03Z

Nessus:

File:Caffeine-free.jpg

2007-06-29T01:02:32Z

Nessus:

Collaboration/Harvard IIC/AstroMed

2007-06-29T00:46:33Z

Nessus: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Mike Halle: BWH/Harvard IIC
* Douglas Alan: Havard IIC
* Jim Miller: GE

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Prior Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Special topic breakout: ITK

2007-06-27T15:42:39Z

Nessus: /* Participants */

'''Tutorial Session on ITK''' (Luis Ibanez)

= Topics =
*How do you efficiently integrate VTK and ITK with respect to reading and writing images? Is there one class that can be used to hold data sets for both libraries?
*How to do FFTs in ITK?
*What type of coordinate space should be used, voxels vs. real space?
*What type of image formats should be used?
*Is there any standard way to read in coefficient files, i.e., algorithm specific parameters?
*How are XML/MRML files parced in ITK/VTK? We want to know how to use the vtkXMLparser and MRML objects to parse our XML files.
*What are the memory and performance issues with ITK?
*How can we debug memory leaks (or force memory collector to start collecting)?
*How can I access the metadata of each slice in a 3D DICOM volume?

= Hands On =

* ITK - VTK Integration
** http://insight-journal.org/dspace/handle/1926/495
* FFT
** Insight/Examples/Filtering/
*** FFTDirectInverse.cxx
*** FFTDirectInverse2.cxx
*** FFTImageFilter.cxx
*** FFTImageFilterFourierDomainFiltering.cxx
*** http://insight-journal.org/dspace/handle/1926/326
*** http://insight-journal.org/dspace/handle/1926/321
* Voxels vs Real Space
** Real Space
* File Formats
** Depends on the purpose...
*** MetaImage
*** Analyze
*** DICOM
*** Nrrd
* Standard for reading coefficients
** Not really...
** It is worth to define one
* XML/MRML Parsing
** Need help from Steve Pieper here (Jim? Alex? Laurent?)
* Memory issues in ITK
** Many Trade offs
** Usually trading computation time versus memory
** ITK only supports shared memory, not distributed memory (MPI)

= Participants =
*Jeff Hawley
*Kunlin Cao
*Kai Ding
*Xiujuan Geng
*James Harris
*Gary Christensen
*Paul Song
*Jake Nickel
*Nick Kiguta
*Alex. Gouaillard
*Csaba Csoma
*Douglas Alan

Collaboration/Harvard IIC/AstroMed

2007-06-21T18:58:43Z

Nessus: /* Additional Information */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Mike Halle: BWH/Harvard IIC
* Douglas Alan: Havard IIC
* Jim Miller: GE

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]
* [http://astromed.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter.
</div>

Collaboration/Harvard IIC/AstroMed

2007-06-21T18:51:56Z

Nessus: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Mike Halle: BWH/Harvard IIC
* Douglas Alan: Havard IIC
* Jim Miller: GE

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===References===

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]

</div>

Collaboration/Harvard IIC/AstroMed

2007-06-21T18:51:35Z

Nessus: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|}

__NOTOC__
===Key Investigators===
* Mike Halle: BWH/Harvard IIC
* Douglas Alan: Havard IIC
* Jim Miller: GE

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

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

<h1>Objective</h1>
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
</div>

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

<h1>Approach, Plan</h1>

Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach, at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
</div>

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

<h1>Progress</h1>

We have implemented an open-source FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

The FITS file converter is available in both source and binary releases [http://astromed.iic.harvard.edu/FITS-reader here].

The scientists who use this software at the Harvard IIC have given conference talks and will be publishing papers on the scientific results that they have achieved using the Slicer-based visualization tools.
</div>

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

===References===

TODO: Replace the following with our papers.

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF].

* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, [http://lanl.arxiv.org/abs/astro-ph/0611400 "Application of Medical Imaging Software to 3D Visualization of Astronomical Data"], 10/2006, ADASS XVI Conference. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ADASSpresentation.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/mborkin_ADASSpresentation.pdf PDF] [http://www.cfa.harvard.edu/COMPLETE/astromed/adass2006/ (linked movies)].

* Michelle A. Borkin, [http://www.cfa.harvard.edu/COMPLETE/papers/borkin.pdf "A COMPLETE Survey of Velocity Features in Perseus"], 5/2006, Harvard University Undergraduate Senior Thesis.

* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604.

=Additional Information=

* [http://astromed.iic.harvard.edu Astronomical Medicine web site]

</div>

Collaboration/Harvard IIC/AstroMed

2007-06-21T18:47:24Z

Nessus:

Collaboration/Harvard IIC/AstroMed

2007-06-21T18:35:39Z

Nessus:

Collaboration/Harvard IIC/AstroMed

2007-06-21T18:34:19Z

Nessus:

Collaboration/Harvard IIC/AstroMed

2007-06-21T16:40:41Z

Nessus:

File:Future-astromed-slicer-mockup.png

2007-06-21T16:09:24Z

Nessus: Mockup of what a future version of Slicer might look like that supports more features desired by the Astronomical Medicine project.

Mockup of what a future version of Slicer might look like that supports more features desired by the Astronomical Medicine project.

Collaboration/Harvard IIC/AstroMed

2007-06-21T16:03:58Z

Nessus:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
|}

__NOTOC__
===Key Investigators===
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

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

<h1>Objective</h1>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h1>Approach, Plan</h1>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...
</div>

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

<h1>Progress</h1>

Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>

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

</div>

===References===
* Fletcher, P.T., Tao, R., Jeong, W.-K., Whitaker, R.T., "A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI," to appear Information Processing in Medical Imaging (IPMI) 2007.
* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., and Gerig, G., "Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis," Medical Image Analysis 10 (2006), 786--798.
* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore J.H., and Gerig, G., Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Lecture Notes in Computer Science LNCS, James S. Duncan and Guido Gerig, editors, Springer Verlag, Vol. 3749, Oct. 2005, pp. 131 -- 138
* C. Goodlett, I. Corouge, M. Jomier, and G. Gerig, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

=Additional Information=
Please link to pages with additional information here.

2007 Programming/Project Week MIT

2007-05-17T21:36:35Z

Nessus: /* Non-Medical Collaborations */

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

== 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
** noon-1pm lunch
** 1-3:30pm Introduce Projects using 4-block slides (all Project Leads)
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9-10am: 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: Non-Linear Registration]]
** 2-3pm: [[Special topic breakout: DWI/DTI]]
** 3-4pm: [[Special topic breakout: KWWidgets]]
** 4-5pm: [[Special topic breakout: Atlases]]
** 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
** 8:30am breakfast
** 10am-noon: Project Progress using 4-block slides
** 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 14, 2007: Complete the top half of [[media:NA-MIC_Latest_4-Block_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# [[Engineering:TCON_2007#2005-06-14|June 14, 2007: TCON#3 Review of 4-Blocks (Structural, DTI, Collaboration, Other)]]
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Review of 4-Blocks (NA-MIC Kit)]]
# 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 (Brad Davis, John Melonakos, 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)
* Slicer3 Tractography editor (Lauren O'Donnell, Raul San Jose)

===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)
** 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, depends on Dan's availability)
** 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 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 (Tentative)
#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
#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
#Rhiannon Carlson, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator
#Csaba Csoma, Johns Hopkins University, Collaborator
#David Gobbi, Queen's University, Collaborator
#Kai Ding, University of Iowa, Gary's student
#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

2007 Programming/Project Week MIT

2007-05-17T21:33:31Z

Nessus: /* Attendee List */

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

== 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
** noon-1pm lunch
** 1-3:30pm Introduce Projects using 4-block slides (all Project Leads)
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9-10am: 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: Non-Linear Registration]]
** 2-3pm: [[Special topic breakout: DWI/DTI]]
** 3-4pm: [[Special topic breakout: KWWidgets]]
** 4-5pm: [[Special topic breakout: Atlases]]
** 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
** 8:30am breakfast
** 10am-noon: Project Progress using 4-block slides
** 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 14, 2007: Complete the top half of [[media:NA-MIC_Latest_4-Block_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# [[Engineering:TCON_2007#2005-06-14|June 14, 2007: TCON#3 Review of 4-Blocks (Structural, DTI, Collaboration, Other)]]
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Review of 4-Blocks (NA-MIC Kit)]]
# 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 (Brad Davis, John Melonakos, 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)
* Slicer3 Tractography editor (Lauren O'Donnell, Raul San Jose)

===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)
** 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, depends on Dan's availability)
** 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 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===

==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 (Tentative)
#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
#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
#Rhiannon Carlson, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator
#Csaba Csoma, Johns Hopkins University, Collaborator
#David Gobbi, Queen's University, Collaborator
#Kai Ding, University of Iowa, Gary's student
#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

2007 Project Half Week

2007-03-30T21:36:14Z

Nessus: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==

This event was successfully concluded on January 12, 2007. A summary powerpoint for this event is available [[image:2007 Project Half Week Summary.ppt| here]].

Some statistics:

For the AHM:
* 96 total attendees: 56 NA-MIC participants, 32 collaborators, 8 EAB+NIH
** 56 NA-MIC Participants breakdown by cores: Core 1 (24), Core 2 (13), Core 3 (15), Core 4 (1), Core 5 (1), Core 6 (1), Core 7 (1)
** 32 Collaborators: Acoustic Med (1), BWH (12), Caltech (1), Duke (1), Harvard IIC (1), Knowledge Vis (1), Mario Negri (1), MIT (2), NWU (3), Stanford (1), MIND (1), UIowa(6), Virginia Tech (1).
* 38 Projects: Structural Analysis (9), Diffusion Image Analysis (7), NA-MIC Kit (10), External Collaborations (11)

==Please note==
* 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.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration2.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Ran Tao - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Image:2007 Project Half Week DTI.ppt|4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]] [[media:2007 AHM Programming Half Week PackagingAndDeployment2.ppt | 4-block PPT Feb 2007]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve, Skip, Alex) [[Media:2007WS3DSlicer.ppt| 4 block PPT Jan 2007]]
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]] [[Execution_Model_Reference_Systems|discussion on reference systems]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Vis-Updated-012606.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh namic1.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
##Mapped Meshing Using ITK - [[Media:2007_AHM_Programming_Half_Week_MappedMesh.ppt|ITK FEM Registration Mapped Meshing Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[image:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]
# Slicer Enhancements for Astronomical Data Cubes ('''Douglas Alan''' IIC, Mike Halle BWH/IIC, Bill Lorensen GE, Jim Miller GE, Wendy Plesniak BWH), [[Media:2006_Summer_Project_Week_Astronomy_FITS_Reader_Prelim_Results.ppt|4-block PPT June 2006]], [[Media:2007_Project_Half_Week_FITSReaderArch.ppt| 4-block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== 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_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: 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#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: 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...

== A History in Wiki Links ==

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