NAMIC Wiki - User contributions [en]

Engineering:TCON 2007

2007-05-01T01:42:32Z

Jags: /* 2007-04-26 */

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Minutes:

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

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

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

==2007-03-29 ==

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

Highlights:

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

==2007-03-22 ==

Agenda:

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

Jim has notes and attendees to add.

==2007-03-15 ==

Agenda:

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

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

Notes:

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

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

==2007-03-08 ==

Agenda:

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

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

==2007-03-01 ==

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

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

==2007-02-22 ==

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

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

== 2007-02-15 ==

Agenda:

Attendees: Jim, Nicole, Tina, Katie, Jags

== 2007-02-08 ==

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

== 2007-02-01 ==

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

== 2007-01-25 ==

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

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

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

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

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

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

== 2007-01-11 ==

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

== 2007-01-04 ==

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

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

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

Mbirn:SpringConference2007

2007-03-21T12:28:19Z

Jags: /* Sessions for AHM: */

== Morphometry BIRN All Hands Meeting - 2007 ==
 
Location: Boston, MA
 
Date: March 21-23, 2007
 
Venue: [http://www.radisson.com/bostonma Radisson Boston]
 
 
Room rates are $159/night, please call the hotel directly at 617-482-1800 and let reservations know that you are with the "mBIRN Spring Meeting 2007" block.
 
 
There will be a Programmer's Day on 3/21 for those people needing extra working time outside of the two meeting days. Contact
Karl Helmer (helmer@nmr.mgh.harvard.edu) for more information.
 
 
We will be kicking off the meeting on 3/21 with a cocktail party social starting at 5:00 pm followed by a dinner at 7:00 pm, both are at the Radisson. 

There is also a group dinner planned on 3/22 at Maggiano's Little Italy (4 Columbus Ave, Boston, MA
(617) 542-3456; across the street from the hotel).
 
 

== Sessions for AHM: ==

'''Wednesday (3/21) ''' ''Note: this session takes place at [http://spl.harvard.edu:8000/pages/directions/1249Boylston/Boylston-facility.html 1249 Boylston Street]'' 
The conference room is on the second floor, room 245, and the phone number
there is 617-525-6224. Once you arrive downstairs call extension 56224 and
someone can come and let you in.

*Morning 
Breakfast: 8AM 
Start: 8:30 AM 
Topic 1: Where are we and where are we going? 
Introduction / Goals of the Meeting - Randy Gollub 
Data Repository Update - Chris Fennema-Notestine 
(5 minute presentations + time for discussion/questions) 
Portal Update - Jeff Grethe, Mark James 
Applications Update: Steve Pieper (Slicer 3) [[media:Slicer3-update-2007-03-21.ppt | slides]]; Nick Schmansky (QDEC: a Freesurfer group-analysis GUI tool) 
Workflows Update: R. Jagadeeswaran (LONI) [[media:Jags_mbirnAHM_March_2007.ppt | slides]]; Shawn Murphy/Mike Mendis (MGH) 
Databases Update - Dan Marcus (XNAT) 

Discussion of the agenda for Wednesday and Thursday 
Move to Breakout Groups 

''Lunch (12-1:00PM)'' 
*Afternoon (1-4PM) 
Database/Application Integration Working Session (Dan Marcus, Steve Pieper, Doug Greve, Tim Olsen) 
mBIRN workflows group (Anthony Kolasny, Tim OBrien, Shawn Murphy, Mike Mendis, Ramil Manansala, Neil Jones) 
 
*Evening (at Radisson) 
Cocktail Reception (@5:30 PM) 
Site Update Presentations (@6:00PM) [[media:MBIRN-BWH-Environment-2007-03-21.ppt | slides about the BWH environment]] 
Dinner (@7:00 PM) 

'''Thursday (3/22)''' 
*Morning 
Breakfast 7:30-8:30 
Introduction – Bruce Rosen 
Chris Fennema-Notestine – update from Data Repository Director 

Specific sessions for the following TBD by discussion on Wednesday's Programmer Day: 
Workflows Working Group-demonstrations of the LDDMM and LONI pipelines 
XCEDE Group (Dan Marcus, Jeff Grethe, Tim O'Brien, Dave Keator,..., includes provenance group) 
Upload Working Group 
Visualization and Analysis Working Group 
 
A parallel DTI Working Session (Susumu Mori, Allen Song, Jonathan Farrell, Bennet Landman, Jim Fallon, Berj Gimi, Anders Dale, Karl Helmer) will run throughout Thursday. 
''DTI session will begin with 5 minute updates from each participating site'' 

''Lunch 12-2PM'' 
Operations Committee Lunch 12-1 PM 

*Afternoon (2-5PM) 
DTI Working Session 
Workflows Working Session 
XCEDE /Query Atlas groups (includes provenance group)
Upload Working Session 
Databases Working Session 

*Evening 
6:30 pm - Dinner at [http://www.google.com/maps?hl=en&safe=off&q=maggiano%27s+little+italy&near=Boston,+MA&cid=0,0,1768425890215287899&ll=42.351418,-71.068375&spn=0,.02&sa=X&oi=local&ct=image Maggiano's Little Italy] (4 Columbus Ave, Boston, MA
(617) 542-3456; across the street from the hotel) 

'''Friday (3/23)''' 
*Morning 
Breakfast (7:30-8:30) 
Opening Remarks - Greg Farber 
Opening Remarks II - Bruce Rosen 
Overview for each Working Group 
Introduction to the BIRN Data Repository - Christine Fennema-Notestine 
Introduction of the Clinical Collaborators - Representatives 
Roundtable discussion with mBIRN clinical collaborators: National Database for Autism Research (NDAR), Specialized Program of Translational Research in Acute Stroke (SPOTRIAS), Framingham Heart Study, NIMH Pediatric Neuroimaging Group.
 

''Lunch (12-1:30PM)'' 

*Afternoon (1:30-4PM) 
Wrap up Session – Discussion of what Morphometry can deliver in the one and
two year timeframes. Incorporation of feedback and needs of the clinical
collaborators. 
Action Items 
Finish @ 4pm
 
 

== ATTENDEES ==
 
MGH: B. Rosen, R. Gollub, K. Helmer, S.Murphy, D. Greve, D. Kennedy, M. Mendis, R. Buckner, N.Schmansky, S. Wallace, B. Fischl, G. Hoffman
 
BWH: N. Aucoin, K. Hayes, S. Pieper, R. Kikinis, W. Plesniak
 
MIT: P.Golland
 
WashU: D. Marcus, T.Olsen, M. Ramaratnam, K. Archie
 
JHU: T. Brown, J.Hennesey, A. Kolasny, M. Miller, S. Mori, J. Farrell, B. Landman, A. Qui
 
Duke: A. Song, J. MacFall, B. Boyd, K. Zhao
 
UCLA: A. Toga, R. Jagadeeswaran
 
UCSD: A. Dale, C. Fennema-Notestine
 
UCI: J. Ames, S. Potkin, J.Turner, D. Wei, D. Keator, J. Fallon, A. Preda
 
BIRN CC: M. James, J. Grethe, V. Astakhov, R. Manansala, N. Jones
 
NIH: E.Collier
 
Other Collaborators: B. Gimi (Children's)
 
NIH CIT: M. McAulliffe, E. McCreedy 
 
Friday’s clinical collaborator round table discussion: 
M. McAulliffe (NDAR) 
G. Harris, O. Wu (SPOTRIAS) 
P. Wolfe, R. Killany, ++ (Framingham Heart Study) 
F. LaLonde (NIMH)

File:Jags mbirnAHM March 2007.ppt

2007-03-21T12:27:18Z

Jags:

Engineering:UCLA

2007-03-08T20:03:26Z

Jags:

#Attended NAMIC AHM, SLC Utah, January 2007
#Attended NAMIC Programming/Project Week @ MIT, June 2006
#Pipeline version 4.0 with Client-Server capabilities now available
#Scalable server which handles 1000's of inputs
#Default visualization component in Pipeline package
#Pipeline Batch mode available - Slicer can now invoke Pipeline in batch-mode with pre-bound workflows
#Integration with IDA, other protocol/software suites in progress
# built NAMIC software [[InstallationPipelines|installation pipelines]]
# attended dissemination workshops [[Dissemination:Workshop_Dec9-10_Boston|2004-12-9 Boston]] and [[Dissemination:Workshop_Feb17-18_2005|2005-2-18 UCSD]]
# attended NAMIC AHM at SLC Utah, January 2006
#Latest build/documentation available at: [http://pipeline.loni.ucla.edu/]
--

Engineering:UCLA

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Engineering:UCLA

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Engineering:UCLA

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Engineering:UCLA

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Engineering:UCLA

2007-03-06T22:48:56Z

Jags:

Engineering:UCLA

2007-03-06T22:48:29Z

Jags:

#Attended NAMIC AHM, SLC Utah, January 2007
#Attended NAMIC Programming/Project Week @ MIT, June 2006
#Pipeline version 4.0 with Client-Server capabilities now available
#Scalable server which handles 1000's of inputs
#Default visualization component in Pipeline package
#Pipeline Batch mode available - Slicer can now invoke Pipeline in batch-mode with pre-bound workflows
#Integration with IDA, other protocol/software suites in progress
--
# built NAMIC software [[InstallationPipelines|installation pipelines]]
# built integrated visualization component
# attended dissemination workshops [[Dissemination:Workshop_Dec9-10_Boston|2004-12-9 Boston]] and [[Dissemination:Workshop_Feb17-18_2005|2005-2-18 UCSD]]
# attended NAMIC AHM at SLC
--

Engineering:UCLA

2007-03-06T22:46:49Z

Jags:

# built NAMIC software [[InstallationPipelines|installation pipelines]]
# built integrated visualization component
# attended dissemination workshops [[Dissemination:Workshop_Dec9-10_Boston|2004-12-9 Boston]] and [[Dissemination:Workshop_Feb17-18_2005|2005-2-18 UCSD]]
# attended NAMIC AHM at SLC
--
#Attended NAMIC AHM, SLC Utah, January 2007
#Attended NAMIC Programming/Project Week @ MIT, June 2006
#Pipeline version 4.0 with Client-Server capabilities now available
#Scalable server which handles 1000's of inputs
#Default visualization component in Pipeline package
#Pipeline Batch mode available - Slicer can now invoke Pipeline in batch-mode with pre-bound workflows
#Integration with IDA, other protocol/software suites in progress

Engineering:UCLA

2007-03-06T22:46:36Z

Jags:

# built NAMIC software [[InstallationPipelines|installation pipelines]]
# built integrated visualization component
# attended dissemination workshops [[Dissemination:Workshop_Dec9-10_Boston|2004-12-9 Boston]] and [[Dissemination:Workshop_Feb17-18_2005|2005-2-18 UCSD]]
# attended NAMIC AHM at SLC
--
#Attended NAMIC AHM, SLC Utah, January 2007
#Attended NAMIC Programming/Project Week @ MIT, June 2006
#Pipeline version 4.0 with Client-Server capabilities now available
#Scalable server which handles 1000's of inputs
#Default visualization component in Pipeline package
#Pipeline Batch mode available - Slicer can now invoke Pipeline in
batch-mode with pre-bound workflows
#Integration with IDA, other protocol/software suites in progress

Slicer3:Pipeline Integration

2007-01-26T04:00:55Z

Jags:

# The main features of the project
## http://pipeline.loni.ucla.edu
# The main outstanding questions that must be answered before you can complete the project ::
## Pipeline -> Slicer3
### Once the API for submission to Slicer3 is released, we can integrate it into the Pipeline.
## Slicer3 -> Pipeline
### We have made considerable progress in making Pipeline more stable, robust and scalable. Detailed progress is listed below ::
#### GUI : A new and improved graphical interface is now available. The gui is now much simpler in design and easier to use. The list of improvements/ new features is as follows :

- Completely new data model/xml
- Significantly easier parameter editing
- Cleaner drag and drop of modules
- Easier list processing
- Stronger type checking (with feedback to help the user)
- Variable can be used on parameter bindings
- Personal Library of workflows and moduels
- Copy/Paste of single modules and groups of modules (and still retain connections)
- Undo/Redo on most operations
- Workflows can be layed out horizontally now
- Faster and easier zooming
- Scalable GUI functionality - is able to handle hundreds of modules in a single workflow

# ## ### #### DataModel : The data model, associated XML descriptions have been simplified greatly. The data model has been decoupled from the execution and the GUI, this component has been completed
#### Translation : The translation portion of the software is responsible for accomodating logic that separates GUI/Execution vs Execution. This component has been completed, it takes the workflow and converts it into a flattened graph (it loses the property of module groups at this stage) and constructs the commands using the data model
#### Validation : The validation portion conducts sanity checks on the workflow. It allows the user to fix errors prior to "actual" execution and informs the user of all steps needed to make the workflow run
#### Execution : The execution portion now is an independent component that is agnostic of the data model and can be invoked on the command line directly. Self-sufficient workflows (with previously bound parameters), can be now invoked and executed from the commandline, bypassing the GUI entirely. Workflows or pipes can now be executed both locally and on the LONI grid. The scalability has dramatically improved from 30 inputs to thousands of inputs per workflow. The changes in the execution model are ::

- Agnostic of the data model
- Minimal synchronization to express sequentiality and/or parallelism
- Local execution and LONI grid execution supported
- Detailed logs to keep track of progress
- Periodic status messages passed to GUI for immediate user feedback
- Scalability of execution allows running > 1000 inputs per workflow

# To start a pipeline on the commandline with parameters:

java -classpath pipeline.client.jar ui.cli.Main -execute prebound_workflow

'''Team Members'''<nowiki>: </nowiki>

* Jagadeeswaran Rajendiran - UCLA

Slicer3:Pipeline Integration

2007-01-26T04:00:36Z

Jags:

# The main features of the project
## http://pipeline.loni.ucla.edu
# The main outstanding questions that must be answered before you can complete the project ::
## Pipeline -> Slicer3
### Once the API for submission to Slicer3 is released, we can integrate it into the Pipeline.
## Slicer3 -> Pipeline
### We have made considerable progress in making Pipeline more stable, robust and scalable. Detailed progress is listed below ::
#### GUI : A new and improved graphical interface is now available. The gui is now much simpler in design and easier to use. The list of improvements/ new features is as follows :

<verbatim>

- Completely new data model/xml
- Significantly easier parameter editing
- Cleaner drag and drop of modules
- Easier list processing
- Stronger type checking (with feedback to help the user)
- Variable can be used on parameter bindings
- Personal Library of workflows and moduels
- Copy/Paste of single modules and groups of modules (and still retain connections)
- Undo/Redo on most operations
- Workflows can be layed out horizontally now
- Faster and easier zooming
- Scalable GUI functionality - is able to handle hundreds of modules in a single workflow

</verabatim>

# ## ### #### DataModel : The data model, associated XML descriptions have been simplified greatly. The data model has been decoupled from the execution and the GUI, this component has been completed
#### Translation : The translation portion of the software is responsible for accomodating logic that separates GUI/Execution vs Execution. This component has been completed, it takes the workflow and converts it into a flattened graph (it loses the property of module groups at this stage) and constructs the commands using the data model
#### Validation : The validation portion conducts sanity checks on the workflow. It allows the user to fix errors prior to "actual" execution and informs the user of all steps needed to make the workflow run
#### Execution : The execution portion now is an independent component that is agnostic of the data model and can be invoked on the command line directly. Self-sufficient workflows (with previously bound parameters), can be now invoked and executed from the commandline, bypassing the GUI entirely. Workflows or pipes can now be executed both locally and on the LONI grid. The scalability has dramatically improved from 30 inputs to thousands of inputs per workflow. The changes in the execution model are ::

- Agnostic of the data model
- Minimal synchronization to express sequentiality and/or parallelism
- Local execution and LONI grid execution supported
- Detailed logs to keep track of progress
- Periodic status messages passed to GUI for immediate user feedback
- Scalability of execution allows running > 1000 inputs per workflow

# To start a pipeline on the commandline with parameters:

java -classpath pipeline.client.jar ui.cli.Main -execute prebound_workflow

'''Team Members'''<nowiki>: </nowiki>

* Jagadeeswaran Rajendiran - UCLA

Slicer3:Pipeline Integration

2007-01-26T04:00:10Z

Jags:

Slicer3:Pipeline Integration

2007-01-26T03:59:51Z

Jags:

# The main features of the project
## http://pipeline.loni.ucla.edu
# The main outstanding questions that must be answered before you can complete the project ::
## Pipeline -> Slicer3
### Once the API for submission to Slicer3 is released, we can integrate it into the Pipeline.
## Slicer3 -> Pipeline
### We have made considerable progress in making Pipeline more stable, robust and scalable. Detailed progress is listed below ::
#### GUI : A new and improved graphical interface is now available. The gui is now much simpler in design and easier to use. The list of improvements/ new features is as follows :

<verbatim>

- Completely new data model/xml
- Significantly easier parameter editing
- Cleaner drag and drop of modules
- Easier list processing
- Stronger type checking (with feedback to help the user)
- Variable can be used on parameter bindings
- Personal Library of workflows and moduels
- Copy/Paste of single modules and groups of modules (and still retain connections)
- Undo/Redo on most operations
- Workflows can be layed out horizontally now
- Faster and easier zooming
- Scalable GUI functionality - is able to handle hundreds of modules in a single workflow

</verbatim?

# ## ### #### DataModel : The data model, associated XML descriptions have been simplified greatly. The data model has been decoupled from the execution and the GUI, this component has been completed
#### Translation : The translation portion of the software is responsible for accomodating logic that separates GUI/Execution vs Execution. This component has been completed, it takes the workflow and converts it into a flattened graph (it loses the property of module groups at this stage) and constructs the commands using the data model
#### Validation : The validation portion conducts sanity checks on the workflow. It allows the user to fix errors prior to "actual" execution and informs the user of all steps needed to make the workflow run
#### Execution : The execution portion now is an independent component that is agnostic of the data model and can be invoked on the command line directly. Self-sufficient workflows (with previously bound parameters), can be now invoked and executed from the commandline, bypassing the GUI entirely. Workflows or pipes can now be executed both locally and on the LONI grid. The scalability has dramatically improved from 30 inputs to thousands of inputs per workflow. The changes in the execution model are ::

- Agnostic of the data model
- Minimal synchronization to express sequentiality and/or parallelism
- Local execution and LONI grid execution supported
- Detailed logs to keep track of progress
- Periodic status messages passed to GUI for immediate user feedback
- Scalability of execution allows running > 1000 inputs per workflow

# To start a pipeline on the commandline with parameters:

java -classpath pipeline.client.jar ui.cli.Main -execute prebound_workflow

'''Team Members'''<nowiki>: </nowiki>

* Jagadeeswaran Rajendiran - UCLA

Engineering:TCON 2007

2007-01-25T20:57:49Z

Jags: /* 2007-01-25 */

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

== 2007-01-25 ==

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

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

Highlights:
*New phone number for TCON next week; email Jim for the number
*Problem with region growing?
*

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

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

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

== 2007-01-11 ==

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

== 2007-01-04 ==

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

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

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

Engineering:TCON 2007

2007-01-18T20:55:06Z

Jags: /* 2007-01-18 */

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

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

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

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

== 2007-01-11 ==

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

== 2007-01-04 ==

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

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

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

EAB Meeting AHM2007

2007-01-12T13:32:21Z

Jags:

Back to [[AHM_2007]]

Information about NA-MIC EAB is available [[EAB|here]].

*Confirmed EAB Attendees:
**Chris Johnson (Chair)
**Sanjoy Mitter
**Sandy Napel
**Godfrey Pearlson
**Carlo Pierpaoli
**Fred Prior
**Michael Ackerman (ex officio)

Schedule for the EAB Meeting at AHM 2007:

* 8-10am:
** 5-min each Site PI Presentations to the EAB:
** What did you do for NA-MIC and/or what did NA-MIC do for you
** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation
*** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[Media:NAMIC_2007_EAB_UTAH.ppt|slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf|slides]])
*** Core 2: GE GRC ([[slides]]), Kitware ([[media:AHM-SLC-Jan2007-EAB-KitwareCore2.ppt|slides]]), UCLA ([[Media:NamicEAB_LONI_2007.ppt|slides]]), UCSD ([[media:NA-MIC_EAB_UCSD_2007v2.ppt|Slides]]), Isomics ([[media:EAB Isomics-2007.ppt | slides]])
*** Core 3: Harvard ([[Media:NA-MIC_EAB_01_12_shenton_2007.ppt|slides]]), Dartmouth ([[Media:NA-MIC_EAB_01_11_Saykin_2007.ppt|slides]]), UCI and U Toronto ([[slides]])
*** Cores 4-6: Service ([[media:AHM-SLC-Jan2007-EAB-KitwareCore4.ppt|slides]]), Dissemination ([[slides]]), Training ([[slides]])
* 10-10:30am: Coffee break
* 10:30am-11am: Discussion of Site PIs with EAB
* 11am-12pm: Closed session of the EAB
* 12pm adjourn

Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]

EAB Meeting AHM2007

2007-01-12T13:31:20Z

Jags:

Back to [[AHM_2007]]

Information about NA-MIC EAB is available [[EAB|here]].

*Confirmed EAB Attendees:
**Chris Johnson (Chair)
**Sanjoy Mitter
**Sandy Napel
**Godfrey Pearlson
**Carlo Pierpaoli
**Fred Prior
**Michael Ackerman (ex officio)

Schedule for the EAB Meeting at AHM 2007:

* 8-10am:
** 5-min each Site PI Presentations to the EAB:
** What did you do for NA-MIC and/or what did NA-MIC do for you
** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation
*** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[Media:NAMIC_2007_EAB_UTAH.ppt|slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf|slides]])
*** Core 2: GE GRC ([[slides]]), Kitware ([[media:AHM-SLC-Jan2007-EAB-KitwareCore2.ppt|slides]]), UCLA ([[Image:NamicEAB LONI 2007.ppt|slides]]), UCSD ([[media:NA-MIC_EAB_UCSD_2007v2.ppt|Slides]]), Isomics ([[media:EAB Isomics-2007.ppt | slides]])
*** Core 3: Harvard ([[Media:NA-MIC_EAB_01_12_shenton_2007.ppt|slides]]), Dartmouth ([[Media:NA-MIC_EAB_01_11_Saykin_2007.ppt|slides]]), UCI and U Toronto ([[slides]])
*** Cores 4-6: Service ([[media:AHM-SLC-Jan2007-EAB-KitwareCore4.ppt|slides]]), Dissemination ([[slides]]), Training ([[slides]])
* 10-10:30am: Coffee break
* 10:30am-11am: Discussion of Site PIs with EAB
* 11am-12pm: Closed session of the EAB
* 12pm adjourn

Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]

EAB Meeting AHM2007

2007-01-12T13:27:41Z

Jags:

Back to [[AHM_2007]]

Information about NA-MIC EAB is available [[EAB|here]].

*Confirmed EAB Attendees:
**Chris Johnson (Chair)
**Sanjoy Mitter
**Sandy Napel
**Godfrey Pearlson
**Carlo Pierpaoli
**Fred Prior
**Michael Ackerman (ex officio)

Schedule for the EAB Meeting at AHM 2007:

* 8-10am:
** 5-min each Site PI Presentations to the EAB:
** What did you do for NA-MIC and/or what did NA-MIC do for you
** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation
*** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[Media:NAMIC_2007_EAB_UTAH.ppt|slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf|slides]])
*** Core 2: GE GRC ([[slides]]), Kitware ([[slides]]), UCLA ([[Image:NamicEAB LONI 2007.ppt | slides]]), UCSD ([[media:NA-MIC_EAB_UCSD_2007v2.ppt|Slides]]), Isomics ([[media:EAB Isomics-2007.ppt | slides]])
*** Core 3: Harvard ([[Media:NA-MIC_EAB_01_12_shenton_2007.ppt|slides]]), Dartmouth ([[Media:NA-MIC_EAB_01_11_Saykin_2007.ppt|slides]]), UCI and U Toronto ([[slides]])
*** Cores 4-6: Service ([[slides]]), Dissemination ([[slides]]), Training ([[slides]])
* 10-10:30am: Coffee break
* 10:30am-11am: Discussion of Site PIs with EAB
* 11am-12pm: Closed session of the EAB
* 12pm adjourn

Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]

EAB Meeting AHM2007

2007-01-12T13:26:58Z

Jags:

Back to [[AHM_2007]]

Information about NA-MIC EAB is available [[EAB|here]].

*Confirmed EAB Attendees:
**Chris Johnson (Chair)
**Sanjoy Mitter
**Sandy Napel
**Godfrey Pearlson
**Carlo Pierpaoli
**Fred Prior
**Michael Ackerman (ex officio)

Schedule for the EAB Meeting at AHM 2007:

* 8-10am:
** 5-min each Site PI Presentations to the EAB:
** What did you do for NA-MIC and/or what did NA-MIC do for you
** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation
*** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[Media:NAMIC_2007_EAB_UTAH.ppt|slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf|slides]])
*** Core 2: GE GRC ([[slides]]), Kitware ([[slides]]), UCLA ([[Image:NamicEAB LONI 2007.ppt]]), UCSD ([[media:NA-MIC_EAB_UCSD_2007v2.ppt|Slides]]), Isomics ([[media:EAB Isomics-2007.ppt | slides]])
*** Core 3: Harvard ([[Media:NA-MIC_EAB_01_12_shenton_2007.ppt|slides]]), Dartmouth ([[Media:NA-MIC_EAB_01_11_Saykin_2007.ppt|slides]]), UCI and U Toronto ([[slides]])
*** Cores 4-6: Service ([[slides]]), Dissemination ([[slides]]), Training ([[slides]])
* 10-10:30am: Coffee break
* 10:30am-11am: Discussion of Site PIs with EAB
* 11am-12pm: Closed session of the EAB
* 12pm adjourn

Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]

EAB Meeting AHM2007

2007-01-12T13:26:23Z

Jags:

Back to [[AHM_2007]]

Information about NA-MIC EAB is available [[EAB|here]].

*Confirmed EAB Attendees:
**Chris Johnson (Chair)
**Sanjoy Mitter
**Sandy Napel
**Godfrey Pearlson
**Carlo Pierpaoli
**Fred Prior
**Michael Ackerman (ex officio)

Schedule for the EAB Meeting at AHM 2007:

* 8-10am:
** 5-min each Site PI Presentations to the EAB:
** What did you do for NA-MIC and/or what did NA-MIC do for you
** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation
*** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[Media:NAMIC_2007_EAB_UTAH.ppt|slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf|slides]])
*** Core 2: GE GRC ([[slides]]), Kitware ([[slides]]), UCLA [[Media:NamicEAB LONI 2007.ppt]], UCSD ([[media:NA-MIC_EAB_UCSD_2007v2.ppt|Slides]]), Isomics ([[media:EAB Isomics-2007.ppt | slides]])
*** Core 3: Harvard ([[Media:NA-MIC_EAB_01_12_shenton_2007.ppt|slides]]), Dartmouth ([[Media:NA-MIC_EAB_01_11_Saykin_2007.ppt|slides]]), UCI and U Toronto ([[slides]])
*** Cores 4-6: Service ([[slides]]), Dissemination ([[slides]]), Training ([[slides]])
* 10-10:30am: Coffee break
* 10:30am-11am: Discussion of Site PIs with EAB
* 11am-12pm: Closed session of the EAB
* 12pm adjourn

Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]

EAB Meeting AHM2007

2007-01-12T13:25:57Z

Jags:

Back to [[AHM_2007]]

Information about NA-MIC EAB is available [[EAB|here]].

*Confirmed EAB Attendees:
**Chris Johnson (Chair)
**Sanjoy Mitter
**Sandy Napel
**Godfrey Pearlson
**Carlo Pierpaoli
**Fred Prior
**Michael Ackerman (ex officio)

Schedule for the EAB Meeting at AHM 2007:

* 8-10am:
** 5-min each Site PI Presentations to the EAB:
** What did you do for NA-MIC and/or what did NA-MIC do for you
** Please include all papers that acknowledge NA-MIC, whether they are published, in press, submitted, or in preparation
*** Core 1: MIT ([[Media:NAMIC_AHM2007_EAB_MIT.ppt|slides]]), U Utah ([[Media:NAMIC_2007_EAB_UTAH.ppt|slides]]), UNC ([[Media:UNCSummary-5Min-EAB-GG.ppt|slides]]), GATech ([[Media:Gatech.namic.2007.ppt|slides]]), MGH ([[Media:NAMIC_MGH_AHM_2007.pdf|slides]])
*** Core 2: GE GRC ([[slides]]), Kitware ([[slides]]), UCLA ([[Media:NamicEAB LONI 2007.ppt]]), UCSD ([[media:NA-MIC_EAB_UCSD_2007v2.ppt|Slides]]), Isomics ([[media:EAB Isomics-2007.ppt | slides]])
*** Core 3: Harvard ([[Media:NA-MIC_EAB_01_12_shenton_2007.ppt|slides]]), Dartmouth ([[Media:NA-MIC_EAB_01_11_Saykin_2007.ppt|slides]]), UCI and U Toronto ([[slides]])
*** Cores 4-6: Service ([[slides]]), Dissemination ([[slides]]), Training ([[slides]])
* 10-10:30am: Coffee break
* 10:30am-11am: Discussion of Site PIs with EAB
* 11am-12pm: Closed session of the EAB
* 12pm adjourn

Here is a link to last year's EAB meeting and slides, for reference: [[Leadership:EAB_Meeting_AHM2006|EAB 2006 Meeting Agenda and Site PI Slides]]

File:NamicEAB LONI 2007.ppt

2007-01-12T13:25:07Z

Jags: EAB LONI 2007 Jags

EAB
LONI
2007
Jags

2007 Project Half Week

2007-01-11T20:57:26Z

Jags: /* NA-MIC Kit */

Back to [[AHM_2007|AHM_2007]]

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

==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]]
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# 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_GroupWiseRegistration.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]]
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.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, 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] [[Media: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]]
#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]]
#Malab-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.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, 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)
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]]
#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_Visualization.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_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.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]].

2007 Project Half Week

2007-01-11T20:57:08Z

Jags: /* NA-MIC Kit */

Back to [[AHM_2007|AHM_2007]]

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

==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]]
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# 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_GroupWiseRegistration.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]]
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.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, 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] [[Media: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]]
#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]]''' ('''JagsTest''') [[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]]
#Malab-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.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, 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)
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]]
#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_Visualization.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_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.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]].

File:2007 Project Half Week Loni Pipeline.ppt

2007-01-10T08:01:11Z

Jags: AHM 2007 LONI Pipeline - UNC shape analysis LONI Pipleine - Slicer3 integration

AHM 2007

LONI Pipeline - UNC shape analysis
LONI Pipleine - Slicer3 integration