NAMIC Wiki - User contributions [en]

2010 Summer Project Week Shape Test Bench

2010-06-25T13:44:03Z

Niethammer:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Caudate_orig.png|Original Caudate Shape.
Image:Caudate_bump.png|Artifical Bump Added to the Tail.
Image:SyntheticImagePerturbations.png|Synthetic perturbation
</gallery>

==Key Investigators==
* UNC: Marc Niethammer
* BWH: Sylvain Bouix

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

<h3>Objective</h3>
* A prototype software to create population of synthetic 3D objects for shape analysis testing and evaluation.

</div>

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

<h3>Approach, Plan</h3>
* Artifical shape changes in the form of: global volume preserving transforms, "dimples and bulges", boundary noise.
* Automatic population creation mimicking real data variability.

</div>

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

<h3>Progress</h3>
* First version of boundary noise creation done.
* Affine transforms for population creation.

<h3>Progress during programming week</h3>
* Created full pipeline to create synthetic shapes with deformable warps based on the following steps:
* Unbiased atlas building from a normal population.
* Creation of a mean shape.
* Introduction of randomized dimples and bumps both parametrically and non-parametrically.
* Creation of population with these changes from inverse deformation fields (from the atlas).
* Wrote a viewer to inspect population.
* Currently a mixture of C++/matlab and shell scripts. To be streamlined ...

</div>
</div>

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

==Delivery Mechanism==

To early to tell. Either a downloadable set of images, or an open source software suite.

==References==

</div>

File:SyntheticImagePerturbations.png

2010-06-25T13:42:15Z

Niethammer: A set of synthetic images deformed and with a prespecified randomized perturbation.

A set of synthetic images deformed and with a prespecified randomized perturbation.

2010 Summer Project Week Shape Test Bench

2010-06-25T13:32:49Z

Niethammer:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Caudate_orig.png|Original Caudate Shape.
Image:Caudate_bump.png|Artifical Bump Added to the Tail.
</gallery>

==Key Investigators==
* UNC: Marc Niethammer
* BWH: Sylvain Bouix

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

<h3>Objective</h3>
* A prototype software to create population of synthetic 3D objects for shape analysis testing and evaluation.

</div>

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

<h3>Approach, Plan</h3>
* Artifical shape changes in the form of: global volume preserving transforms, "dimples and bulges", boundary noise.
* Automatic population creation mimicking real data variability.

</div>

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

<h3>Progress</h3>
* First version of boundary noise creation done.
* Affine transforms for population creation.

<h3>Progress during programming week</h3>
* Created full pipeline to create synthetic shapes with deformable warps based on the following steps:
* Unbiased atlas building from a normal population.
* Creation of a mean shape.
* Introduction of randomized dimples and bumps both parametrically and non-parametrically.
* Creation of population with these changes from inverse deformation fields (from the atlas).
* Wrote a viewer to inspect population.
* Currently a mixture of C++/matlab and shell scripts. To be streamlined ...

</div>
</div>

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

==Delivery Mechanism==

To early to tell. Either a downloadable set of images, or an open source software suite.

==References==

</div>

Microscopy Image Analysis

2010-06-22T18:28:33Z

Niethammer: /* Participants */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
* Wednesday afternoon - Microscopy Breakout Session ( Location: [http://whereis.mit.edu/?go=32 Kiva])
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Palaniappan Lab- Univ of Missouri
*** 1:40pm: Machiraju Lab- Ohio State Univ
**** Shantanu Singh - Large Scale Analysis of Cellular Phenotypes in the Tumor Microenvironment
**** Liya Ding - Image Analysis of Large Histology Datasets using ITK
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network / President Cosmo Software
** 2:40pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week using your project page
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Liya Ding, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute, CompuCyte Corporation
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Andinet Enquobahrie, Kitware
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.
# Alex Yarmarkovich, Isomics, Inc.
# Curtis Lisle, KnowledgeVis
# Tammy Riklin Raviv, CSAIL, MIT
# Marc Niethammer, UNC Chapel Hill

DBP2:UNC:Cortical Thickness Roadmap

2007-08-23T13:00:28Z

Niethammer: /* Roadmap */

== Roadmap ==

Group analysis of regional and local cortical thickness of the young brain (2 years old) is one goal of the [[DBP2:UNC | UNC DBP]]. This page describes the technology roadmap for cortical thickness analysis in the NA-MIC Kit.

Ultimately, the NA-MIC Kit will provide a workflow for individual and group analysis of cortical thickness. This workflow will be implemented as a set of Slicer3 modules that can be used interactively within the Slicer3 application as well as in batch on a computing cluster using BatchMake. The main modules will include:

; A - White matter/gray matter segmentation :
:* UNC has a segmentation technique implemented in an ITK framework for segmenting white matter and gray matter in the young brain. This technique will be converted into a Slicer3 [[Slicer3:Execution Model Documentation | command line module]]
:** Since this segmentation technique exists in an ITK framework, the integration into Slicer3 is low risk and should be completed over the next couple of months (mid fall)
:* UNC will also investigate adapting the Slicer3 EM Segment module to their young brain studies. Here, UNC will adapt the UNC atlas of the 2 year old brain to provide priors for the EM Segment module
:** This will be a good test case for applying the Slicer3 EM Segment module to a slightly different application. UNC should work through the training material on the Slicer3 EM Segment module and then refer to Brad Davis and Kilian Pohl as needed.
:** This also should be completed before the AHM.
; B - Local cortical thickness measurement :
:* UNC has an algorithm to measure local cortical thickness given a labeling of white matter and gray matter. This technique will be converted into a Slicer3 command line module
:** This technique is non-symmetric and sparse (only computing distances where they can be computed reliably).
:** It is expected that this module should be available before the AHM.
;** Marc Niethammer was developing a [[Algorithm:Harvard:Thickness Slicer3 Module|technique]] at a previous project week that would be symmetric. This could be an alternative used as a comparison.
; C - Subject comparison :
:* Regional as well as local subject comparisons are needed
:* Regional analysis will require precise deformable registration to a young brain atlas
:** NA-MIC Kit tools can be applied here
:* Local analysis requires techniques which are not currently in the NA-MIC Kit
:** Freesurfer could be used for the local analysis (but it is not in the NA-MIC Kit)
:** Ipek is developing local analysis tools and may have a tool available in Fall 2008.
; D - Performance characterization and validation :
:* Characterize response based on signal noise, patient motion, etc.
:* Comparison to other tools (FreeSurfer)

===To do===
* Assign owners to tasks
* Define schedule

===Staffing Plan===

* Clement is the DBP resource charged with adapting the tools in the NA-MIC Kit to the DBP needs
* Martin is the algorithm core contact
* Jim is the engineering core contact

===Schedule===

* '''xx/xx/2007''' - White matter/gray matter segmentation of the young brain using UNC technique as a Slicer3 module
* '''xx/xx/2007''' - White matter/gray matter segmentation of the young brain using the Slicer3 EM Segment module
* '''xx/xx/2007''' - Cortical thickness measurement using UNC technique as a Slicer3 module
* '''xx/xx/2007''' - Cortical thickness measurement using Marc Niethammer's approach as a Slicer3 module
* '''xx/xx/2007''' - Deformable registration of young brain regional atlas
* '''xx/xx/2007''' - Regional analysis of cortical thickness as a Slicer3 module
* '''xx/xx/2007''' - BatchMake workflow
* '''xx/xx/2007''' - Groupwise regional analysis of cortical thickness as a NA-MIC Workflow
* '''xx/xx/200x''' - Groupwise local analysis of cortical thickness as a NA-MIC Workflow

===Team and Institute===
*Co-PI: Heather Cody Hazlett, PhD, (heather_cody at med.unc.edu, Ph: 919-966-4099)
*Co-PI: Joseph Piven, MD
*NA-MIC Engineering Contact: Jim Miller, GE Research
*NA-MIC Algorithms Contact: Martin Styner, UNC

SanteFe.Tractography.Conference

2007-08-14T13:56:20Z

Niethammer: /* Conference Attendees */

= Goals =
We in NA-MIC, and our collaborating colleagues from BIRN, NAC and UIowa, are in a unique position to make a substanital contribution to the field of knowledge concerning the validation of medical image processing of Diffusion Tensor Image data. Among our faculty are leaders in the field of not only DTI analysis algorithm development, but also of validation and calibration. We seek to use our unique opportunity for multi-site collaboration to advance knowledge in this area for the benefit of clinical and computational scientists.

* To compare and contrast the results of tractography algorithms included in or supported by the NA-MIC Toolkit on a benchmark dataset of Diffusion Tensor Imaging (DTI) data.<br />
* To develop a framework for systematically and statistically comparing and contrasting these outcome measures mapped to specific manuscript preparation.<br />
* To map out appropriate leadership for each of the proposed manuscripts. <br />
* To initiate development of tutorials for tractography algorithms not yet in the NAMIC Training Compendium.<br />
* To propose methods for NA-MIC benchmarks of calibration and validation of tractography algorithms for further discussion at the 2008 AHM.<br />

== Conference Logistics ==

* October 1-2, 2007, 8:00 AM- 5:00 PM<br />
* The workshop is being held in the Governors Room at the Inn of the Governors, 101 W. Alameda, Sante Fe, NM 87501, 1-800-234-4534, http://www.innofthegovernors.com/ <br />
* We have booked a block of rooms for $169.00/night for single or double occupancy September 30- October 3, 2007 (Sunday through Tuesday nights). Our reservation code is "NAMIC" and the deadline for reservations is August 31, 2007. The price includes a full breakfast buffet, wireless internet access in the lobby, meeting room and sleeping rooms at no additional cost. <br />
* Fly into Albuquerque, NM. Information about shuttles from the airport to the hotel can be found here http://www.sandiashuttle.com/.

Many grateful thanks to John Rasure and Debbie Lynch of the MIND Institute for their assistance in making these arrangements.

==Registration==
* '''To register, add your name to the list of attendees below and make your flight and hotel reservations'''

* Questions about logistics and the content of the Conference should be addressed to Randy Gollub (rgollub at partners.org).

* '''This Conference is supported by the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics'''.

== Conference Attendees ==

* Ross Whitaker, PhD
* Guido Gerig, PhD
* Casey Goodlett, Utah
* Carl-Fredrik Westin, PhD
* Marek Kubicki, MD, PhD
* Sylvain Bouix, PhD
* [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School (Department of Psychiatry and Martinos Center, Department of Radiology, Massachussets General Hospital)
* [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School (Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital)
* H. Jeremy Bockholt, The MIND Institute
* [[User:Melonakos|John Melonakos]], Georgia Tech
* Ron Kikinis, MD
* Tom Fletcher, Utah
* Dennis Jen, MGH
* Allen Song, PhD Duke
* Tri Ngo, BWH
* Marc Niethammer, BWH
<br>

== Preparation for Workshop -- ''Important Information for all attendees'' ==

Suggestions: [[July31T-con |Notes from July 31 Planning T-con with detailed "To Dos"]]

Suggested background reading for workshop:<br />

#[[Media:AHM2006-validation-DTI-gg.ppt| Guido's 2006 AHM presentation on Validation strategies for DTI analysis]]
#[[Media:DWI.reproducibility.pdf]]
#[[http://cds.ismrm.org/protected/DiffusionWorkshop05 If any of you attended the 2005 ISMRM Workshop on Methods for Quantitative Diffusion of MRI of Human Brain and can get us access to the detailed summary, I have seen it and it might be very useful]]
#Presentations by and Fitzpatrick from the [http://idm.univ-rennes1.fr/VMIP/miccai2003/presentations.html MICCAI 2003 Tutorial on Validation in Medical Image Processing]
#Peruse the webpages associated with the [http://www.vuse.vanderbilt.edu/~image/registration/ Retrospective Image Registration Evaluation project]
#[http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/10818/34114/01624925.pdf anyone have access to this?]
#[[Media:BrainTissueClassifiers_BouixNeuroimage2007.pdf| Sylvain's segmentation comparison manuscript]]
#[[Media:MonkeyDTIStudy_Neuroimage2007.pdf| CF Westin's experimental study manuscript]]

Please complete the following items prior to the workshop.
<span style="background-color: yellow">'''This is hands-on Conference. All participants must come with their own computer loaded with the calibration data and the results of their own algorithm analysis. '''</span><br />

<span style="background-color: orange">'''Benchmark Datasets'''</span>

== Agenda ==

=== '''October 1, Meeting 8:30 AM - 5 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:40 AM '''Goals of Conference'''
* 8:40 - 10:15 AM '''presentations of results from each of the participants & discussion''' see
* 10:15 -10:30 Coffee Break
* 10:30 - 11:45 AM '''continue presentations of results from each of the participants & discussion'''
* 11:45 - 1:00 Lunch together at local restaurant
* 1:00 - 3:00 PM '''Discuss methods and metrics for contrasting/comparing tractography outcome measures'''
* 3:00 - 3:15 PM Coffee Break
* 3:15 - 5:00 PM '''Continue to discuss methods and metrics for contrasting/comparing tractography outcome measures'''

* 7:00 PM Dinner at local resturant(s) to be found by wandering around town

=== '''October 2, 8:30 AM - 5 PM''' ===
* 7:30- 8:30 AM Enjoy the breakfast buffet at the hotel
* 8:30 - 8:40 AM '''Synopsis of yesterday's accomplishments'''
* 8:40 - 10:15 '''Discuss what to do next on this project'''
* 10:15 -10:30 Coffee Break
* 10:30 - 11:45 '''Continue to formulate a plan for next steps on this project'''
* 11:45 - 1:00 PM Lunch together at local restaurant
* 1:00 - 3:00 PM '''?'''
* 3:00 - 3:15 PM Coffee Break
* 3:15 - 5:00 PM Formulation of action plan and assignment of tasks

<br />

Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project Page]]

July31T-con/PlayingWithTheDiffusionData

2007-08-03T15:58:09Z

Niethammer:

== Exploring the Upsampling of the BWH Diffusion Data ==

Extracting one a slice for one of the gradient directions of the diffusion data results in an image like this: <br>

[[Image:original.png|500px]]

A two-dimensional Fourier transform leads the following magnitude images (uncentered and centered):

[[Image:fouriermagnitude.png|500px]]
[[Image:fouriermagnitude-centered.png|500px]]

Representing this in the log-domain results in

[[Image:logfouriermagnitude.png|500px]]
[[Image:logfouriermagnitude-centered.png|500px]]

Unfortunately, we don't see nice blue regions that we would have expected from ideal zero-padding.
Instead it looks a little "salt-and-peppery." Is this a scanner discretization effect?

Cutting away everything that should ideally be zero gives this Fourier log-image:

[[Image:Logfouriermagnitude-centered-and-cut.png|500px]]

An inverse Fourier transform followed by discretization results in:

[[Image:reconstructed.png|500px]]

The result is slighly smoother than the original, which is sensible since we essentially low-pass
filtered the result.

The difference between original and reconstruction is not great, but still shows a little bit of structure:

[[Image:reconstruction-diffference.png|500px]]

In case you want to recreate the results. Here is the matlab script [[media:dwiTstScript.m|dwiTstScript.m]]. And here is the data [[media:SampleDWIDataSlice.tar.gz|SampleDWIDataSlice.tar.gz]].

July31T-con/PlayingWithTheDiffusionData

2007-08-03T15:56:10Z

Niethammer: diffusion data downsampling test

== Exploring the Upsampling of the BWH Diffusion Data ==

Extracting one a slice for one of the gradient directions of the diffusion data results in an image like this: <br>

[[Image:original.png|500px]]

A two-dimensional Fourier transform leads the following magnitude images (uncentered and centered):

[[Image:fouriermagnitude.png|500px]]
[[Image:fouriermagnitude-centered.png|500px]]

Representing this in the log-domain results in

[[Image:logfouriermagnitude.png|500px]]
[[Image:logfouriermagnitude-centered.png|500px]]

Cutting away everything that should ideally be zero gives this Fourier log-image:

[[Image:Logfouriermagnitude-centered-and-cut.png|500px]]

An inverse Fourier transform followed by discretization results in:

[[Image:reconstructed.png|500px]]

The result is slighly smoother than the original, which is sensible since we essentially low-pass
filtered the result.

The difference between original and reconstruction is not great, but still shows a little bit of structure:

[[Image:reconstruction-diffference.png|500px]]

In case you want to recreate the results. Here is the matlab script [[media:dwiTstScript.m|dwiTstScript.m]]. And here is the data [[media:SampleDWIDataSlice.tar.gz|SampleDWIDataSlice.tar.gz]].

File:DwiTstScript.m

2007-08-03T15:48:34Z

Niethammer:

File:SampleDWIDataSlice.tar.gz

2007-08-03T15:47:25Z

Niethammer:

File:Logfouriermagnitude-centered-and-cut.png

2007-08-03T15:45:41Z

Niethammer:

File:Reconstruction-diffference.png

2007-08-03T15:37:09Z

Niethammer:

File:Reconstructed.png

2007-08-03T15:37:00Z

Niethammer:

File:Original.png

2007-08-03T15:36:49Z

Niethammer:

File:Logfouriermagnitude-centered.png

2007-08-03T15:36:39Z

Niethammer:

File:Logfouriermagnitude.png

2007-08-03T15:36:29Z

Niethammer:

File:Fouriermagnitude-centered.png

2007-08-03T15:36:19Z

Niethammer:

File:Fouriermagnitude.png

2007-08-03T15:36:06Z

Niethammer:

July31T-con

2007-08-03T15:34:09Z

Niethammer: link to diffusion data exploration page

'''In attendence''' (add your name if you were there but I didn't note it below):
Guido Gerig, Ron Kikinis, Casey Goodlett, Randy Gollub, Ross Whitaker, Dennis Jen, Lauren O'Donnell, Karl Helmer, Vince Magnotta, John Melanakos, CF Westin, Tri Ngo, Doug Markant, Sonia Pujol

<br>

# Data format issues: Issues under email discussion currently; [[July31T-con/PlayingWithTheDiffusionData | Some data exploration ]]
## Voxel resolution: non-isotropic native resolution vs. upsampling vs. downsampling (to be discussed and decided on common preprocessing)
### Native grid size is 144x144x81 [FOV: 240mm] with voxel size 1.667x1.667x1.7
### Provided data is 256x256x81 [FOV: 240mm] with voxel size 0.9375x0.9375x1.7
## Eddy Current distortion correction: both uncorrected and corrected datasets are available (we need a consensus on which to use. No comparison to determine quality of correction has yet been done.)
# Input/Output formats
## Input/Output image volumes should be in nrrd format using the standard NA-MIC DTI conventions [NAMIC_Wiki:DTI:Nrrd_format]
## Streamlines should be in vtk format [legacy or XML vtk format] including the tensor information at each point along the fiber tract
## Other output formats (such as statistics spreadsheets, graphs, etc. ) should be documented by the groups
<br>

'''Action Items:''' <br>
# All algorithm developers will make sure the wiki page for this project correctly relfects the details of their algorithm and participation.
# All agorithm developers will run their software on the data as described above by Guido.
# All agorithm developers will keep laboratory notes on as many details of the processing pipeline as they can and summarize this information in a Lab Report to be shared with the group in Sante Fe. The metrics that were mentioned included: detailed methods, processing steps, time to run each step, user interaction or tweaks that needed to be made, size of resultant files, processor requirements, etc.
# All algorithm developers will generate final results both by subject and group with output measures that they deem most informative. The summarized information including images of the results and any metrics to be put into a final Powerpoint report to be shared with the group in Sante Fe.
# The above two items should be a single presentation.
# Marek and his group will add specific clinically relevant hypotheses for how each tract differs between healthy and matched schizophrenic subjects.
# Algorithm developers will use the page to post their ideas for statistical approaches to summarize, compare and contrast the data.
# Sonia, with support of her mentors, will draft an outline to be used to guide our discussion in Sante Fe
# Randy will extend an invitation to Carlo Piepoli, Susumu Mori, Allen Song and Tim Behrens and amend the wiki to let interested outsiders contact her to inquire about participation. She will ensure that the meeting retains its focus on NAMIC work but welcomes outside expertise and potential collaborations.
# Agenda for the 2 days has been updated and is open to further discussion from the group.
<br>
'''Miscellaneous ideas:'''
*Ron/Ross suggested that this Conference be a "dry run" for a future MICCAI session on this same topic.
*Another question to be considered at the meeting is whether this particular dataset is the optimal one to use for this work. Probably we are fine for Sante Fe, but going forward, should we consider a dataset that was collected with a isotropic voxels and other considerations raised during our discussion?

Return to [[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures | Contrasting Tractography Project Page]] <br>
Return to [[SanteFe.Tractography.Conference | SanteFe Tractography Conference Page]]

Projects/Diffusion/2007 Project Week EPI Distortion correction using field maps

2007-06-25T23:20:14Z

Niethammer: added pointer to data

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

|}

__NOTOC__
===Key Investigators===
* BWH: Marek Kubicki
* Anyone else who is interesting in helping

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

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

<h1>Objective</h1>
EPI data collected for DTI and fMRI analysis are spatially distorted, due to susceptibility/chemical shift artifacts. Our VCFS pilot data have been collected using parallel imaging, which reduces distortions, but does not eliminate them. In our data, we see artifacts in the inferior temporal and inferior frontal brain regions. As suggested by Bruce Fischl at the last Core1 meeting, we collected field maps to calculate distortions, which information could be then used to "undistort" images.

</div>

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

<h1>Approach, Plan</h1>

In the series of field mapping, we acquired two sets of images with different TEs (9 and 15 ms). In each set, we have real images, imaginary images, and magnitude images for each slice location. Therefore, total number of images in the series is 2*3*85. We have one dataset that includes sMRI, DTI and fMRI, and need help with distortion correction.

Data can be found on BIRN at: <br>
/home/Projects/NAMIC__0003/Files/PNL/3T_EPI_distortion_correction_data_sample

</div>

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

<h1>Progress</h1>

</div>

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

</div>

2007 Core 1 Meeting

2007-05-22T17:15:13Z

Niethammer: /* Attendees */

== Agenda ==

*May 30 -
** 8:30am Remarks (Whitaker)
*** Introductions
*** Discuss goals and agenda
** 9:00am Driving Biological problems '''[[2007_Core_1_Meeting_DBP_Guidlines|(Guidelines for talks)]]'''
*** Marek Kubicki - Harvard/B&W
*** Gabor Fichtinger - Johns Hopkins
*** (break)
*** H. Jeremy Bockholt - Mind Institute
*** Heather Cody - UNC
**12:00pm Lunch
** 1:00pm Invited Talk: Daniel Rueckert. "Quantification of brain development during early childhood using non-rigid registration". ([http://www.csail.mit.edu/events/eventcalendar/calendar.php?show=event&id=1484 talk announcement])
** 2:00pm Break out sessions with DPBs
** 3:30pm Break
** 3:45-6:00pm Core 1 presentations
*** John Melonakos (Georgia Tech) - TBD
*** MGH (name)
*** MIT (name)
*** UNC (name)
*** Tom Fletcher (Utah), "Volumetric Connectivity for analysis of DTI"
*May 31
** 8:30am Core 1 presentations
*** Utah "Nonparametric Shape Modeling of Object Complexes" (Speaker TBD)
*** UNC (name)
*** (break)
*** Mert Sabuncu (MIT), "Population Analysis of Anatomical Variability"
*** MGH (name)
*** John Melonakos (Georgia Tech) - TBD
** 12:30pm Lunch
** 1pm Strategic planning, software
*** Progress/interactions with DBPs
*** Software contributions and Core 2 interactions
*** Performance assessment and renewal
** 5pm Finish

== Logistics ==

'''Dates:''' May 30-31, 2007.

Please plan to travel on May 29, so that we can start in the morning of May 30.
The meeting will be two full days; please plan to stay until 5pm on May31.

'''Location:''' MIT.

The meeting will take place in the Kiva conference room, on the 4th floor of Stata Center. We will post signs in the building, directing you to the conference room.

'''Food:''' Breakfast and lunch will be provided on May 30-31. We will also organize people into groups to go out for dinner on May 30. There are plenty of restaurants around Central Square and MIT.

'''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]]. Please book your rooms early.

== Attendees ==

* Ross Whitaker
* Polina Golland (MIT)
* Ron Kikinis
* Guido Gerig(UNC)
* Heather Cody Hazlett (UNC Autism DBP)
* Allen Tannenbaum
* John Melonakos
* H. Jeremy Bockholt (MIND/UNM)
* Harvard Core 3: Marek Kubicki
* Mert R Sabuncu (MIT CSAIL)
* Lilla Zollei (NMR, MGH)
* Serdar K Balci (MIT CSAIL)
* Ulas Ziyan (MIT)
* Tom Fletcher (Utah)
* Josh Cates (Utah - tentative)
* Gabor Fichtinger (JHU)
* Jim Miller (GE Research)
* Dennis Jen
* Sandy Wells (BWH, MIT)
* Marc Niethammer (BWH, Core 3)

2007 Programming/Project Week MIT

2007-05-17T16:15:38Z

Niethammer: /* 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.

===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.

=== Agenda===

* 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
** 9-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]] (Tempany, Fichtinger, Burdette groups from BWH/JHU/Queens/AcousticMed)
** noon lunch
** 1-2pm: [[Special topic breakout: Non-Linear Registration]] (TBD)
** 2-3pm: [[Special topic breakout: DWI/DTI]] (?)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday
** 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)

===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)
** MRML Scenes for the Execution Model, including transforms (Jim Miller, Brad Davis, Nicole Aucoin, 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)
* 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)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics)
** [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma JHU, David Gobbi Queen's)
** [[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)
** [[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)
* [[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)

===Non-Medical Collaborations===

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

Projects:ShapeAnalysisOfCaudateAndCorpusCallosum

2007-04-23T14:37:29Z

Niethammer:

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

'''Objective:''' To improve shape analysis of the caudate and to parcellate the corpus callosum based on function.

'''Progress:'''

* UNC applied shape analysis pipeline to a dataset of manually segmented caudates of males with and without schizoptypal personality disorders. Differences were found mainly on the right caudates. No differences were found for regional parcellations of the corpus callosum.
* The open source shape analysis pipeline was transfered and installed at Harvard PNL.
* Harvard applied the UNC shape analysis software to a new dataset of manually segmented caudates of females with and without schizotypal personality disorder. The results confirmed previous findings in the male dataset. Statistically significant shape differences for the right caudate were found (see Fig 1).
* A less stringent method to correct for multiple comparisons (false discovery rate; FDR) was implemented (UNC) and applied to the the male and female caudata datasets (see Fig 2).

'''Key Investigators:'''

* Harvard PNL: Sylvain Bouix, Marek Kubicki, James Levitt, Marc Niethammer, Martha Shenton
* UNC: Martin Styner, Isabelle Corouge, Guido Gerig
* Georgia Tech: Delphine Nain, Allen Tannenbaum

{|
|+ '''Fig 1. Right female caudate results'''
|valign="top"|[[Image:Rawpval_rc_back_min.png|thumb|252px|Medial]]
|valign="top"|[[Image:Rawpval_rc_front_min.png|thumb|277px|Lateral]]
|valign="top"|[[Image:Rawpval_rc_colorbar_min.png|thumb|52px|p value]]
|}

{|
|+ '''Fig 2. Right female caudate results, corrected for multiple comparisons (FDR)'''
|valign="top"|[[Image:Female_right_medial_ICV_caudate_FDR_pvalue_cropped.png|thumb|252px|Medial]]
|valign="top"|[[Image:Female right lateral ICV caudate FDR pvalue cropped.png|thumb|277px|Lateral]]
|valign="top"|[[Image:FemaleFDRcolorbar.png|thumb|52px|p value]]
|}

'''Links:'''

* [[Progress_Report:Shape_Analysis|Shape Analysis Progress Report]]
* [[DBP:Harvard:Collaboration:UNC|DBP:Harvard:Collaboration:UNC]]
* [[DataRepository#Brockton_VA.2FHarvard_Structural_and_DTI_Images|Male caudate data]]

File:FemaleFDRcolorbar.png

2007-04-23T14:35:05Z

Niethammer:

File:Female right medial ICV caudate FDR pvalue cropped.png

2007-04-23T14:34:24Z

Niethammer:

File:Female right lateral ICV caudate FDR pvalue cropped.png

2007-04-23T14:33:57Z

Niethammer:

Projects:GenusZeroSlicer3Module

2007-04-23T14:26:46Z

Niethammer:

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

'''Objective:''' Implement a Slicer 3 module to perform topology correction of voxel data to ensure a genus zero surface when extracting an iso-surface from the voxel data using marching cubes. This is useful for rendering purposes as well as an initial step for shape analysis methods relying on surfaces with spherical topology (i.e., genus 0, one connected component).

'''Progress:''' Finished the Slicer 3 module based on previous work by Steve Haker and Michael Rabes. A full ITK implementation is currently in progress (Michael Rabes).

'''Key Investigators:'''
* Steve Haker, Michael Rabes, Marc Niethammer, Sylvain Bouix, Steve Pieper.

'''Slides from the programming week:'''[[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]

[[Image:GenusZeroGUI.png|left|thumb|300px|Automatically generated GUI of the thickness Slicer 3 module.]]

File:GenusZeroGUI.png

2007-04-23T14:25:40Z

Niethammer:

Projects:ThicknessSlicer3Module

2007-04-23T14:15:18Z

Niethammer:

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

'''Objective:''' Implement a simple command line module for Slicer 3 enabling thickness measurements on appropriate labelmaps (voxel data).
Thickness measurements are performed using correspondences induced by the solution of Laplace's equation.

'''Progress:''' Finished an initial implementation.

'''Key Investigators:'''
* Marc Niethammer, Sylvain Bouix, Steve Pieper.

'''Slides from the programming week:'''
[[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]

[[Image:ThicknessGUI.png|left|thumb|300px|Automatically generated GUI of the thickness Slicer 3 module.]]

File:ThicknessGUI.png

2007-04-23T14:12:54Z

Niethammer:

Projects:ThicknessSlicer3Module

2007-04-23T14:11:18Z

Niethammer:

Projects:LMMSERicianDWINoiseRemoval

2007-04-23T13:35:14Z

Niethammer:

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

'''Objective:''' Provide a way for noise removal in diffusion weighted images incorporating the Rician noise model. The Rician noise level is estimated automatically and used to parametrize the local
Linear Minimum Mean Squared Error estimator.

'''Progress:''' The method was evaluated on real and synthetic datasets. A Slicer 3 module was developed.

''References:''
* Aja-Fernandez, S., Alberola-Lopez, C., Westin, C.F., "Filtering and noise estimation in magnitude MRI and Rician distributed images," submitted to IEEE Transactions on Image Processing.
* Aja-Fernandez, S., Niethammer, M., Kubicki, M., Shenton, M.E., Westin, C.-F., "Restoration of DWI data using a Rician LMMSE estimator," submitted to MRM.

'''Key Investigators:'''
* Santiago Aja-Fernandez, Marc Niethammer, Marek Kubicki, Martha Shenton, Carl-Fredrik Westin.

'''Example results:'''

[[Image:Glyph_orig_rician_LMMSE.png|left|thumb|300px|FA values and direction of major tensor eigenvalue based on original DWI data.]]

[[Image:Glyph_f10_rician_LMMSE.png|left|thumb|300px|FA values and direction of major tensor eigenvalue after filtering the DWI data using the LMMSE filter.]]

Projects:LMMSERicianDWINoiseRemoval

2007-04-23T13:33:02Z

Niethammer:

'''Objective:''' Provide a way for noise removal in diffusion weighted images incorporating the Rician noise model. The Rician noise level is estimated automatically and used to parametrize the local
Linear Minimum Mean Squared Error estimator.

'''Progress:''' The method was evaluated on real and synthetic datasets. A Slicer 3 module was developed.

''References:''
* Aja-Fernandez, S., Alberola-Lopez, C., Westin, C.F., "Filtering and noise estimation in magnitude MRI and Rician distributed images," submitted to IEEE Transactions on Image Processing.
* Aja-Fernandez, S., Niethammer, M., Kubicki, M., Shenton, M.E., Westin, C.-F., "Restoration of DWI data using a Rician LMMSE estimator," submitted to MRM.

'''Key Investigators:'''
* Santiago Aja-Fernandez, Marc Niethammer, Marek Kubicki, Martha Shenton, Carl-Fredrik Westin.

'''Example results:'''

[[Image:Glyph_orig_rician_LMMSE.png|left|thumb|300px|FA values and direction of major tensor eigenvalue based on original DWI data.]]

[[Image:Glyph_f10_rician_LMMSE.png|left|thumb|300px|FA values and direction of major tensor eigenvalue after filtering the DWI data using the LMMSE filter.]]

File:Glyph orig rician LMMSE.png

2007-04-23T13:20:10Z

Niethammer:

File:Glyph f10 rician LMMSE.png

2007-04-23T13:19:28Z

Niethammer:

Projects:DiffusionMeasuresAlongFiberTracts

2007-04-17T15:10:32Z

Niethammer:

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

'''Objective:''' To quantify changes in diffusion properties along the cingulum bundle for schizophrenics and normal controls.

'''Progress:''' We improved the diffusion MRI module in slicer to allow for a better fiber selection (based on multiple regions of interest) as well as fiber clustering. We set up a processing pipeline to allow for statistical computations of fiber diffusion properties across the fibers of a fiber bundle and along the bundle itself. Further, we are in the process of developing a continuous representation of fiber bundles (see Figure) to allow for a more geometric computation of bundle diffusion quantities.

'''Key Investigators:'''

* Harvard PNL: Marc Niethammer, Sylvain Bouix, Marek Kubicki, Mark Dreusicke, Martha Shenton
* MIT: CF Westin, Lauren O'Donnell, Raul San Jose

'''Links:'''

* [[DBP:Harvard:Collaboration:MITDTI|DBP:Harvard:Collaboration:MITDTI]]
* http://pnl.bwh.harvard.edu/index.html

[[Image:Cingulum_reseeded_withtrajectories.png|left|thumb|500px|Cingulum bundle with arclength parameterization.]]

Projects:CorpusCallosumRegionalFAAnalysis

2007-04-17T15:04:57Z

Niethammer:

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

'''Objective:''' To quantify diffusion fractional anisotropy (FA) differences between controls and schizophrenia subjects within anatomicaly defined portions of the corpus callosum.

'''Progress:'''

* We are in the process of applying population clustering algorythm to the NAMIC chronic schizophrenia data. Corpus callosum masks have been already drawn manually in slicer, and combined with fiber tractography clustering output. Several clusters of fiber tracts going through the corpus callosum have been identified, and now corpus masks will be back-painted and separated according to clusters.
* In a separate analysis, a probabilistic regional parcellation shape model derived by tracking inter-hemispheric lobar DTI connections has been applied. The corpus callosum contours and respective 4 probabilistic parcellations were computed from the structural MRI automatically using a Fourier descriptor based active shape segmentation. The probabilistic masks were non-rigidly registered to the DTI base image and used for probabilistic histogram computation of the FA.

'''References'''

M. Styner, R. Gimpel Smith, C. Cascio, I. Oguz, M. JomierL: Corpus Callosum Subdivision based on a Probabilistic Model of Inter-hemispheric Connectivity, Medical Image Computing and Computer Assisted Interventions 2005, LNCS 3750, pp. 765-772.

'''Key Investigators:'''

* Harvard PNL: Marek Kubicki, Mark Dreusicke, Doug Markant, Martha Shenton
* MIT: Lauren O'Donnell, Carl-Fredrik Westin
* UNC: Martin Styner

<br />'''Links:'''

* [[DBP:Harvard:Collaboration:MITDTI|DBP:Harvard:Collaboration:MITDTI]]

<br />
[[Image:FACorpus.png|[[Image:magnify-clip.png|Enlarge]]]]

File:DwiTstCase.tar.gz

2007-02-07T17:53:36Z

Niethammer: DWI test case with 6 slices and 51 directions plus 8 baselines.

DWI test case with 6 slices and 51 directions plus 8 baselines.

2007 Project Half Week

2007-02-01T19:45:15Z

Niethammer: /* Structural Analysis */

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]]

===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]] [[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)
#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

2007-01-09T18:39:02Z

Niethammer: /* 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]]
# Scripts to run and visualize [[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]] ‎
#SVM Shape Analysis (Brad, Polina, Martin)
#[[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: Congealing with B-spline (Lilla, Stephen)
## 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 Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|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|Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4-block ppt]]
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[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|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]] '''Haiying'''
###[[Slicer3:EM|EMSegment Interface]] '''Brad Davis'''
###[[Slicer3:Slicer_Daemon|Slicer Daemon Interface (for unu, matlab)]] '''Steve Pieper''' (merged with Katharina Quintus's project using Slicer Daemon)
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##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|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[Image:2007_Project_Half_Week_GridExecution.ppt]]
#Tractography in Slicer3 (Lauren, Raul)
#Malab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

===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]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]
#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:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 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)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT Jan 2007]] (Kilian Pohl, Chris Wyatt)

== 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

2007-01-09T00:43:34Z

Niethammer: /* Structural Analysis */

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]]
# Scripts to run and visualize [[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]] ‎
#SVM Shape Analysis (Brad, Polina, Martin)
#[[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: Congealing with B-spline (Lilla, Stephen)
## 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 Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[Image:2007_Project_Half_Week_GridExecution.ppt]]
#Tractography in Slicer3 (Lauren, Raul)
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

===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]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]
#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:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 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)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT Jan 2007]] (Kilian Pohl, Chris Wyatt)

== 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

2007-01-09T00:43:15Z

Niethammer: /* Structural Analysis */

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]]
# Scripts to run and visualize [[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]] ‎
#SVM Shape Analysis (Brad, Polina, Martin)
#[[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: Congealing with B-spline (Lilla, Stephen)
## 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), [[Meida: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 Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[Image:2007_Project_Half_Week_GridExecution.ppt]]
#Tractography in Slicer3 (Lauren, Raul)
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

===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]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]
#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:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 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)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT Jan 2007]] (Kilian Pohl, Chris Wyatt)

== 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 ThicknessImageFilter.ppt

2007-01-09T00:42:10Z

Niethammer:

File:2007 Project Half Week GenusZeroImageFilter.ppt

2007-01-09T00:41:56Z

Niethammer:

File:2007 Project Half Week Caudate Paper.ppt

2007-01-09T00:41:34Z

Niethammer:

2007 Project Half Week

2007-01-09T00:40:37Z

Niethammer: /* Structural Analysis */

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]]
# Scripts to run and visualize [[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]] ‎
#SVM Shape Analysis (Brad, Polina, Martin)
#[[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: Congealing with B-spline (Lilla, Stephen)
## 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), [[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 Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[Image:2007_Project_Half_Week_GridExecution.ppt]]
#Tractography in Slicer3 (Lauren, Raul)
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

===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]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]
#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:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 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)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT Jan 2007]] (Kilian Pohl, Chris Wyatt)

== 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]].