NAMIC Wiki - User contributions [en]

DBP2:Harvard:Brain Segmentation Roadmap

2010-01-03T12:37:26Z

Jvs:

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Collaborations]], [[DBP2:Harvard|Harvard DBP 2]]
__NOTOC__
=Stochastic Tractography for VCFS=
== Roadmap ==

The main goal of this project is to develop end-to-end application that would be used to characterize anatomical connectivity abnormalities in the brain of patients with velocardiofacial syndrome (VCFS), and to link this information with deficits in schizophrenia. This page describes the technology roadmap for stochastic tractography, using newly acquired 3T data, NAMIC tools and slicer 3.

== Algorithm ==

[[Image:IC_sto_new.png|thumb|right|200px|<font size=1> Figure 1: Comparison of deterministic and stochastic tractography algorithms</font>]]
; A-Description
* Most tractography methods estimate fibers by tracing the maximum direction of diffusion. A limitation of this approach is that, in practice, several factors introduce uncertainty in the tracking procedure, including, noise, splitting and crossing fibers, head motion and image artifacts. To address this uncertainty, stochastic tractography methods have been developed to quantify the uncertainty associated with estimated fibers (Bjornemo et al., 2002). Method uses a propagation model based on stochastics and regularization, which allows paths originating at one point to branch and return a probability distribution of possible paths. The method utilizes principles of a statistical Monte Carlo method called Sequential Importance Sampling and Resampling (SISR). Based on probability functions, using a sequential importance sampling technique ([http://lmi.bwh.harvard.edu/papers/pdfs/2002/bjornemoMICCAI02.pdf Bjornemo et al., 2002]), one can generate thousands of fibers starting in the same point by sequentially drawing random step directions. This gives a very rich model of the fiber distribution, as contrasted with single fibers produced by conventional tractography methods. Moreover, from a large number of sampled paths, probability maps can be generated, providing better estimates of connectivity between several anatomical locations. A comparison of the algorithms can be seen here. (Figure 1)

[[Image:StochasticPic.PNG|thumb|right|200px|<font size=1>Figure 2: Stochastic tractography of uncinate fasciculis on anatomical data (left) and cingulum bungle on fMRI scan (right)</font>]]
; B-Possible Applications
* Since diffusion direction uncertainty within the gray matter is quite significant; principal diffusion direction approaches usually do not work for tracking between two gray matter regions. Thus if one requires finding connections between a priori selected anatomical gray matter regions, defined either by anatomical segmentations (in case of using structural ROI data), or functional activations (in case of megring DTI with fMRI), stochastic tractography seems to be the method of choice. Here is an example of this application to anatomical data (Figure 2, left image) and to fMRI data (Figure 2, right image).

* Stochastic Tractography is also comparable, if not better, in defining large white matter fiber bundles, especially those traveling through white matter regions characterized by increased diffusion uncertainty (fiber crossings). Example of such application to internal capsule. (Figure 3)

[[Image:IC-comp-new.png|thumb|right|200px|<font size=1>Figure 3: Streamline vs. stochastic tractography of the Internal Capsule</font>]]
; C-References

* [http://lmi.bwh.harvard.edu/papers/pdfs/2002/bjornemoMICCAI02.pdf Björnemo M, Brun A, Kikinis R, Westin CF. Regularized stochastic white matter tractography using diffusion tensor MRI. In Fifth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'02). Tokyo, Japan, 2002;435-442.]
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]

[[Image:StochasticGUI1.PNG|thumb|right|200px|<font size=1> Figure 4: Python Stochastic Tractography GUI </font>]]

==Module==
Can be found in: MODULES > PYTHON MODULES > PYTHON STOCHASTIC TRACTOGRAPHY
;Functionality of Python Stochastic Tractography module in Slicer 3.0
* IO:
Module reads files (DWI and ROIs) in nhdr format.
* Smoothing:
One can smooth the DWI data (only Gausian smoothing is supported at this time). We recommend it if the data is noisy.
* Brain Mask:
The Brain mask defines the volume in which the tensor will be computed and the tracts evaluated.
*Diffusion Tensor:
This step calculates the tensor and can output anisotropy indices (FA/Mode/Trace)
*Tractography:
Parameters that need to be adjusted:
:1. The amount of tracts that will be seeded from each voxel (we recommend between 500 and 1000 tracts, depending on the workstation power- 1000 tracts per voxel seeded within the large ROI for high resolution DWI can take a long time to compute).
:2. Maximum tract length (in mm), this can eliminate long, unwanted tracts if the regions for which connection is measured are located close to each other
:3. Step Size: distance between each re-estimation of tensors, usually between 0.5 and 1 mm
:4. Stopping criteria. This can be used on the top of WM mask, to terminate tracts (in case they really want to travel through the CSF, for example).
*Connectivity Map:
This step creates output probability maps.
:1. binary: each voxel is counted only once if at least one fiber pass through it
:2. cumulative: tracts are summed by voxel independently
:3. weighted: tracts are summed by voxel depending on their length
*Length Based:
This step will output only either the shortest 1/3, middle 1/3, or longest 1/3 of the tracts.
*Vicinity
This step traces back n number of steps from tract endpoint to check if track crosses target ROI. If so, tract is included.
*Threshold
This step will reject tracts whose endpoints are lower than the threshold value).
*Spherical ROI vicinity
This will make the ROI a sphere based on the ROI’s center of gravity (with the sphere’s radius being the distance from the center to the ROI’s furthest point). This sphere can be inflated by raising the Vicinity level to the number of steps you’d like to increase the ROI’s size by.

Then, probability maps can be saved as ROIs, and either used directly, or thresholded (at certain probability, step claimed by few publications to remove noise) in slicer to mask and compute average FA, Mode, Trace for entire connection. Diffusion indices can be also weighted by the probability of connection for each voxel.

:* Module documentation can be found here:
:**[[Media:IJdata.tar.gz|Training Dataset]]
:**[[Media:Stochastic_June09_1.ppt|Training Presentation]]
:**[[Media:Helix.zip|Sample Helix Dataset]]

==Work Accomplished==
[[Image:helix_withsmoothing.png|thumb|right|200px|<font size=1>Figure 6: Stochastic tractography from a single ROI on helix phantom</font>]]
; A - Optimization and testing of stochastic tractography algorithm :
:* Original methodological paper, as well as our first attempts to use the algorithm (CC+ and matlab scripts) have been done on old "NAMIC" 1.5T LSDI data ([https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&CPq_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FHarvard%2Farchive_morph&up=CPq&JavaScript=enabled Structural MRI] and [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&up=7li&7li_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FHarvard%2Farchive_diffusion&JavaScript=enabled DTI data]).
:* Tri worked hard on making sure algorithm works on new high resolution 3T data (available here: [https://portal.nbirn.net/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=moveUpDir&gv7_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FPNL%2F3T_strct_dti_fmri%2Fcase01017&up=gv7&JavaScript=enabled|PNL 3T Data]).
:* Tests have been done also on the spiral diffusion phantom, to make sure diffusion directions and scanner coordinates are handled properly by the algorithm (Figure 6).

; B - Clinical Applications

:* Algorithm was used to trace and analyze anterior limb of the internal capsule on 1.5T data. It generated reacher representation of frontal fiber projections, it also turned out to be more sensitive to group differences in white matter integrity that conventional deterministic tractography (see Figure 6).
:* Algorithm was also used to trace smaller white matter fiber tracts, such as Cingulum, Fornix, Uncinate Fasciculus, Arcuate Fasciculus on 3T "Santa Fe" dataset (http://www.na-mic.org/Wiki/index.php/SanteFe.Tractography.Conference)

; C - References

:* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
:* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, de Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
:* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
:* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
:* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
:* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

== Work in Progress ==

; A - Optimization and Testing of stochastic tractography module :
:* Julien is testing now separate components of work flow, including the masks, and impact of their precision on stochastic output, as well as impact of number of seeding points on tractography results.
:* At the same time, we are testing the module on a Max Plank dataset of Anna Rotarska-Jagiela by looking at the connections through the corpus callosum of the left auditory cortex to the right auditory cortex as defined by fMRI activation maps as well as running this data for the tractography comparison project.
:* We are discussing possibility of adding project specific functionality to module, such as third ROI to guide tractography, nonlinear registration button for merging fMRI and DTI data.

; B - Related Clinical Projects

;* Arcuate Fasciculus Extraction Project
[[Image:STArcuate.jpg|thumb|right|200px|<font size=1>Figure 7: The arcuate fasciculus including seed, midpoint and target ROI's.</font>]]
We have started the project of investigating Arcuate Fasciculus using Stochastic Tractography (Figure 7). This structure is especially important in both VCFS and schizophrenia, as it connects language related areas (Brocka and Wernicke's), and is involved in language processing quite disturbed in schizophrenia patients. It also can not be reliably traced using deterministic tractography.
:Project involves:
:* Whole brain segmentation, and automatic extraction of regions interconnected by Arcuate Fasciculus (Inferior frontal and Superior Temporal Gyri).
:* White matter segmentation, in order to prevent algorithm from traveling through the ventricles, where diffusivity is high.
:* Non-linear registration of labelmaps to the DTI space.
:* Seeding tracts. We have piloted it using 5000 seeds per voxel, however it is quite time consuming running it on even most powerful computers in the lab, so we have experimented with smaller number of seeds per voxel. We tested 1000 seeds, which gave virtually identical results.
:* Extracting path of interest, and calculating FA along the path for group comparison. Presentation of previous results for 7 schizophrenics and 12 control subjects, can be found here: [[Media:NAMIC_AHM_Arcuate.ppt|Progress Report Presentation]].
:* Results presentation and paper submission. Abstract was accepted and results presented at the World Biological Psychiatry Symposium in Venice, Italy. Paper is in preparation.

[[Image:connectivity1.jpg|thumb|right|200px|<font size=1>Figure 8: Maps of inferior frontal cortex (Broca) connectivity in controls and patients with schizophrenia.</font>]]

;* Semantic Network Connectivity Project
We use combination of fMRI and DTI data to define and characterize functional and anatomical connectivity within the semantic processing network in schizophrenia.
:Project involves:
:* fMRI data analysis and identification of functional nodes involved in semantic processing in healthy controls and seubjects with schizophrenia
:* Analysis of functional connectivity (using FSL) between nodes of semantic network
:* Whole brain Voxel Based analysis of DTI data in same population
:* Use of stochastic tractography to identify connections between functional nodes
:* Correlational analysis involving anatomical and functional connectivity data.
:* Results presentation and paper submission. Data was presented at HBM conference in 2007, paper has been submitted to HBM.
:* <font color="red">'''New: '''</font>June 10th 2009, paper accepted for publication in Human Brain Mapping: "Functional and Anatomical Connectivity Abnormalities in Left Inferior Frontal Gyrus in Schizophrenia" by Jeong, Wible, Hashimoto and Kubicki, HBM in Press

[[Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|thumb|right|200px|<font size=1>Figure 9: Brain automatic segmentation of subject with VCFS.</font>]]

;* Anatomical Connectivity Abnormalities in VCFS
We use combination of structural MRI and DTI to investigate anatomical abnormalities that would characterize patients with VCFS, and relationship of these abnormalities to those observed in schizophrenia.
:Project involves:
:* Whole brain, automatic segmentation of brain images obtained from patients with VCFS in order to identify structures involved in this disease.
:* Registration between anatomical and DTI scans (manual skull stripping followed by linear followed by nonlinear registration of SPGRs to DTI space).
:* Use of stochastic tractography to identify connections between gray matter regions identified in the disease.
:* Extracting paths of interest, and calculating FA along the paths for group comparison.
:* Correlational analysis involving anatomical and connectivity data, clinical information and genetic data.
:* Results presentation and paper submission. First step of data analysis has been already accomplished, we are in the process of registering structural and DTI data and preparing DTI data for stochastic tractography analysis. We plan to submit an abstract with study results for Biological Psychiatry symposium (dedline December 2009).

[[Image:Anna.png|thumb|right|200px|<font size=1>Figure 10: Max Plank data showing tracts through the corpus connecting 2 cortical ROIs defined by fMRI activations.</font>]]

;* Study of Default Network
We have started collaboration with Department of Neurophysiology Max Planck Institute in Frankfurt (Anna Rotarska contact person). They have dataset containing DTI and resting state fMRI in schizophrenia, and want to use stochastic tractography to measure integrity of anatomical connections within the default network in schizophrenia. Their fMRI data has been co-registered with anatomical scans, and has been put it into DTI space. Figure 8 shows pilot data of the white matter connections through the corpus callosum between the left and the right auditory cortex ROIs as defined by fMRI data. This data will be also used to test robustness of our module, since data was collected on a different scanner (3T Philips).

;* Tractography Comparison Project
We are also working on a [http://www.na-mic.org/Wiki/index.php/SanteFe.Tractography.Conference tractography comparison project]dataset, where we apply stochastic tractography to phantom, as well as test dataset.

===Staffing Plan===

* Sylvain and Yogesh are the DBP resources charged with adapting the tools in the NA-MIC Kit to the DBP needs
* Doug Markant, our NAMIC RA has left the lab, and now Doug Terry, is a new NAMIC RA.
* Julien is our new NAMIC software engineer. He is responsible for improving the STM (Stochastic Tractography Module), and making sure software works with STM compliant datasets.
[[Link Progress| Development Progress]]
* Polina is the algorithm core contact
* Brad is the engineering core contact

===Schedule===

* '''10/2007''' - Optimization of Stochastic Tractography algorythm for 1.5T data.
* '''10/2007''' - Algorythm testing on Santa Fe data set and diffusion phantom.
* '''06/2008''' - Optimization of Stochastic Tractography algorythm for 3T data.
* '''11/2008''' - Slicer 3 module prototype using python.
* '''12/2008''' - Slicer 3 module official release
* '''12/2008''' - Documentation and packaging for dissemination.
* '''12/2008''' - First clinical application of stochastic tractography module.
* '''01/2009''' - First draft of the clinical paper.
* '''05/2009''' - Distortion correction and nonlinear registration added to the module
* '''05/2009''' - Symposium on tractography, including stochastic methods at World Biological Psychiatry Symposium in Florence, Italy.
* '''05/2009''' - Presentation of Arcuate Fasciculus findings at World Biological Psychiatry Symposium in Florence, Italy.
* '''07/2009''' - Summer Programming week- work on optimizing and speeding up data processing, releasing second generation of software that includes preprocessing pipeline.
* '''07/2009''' - Continue working on clinical collaborative studies using stochastic tractography module.
* '''12/2009''' - Submission of abstracts reporting findings of several clinical studies involving stochastic tractography, including anatomical connectivity abnormalities in patients with VCFS and anatomical and functional connectivity abnormalities in schizophrenia.

===Team and Institute===
*PI: Marek Kubicki (kubicki at bwh.harvard.edu)
*DBP2 Investigators: Sylvain Bouix, Yogesh Rathi, Julien de Siebenthal
*NA-MIC Engineering Contact: Brad Davis, Kitware
*NA-MIC Algorithms Contact: Polina Gollard, MIT

===Publications===

''In print''

*[http://www.na-mic.org/pages/Special:Publications?text=Kubicki+AND+Westin+AND+DTI&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked| NA-MIC Publications Database - Clinical Applications]

*[http://www.na-mic.org/pages/Special:Publications?text=Ngo+AND+Golland&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked| NA-MIC Publications Database - Algorithms Development]

[[Category: Schizophrenia]] [[Category: Diffusion MRI]] [[Category: Segmentation]]

Python Stochastic Tractography Tutorial

2009-09-28T22:29:20Z

Jvs:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Cc_01.png|thumb|340px|Model of the Corpus Callosum from Stochastic Tractography (coronal) ]]
|[[Image:Cc_02.png|thumb|340px|Model of the Corpus Callosum from Stochastic Tractography (sagittal) ]]
|[[Image:helix_withsmoothing.png|thumb|220px|Stochastic Tractography on Phantom]]
|}

__NOTOC__

===Key Investigators===
*PI: Marek Kubicki (kubicki at bwh.harvard.edu)
*DBP2 Investigators: Sylvain Bouix, Yogesh Rathi, Julien de Siebenthal, RA Doug Terry
*NA-MIC Engineering Contact: Brad Davis, Kitware
*NA-MIC Algorithms Contact: Polina Gollard, MIT

Go to [http://www.slicer.org/slicerWiki/index.php/Modules:StochasticTractography-Documentation-3.4 Slicer 3.4 module documentation] for more information

===Tutorial===
*[[Media:IJData.tar.gz|Training Dataset]]
*[[Media:Stochastic_June09_2.ppt|Training Presentation]]
*[[Media:Helix.zip|Sample Helix Dataset]]

__NOTOC__
<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">
<h1>Objective</h1>
To address the uncertainty of deterministic tractography methods, stochastic tractography methods have been developed to quantify the uncertainty associated with estimated fibers (Bjornemo et al., 2002). Method uses a propagation model based on stochastics and regularization, which allows paths originating at one point to branch and return a probability distribution of possible paths. One can generate thousands of fibers starting in the same point by sequentially drawing random step directions. This gives a very rich model of the fiber distribution, as contrasted with single fibers produced by conventional tractography methods. Moreover, from a large number of sampled paths, probability maps can be generated, providing better estimates of connectivity between several anatomical locations.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
This tutorial will walk users through the multiple stages of the python stochastic tractography module, where the inputs are a DWI and a region of interest labelmap. This will include:
# Loading the Volumes
# Extracting DWI and getting Baseline DWI threshold levels
# Using features of the module including smoothing, brain mask generation, and other settings.
# Generating a Connectivity Map, which is able to be thresholded and customized.
</div>

<div style="width: 27%; float: left;">
<h1>Progress</h1>
*A tutorial has been developed and data is available for tutorial.
*We have started the project of investigating Arcuate Fasciculus using Stochastic Tractography. This structure is especially important in both VCFS and schizophrenia, as it connects language related areas (Brocka and Wernicke's), and is involved in language processing quite disturbed in schizophrenia patients. It also can not be reliably traced using deterministic tractography.
</div>

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

File:Stochastic June09 2.ppt

2009-09-28T22:28:45Z

Jvs:

Python Stochastic Tractography Tutorial

2009-09-28T21:32:10Z

Jvs:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Cc_01.png|thumb|340px|Model of the Corpus Callosum from Stochastic Tractography (coronal) ]]
|[[Image:Cc_02.png|thumb|340px|Model of the Corpus Callosum from Stochastic Tractography (sagittal) ]]
|[[Image:helix_withsmoothing.png|thumb|220px|Stochastic Tractography on Phantom]]
|}

__NOTOC__

===Key Investigators===
*PI: Marek Kubicki (kubicki at bwh.harvard.edu)
*DBP2 Investigators: Sylvain Bouix, Yogesh Rathi, Julien de Siebenthal, RA Doug Terry
*NA-MIC Engineering Contact: Brad Davis, Kitware
*NA-MIC Algorithms Contact: Polina Gollard, MIT

Go to [http://www.slicer.org/slicerWiki/index.php/Modules:StochasticTractography-Documentation-3.4 Slicer 3.4 module documentation] for more information

===Tutorial===
*[[Media:IJData.tar.gz|Training Dataset]]
*[[Media:Stochastic_June09_1.ppt|Training Presentation]]
*[[Media:Helix.zip|Sample Helix Dataset]]

__NOTOC__
<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">
<h1>Objective</h1>
To address the uncertainty of deterministic tractography methods, stochastic tractography methods have been developed to quantify the uncertainty associated with estimated fibers (Bjornemo et al., 2002). Method uses a propagation model based on stochastics and regularization, which allows paths originating at one point to branch and return a probability distribution of possible paths. One can generate thousands of fibers starting in the same point by sequentially drawing random step directions. This gives a very rich model of the fiber distribution, as contrasted with single fibers produced by conventional tractography methods. Moreover, from a large number of sampled paths, probability maps can be generated, providing better estimates of connectivity between several anatomical locations.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
This tutorial will walk users through the multiple stages of the python stochastic tractography module, where the inputs are a DWI and a region of interest labelmap. This will include:
# Loading the Volumes
# Extracting DWI and getting Baseline DWI threshold levels
# Using features of the module including smoothing, brain mask generation, and other settings.
# Generating a Connectivity Map, which is able to be thresholded and customized.
</div>

<div style="width: 27%; float: left;">
<h1>Progress</h1>
*A tutorial has been developed and data is available for tutorial.
*We have started the project of investigating Arcuate Fasciculus using Stochastic Tractography. This structure is especially important in both VCFS and schizophrenia, as it connects language related areas (Brocka and Wernicke's), and is involved in language processing quite disturbed in schizophrenia patients. It also can not be reliably traced using deterministic tractography.
</div>

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

File:IJData.tar.gz

2009-09-28T21:31:57Z

Jvs:

EPI Correction in Slicer3

2009-07-06T15:05:23Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:01053_before.png|Before correction
Image:01053_after.png|After correction
</gallery>

==Key Investigators==
* GE: Jim Miller
* BWH: Sylvain Bouix, Julien de Siebenthal
* Utah: Ran Tao, Tom Fletcher, Ross Whitaker

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

<h3>Objective</h3>

The objective of this project is to integrate EPI distortion correction module into Slicer, which implement the variational method.

</div>

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

<h3>Approach, Plan</h3>

Our goals for the project week are:
*Integrate EPI distortion correction module into Slicer3

*Perform and evaluate results on BWH brain dataset.

</div>

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

<h3>Progress</h3>

*The code is integrated into Slicer3.
*Compare to the results with B-spline registration

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

==References==
*[http://www.cs.utah.edu/~rantao/OpenSource/EPICorrectionCode.tgz EPI Correction Code]

Summer2009:Implementing parallelism in python

2009-07-06T15:04:12Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of running computational intensive simulations with the python language.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to subdivide highly intensive computational tasks and profit of the parallelism offered by current multicore machines.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* Achieved software for parallelizing python tasks. It uses parallel python for that purpose and was tested successfully on fat nodes and the cluster at SPL.
* Improved performance
* Completed parallelization of connection filtering
* Completed batch for different studies configuration
* Checked in under the Slicer trunk - the package is found under <your slicer3 path>/lib/Slicer3/Plugins/StochasticTractographyServerMP

</div>
</div>

==References==

Summer2009:Implementing parallelism in python

2009-07-06T15:03:54Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of running computational intensive simulations with the python language.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to subdivide highly intensive computational tasks and profit of the parallelism offered by current multicore machines.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* Achieved software for parallelizing python tasks. It uses parallel python for that purpose and was tested successfully on fat nodes and the cluster at SPL.
* Improved performance
* Completed parallelization of connection filtering
* Completed batch for different studies configuration
* commit under the Slicer trunk - the package is found under <your slicer3 path>/lib/Slicer3/Plugins/StochasticTractographyServerMP

</div>
</div>

==References==

Summer2009:Using cython

2009-06-28T21:17:21Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of accelerating the stochastic tractography code developed in python and part of the current version of Slicer 3.4.

</div>

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

<h3>Approach, Plan</h3>
Cython is used to develop a direct way of integrating native C code where python bytecode is too slow and hinders performance of the algorithm.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* Implemented Cython code for tensor and fiber tracking
* Performance depends mainly of the nature of the Python code - if numpy adequately used (vectorization...) - no significant difference with C performance

</div>
</div>

==References==

Summer2009:Implementing parallelism in python

2009-06-27T15:09:25Z

Jvs:

Summer2009:Using client server paradigm with python and slicer

2009-06-27T15:06:17Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are interested to run intensive tasks from the Slicer python directly.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to defer intensive computational task into another process communicating remotely with the Slicer process.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* Achieved software for enabling a client-server python. It uses basic socket mechanism for that purpose and was tested successfully. It mimics CLI modules written in C++.
* Enhanced options (client side) to setup the module
* Study possibility of using Pyro (RPC) to replace socket library
* Reflect on how to improve the slicer daemon mechanism - would be nice to have a RPC-like mechanism integrated in Slicer for python development (Pyro?)

</div>
</div>

==References==

Summer2009:VCFS

2009-06-27T14:52:23Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Back to Projects List]]
Image:Anna.png|Tracts through the corpus connecting two cortical regions defined by fMRI activation.
Image:Image5.jpeg|Display of Anterior Cingulate Cortex (ACC) and Orbito-Frontal Cortex (OFC).
Image:Image11.jpeg|Population study on ACC to OFC connection using stochastic tractography showed significant FA reduction in schizophrenics.
Image:01040-lh-all-3D-cropped.png|stochastic tractography of IFG-STG (arcuate) and IFG-occipital (IOFF) connections.
Image:FA IFG-Occ scatter.jpg|Significant finding in left IFG-occipital connections suggests decreased integrity of fiber tracts involved in language processing in schizophrenia.
Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|VCFS segmentation results to be used as seed regions for stochastic tracking.
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix, Marek Kubicki

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

<h3>Objective</h3>
To create an end-to-end analysis pipeline to study white matter anomalies using a stochastic tractography algorithm in VCFS population.

See our [[DBP2:Harvard:Brain_Segmentation_Roadmap| Roadmap]] for more details.

</div>

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

<h3>Approach, Plan</h3>
Our approach involves the implementation of a stochastic tractography algorithm in python that can be used both within and outside of the slicer framework.

Our plan for the project week is to integrate diffusion weighted imaging preprocessing steps to the pipeline in particular:
* Rician Noise Removal
* EPI distortion correction
* Eddy current correction

We will also be testing pipeline on VCFS population, now that we have enough subjects to start a study and some encouraging gray matter segmentation results.

</div>

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

<h3>Progress</h3>
* Achieved ITK integration through WrapITK into the python pipeline
** cmake were adapted to reduce the so called 'combinatorial explosion' to a reasonable compilation cycle (<1h on my laptop)
** alternative under discussion for the Slicer side: weave seems to be a better candidate
* Tested numpy conversion to/from VTK/ITK
* Ongoing : EPI distortion correction under test
** Rician & EPI are cmake ready for python wrapping
* Even if not perfect, WrapITK allows:
** to build efficient VTK/ITK pipeline - with the python benefits
** to integrate easily a C++ class developed in ITK/VTK: it is just up to write a small cmake configuration file
** >90% of ITK and VTK classes are usable at once
** quite cumbersome to understand why people argue against it ;-)

</div>
</div>

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

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, von Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

</div>

Summer2009:VCFS

2009-06-27T14:49:50Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Back to Projects List]]
Image:Anna.png|Tracts through the corpus connecting two cortical regions defined by fMRI activation.
Image:Image5.jpeg|Display of Anterior Cingulate Cortex (ACC) and Orbito-Frontal Cortex (OFC).
Image:Image11.jpeg|Population study on ACC to OFC connection using stochastic tractography showed significant FA reduction in schizophrenics.
Image:01040-lh-all-3D-cropped.png|stochastic tractography of IFG-STG (arcuate) and IFG-occipital (IOFF) connections.
Image:FA IFG-Occ scatter.jpg|Significant finding in left IFG-occipital connections suggests decreased integrity of fiber tracts involved in language processing in schizophrenia.
Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|VCFS segmentation results to be used as seed regions for stochastic tracking.
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix, Marek Kubicki

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

<h3>Objective</h3>
To create an end-to-end analysis pipeline to study white matter anomalies using a stochastic tractography algorithm in VCFS population.

See our [[DBP2:Harvard:Brain_Segmentation_Roadmap| Roadmap]] for more details.

</div>

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

<h3>Approach, Plan</h3>
Our approach involves the implementation of a stochastic tractography algorithm in python that can be used both within and outside of the slicer framework.

Our plan for the project week is to integrate diffusion weighted imaging preprocessing steps to the pipeline in particular:
* Rician Noise Removal
* EPI distortion correction
* Eddy current correction

We will also be testing pipeline on VCFS population, now that we have enough subjects to start a study and some encouraging gray matter segmentation results.

</div>

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

<h3>Progress</h3>
* Achieved ITK integration through WrapITK into the python pipeline
** cmake were adapted to reduce the so called 'combinatorial explosion' to a reasonable compilation cycle (<1h on my laptop)
** alternative under discussion for the Slicer side: weave seems to be a better candidate
* Tested numpy conversion to/from VTK/ITK
* Ongoing : EPI distortion correction under test
** Rician & EPI are cmake ready for python wrapping
* Even if not perfect, wrapitk allows:
** to build efficient VTK/ITK pipeline - with the python benefits
** to integrate easily a C++ class developed in ITK/VTK up to setup a cmake configuration file
** >90% of ITK and VTK classes are usable at once
** quite cumbersome to understand why people argue against it ;-)

</div>
</div>

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

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, von Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

</div>

Summer2009:VCFS

2009-06-27T14:49:30Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Back to Projects List]]
Image:Anna.png|Tracts through the corpus connecting two cortical regions defined by fMRI activation.
Image:Image5.jpeg|Display of Anterior Cingulate Cortex (ACC) and Orbito-Frontal Cortex (OFC).
Image:Image11.jpeg|Population study on ACC to OFC connection using stochastic tractography showed significant FA reduction in schizophrenics.
Image:01040-lh-all-3D-cropped.png|stochastic tractography of IFG-STG (arcuate) and IFG-occipital (IOFF) connections.
Image:FA IFG-Occ scatter.jpg|Significant finding in left IFG-occipital connections suggests decreased integrity of fiber tracts involved in language processing in schizophrenia.
Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|VCFS segmentation results to be used as seed regions for stochastic tracking.
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix, Marek Kubicki

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

<h3>Objective</h3>
To create an end-to-end analysis pipeline to study white matter anomalies using a stochastic tractography algorithm in VCFS population.

See our [[DBP2:Harvard:Brain_Segmentation_Roadmap| Roadmap]] for more details.

</div>

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

<h3>Approach, Plan</h3>
Our approach involves the implementation of a stochastic tractography algorithm in python that can be used both within and outside of the slicer framework.

Our plan for the project week is to integrate diffusion weighted imaging preprocessing steps to the pipeline in particular:
* Rician Noise Removal
* EPI distortion correction
* Eddy current correction

We will also be testing pipeline on VCFS population, now that we have enough subjects to start a study and some encouraging gray matter segmentation results.

</div>

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

<h3>Progress</h3>
* Achieved ITK integration through WrapITK into the python pipeline
** cmake were adapted to reduce the so called 'combinatorial explosion' to a reasonable compilation cycle (<1h on my laptop)
** alternative under discussion for the Slicer side: weave seems to be a better candidate
* Tested numpy conversion to/from VTK/ITK
* Ongoing : EPI distortion correction under test
** Rician & EPI are cmake ready for python wrapping
* Even if not perfect, wrapitk allows:
** to build efficient VTK/ITK pipeline - with the python benefits
** to integrate easily a C++ class developed in ITK/VTK up to setup a cmake configuration file
** >90% of ITK and VTK classes are usable at once
** quite cumbersome to know why people argue against it ;-)

</div>
</div>

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

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, von Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

</div>

Summer2009:VCFS

2009-06-27T14:42:43Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Back to Projects List]]
Image:Anna.png|Tracts through the corpus connecting two cortical regions defined by fMRI activation.
Image:Image5.jpeg|Display of Anterior Cingulate Cortex (ACC) and Orbito-Frontal Cortex (OFC).
Image:Image11.jpeg|Population study on ACC to OFC connection using stochastic tractography showed significant FA reduction in schizophrenics.
Image:01040-lh-all-3D-cropped.png|stochastic tractography of IFG-STG (arcuate) and IFG-occipital (IOFF) connections.
Image:FA IFG-Occ scatter.jpg|Significant finding in left IFG-occipital connections suggests decreased integrity of fiber tracts involved in language processing in schizophrenia.
Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|VCFS segmentation results to be used as seed regions for stochastic tracking.
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix, Marek Kubicki

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

<h3>Objective</h3>
To create an end-to-end analysis pipeline to study white matter anomalies using a stochastic tractography algorithm in VCFS population.

See our [[DBP2:Harvard:Brain_Segmentation_Roadmap| Roadmap]] for more details.

</div>

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

<h3>Approach, Plan</h3>
Our approach involves the implementation of a stochastic tractography algorithm in python that can be used both within and outside of the slicer framework.

Our plan for the project week is to integrate diffusion weighted imaging preprocessing steps to the pipeline in particular:
* Rician Noise Removal
* EPI distortion correction
* Eddy current correction

We will also be testing pipeline on VCFS population, now that we have enough subjects to start a study and some encouraging gray matter segmentation results.

</div>

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

<h3>Progress</h3>
* Achieved ITK integration through WrapITK into the python pipeline
** cmake were adapted to reduce the so called 'combinatorial explosion' to a reasonable compilation cycle (<1h on my laptop)
** alternative under discussion for the Slicer side: weave seems to be a better candidate
* Tested numpy conversion to/from VTK/ITK
* Ongoing : EPI distortion correction under test
** Rician & EPI are cmake ready for python wrapping

</div>
</div>

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

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, von Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

</div>

Summer2009:VCFS

2009-06-27T14:37:17Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Back to Projects List]]
Image:Anna.png|Tracts through the corpus connecting two cortical regions defined by fMRI activation.
Image:Image5.jpeg|Display of Anterior Cingulate Cortex (ACC) and Orbito-Frontal Cortex (OFC).
Image:Image11.jpeg|Population study on ACC to OFC connection using stochastic tractography showed significant FA reduction in schizophrenics.
Image:01040-lh-all-3D-cropped.png|stochastic tractography of IFG-STG (arcuate) and IFG-occipital (IOFF) connections.
Image:FA IFG-Occ scatter.jpg|Significant finding in left IFG-occipital connections suggests decreased integrity of fiber tracts involved in language processing in schizophrenia.
Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|VCFS segmentation results to be used as seed regions for stochastic tracking.
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix, Marek Kubicki

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

<h3>Objective</h3>
To create an end-to-end analysis pipeline to study white matter anomalies using a stochastic tractography algorithm in VCFS population.

See our [[DBP2:Harvard:Brain_Segmentation_Roadmap| Roadmap]] for more details.

</div>

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

<h3>Approach, Plan</h3>
Our approach involves the implementation of a stochastic tractography algorithm in python that can be used both within and outside of the slicer framework.

Our plan for the project week is to integrate diffusion weighted imaging preprocessing steps to the pipeline in particular:
* Rician Noise Removal
* EPI distortion correction
* Eddy current correction

We will also be testing pipeline on VCFS population, now that we have enough subjects to start a study and some encouraging gray matter segmentation results.

</div>

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

<h3>Progress</h3>
* Achieved itk integration through WrapITK into the python pipeline
** alternative under discussion for the Slicer side: weave seems to be a better candidate
* Tested numpy conversion to/from VTK/ITK
* Ongoing : EPI distortion correction under test

</div>
</div>

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

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, von Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

</div>

Summer2009:VCFS

2009-06-27T14:36:03Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Back to Projects List]]
Image:Anna.png|Tracts through the corpus connecting two cortical regions defined by fMRI activation.
Image:Image5.jpeg|Display of Anterior Cingulate Cortex (ACC) and Orbito-Frontal Cortex (OFC).
Image:Image11.jpeg|Population study on ACC to OFC connection using stochastic tractography showed significant FA reduction in schizophrenics.
Image:01040-lh-all-3D-cropped.png|stochastic tractography of IFG-STG (arcuate) and IFG-occipital (IOFF) connections.
Image:FA IFG-Occ scatter.jpg|Significant finding in left IFG-occipital connections suggests decreased integrity of fiber tracts involved in language processing in schizophrenia.
Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|VCFS segmentation results to be used as seed regions for stochastic tracking.
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix, Marek Kubicki

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

<h3>Objective</h3>
To create an end-to-end analysis pipeline to study white matter anomalies using a stochastic tractography algorithm in VCFS population.

See our [[DBP2:Harvard:Brain_Segmentation_Roadmap| Roadmap]] for more details.

</div>

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

<h3>Approach, Plan</h3>
Our approach involves the implementation of a stochastic tractography algorithm in python that can be used both within and outside of the slicer framework.

Our plan for the project week is to integrate diffusion weighted imaging preprocessing steps to the pipeline in particular:
* Rician Noise Removal
* EPI distortion correction
* Eddy current correction

We will also be testing pipeline on VCFS population, now that we have enough subjects to start a study and some encouraging gray matter segmentation results.

</div>

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

<h3>Progress</h3>
* Achieved itk integration through WrapITK into the python pipeline
** alternative under discussion for the Slicer side: weave seems to be ideal
* Tested numpy conversion to/from VTK/ITK
* Ongoing : EPI distortion correction under test

</div>
</div>

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

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, von Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

</div>

Summer2009:VCFS

2009-06-27T14:34:38Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Back to Projects List]]
Image:Anna.png|Tracts through the corpus connecting two cortical regions defined by fMRI activation.
Image:Image5.jpeg|Display of Anterior Cingulate Cortex (ACC) and Orbito-Frontal Cortex (OFC).
Image:Image11.jpeg|Population study on ACC to OFC connection using stochastic tractography showed significant FA reduction in schizophrenics.
Image:01040-lh-all-3D-cropped.png|stochastic tractography of IFG-STG (arcuate) and IFG-occipital (IOFF) connections.
Image:FA IFG-Occ scatter.jpg|Significant finding in left IFG-occipital connections suggests decreased integrity of fiber tracts involved in language processing in schizophrenia.
Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|VCFS segmentation results to be used as seed regions for stochastic tracking.
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix, Marek Kubicki

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

<h3>Objective</h3>
To create an end-to-end analysis pipeline to study white matter anomalies using a stochastic tractography algorithm in VCFS population.

See our [[DBP2:Harvard:Brain_Segmentation_Roadmap| Roadmap]] for more details.

</div>

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

<h3>Approach, Plan</h3>
Our approach involves the implementation of a stochastic tractography algorithm in python that can be used both within and outside of the slicer framework.

Our plan for the project week is to integrate diffusion weighted imaging preprocessing steps to the pipeline in particular:
* Rician Noise Removal
* EPI distortion correction
* Eddy current correction

We will also be testing pipeline on VCFS population, now that we have enough subjects to start a study and some encouraging gray matter segmentation results.

</div>

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

<h3>Progress</h3>
* Achieved itk integration through WrapITK into the python pipeline
* Tested further numpy conversion to/from VTK/ITK
* Ongoing : EPI distortion correction under test

</div>
</div>

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

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, von Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

</div>

Summer2009:VCFS

2009-06-27T14:03:40Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Back to Projects List]]
Image:Anna.png|Tracts through the corpus connecting two cortical regions defined by fMRI activation.
Image:Image5.jpeg|Display of Anterior Cingulate Cortex (ACC) and Orbito-Frontal Cortex (OFC).
Image:Image11.jpeg|Population study on ACC to OFC connection using stochastic tractography showed significant FA reduction in schizophrenics.
Image:01040-lh-all-3D-cropped.png|stochastic tractography of IFG-STG (arcuate) and IFG-occipital (IOFF) connections.
Image:FA IFG-Occ scatter.jpg|Significant finding in left IFG-occipital connections suggests decreased integrity of fiber tracts involved in language processing in schizophrenia.
Image:ScreenshotFreeSurferDeepMatterSagitalView-vcase1-2009-06-12.jpg|VCFS segmentation results to be used as seed regions for stochastic tracking.
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix, Marek Kubicki

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

<h3>Objective</h3>
To create an end-to-end analysis pipeline to study white matter anomalies using a stochastic tractography algorithm in VCFS population.

See our [[DBP2:Harvard:Brain_Segmentation_Roadmap| Roadmap]] for more details.

</div>

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

<h3>Approach, Plan</h3>
Our approach involves the implementation of a stochastic tractography algorithm in python that can be used both within and outside of the slicer framework.

Our plan for the project week is to integrate diffusion weighted imaging preprocessing steps to the pipeline in particular:
* Rician Noise Removal
* EPI distortion correction
* Eddy current correction

We will also be testing pipeline on VCFS population, now that we have enough subjects to start a study and some encouraging gray matter segmentation results.

</div>

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

<h3>Progress</h3>
* EPI is under test
* Achieved itk integration through WrapITK into the python pipeline
* Tested further numpy conversion to/from VTK/ITK

</div>
</div>

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

==References==
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]
* [http://www.na-mic.org/Wiki/index.php/Media:dougt_poster.pdf Terry DP, Rausch AC, Alvarado JL, Melonakos ED, Markant D, Westin CF, Kikinis R, von Siebenthal J, Shenton ME, Kubicki M. White Matter Properties of Emotion Related Connections in Schizophrenia. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* [http://www.na-mic.org/Wiki/index.php/Media:Jorge_poster.pdf Alvarado JL, Terry DP, Markant D, Ngo T, Kikinis R, Westin CF, McCarley RW, Shenton ME, Kubicki M. Study of Language-Related White Matter Tract Connections in Schizophrenia using Diffusion Stochastic Tractography. Poster presented at the 2009 Mysell Poster Day, Dept. of Psychiatry, Harvard Medical School, April 2009]
* Melonakos ED, Shenton ME, Markant D, Alvarado J, Westin CF, Kubicki M. White Matter Properties of Orbitofrontal Connections in Schizophrenia. Poster being presented at the 64th Meeting of the Society of Biological Psychiatry. Vancouver, BC. May 2009.
* Kubicki, M. Khan, U., Bobrow, L., O'Donnell, L. Pieper, S. Westin, CF., Shenton, ME. New Methods for Assessing Whole Brain DTI Abnormalities in Schizophrenia. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.
* Kubicki, M., Markant, D., Ngo, T., Westin, CF., McCarley, RW., Shenton, ME. Study of Language Related White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Presentation given at the International Congress of World Psychiatric Association. Florence, Italy. April 2009.

</div>

Summer2009:Using client server paradigm with python and slicer

2009-06-26T22:15:56Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are interested to run intensive tasks from the Slicer python directly.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to defer intensive computational task into another process communicating remotely with the Slicer process.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* Software for enabling a client-server paradigm is done. It uses basic socket mechanism for that purpose and was tested successfully. It mimics CLI modules written in C++.
* Enhanced options (client side) to setup the module
* Study possibility of using Pyro (RPC) to replace socket mechanism

</div>
</div>

==References==

Summer2009:Implementing parallelism in python

2009-06-26T22:10:42Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of running computational intensive simulations with the python language.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to subdivide highly intensive computational tasks and profit of the parallelism offered by current multicore machines.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* Software for parallelizing python tasks is done. It uses parallel python for that purpose and was tested successfully on fat nodes and the cluster at SPL.
* Improved performance
* Completed parallelization of connection filtering
* Completed batch for different studies configuration

</div>
</div>

==References==

Summer2009:Using cython

2009-06-26T22:09:59Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of accelerating the stochastic tractography code developed in python and part of the current version of Slicer 3.4.

</div>

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

<h3>Approach, Plan</h3>
Cython is used to develop a direct way of integrating native C code where python bytecode is too slow and hinders performance of the algorithm.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* Cython code for tensor and fiber tracking done
* Performance depends mainly of the nature of the Python code - if numpy adequately used (vectorization...) - no significant difference with C performance

</div>
</div>

==References==

Summer2009:Using CUDA for stochastic tractography

2009-06-26T22:07:03Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
Stochastic tractography does not provide interactive visualization so far due to its intensive computational needs.

</div>

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

<h3>Approach, Plan</h3>
Idea would be to visualize online paths generated in a point of interest like a fiducial. This approach would be based on the online visualization of streamline tractography done by moving a fiducial interactively.

During the summer week, we will continue our work to develop a concrete solution in investigating acceleration means based mainly on CUDA.
</div>

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

<h3>Progress</h3>
* Cuda was integrated through PyCuda with support for numpy arrays syntax
* Check compilation&instalation under Linux&Windows
* Implemented part of the tractography algorithm in kernel
* Tested direct call to driver api - ok
* Tested driver kernels (simple matrix operations) - ok
* Still need to complete the whole tractography algorithm in kernel mode

</div>
</div>

==References==

Summer2009:Using CUDA for stochastic tractography

2009-06-26T22:06:34Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
Stochastic tractography does not provide interactive visualization so far due to its intensive computational needs.

</div>

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

<h3>Approach, Plan</h3>
Idea would be to visualize online paths generated in a point of interest like a fiducial. This approach would be based on the online visualization of streamline tractography done by moving a fiducial interactively.

During the summer week, we will continue our work to develop a concrete solution in investigating acceleration means based mainly on CUDA.
</div>

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

<h3>Progress</h3>
* Cuda was integrated through PyCuda with support for numpy arrays syntax
* Check compilation&instalation under Linux&Windows
* Implemented part of the tractography algorithm in kernel
* Tested direct call to driver api - ok
* Tested driver kernels (simple matrix operations)
* Still need to complete the whole tractography algorithm in kernel mode

</div>
</div>

==References==

Summer2009:Implementing parallelism in python

2009-06-26T22:03:27Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of running computational intensive simulations with the python language.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to subdivide highly intensive computational tasks and profit of the parallelism offered by current multicore machines.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* software for parallelizing python tasks is done. It uses parallel python for that purpose and was tested successfully on fat nodes and the cluster at SPL.
* improved performance with cache mechanism
* complete parallelization of connection filtering
* complete batch for different studies configuration

</div>
</div>

==References==

Summer2009:Using cython

2009-06-26T22:01:07Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of accelerating the stochastic tractography code developed in python and part of the current version of Slicer 3.4.

</div>

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

<h3>Approach, Plan</h3>
Cython is used to develop a direct way of integrating native C code where python bytecode is too slow and hinders performance of the algorithm.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
* cython code for tensor and fiber tracking done
* performance depends mainly of the nature of the Python code - if numpy adequately used (vectorization...) - no significant difference with C performance

</div>
</div>

==References==

Summer2009:Using CUDA for stochastic tractography

2009-06-26T21:50:55Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
Stochastic tractography does not provide interactive visualization so far due to its intensive computational needs.

</div>

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

<h3>Approach, Plan</h3>
Idea would be to visualize online paths generated in a point of interest like a fiducial. This approach would be based on the online visualization of streamline tractography done by moving a fiducial interactively.

During the summer week, we will continue our work to develop a concrete solution in investigating acceleration means based mainly on CUDA.
</div>

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

<h3>Progress</h3>
* Cuda was integrated through PyCuda with support for numpy arrays syntax
* direct call to driver api tested
* driver kernels tested (simple matrix operations)

</div>
</div>

==References==

Summer2009:Using CUDA for stochastic tractography

2009-06-26T21:50:34Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
Stochastic tractography does not provide interactive visualization so far due to its intensive computational needs.

</div>

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

<h3>Approach, Plan</h3>
Idea would be to visualize online paths generated in a point of interest like a fiducial. This approach would be based on the online visualization of streamline tractography done by moving a fiducial interactively.

During the summer week, we will continue our work to develop a concrete solution in investigating acceleration means based mainly on CUDA.
</div>

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

<h3>Progress</h3>
* Cuda was integrated through PyCuda with support for numpy arrays syntax
* direct call to driver api tested
* driver kernels tested (simple matrices operations)

</div>
</div>

==References==

2009 Summer Project Week

2009-06-11T14:46:59Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

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

===CUDA Projects===

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

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

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

2009 Summer Project Week

2009-06-09T22:36:26Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev, C-F Westin)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan M, Florin, Ron, Wendy, Tim, Misha)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Dan Marcus)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus, Dan Blezek, Tim Olsen)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

===NA-MIC Engineering Projects===
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, James Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal, Sylvain Bouix)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

2009 Summer Project Week

2009-06-09T22:15:13Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev, C-F Westin)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan M, Florin, Ron, Wendy, Tim, Misha)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Dan Marcus)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus, Dan Blezek, Tim Olsen)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

===NA-MIC Engineering Projects===
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, James Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

2009 Summer Project Week

2009-06-09T22:14:14Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev, C-F Westin)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan M, Florin, Ron, Wendy, Tim, Misha)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Dan Marcus)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus, Dan Blezek, Tim Olsen)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

===NA-MIC Engineering Projects===
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography code]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, James Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

Summer2009:Using CUDA for stochastic tractography

2009-06-09T20:31:06Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
Stochastic tractography does not provide interactive visualization so far due to its intensive computational needs.

</div>

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

<h3>Approach, Plan</h3>
Idea would be to visualize online paths generated in a point of interest like a fiducial. This approach would be based on the online visualization of streamline tractography done by moving a fiducial interactively.

During the summer week, we will continue our work to develop a concrete solution in investigating acceleration means based mainly on CUDA.
</div>

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

<h3>Progress</h3>
To be achieved during the summer week...

</div>
</div>

==References==

Summer2009:Using cython

2009-06-09T20:30:28Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of accelerating the stochastic tractography code developed in python and part of the current version of Slicer 3.4.

</div>

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

<h3>Approach, Plan</h3>
Cython is used to develop a direct way of integrating native C code where python bytecode is too slow and hinders performance of the algorithm.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
To be achieved during the summer week...

</div>
</div>

==References==

Summer2009:Using cython

2009-06-09T20:30:13Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of accelerating the stochastic tractography code developed in python and part of the current version of Slicer 3.4.

</div>

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

<h3>Approach, Plan</h3>
Cython is used to develop a direct way of integrating native C code where python bytecode is too slow and hinders performance of the algorithm.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
To be achieved during the week...

</div>
</div>

==References==

Summer2009:Using cython

2009-06-09T20:28:55Z

Jvs: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * BWH: Julien de Siebenthal, Sylvain Bouix <div st...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of accelerating the stochastic tractography code developed in python and part of the current version of Slicer 3.4.

</div>

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

<h3>Approach, Plan</h3>
Cython is used to develop a direct way of integrating native C code where python bytecode is too slow and hinders performance of the algorithm.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>

</div>
</div>

==References==

2009 Summer Project Week

2009-06-09T20:23:25Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev, C-F Westin)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan M, Florin, Ron, Wendy, Tim, Misha)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Dan Marcus)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus, Dan Blezek, Tim Olsen)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

===NA-MIC Engineering Projects===
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_cython| Accelerating python with cython applied to stochastic tractography code]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, James Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

2009 Summer Project Week

2009-06-09T19:16:36Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev, C-F Westin)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan M, Florin, Ron, Wendy, Tim, Misha)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Dan Marcus)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus, Dan Blezek, Tim Olsen)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

===NA-MIC Engineering Projects===
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, James Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

2009 Summer Project Week

2009-06-09T19:16:07Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev, C-F Westin)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan M, Florin, Ron, Wendy, Tim, Misha)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Dan Marcus)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus, Dan Blezek, Tim Olsen)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

===NA-MIC Engineering Projects===
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, James Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)
#[[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

2009 Summer Project Week

2009-06-09T19:15:13Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev, C-F Westin)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan M, Florin, Ron, Wendy, Tim, Misha)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Dan Marcus)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus, Dan Blezek, Tim Olsen)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

===NA-MIC Engineering Projects===
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, James Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

2009 Summer Project Week

2009-06-09T19:14:32Z

Jvs:

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

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev, C-F Westin)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan M, Florin, Ron, Wendy, Tim, Misha)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Dan Marcus)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus, Dan Blezek, Tim Olsen)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

===NA-MIC Engineering Projects===
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, James Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

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

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

Summer2009:Using CUDA for stochastic tractography

2009-06-09T19:11:52Z

Jvs:

Summer2009:Using CUDA for stochastic tractography

2009-06-09T19:09:59Z

Jvs: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * BWH: Julien de Siebenthal, Sylvain Bouix <div st...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
Stochastic tractography does not provide easy realtime visualization.

</div>

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

<h3>Approach, Plan</h3>
Idea would be to visualize online ways paths are generated in a point of interest. This approach mimics the online visualization of streamline tractography by moving a fiducial interactively.

During the summer week, we will continue our work to develop a concrete solution in investigating acceleration means based mainly on CUDA.
</div>

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

<h3>Progress</h3>

</div>
</div>

==References==

Summer2009:Using client server paradigm with python and slicer

2009-06-09T19:05:20Z

Jvs: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * BWH: Julien de Siebenthal, Sylvain Bouix <div st...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are interested to run intensive tasks from the Slicer python directly.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to defer intensive computational task into another process communicating remotely with the Slicer process.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
Software for enabling a client-server paradigm is done. It uses basic socket mechanism for that purpose and was tested successfully. It mimics CLI modules written in C++.

</div>
</div>

==References==

Summer2009:Implementing parallelism in python

2009-06-09T18:59:13Z

Jvs:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of running computational intensive simulations with the python language.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to subdivide highly intensive computational tasks and profit of the parallelism offered by current multicore machines.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
Software for parallelizing python tasks is done. It uses parallel python for that purpose and was tested successfully on fat nodes and the cluster at SPL.

</div>
</div>

==References==

Summer2009:Implementing parallelism in python

2009-06-09T18:43:31Z

Jvs: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * BWH: Julien de Siebenthal, Sylvain Bouix <div st...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Julien de Siebenthal, Sylvain Bouix

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

<h3>Objective</h3>
We are investigating ways of running highly computational intensive simulations with the python language.

</div>

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

<h3>Approach, Plan</h3>
Our approach is to subdivide highly intensive computational tasks and profit of the parallelism offered by current multicore machines.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.
</div>

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

<h3>Progress</h3>
Software for parallelizing python tasks is done. It uses parallel python for that purpose and was tested successfully on fat nodes and the cluster at SPL.

</div>
</div>

==References==

2009 Summer Project Week

2009-06-02T01:53:16Z

Jvs:

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Ziv)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiaodong, Snehashis Roy)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech

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

2009 Summer Project Week

2009-06-02T01:48:29Z

Jvs:

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Ziv)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiaodong, Snehashis Roy)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech

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

2009 Summer Project Week

2009-06-02T01:47:13Z

Jvs:

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Ziv)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiaodong, Snehashis Roy)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien)
# [[Summer2009:Using_client_server_paradigm_with_python| Deferring heavy computational tasks in python]] (Julien)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech

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

2009 Summer Project Week

2009-06-02T01:46:23Z

Jvs:

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

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

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

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

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Ziv)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiaodong, Snehashis Roy)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien)
# [[Summer2009:Using_client_server_with_python| Deferring heavy computational tasks in python]] (Julien)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

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

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech

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