NAMIC Wiki - User contributions [en]

2012 Winter Project Week:ScriptView

2012-01-13T17:02:39Z

Montillo: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:Subj1_II.png|Subject1.
Image:Subj2_II.png|Subject2.
Image:Subj3_II.png|Subject3.
</gallery>

==Key Investigators==
* GE Research: Albert Montillo (montillo@ge.com)

* Isomics: Steve Pieper

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

<h3>Objective</h3>
Programmatically setup 3D Slicer to view data from different subjects while applying the same consistent view. Save screen image to PNG.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to create a template MRML scene file and reuse it for each subject. MRML scene stores relative paths to items in the scene such as volumes. Python script is passed to Slicer to load the scene per subject and save image.<foo>.

</div>

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

<h3>Progress</h3>
The python script has been tested on folder with multiple subject subfolders. All subject folders use same file names for scene elements so that same MRML file works for all subjects. MRML scene need only be setup once, for one subject, then reused for each subject.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as a python script.

</div>

2012 Winter Project Week:ScriptView

2012-01-13T16:35:09Z

Montillo: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:Subj1_II.png|Subject1.
Image:Subj2_II.png|Subject2.
Image:Subj3_II.png|Subject3.
</gallery>

==Key Investigators==
* GE Research: Albert Montillo (montillo@ge.com)

Many thanks to : Steve Pieper

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

<h3>Objective</h3>
Programmatically setup 3D Slicer to view data from different subjects while applying the same consistent view. Save screen image to PNG.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to create a template MRML scene file and reuse it for each subject. MRML scene stores relative paths to items in the scene such as volumes. Python script is passed to Slicer to load the scene per subject and save image.<foo>.

</div>

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

<h3>Progress</h3>
The python script has been tested on folder with multiple subject subfolders. All subject folders use same file names for scene elements so that same MRML file works for all subjects. MRML scene need only be setup once, for one subject, then reused for each subject.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as a python script.

</div>

2012 Winter Project Week:ScriptView

2012-01-13T16:21:52Z

Montillo: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:Subj1_II.png|Subject1.
Image:Subj2_II.png|Subject2.
Image:Subj3_II.png|Subject3.
</gallery>

==Key Investigators==
* GE Research: Albert Montillo

Many thanks to : Steve Pieper (Isomics)

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

<h3>Objective</h3>
Programmatically setup 3D Slicer to view data from different subjects while applying the same consistent view. Save screen image to PNG.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to create a template MRML scene file and reuse it for each subject. MRML scene stores relative paths to items in the scene such as volumes. Python script is passed to Slicer to load the scene per subject and save image.<foo>.

</div>

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

<h3>Progress</h3>
The python script has been tested on folder with multiple subject subfolders. All subject folders use same file names for scene elements so that same MRML file works for all subjects. MRML scene need only be setup once, for one subject, then reused for each subject.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as a python script.

</div>

2012 Winter Project Week:ScriptView

2012-01-13T16:17:37Z

Montillo:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:Subj1_II.png|Subject1.
Image:Subj2_II.png|Subject2.
Image:Subj3_II.png|Subject3.
</gallery>

==Key Investigators==
* GE Research: Albert Montillo

Many thanks to : Steve Pieper (Isomics)

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

<h3>Objective</h3>
Programmatically setup 3D Slicer to view data from different subjects while applying the same consistent view. Save screen image to PNG.

</div>

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

<h3>Approach, Plan</h3>

Our approach is create a template MRML scene file and reuse it for each subject. MRML scene stores relative paths to items in the scene such as volumes. Python script is passed to Slicer to load dthe scene per subject and save image.<foo>.

</div>

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

<h3>Progress</h3>
The python script has been tested on folder with multiple subject subfolders. All subject folders use same file names for scene elements so that same MRML file works for all subjects. MRML scene need only be setup once, for one subject, then reused for each subject.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as a python script.

</div>

2012 Winter Project Week:ScriptView

2012-01-13T16:17:00Z

Montillo:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:Subj1_II.|Subject1.
Image:Subj2_II.|Subject2.
Image:Subj3_II.|Subject3.
</gallery>

==Key Investigators==
* GE Research: Albert Montillo

Many thanks to : Steve Pieper (Isomics)

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

<h3>Objective</h3>
Programmatically setup 3D Slicer to view data from different subjects while applying the same consistent view. Save screen image to PNG.

</div>

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

<h3>Approach, Plan</h3>

Our approach is create a template MRML scene file and reuse it for each subject. MRML scene stores relative paths to items in the scene such as volumes. Python script is passed to Slicer to load dthe scene per subject and save image.<foo>.

</div>

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

<h3>Progress</h3>
The python script has been tested on folder with multiple subject subfolders. All subject folders use same file names for scene elements so that same MRML file works for all subjects. MRML scene need only be setup once, for one subject, then reused for each subject.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as a python script.

</div>

File:Subj3 II.png

2012-01-13T16:15:44Z

Montillo:

File:Subj2 II.png

2012-01-13T16:14:54Z

Montillo:

File:Subj1 II.png

2012-01-13T16:13:52Z

Montillo:

2012 Winter Project Week:ScriptView

2012-01-13T16:12:03Z

Montillo:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Subject1.
Image:genuFAp.jpg|Subject2.
Image:genuFAp.jpg|Subject3.
</gallery>

==Key Investigators==
* GE Research: Albert Montillo

Many thanks to : Steve Pieper (Isomics)

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

<h3>Objective</h3>
Programmatically setup 3D Slicer to view data from different subjects while applying the same consistent view. Save screen image to PNG.

</div>

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

<h3>Approach, Plan</h3>

Our approach is create a template MRML scene file and reuse it for each subject. MRML scene stores relative paths to items in the scene such as volumes. Python script is passed to Slicer to load dthe scene per subject and save image.<foo>.

</div>

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

<h3>Progress</h3>
The python script has been tested on folder with multiple subject subfolders. All subject folders use same file names for scene elements so that same MRML file works for all subjects. MRML scene need only be setup once, for one subject, then reused for each subject.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as a python script.

</div>

2012 Winter Project Week:ScriptView

2012-01-13T16:11:13Z

Montillo: /* Key Investigators */

2012 Winter Project Week:ScriptView

2012-01-13T16:06:41Z

Montillo:

2012 Winter Project Week:ScriptView

2012-01-13T16:05:11Z

Montillo: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Key Investigators==
* GE Research: Albert Montillo
* Isomics: Steve Pieper

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

<h3>Objective</h3>
Programmatically setup 3D Slicer to view data from different subjects while applying the same consistent view. Save screen image to PNG.

</div>

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

<h3>Approach, Plan</h3>

Our approach is create a template MRML scene file and reuse it for each subject. MRML scene stores relative paths to items in the scene such as volumes. Python script is passed to Slicer to load dthe scene per subject and save image.<foo>.

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

2012 Winter Project Week:ScriptView

2012-01-13T16:00:44Z

Montillo:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

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

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

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h3>Approach, Plan</h3>

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

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

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

2012 Winter Project Week

2012-01-13T15:59:35Z

Montillo: /* NA-MIC Kit Internals */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== [[AHM_2012#Agenda|'''AGENDA''']] and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:GeometricMetamorphosisTBI|Geometric Metamorphosis for TBI]] (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
* [[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger, Isaiah Norton, Jayashree)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen, Junichi Tokuda)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Isaiah Norton, Mehdi Moradi, Tamas Ungi)
*[[2012_Winter_Project_Week:LaserAblationAndGuidance|Slicer-BrainLab integration for laser ablation]] (Erol Yeniaras, Isaiah Norton, Pratik Patel)
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer for Neurosurgery]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]
* [[2012_Winter_Project_Week:CTLiverRegistration|Register liver CT images for tumor progress monitoring]] (Karl Diedrich, Nobuhiko Hata, Atsushi Yamada)
* [[2012_Winter_Project_Week:Fast Multi-modal Registration|Fast Registration with User-guidance for AMIGO]] (Dave Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:UKFTractography|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plesniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
*[[2012_Project_Week:RemoveSlicerLegacyCode|Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)]]
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra, Dave Welch)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)
*[[2012_Winter_Project_Week:ScriptView|Consistent, scripted setup of Slicer view for multiple subjects]] (Albert, Steve)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[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 December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). 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...

2012 Winter Project Week

2012-01-13T15:58:11Z

Montillo: /* NA-MIC Kit Internals */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== [[AHM_2012#Agenda|'''AGENDA''']] and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:GeometricMetamorphosisTBI|Geometric Metamorphosis for TBI]] (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
* [[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger, Isaiah Norton, Jayashree)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen, Junichi Tokuda)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Isaiah Norton, Mehdi Moradi, Tamas Ungi)
*[[2012_Winter_Project_Week:LaserAblationAndGuidance|Slicer-BrainLab integration for laser ablation]] (Erol Yeniaras, Isaiah Norton, Pratik Patel)
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer for Neurosurgery]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]
* [[2012_Winter_Project_Week:CTLiverRegistration|Register liver CT images for tumor progress monitoring]] (Karl Diedrich, Nobuhiko Hata, Atsushi Yamada)
* [[2012_Winter_Project_Week:Fast Multi-modal Registration|Fast Registration with User-guidance for AMIGO]] (Dave Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:UKFTractography|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plesniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
*[[2012_Project_Week:RemoveSlicerLegacyCode|Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)]]
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra, Dave Welch)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)
*[[2012_Project_Week:ScriptView|Consistent, scripted setup of Slicer view for multiple subjects]] (Albert, Steve)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[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 December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). 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...

2012 Winter Project Week:ScriptView

2012-01-13T15:56:24Z

Montillo: Created page with '__NOTOC__ <gallery> Image:PW-SLC2012.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention 2012_Winter_Project_Week:<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

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

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

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h3>Approach, Plan</h3>

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

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

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>