NAMIC Wiki - User contributions [en]

FMA (Protege) links to Slicer

2008-06-20T20:11:56Z

Vissu 330:

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|SPN Ontology visualization in Query Atlas.]]

|}

__NOTOC__

===Key Investigators===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

<h1>Objective</h1>

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies of brain based on Protege's frame based representation.

</div>

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

<h1>Approach, Plan</h1>
Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build
a query-engine that allows a software program to navigate through protege ontologies. We will use this capability to develop an ontology browser for FMA.

</div>

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

<h1>Progress</h1>
Our plan for the project week is to work on
1. Integration of FMA browser with QueryAtlas.
2. Assesment of appropriate prefuse data-structures to hold FMA ontology data.
3. Integration of Query engine to Ion-Florin et al's physiological ontology of brain.

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T20:10:39Z

Vissu 330: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Key Investigators===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

<h1>Objective</h1>

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies of brain based on Protege's frame based representation.

</div>

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

<h1>Approach, Plan</h1>
Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build
a query-engine that allows a software program to navigate through protege ontologies. We will use this capability to develop an ontology browser for FMA.

</div>

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

<h1>Progress</h1>
Our plan for the project week is to work on
1. Integration of FMA browser with QueryAtlas.
2. Assesment of appropriate prefuse data-structures to hold FMA ontology data.
3. Integration of Query engine to Ion-Florin et al's physiological ontology of brain.

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T20:09:57Z

Vissu 330: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Key Investigators===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

<h1>Objective</h1>

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies of brain based on Protege's frame based representation.

</div>

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

<h1>Approach, Plan</h1>
Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build
a query-engine that allows a software program to navigate through protege ontologies. We will use this capability to develop a ontology browser for FMA.

</div>

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

<h1>Progress</h1>
Our plan for the project week is to work on
1. Integration of FMA browser with QueryAtlas.
2. Assesment of appropriate prefuse data-structures to hold FMA ontology data.
3. Integration of Query engine to Ion-Florin et al's physiological ontology of brain.

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T20:09:46Z

Vissu 330: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Key Investigators===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

<h1>Objective</h1>

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies of brain based on Protege's frame based representation.

</div>

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

<h1>Approach, Plan</h1>
Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build
a query-engine that allows a software program to navigate through protege ontologies. We will use this capability to develop a ontology browser for FMA.

</div>

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

<h1>Progress</h1>
Our plan for the project week is to work on
1. Integration of FMA browser with QueryAtlas.
2. Assesment of appropriate prefuse data-structures to hold FMA ontology data.
2. Integration of Query engine to Ion-Florin et al's physiological ontology of brain.

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T20:08:34Z

Vissu 330: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Key Investigators===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

<h1>Objective</h1>

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies of brain based on Protege's frame based representation.

</div>

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

<h1>Approach, Plan</h1>
Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build
a query-engine that allows a software program to navigate through protege ontologies. We will use this capability to develop a ontology browser for FMA.

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

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

<h1>Progress</h1>

1. Integration of FMA browser with Atlas.
2. Integration of Query engine to Ion-Florin et al's physiological ontology of brain.

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T20:08:18Z

Vissu 330: /* Instructions for Use of this Template */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Key Investigators===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

<h1>Objective</h1>

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies of brain based on Protege's frame based representation.

</div>

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

<h1>Approach, Plan</h1>
Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build
a query-engine that allows a software program to navigate through protege ontologies. We will use this capability to develop a ontology browser for FMA.
<foo>.

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

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

<h1>Progress</h1>

1. Integration of FMA browser with Atlas.
2. Integration of Query engine to Ion-Florin et al's physiological ontology of brain.

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T20:08:03Z

Vissu 330: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

<h1>Objective</h1>

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies of brain based on Protege's frame based representation.

</div>

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

<h1>Approach, Plan</h1>
Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build
a query-engine that allows a software program to navigate through protege ontologies. We will use this capability to develop a ontology browser for FMA.
<foo>.

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

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

<h1>Progress</h1>

1. Integration of FMA browser with Atlas.
2. Integration of Query engine to Ion-Florin et al's physiological ontology of brain.

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T20:02:27Z

Vissu 330: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

<h1>Objective</h1>

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies based on Protege's frame based representation.

</div>

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

<h1>Approach, Plan</h1>

Our plan is to integrate capabilities to browse foundational model of anatomy (FMA)'s ontology with the QueryAtlas ontology browser. <foo>.

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T19:59:24Z

Vissu 330: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos
* Stanford: Michael Hall.

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

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

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

</div>

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

<h1>Approach, Plan</h1>

Our plan is to integrate capabilities to browse foundational model of anatomy (FMA)'s ontology with the QueryAtlas ontology browser. <foo>.

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T19:56:20Z

Vissu 330: /* References */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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===
* GE: Viswanath Avasarala, Jim Miller
* Utah: Tom Fletcher, Ross Whitaker

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

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

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

</div>

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

<h1>Approach, Plan</h1>

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

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T19:55:52Z

Vissu 330: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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===
* GE: Viswanath Avasarala, Jim Miller
* Utah: Tom Fletcher, Ross Whitaker

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

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

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

</div>

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

<h1>Approach, Plan</h1>

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

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* A Prototype Symbolic Model of Canonical Functional Neuroanatomy of the Motor System
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T19:55:00Z

Vissu 330:

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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%;">

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

</div>

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

<h1>Approach, Plan</h1>

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

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* A Prototype Symbolic Model of Canonical Functional Neuroanatomy of the Motor System
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
* Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

FMA (Protege) links to Slicer

2008-06-20T19:52:29Z

Vissu 330:

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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%;">

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

</div>

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

<h1>Approach, Plan</h1>

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

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* Florin's paper on the functional ontology
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*

FMA (Protege) links to Slicer

2008-06-20T19:52:10Z

Vissu 330:

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brani ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]

|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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%;">

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

</div>

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

<h1>Approach, Plan</h1>

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

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* Florin's paper on the functional ontology
*C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
*

FMA (Protege) links to Slicer

2008-06-20T19:50:03Z

Vissu 330:

File:SmallOntologyBrowser.png

2008-06-20T19:47:34Z

Vissu 330: uploaded a new version of "Image:SmallOntologyBrowser.png"

FMA (Protege) links to Slicer

2008-06-20T19:40:12Z

Vissu 330:

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brani ]]
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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%;">

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

</div>

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

<h1>Approach, Plan</h1>

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

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* Florin's paper on the functional ontology
* Transcribing the FMA
* FMA

FMA (Protege) links to Slicer

2008-06-20T19:39:24Z

Vissu 330:

{|
|[[Image:Fma.JPG|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/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%;">

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

</div>

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

<h1>Approach, Plan</h1>

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

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

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

<h1>Progress</h1>

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

</div>

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

</div>

===References===
* Florin's paper on the functional ontology
* Transcribing the FMA
* FMA

File:Fma.JPG

2008-06-20T19:38:37Z

Vissu 330: Exploration of Foundational Model of Anatomy

Exploration of Foundational Model of Anatomy