NAMIC Wiki - User contributions [en]

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-18T15:19:41Z

Yang:

{|
|[[Image:ProjectWeek-2008.png|thumb|360px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:DTIReg.JPG|thumb|420px|The non-linear DTI registration plugin.]]
|}
__NOTOC__
===Key Investigators===
*Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
*Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
*Yang Li <Yang.Li@uphs.upenn.edu>
*Luke Bloy <lbloy@seas.upenn.edu>

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

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

<h1>Objective</h1>

To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [http://www.rad.upenn.edu/sbia]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.

</div>

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

<h1>Approach, Plan</h1>
*DTI registration: has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
*DTI Statistics: SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
*HARDI registration: This is being developed in ITK, building on HARDI representation format currently under development
*HARDI statistics: being developed in ITK

</div>

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

<h1>Progress</h1>
*DTI Registration: plugin is ready and will be demonstrated
To do: Replace the affine registration component, help file, speed, version control
*Need help with:
1. General representation for registration in ITK

2. Code for Demons DTI registration for comparison

3. Visualization: tensor glyphs and ODFs

</div>

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

</div>
===References===
This work was supported in part by NIH grants .

* [http://www.rad.upenn.edu/sbia Link to SBIA web site: ]
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, in MICCAI 2008, New York.
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, in SPIE Medical Imaging 2008, San Diego.
* [https://www.rad.upenn.edu/sbia/papers/181.pdf R. Verma, P. Khurd, C. Davatzikos, On Analyzing Diffusion Tensor Images by Identifying Manifold Structure using Isomaps, IEEE Transactions on Medical Imaging, 772-778, Vol. 26, No. 6, 2007 (need access to IEEE explore to view papers) ]
* [https://www.rad.upenn.edu/sbia/papers/177.pdf P. Khurd, R. Verma and C. Davatzikos, Kernel-based Manifold Learning for Statistical Analysis of Diffusion Tensor Images, Information Processing in Medical Imaging (IPMI), 581-593, Vol. 4584, 2007 ]

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-18T15:13:56Z

Yang:

{|
|[[Image:ProjectWeek-2008.png|thumb|360px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:DTIReg.JPG|thumb|420px| The DTI non-linear registration plugin.]]
|}
__NOTOC__
===Key Investigators===
*Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
*Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
*Yang Li <Yang.Li@uphs.upenn.edu>
*Luke Bloy <lbloy@seas.upenn.edu>

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

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

<h1>Objective</h1>

To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [http://www.rad.upenn.edu/sbia]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.

</div>

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

<h1>Approach, Plan</h1>
*DTI registration: has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
*DTI Statistics: SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
*HARDI registration: This is being developed in ITK, building on HARDI representation format currently under development
*HARDI statistics: being developed in ITK

</div>

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

<h1>Progress</h1>
*DTI Registration: plugin is ready and will be demonstrated
To do: Replace the affine registration component, help file, speed, version control
*Need help with:
1. General representation for registration in ITK

2. Code for Demons DTI registration for comparison

3. Visualization: tensor glyphs and ODFs

</div>

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

</div>
===References===
This work was supported in part by NIH grants .

* [http://www.rad.upenn.edu/sbia Link to SBIA web site: ]
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, in MICCAI 2008, New York.
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, in SPIE Medical Imaging 2008, San Diego.
* [https://www.rad.upenn.edu/sbia/papers/181.pdf R. Verma, P. Khurd, C. Davatzikos, On Analyzing Diffusion Tensor Images by Identifying Manifold Structure using Isomaps, IEEE Transactions on Medical Imaging, 772-778, Vol. 26, No. 6, 2007 (need access to IEEE explore to view papers) ]
* [https://www.rad.upenn.edu/sbia/papers/177.pdf P. Khurd, R. Verma and C. Davatzikos, Kernel-based Manifold Learning for Statistical Analysis of Diffusion Tensor Images, Information Processing in Medical Imaging (IPMI), 581-593, Vol. 4584, 2007 ]

File:DTIReg.JPG

2008-06-18T15:09:11Z

Yang:

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-18T14:28:22Z

Yang: /* References */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|}
__NOTOC__
===Key Investigators===
*Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
*Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
*Yang Li <Yang.Li@uphs.upenn.edu>
*Luke Bloy <lbloy@seas.upenn.edu>

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

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

<h1>Objective</h1>

To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [http://www.rad.upenn.edu/sbia]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.

</div>

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

<h1>Approach, Plan</h1>
*DTI registration: has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
*DTI Statistics: SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
*HARDI registration: This is being developed in ITK, building on HARDI representation format currently under development
*HARDI statistics: being developed in ITK

</div>

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

<h1>Progress</h1>
*DTI Registration: plugin is ready and will be demonstrated
To do: Replace the affine registration component, help file, speed, version control
*Need help with:
1. General representation for registration in ITK

2. Code for Demons DTI registration for comparison

3. Visualization: tensor glyphs and ODFs

</div>

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

</div>
===References===
This work was supported in part by NIH grants .

* [http://www.rad.upenn.edu/sbia Link to SBIA web site: ]
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, in MICCAI 2008, New York.
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, in SPIE Medical Imaging 2008, San Diego.
* [https://www.rad.upenn.edu/sbia/papers/181.pdf R. Verma, P. Khurd, C. Davatzikos, On Analyzing Diffusion Tensor Images by Identifying Manifold Structure using Isomaps, IEEE Transactions on Medical Imaging, 772-778, Vol. 26, No. 6, 2007 (need access to IEEE explore to view papers) ]
* [https://www.rad.upenn.edu/sbia/papers/177.pdf P. Khurd, R. Verma and C. Davatzikos, Kernel-based Manifold Learning for Statistical Analysis of Diffusion Tensor Images, Information Processing in Medical Imaging (IPMI), 581-593, Vol. 4584, 2007 ]

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-17T20:59:27Z

Yang:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
*Ragini Verma, PhD (ragini.verma at rad.upenn.edu) [http://www.rad.upenn.edu/sbia], Christos Davatzikos, Yang Li, Luke Bloy

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

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

<h1>Objective</h1>

Detailed information about SBIA can be found here [http://www.rad.upenn.edu/sbia]

</div>

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

<h1>Approach, Plan</h1>

</div>

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

<h1>Progress</h1>

</div>

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

</div>

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-17T20:54:15Z

Yang:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Normalization.JPG|thumb|640px|Spatial normalization of 5 mouse brains. (a) Color map of the template. (b) Color map
of the group averaged image. (c) Edges extracted from FA map of group averaged image superimposed
on the FA map of template.]]
|}

__NOTOC__

===Key Investigators===
*Ragini Verma, PhD (ragini.verma at rad.upenn.edu) [http://www.rad.upenn.edu/sbia], Christos Davatzikos, Yang Li, Luke Bloy

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

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

<h1>Objective</h1>

Detailed information about SBIA can be found here [http://www.rad.upenn.edu/sbia]

</div>

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

<h1>Approach, Plan</h1>

</div>

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

<h1>Progress</h1>

</div>

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

</div>

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-17T20:53:12Z

Yang:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Normalization.JPG|thumb|320px|Spatial normalization of 5 mouse brains. (a) Color map of the template. (b) Color map
of the group averaged image. (c) Edges extracted from FA map of group averaged image superimposed
on the FA map of template.]]
|}

__NOTOC__

===Key Investigators===
*Ragini Verma, PhD (ragini.verma at rad.upenn.edu) [http://www.rad.upenn.edu/sbia], Christos Davatzikos, Yang Li, Luke Bloy

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

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

<h1>Objective</h1>

Detailed information about SBIA can be found here [http://www.rad.upenn.edu/sbia]

</div>

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

<h1>Approach, Plan</h1>

</div>

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

<h1>Progress</h1>

</div>

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

</div>

File:Normalization.JPG

2008-06-17T20:51:21Z

Yang:

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-17T20:43:51Z

Yang: