NAMIC Wiki - User contributions [en]

2014 Summer Project Week:DRAMMS Slicer

2014-06-25T15:34:33Z

Ouyangming:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for '''2D-to-2D''' and '''3D-to-3D''' cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for '''spatial-temporal (4D)''' registration and '''population-wise''' registration. Some typical applications include:

* atlas construction in a population (infants, neonates, adults, ...);
* multi-atlas based structure segmentation (brain, prostate, ...);
* multi-modal registration (we had some success in histology-MRI registration of the prostate and mouse brain, looking for data for validation);
* registration under a partial loss of correspondences(such as tumor/lesion-bearing images to normal-appearance images);
* quantification of 4D tumor changes;
* study of early-life longitudinal neuro-deveolopment;
* maintenance of 4D segmentation consistency.

Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast [[https://drive.google.com/file/d/0B1RDNI9g7RfrTHhpU21semdYYjA/edit?usp=sharing DRAMMS_in_Breast_Registration]] registration tasks.

The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software Website]

* [http://www.cbica.upenn.edu/sbia/software/dramms/_downloads/DRAMMS_Software_Manual.pdf DRAMMS Software Manual (pdf)]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [https://drive.google.com/file/d/0B1RDNI9g7RfrTHhpU21semdYYjA/edit?usp=sharing Evaluation of DRAMMS in Longitudinal Breast Registration]

2014 Summer Project Week:DRAMMS Slicer

2014-06-24T01:54:26Z

Ouyangming:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for '''2D-to-2D''' and '''3D-to-3D''' cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for '''spatial-temporal (4D)''' registration and '''population-wise''' registration. Some typical applications include:

* atlas construction in a population (infants, neonates, adults, ...);
* multi-atlas based structure segmentation (brain, prostate, ...);
* multi-modal registration (we had some success in histology-MRI registration of the prostate and mouse brain, looking for data for validation);
* registration under a partial loss of correspondences(such as tumor/lesion-bearing images to normal-appearance images);
* quantification of 4D tumor changes;
* study of early-life longitudinal neuro-deveolopment;
* maintenance of 4D segmentation consistency.

Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration (a journal article accepted pending minor revision) tasks.

The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software Website]

* [http://www.cbica.upenn.edu/sbia/software/dramms/_downloads/DRAMMS_Software_Manual.pdf DRAMMS Software Manual (pdf)]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration (a journal article accepted pending minor revision)]

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T18:52:35Z

Ouyangming: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for '''2D-to-2D''' and '''3D-to-3D''' cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for '''spatial-temporal (4D)''' registration and '''population-wise''' registration. Some typical applications include:

* atlas construction in a population (infants, neonates, adults, ...);
* multi-atlas based structure segmentation (brain, prostate, ...);
* multi-modal registration (we had some success in histology-MRI registration of the prostate and mouse brain, looking for data for validation);
* registration under a partial loss of correspondences(such as tumor/lesion-bearing images to normal-appearance images);
* quantification of 4D tumor changes;
* study of early-life longitudinal neuro-deveolopment;
* maintenance of 4D segmentation consistency.

Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration (a journal article accepted pending minor revision) tasks.

The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration (a journal article accepted pending minor revision)]

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T18:52:22Z

Ouyangming: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for '''2D-to-2D''' and '''3D-to-3D''' cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for '''spatial-temporal (4D)''' registration and '''population-wise''' registration. Some typical applications include:

* atlas construction in a population (infants, neonates, adults, ...);
* multi-atlas based structure segmentation (brain, prostate, ...);
* multi-modal registration (we had some success in histology-MRI registration of the prostate and mouse brain, looking for data for validation);
* registration under a partial loss of correspondences(such as tumor/lesion-bearing images to normal-appearance images);
* quantification of 4D tumor changes;
* study of early-life longitudinal neuro-deveolopment;
* maintenance of 4D segmentation consistency.

Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration (a journal article accepted pending minor revision) tasks.

The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration (a journal article accepted pending minor revision)]

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T18:51:38Z

Ouyangming: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for '''2D-to-2D''' and '''3D-to-3D''' cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for '''spatial-temporal (4D)''' registration and '''population-wise''' registration. Some typical applications include:

* quantification of 4D tumor changes;
* study of early-life longitudinal neuro-deveolopment;
* maintenance of 4D segmentation consistency;
* atlas construction in a population (infants, neonates, adults, ...);
* multi-atlas based structure segmentation (brain, prostate, ...);
* multi-modal registration (we had some success in histology-MRI registration of the prostate and mouse brain, looking for data for validation);
* registration under a partial loss of correspondences(such as tumor/lesion-bearing images to normal-appearance images).

Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration (a journal article accepted pending minor revision) tasks.

The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration (a journal article accepted pending minor revision)]

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T18:35:16Z

Ouyangming: /* References */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for '''2D-to-2D''' and '''3D-to-3D''' cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for '''spatial-temporal (4D)''' registration and '''population-wise''' registration. Some typical applications include:

* quantification of 4D tumor changes;
* study of early-life longitudinal neuro-deveolopment;
* maintenance of 4D segmentation consistency;
* atlas construction in a population (infants, neonates, adults, ...);
* multi-atlas based structure segmentation (brain, prostate, ...);
* multi-modal registration (we had some success in histology-MRI registration of the prostate and mouse brain, looking for data for validation).

Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration (a journal article accepted pending minor revision) tasks.

The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration (a journal article accepted pending minor revision)]

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T18:34:55Z

Ouyangming: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for '''2D-to-2D''' and '''3D-to-3D''' cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for '''spatial-temporal (4D)''' registration and '''population-wise''' registration. Some typical applications include:

* quantification of 4D tumor changes;
* study of early-life longitudinal neuro-deveolopment;
* maintenance of 4D segmentation consistency;
* atlas construction in a population (infants, neonates, adults, ...);
* multi-atlas based structure segmentation (brain, prostate, ...);
* multi-modal registration (we had some success in histology-MRI registration of the prostate and mouse brain, looking for data for validation).

Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration (a journal article accepted pending minor revision) tasks.

The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration]

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T18:29:49Z

Ouyangming: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for '''2D-to-2D''' and '''3D-to-3D''' cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for '''spatial-temporal (4D)''' registration (for the quantification of tumor changes, the study of neuro-deveolopment, and maintenance of 4D segmentation consistency) and '''population-wise''' registration (for atlas constructions). Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration tasks. The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration]

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T13:23:30Z

Ouyangming: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It was designed for 2D-to-2D and 3D-to-3D cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for spatial-temporal (4D) longitudinal registration (for the quantification of tumor changes, neuro-deveolopment) and population-wise registration (for atlas constructions). Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration tasks. The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures, and to deal with registration under a partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration]

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T12:46:47Z

Ouyangming: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Randy Gollub, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==

[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]] is a general-purpose, fully-automated, deformable image registration algorithm and software package. It is suitable for 2D-to-2D and 3D-to-3D cross-subject, longitudinal, multi-modal registration tasks, and has been recently extended for spatial-temporal (4D) longitudinal registration (for the quantification of tumor changes, neuro-deveolopment) and population-wise registration (for atlas constructions). Several evaluation studies comparing DRAMMS with many state-of-the-art registration algorithms are also being documented for brain [[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 DRAMMS_in_Brain_Registration]], cardiac [[http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 DRAMMS_in_Cardiac_Registration]], breast registration tasks. The integration of DRAMMS into Slicer is expected to bring more diverse deformable registration options into Slicer, especially an option to deal with registration of both brain and non-brain structures and to deal with registration under partial loss of correspondences.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

* [http://www.sciencedirect.com/science/article/pii/S1361841510000940 DRAMMS Algorithm]

* [http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS Software]

* [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6834815&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A4359023%29 Evaluation of DRAMMS in Across-Subject Brain Registration]

* [http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_22 Evaluation of DRAMMS in Across-Subject Cardiac Registration]

* [Evaluation of DRAMMS in Longitudinal Breast Registration]

2014 Summer Project Week

2014-06-23T12:31:03Z

Ouyangming: /* Slicer4 Extensions */

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)
<br>
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]

<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==Huntington's Disease==
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp)
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)

==TBI==
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Stroke==
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==Image-Guided Therapy==

* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer(WPI), Nirav Patel(WPI), Nobuhiko Hata (BWH) )
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
*[[2014_Summer_Project_Week:Intraoperative_Registration_of_preoperative_CT_and_C-arm_CT_of_the_lung | Intraoperative Registration of preoperative CT and C-arm CT of the lung]] (Katharina Breininger, Jay Jagadeesan)

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, University College Cork (UCC), Ireland)

==[http://qiicr.org QIICR]==
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})

==Feature Extraction==
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)

==Brain==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders | CAD Toolbox for Neurological Disorders]] (Sidong Liu, Siqi Liu, Fan Zhang, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis)
*[[2014_Summer_Project_Week:Longitudinal_patient_specific_DTI_analysis | Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia]] (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Kevin Wang, Andras Lasso)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Saskia Camps, SPL, saskiacamps@gmail.com
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Robin Kouver, BWH/SPL, r.kouver@gmail.com
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
#Yangming Li, University of Washington, ymli81@uw.edu
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week

2014-06-23T12:27:42Z

Ouyangming: /* Slicer4 Extensions */

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)
<br>
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]

<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==Huntington's Disease==
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp)
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)

==TBI==
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Stroke==
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==Image-Guided Therapy==

* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer(WPI), Nirav Patel(WPI), Nobuhiko Hata (BWH) )
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
*[[2014_Summer_Project_Week:Intraoperative_Registration_of_preoperative_CT_and_C-arm_CT_of_the_lung | Intraoperative Registration of preoperative CT and C-arm CT of the lung]] (Katharina Breininger, Jay Jagadeesan)

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, University College Cork (UCC), Ireland)

==[http://qiicr.org QIICR]==
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})

==Feature Extraction==
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)

==Brain==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders | CAD Toolbox for Neurological Disorders]] (Sidong Liu, Siqi Liu, Fan Zhang, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis)
*[[2014_Summer_Project_Week:Longitudinal_patient_specific_DTI_analysis | Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia]] (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Kevin Wang, Andras Lasso)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)
*[[2014_Summer_Project_Week:DRAMMS_Slicer| DRAMMS deformable registration integrated into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Saskia Camps, SPL, saskiacamps@gmail.com
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Robin Kouver, BWH/SPL, r.kouver@gmail.com
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
#Yangming Li, University of Washington, ymli81@uw.edu
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week:DRAMMS Slicer

2014-06-23T12:26:27Z

Ouyangming:

2014-06-23T11:32:42Z

Ouyangming:

2014 Project Week Template

2014-06-23T11:30:24Z

Ouyangming:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>
Image:Dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==
[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]]: DRAMMS is a general-purpose, fully-automated, deformable image registration algorithm and software package. It is suitable for cross-subject, longitudinal, multi-modal registration tasks.

2014 Project Week Template

2014-06-23T11:28:06Z

Ouyangming:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>
Image:dramms-logo.png|[[http://www.cbica.upenn.edu/sbia/software/dramms/ |DRAMMS Website]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To integrate the DRAMMS deformable registration software into 3DSlicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Starting from the current stand-alone DRAMMS version (academic- but not commercial-friendly), figure out the necessary interface to integrate it into Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==
[[http://www.cbica.upenn.edu/sbia/software/dramms/ DRAMMS]]: DRAMMS is a general-purpose, fully-automated, deformable image registration algorithm and software package. It is suitable for cross-subject, longitudinal, multi-modal registration tasks.

2014 Project Week Template

2014 Project Week Template

2014-06-23T11:02:00Z

Ouyangming: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* MGH: Yangming Ou, Jayashree Kalpathy-Cramer
* Isomics: Steve Pieper
* UPenn: Christos Davatzikos
* BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Project Week Template

2014-06-23T11:01:23Z

Ouyangming: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

MGH: Yangming Ou, Jayashree Kalpathy-Cramer
BWH: Andriy Fedorov, Tina Kapur, Ron Kikinis
Isomics: Steve Pieper
UPenn: Christos Davatzikos

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>