NAMIC Wiki - User contributions [en]

CIP and Nipype

2015-01-09T16:27:27Z

Rharmo:

<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
[[File:labeledCT.png]]__NOTOC__
</gallery>

==Key Investigators==
Rola Harmouche, James Ross, Alex Yarmakovich

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype or Vistrails for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first task is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows (nipype/Vistrails) for the following tasks:
** computing body composition (ex pectoralis muscles, subcutaneous fat, visceral fat, paravertebral muscles...) phenotypes from pre-labeled CT data. The phenotypes consist of cross sectional areas of each label and CT intensity statistics within the labeled region
[[File:LungParenchyma.png|290px]]
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Generated nipype interfaces for the CLIs available as part of the chest imaging platform and for python and for python classes
* Implemented an example workflow for the generation of lung parenchyma phenotypes
[[File:parenchyma_workflow_graph.dot.png|290px]]
[[File:command_line.png|290px]]
</div>
</div>

CIP and Nipype

2015-01-09T02:07:22Z

Rharmo:

<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
[[File:labeledCT.png]]__NOTOC__
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype or Vistrails for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first task is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows (nipype/Vistrails) for the following tasks:
** computing body composition (ex pectoralis muscles, subcutaneous fat, visceral fat, paravertebral muscles...) phenotypes from pre-labeled CT data. The phenotypes consist of cross sectional areas of each label and CT intensity statistics within the labeled region
[[File:LungParenchyma.png|290px]]
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Generated nipype interfaces for the CLIs available as part of the chest imaging platform and for python and for python classes
* Implemented an example workflow for the generation of lung parenchyma phenotypes
[[File:parenchyma_workflow_graph.dot.png|290px]]
[[File:command_line.png|290px]]
</div>
</div>

File:Command line.png

2015-01-09T02:05:19Z

Rharmo:

File:LungParenchyma.png

2015-01-09T01:52:20Z

Rharmo:

CIP and Nipype

2015-01-09T01:35:31Z

Rharmo: /* Project Description */

<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
[[File:labeledCT.png]]__NOTOC__
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype or Vistrails for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first task is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows (nipype/Vistrails) for the following tasks:
** computing body composition (ex pectoralis muscles, subcutaneous fat, visceral fat, paravertebral muscles...) phenotypes from pre-labeled CT data. The phenotypes consist of cross sectional areas of each label and CT intensity statistics within the labeled region
[[File:labeledCT.png]]
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Generated nipype interfaces for the CLIs available as part of the chest imaging platform and for python and for python classes
* Implemented an example workflow for the generation of lung parenchyma phenotypes
[[File:parenchyma_workflow_graph.dot.png]]
</div>
</div>

File:Parenchyma workflow graph.dot.png

2015-01-09T01:34:31Z

Rharmo:

CIP and Nipype

2015-01-09T01:25:01Z

Rharmo: /* Project Description */

<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
[[File:labeledCT.png]]__NOTOC__
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype or Vistrails for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first task is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows (nipype/Vistrails) for the following tasks:
** computing body composition (ex pectoralis muscles, subcutaneous fat, visceral fat, paravertebral muscles...) phenotypes from pre-labeled CT data. The phenotypes consist of cross sectional areas of each label and CT intensity statistics within the labeled region
[[File:labeledCT.png]]
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Generated nipype interfaces for the CLIs available as part of the chest imaging platform and for python and for python classes
* Implemented an example workflow for the generation of lung parenchyma phenotypes
[[File:labeledCT.png]]
</div>
</div>

CIP and Nipype

2015-01-05T20:38:52Z

Rharmo: /* Project Description */

<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
[[File:labeledCT.png]]__NOTOC__
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype or Vistrails for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows (nipype/Vistrails) for the following tasks:
** computing body composition (ex pectoralis muscles, subcutaneous fat, visceral fat, paravertebral muscles...) phenotypes from pre-labeled CT data. The phenotypes consist of cross sectional areas of each label and CT intensity statistics within the labeled region
[[File:labeledCT.png]]
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

CIP and Nipype

2015-01-04T00:01:07Z

Rharmo:

<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
[[File:labeledCT.png]]__NOTOC__
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows for the following tasks:
** computing body composition (ex pectoralis muscles, subcutaneous fat, visceral fat, paravertebral muscles...) phenotypes from pre-labeled CT data. The phenotypes consist of cross sectional areas of each label and CT intensity statistics within the labeled region
[[File:labeledCT.png]]
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

File:LabeledCT.png

2015-01-03T23:59:06Z

Rharmo:

CIP and Nipype

2015-01-03T23:58:11Z

Rharmo:

[[File:labeledCT.png]]__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows for the following tasks:
** computing body composition (ex pectoralis muscles, subcutaneous fat, visceral fat, paravertebral muscles...) phenotypes from pre-labeled CT data. The phenotypes consist of cross sectional areas of each label and CT intensity statistics within the labeled region
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

CIP and Nipype

2015-01-03T23:55:36Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows for the following tasks:
** computing body composition (ex pectoralis muscles, subcutaneous fat, visceral fat, paravertebral muscles...) phenotypes from pre-labeled CT data. The phenotypes consist of cross sectional areas of each label and CT intensity statistics within the labeled region
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

CIP and Nipype

2015-01-03T22:40:22Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We now have a suite of CLIs and python scripts for the processing and the analysis of chest images ready to be incorporated in Slicer as part of the Chest Imaging Platform Extension. This week we will be specifically focusing on defining clinically relevant chest image processing workflows that utilize the CLIs and scripts and implementing the workflows in nipype for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Our first is to generate nipype interfaces from the slicer CLIs and python scripts
* Define and implement a set of workflows for the following tasks:
** computing body composition phenotypes from pre-labeled CT data (cross sectional areas of labels and CT intensity statistics within the labeled region)
** computing lung parenchyma phenotypes from CT data

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T14:29:06Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Screen_Shot_2014-06-27_at_9.50.20_AM.png| GUI
</gallery>

==Key Investigators==
Rola Harmouche, Jorge Onieva, James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a method for the segmentation of the pectoralis muscle on chest CT images using graph cuts and a subject-tailored atlas. The atlas is built by selecting a subset of training data that shares high similarity with the test case, by making use of pairwise registrations. Our objective is to develop a slicer python module for the segmentation of pectoralis muscles on 2D CT images.
* We would like to refine some parts of the segmentation process, particularly, the image-based registration between the test and training cases.
* We want to modularize and abstract some components of the segmentation, particularly the atlas creation.
* We also want to incorporate the segmentation module into a nipype work flow for its deployment in high performance computing environments.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We have previously developed a library of tools ported all of our available tools for the processing and the analysis of chest images (chest imaging platform) and have ported them into slicer CLIs.
* The python module will make use of the previously developed CLIs within the chestimaging platform, and of recently developed python scripts.
* We also aim to, if time permits, define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes and for parameter testing, and to use to those interfaces to find the optimal parameters for the pairwise registration.</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Worked on ensuring that the python packages that we need can be compatible with Slicer (thanks to Hans Johnson and Steve Pieper). Dealt with many compatibility issues (numpy, scipy, scikit, pygco) between the code that was developed using Canopy python and Slicer's python .
* Got help with the image-based registration between the test and training cases from Bradley Lowekamp using SimpleITK. He gave me an ipython notebook.
* Incorporating the segmentation code into a python module (but without the atlas creation for now). It successfully runs bit we are still having trouble visualizing the output.

</div>
</div>

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T14:14:05Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Screen_Shot_2014-06-27_at_9.50.20_AM.png| GUI
</gallery>

==Key Investigators==
Rola Harmouche, Jorge Onieva, James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a method for the segmentation of the pectoralis muscle on chest CT images using graph cuts and a subject-tailored atlas. The atlas is built by selecting a subset of training data that shares high similarity with the test case, by making use of pairwise registrations. Our objective is to develop a slicer python module for the segmentation of pectoralis muscles on 2D CT images.
* We would like to refine some parts of the segmentation process, particularly, the image-based registration between the test and training cases.
* We want to modularize and abstract some components of the segmentation, particularly the atlas creation.
* We also want to incorporate the segmentation module into a nipype work flow for its deployment in high performance computing environments.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We have previously developed a library of tools ported all of our available tools for the processing and the analysis of chest images (chest imaging platform) and have ported them into slicer CLIs.
* The python module will make use of the previously developed CLIs within the chestimaging platform, and of recently developed python scripts.
* We also aim to, if time permits, define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes and for parameter testing, and to use to those interfaces to find the optimal parameters for the pairwise registration.</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Worked on ensuring that the python packages that we need can be compatible with Slicer (thanks to Hans and Steve). Dealt with many compatibility issues (numpy, scipy, scikit, pygco) between the code that was developed using Canopy python and Slicer's python .
* Got help with the image-based registration between the test and training cases from Brad using SimpleITK. He gave me an ipython notebook.
* Incorporating the segmentation code into a python module (but without the atlas creation for now). It successfully runs bit we are still having trouble visualizing the output.

</div>
</div>

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T14:05:56Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Screen_Shot_2014-06-27_at_9.50.20_AM.png| GUI
</gallery>

==Key Investigators==
Rola Harmouche, Jorge Onieva, James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a method for the segmentation of the pectoralis muscle on chest CT images using graph cuts and a subject-tailored atlas. The atlas is built by selecting a subset of training data that shares high similarity with the test case, by making use of pairwise registrations. Our objective is to develop a slicer python module for the segmentation of pectoralis muscles on 2D CT images.
* We would like to refine some parts of the segmentation process, particularly, the image-based registration between the test and training cases.
* We want to modularize and abstract some components of the segmentation, particularly the atlas creation.
* We also want to incorporate the segmentation module into a nipype work flow for its deployment in high performance computing environments.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We have previously developed a library of tools ported all of our available tools for the processing and the analysis of chest images (chest imaging platform) and have ported them into slicer CLIs.
* The python module will make use of the previously developed CLIs within the chestimaging platform, and of recently developed python scripts.
* We also aim to, if time permits, define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes and for parameter testing, and to use to those interfaces to find the optimal parameters for the pairwise registration.</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Worked on ensuring that the python packages that we need can be compatible with Slicer (thanks to Hans and Steve). Dealt with many compatibility issues between the code that was developed using Canopy python.
* Got help with the image-based registration between the test and training cases from Brad using SimpleITK. He gave me an ipython notebook.
* Incorporating the segmentation code into a python module (but without the atlas creation for now). It successfully runs bit we are still having trouble visualizing the output.

</div>
</div>

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T14:03:57Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Screen_Shot_2014-06-27_at_9.50.20_AM.png| GUI
</gallery>

==Key Investigators==
Rola Harmouche, Jorge Onieva, James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a method for the segmentation of the pectoralis muscle on chest CT images using graph cuts and a subject-tailored atlas. The atlas is built by selecting a subset of training data that shares high similarity with the test case, by making use of pairwise registrations. Our objective is to develop a slicer python module for the segmentation of pectoralis muscles on 2D CT images.
* We would like to refine some parts of the segmentation process, particularly, the image-based registration between the test and training cases.
* We want to modularize and abstract some components of the segmentation, particularly the atlas creation.
* We also want to incorporate the segmentation module into a nipype work flow for its deployment in high performance computing environments.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We have previously developed a library of tools ported all of our available tools for the processing and the analysis of chest images (chest imaging platform) and have ported them into slicer CLIs.
* The python module will make use of the previously developed CLIs within the chestimaging platform, and of recently developed python scripts.
* We also aim to, if time permits, define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes and for parameter testing, and to use to those interfaces to find the optimal parameters for the pairwise registration.</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Worked on ensuring that the python packages that we need can be compatible with Slicer (thanks to Hans and Steve). Dealt with many compatibility issues between the code that was developed using Canopy python.
* Got help with the image-based registration between the test and training cases from Brad using SimpleITK. He gave me an ipython notebook.

</div>
</div>

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T14:03:30Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Rola Harmouche, Jorge Onieva, James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a method for the segmentation of the pectoralis muscle on chest CT images using graph cuts and a subject-tailored atlas. The atlas is built by selecting a subset of training data that shares high similarity with the test case, by making use of pairwise registrations. Our objective is to develop a slicer python module for the segmentation of pectoralis muscles on 2D CT images.
* We would like to refine some parts of the segmentation process, particularly, the image-based registration between the test and training cases.
* We want to modularize and abstract some components of the segmentation, particularly the atlas creation.
* We also want to incorporate the segmentation module into a nipype work flow for its deployment in high performance computing environments.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We have previously developed a library of tools ported all of our available tools for the processing and the analysis of chest images (chest imaging platform) and have ported them into slicer CLIs.
* The python module will make use of the previously developed CLIs within the chestimaging platform, and of recently developed python scripts.
* We also aim to, if time permits, define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes and for parameter testing, and to use to those interfaces to find the optimal parameters for the pairwise registration.</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Worked on ensuring that the python packages that we need can be compatible with Slicer (thanks to Hans and Steve). Dealt with many compatibility issues between the code that was developed using Canopy python.
* Got help with the image-based registration between the test and training cases from Brad using SimpleITK. He gave me an ipython notebook.

Image:Screen_Shot_2014-06-27_at_9.50.20_AM.png| GUI

[[File:]
</div>
</div>

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T14:01:49Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Rola Harmouche, Jorge Onieva, James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a method for the segmentation of the pectoralis muscle on chest CT images using graph cuts and a subject-tailored atlas. The atlas is built by selecting a subset of training data that shares high similarity with the test case, by making use of pairwise registrations. Our objective is to develop a slicer python module for the segmentation of pectoralis muscles on 2D CT images.
* We would like to refine some parts of the segmentation process, particularly, the image-based registration between the test and training cases.
* We want to modularize and abstract some components of the segmentation, particularly the atlas creation.
* We also want to incorporate the segmentation module into a nipype work flow for its deployment in high performance computing environments.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We have previously developed a library of tools ported all of our available tools for the processing and the analysis of chest images (chest imaging platform) and have ported them into slicer CLIs.
* The python module will make use of the previously developed CLIs within the chestimaging platform, and of recently developed python scripts.
* We also aim to, if time permits, define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes and for parameter testing, and to use to those interfaces to find the optimal parameters for the pairwise registration.</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Worked on ensuring that the python packages that we need can be compatible with Slicer (thanks to Hans and Steve). Dealt with many compatibility issues between the code that was developed using Canopy python.
* Got help with the image-based registration between the test and training cases from Brad using SimpleITK. He gave me an ipython notebook.

[[File:Screen_Shot_2014-06-27_at_9.50.20_AM.png]]
</div>
</div>

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T14:00:39Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Rola Harmouche, Jorge Onieva, James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a method for the segmentation of the pectoralis muscle on chest CT images using graph cuts and a subject-tailored atlas. The atlas is built by selecting a subset of training data that shares high similarity with the test case, by making use of pairwise registrations. Our objective is to develop a slicer python module for the segmentation of pectoralis muscles on 2D CT images.
* We would like to refine some parts of the segmentation process, particularly, the image-based registration between the test and training cases.
* We want to modularize and abstract some components of the segmentation, particularly the atlas creation.
* We also want to incorporate the segmentation module into a nipype work flow for its deployment in high performance computing environments.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We have previously developed a library of tools ported all of our available tools for the processing and the analysis of chest images (chest imaging platform) and have ported them into slicer CLIs.
* The python module will make use of the previously developed CLIs within the chestimaging platform, and of recently developed python scripts.
* We also aim to, if time permits, define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes and for parameter testing, and to use to those interfaces to find the optimal parameters for the pairwise registration.</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Worked on ensuring that the python packages that we need can be compatible with Slicer (thanks to Hans and Steve). Dealt with many compatibility issues between the code that was developed using Canopy python.
* Got help with the image-based registration between the test and training cases from Brad using SimpleITK. He gave me an ipython notebook.

[[File:Screen Shot 2014-06-27 at 9.50.20 AM.jpg]]
</div>
</div>

File:Screen Shot 2014-06-27 at 9.50.20 AM.png

2014-06-27T13:59:45Z

Rharmo:

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T13:28:18Z

Rharmo:

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T13:27:32Z

Rharmo:

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-27T12:17:54Z

Rharmo: /* Project Description */

2014 Summer Project Week: Pectoralis muscle segmentation

2014-06-23T16:15:51Z

Rharmo:

2014 Summer Project Week

2014-06-20T21:48:02Z

Rharmo: Undo revision 86013 by Rharmo (Talk)

__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'''
|
|'''10-11:30pm''' <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>
'''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]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|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/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

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

==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)

==Atrial Fibrillation==

==Huntington's Disease==

==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)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[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)

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* 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)

==Radiation Therapy==
*[[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)

==Chronic Obstructive Pulmonary Disease ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)

==[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})

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[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? Dirk?)
*[[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)

==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)

==Other==
*[[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:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (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)
*[[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)
*[[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)

== '''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
#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

2014-06-20T21:44:36Z

Rharmo: /* Chronic Obstructive Pulmonary Disease */

__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'''
|
|'''10-11:30pm''' <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>
'''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]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|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/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

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

==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)

==Atrial Fibrillation==

==Huntington's Disease==

==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)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[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)

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* 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)

==Radiation Therapy==
*[[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)

==Chronic Obstructive Pulmonary Disease ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation on CT| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)

==[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})

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[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? Dirk?)
*[[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)

==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)

==Other==
*[[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:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (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)
*[[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)
*[[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)

== '''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
#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: Pectoralis muscle segmentation

2014-06-20T21:43:27Z

Rharmo: Created page with '__NOTOC__ <gallery> Image:PW-SLC2014.png|Projects List </gallery> ==Key Investigators== Rola Harmouche, James Ross, Raul San Jose ==Projec…'

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Rola Harmouche, James Ross, Raul San Jose

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a method for the segmentation of the pectoralis muscle on chest CT images using graph cuts and a subject-tailored atlas. The atlas is built by selecting a subset of training data that shares high similarity with the test case, by making use of pairwise registrations. Our objective is to develop a slicer python module for the segmentation of pectoralis muscles on 2D CT images.
* We would like to refine some parts of the segmentation process, particularly, the image-based registration between the test and training cases.
* We want to modularize and abstract some components of the segmentation, particularly the atlas creation.
* We also want to incorporate the segmentation module into a nipype work flow for its deployment in high performance computing environments.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* We have previously developed a library of tools ported all of our available tools for the processing and the analysis of chest images (chest imaging platform) and have ported them into slicer CLIs.
* The python module will make use of the previously developed CLIs within the chestimaging platform, and of recently developed python scripts.
* We also aim to, if time permits, define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes and for parameter testing, and to use to those interfaces to find the optimal parameters for the pairwise registration.</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
</div>
</div>

2014 Summer Project Week

2014-06-20T21:38:59Z

Rharmo: /* Chronic Obstructive Pulmonary Disease */

2014 Winter Project Week:Slicer CIP Modules

2014-01-09T23:39:10Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Screen Shot 2014-01-09 at 5.29.55 PM.png|[[Lung registration output]]
</gallery>

==Key Investigators==

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by incorporating them into Slicer as command line extension modules, Python modules, and through a nipype work flow for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
* In the past few months, we have ported most of the available tools to CLIs
* The library contains a set of tools for image processing, segmentation and airway and vessel generation using particles and inspection. Some of these tools are described in the works by Ross et al. and Kindlmann et. al. Our plan for the project week is to develop a few python modules that execute a flow of commands using a sequence of CLIs in order to perform lung and lobe segmentation, and lung atlas to patient registration. The python modules should be available via both a graphical user interface and the command line. We also aim to define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Private github repository: https://github.com/acil-bwh/SlicerCIP
* Implemented a simple Python module that calls multiple CLIs in order to register a probabilistic lung atlas to a new patient CT volume
</div>
</div>

File:Screen Shot 2014-01-09 at 5.29.55 PM.png

2014-01-09T23:33:59Z

Rharmo: uploaded a new version of "File:Screen Shot 2014-01-09 at 5.29.55 PM.png"

File:Screen Shot 2014-01-09 at 5.29.55 PM.png

2014-01-09T23:32:52Z

Rharmo:

2014 Winter Project Week:Slicer CIP Modules

2014-01-09T23:26:23Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by incorporating them into Slicer as command line extension modules, Python modules, and through a nipype work flow for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
* In the past few months, we have ported most of the available tools to CLIs
* The library contains a set of tools for image processing, segmentation and airway and vessel generation using particles and inspection. Some of these tools are described in the works by Ross et al. and Kindlmann et. al. Our plan for the project week is to develop a few python modules that execute a flow of commands using a sequence of CLIs in order to perform lung and lobe segmentation, and lung atlas to patient registration. The python modules should be available via both a graphical user interface and the command line. We also aim to define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Private github repository: https://github.com/acil-bwh/SlicerCIP
* Implemented a simple Python module that calls multiple CLIs in order to register a probabilistic lung atlas to a new patient CT volume
</div>
</div>

2014 Winter Project Week:Slicer CIP Modules

2014-01-09T22:51:42Z

Rharmo:

File:Screen Shot 2014-01-09 at 5.27.07 PM.png

2014-01-09T22:49:56Z

Rharmo:

2014 Winter Project Week:Slicer CIP Modules

2014-01-09T22:48:48Z

Rharmo: /* Project Description */

2014 Winter Project Week:Slicer CIP Modules

2014-01-06T02:48:51Z

Rharmo: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by incorporating them into Slicer as command line extension modules, Python modules, and through a nipype work flow for their deployment in high performance computing environments.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* The library contains a set of tools for image processing, segmentation and airway and vessel generation using particles and inspection. Some of these tools are described in the works by Ross et al. and Kindlmann et. al. Our plan for the project week is to develop a few python modules that execute a flow of commands using a sequence of CLIs in order to perform lung and lobe segmentation, and lung atlas to patient registration. The python modules should be available via both a graphical user interface and the command line. We also aim to define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
* In the past few months, we have ported most of the available tools to CLIs

</div>
</div>

2013 Summer Project Week:Nipype CLI Integration

2013-06-21T14:16:00Z

Rharmo: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Rola Harmouche,Demian Wassermann, Raul San Jose (BWH)

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

<h3>Objective</h3>
We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by incorporating them into Slicer as command line extension modules and through a nipype work flow for their deployment in high performance computing environments.

</div>

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

<h3>Approach, Plan</h3>
The library contains a set of tools for image processing, segmentation and airway and vessel generation using particles and inspection. Some of these tools are described in the works by Ross et al. and Kindlmann et. al. Our plan for the project week is to port most of these tools to the CLI infrastructure and to define nipype interfaces.

</div>

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

<h3>Progress</h3>
* The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
* This week we decided to deliver the tools through several extensions consisting of python modules. Each module executes a flow of commands by calling CLIs
* We completed the CLIs for 1 of the extensions (as an example), and are working on the scripted module

[[File:CLI-ScreenShot.png]]

</div>
</div>

==Delivery Mechanism==
This work will be delivered to the NA-MIC Kit as a

Slicer Module
Extension -- commandline

==References==
* James C. Ross, R. San Jose Estepar, G. Kindlmann, Alejandro Diaz, C.-F. Westin, Edwin K. Silverman, George R. Washko, [Automatic Lung Lobe Segmentation Using Particles, Thin Plate Splines, and Maximum a Posteriori Estimation] Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2010 Volume 6363, Pages 163-171, 2010
* Gordon Kindlmann, Raúl San José Estépar, Stephen M. Smith, Carl-Fredrik Westin. Sampling and Visualizing Creases with Scale-Space Particles. IEEE Transactions on Visualization and Computer Graphics. 2009; 15(6):1415-1424.
* San José Estépar, R. et al., 2012. Computational Vascular Morphometry for the Assessment of Pulmonary Vascular Disease based on Scale-Space Particles. In Proceedings of the 9th IEEE International Symposium on Biomedical Imaging (ISBI) 2012. Barcelona, pp. 1479–1482.

File:CLI-ScreenShot.png

2013-06-21T14:12:30Z

Rharmo:

2013 Summer Project Week:Nipype CLI Integration

2013-06-21T02:27:46Z

Rharmo: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Rola Harmouche,Demian Wassermann, Raul San Jose (BWH)

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

<h3>Objective</h3>
We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by incorporating them into Slicer as command line extension modules and through a nipype work flow for their deployment in high performance computing environments.

</div>

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

<h3>Approach, Plan</h3>
The library contains a set of tools for image processing, segmentation and airway and vessel generation using particles and inspection. Some of these tools are described in the works by Ross et al. and Kindlmann et. al. Our plan for the project week is to port most of these tools to the CLI infrastructure and to define nipype interfaces.

</div>

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

<h3>Progress</h3>
* The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
* This week we decided to deliver the tools through several extensions consisting of python modules. Each module executes a flow of commands by calling CLIs
* We completed the CLIs for 1 of the extensions (as an example), and are working on the scripted module

</div>
</div>

==Delivery Mechanism==
This work will be delivered to the NA-MIC Kit as a

Slicer Module
Extension -- commandline

==References==
* James C. Ross, R. San Jose Estepar, G. Kindlmann, Alejandro Diaz, C.-F. Westin, Edwin K. Silverman, George R. Washko, [Automatic Lung Lobe Segmentation Using Particles, Thin Plate Splines, and Maximum a Posteriori Estimation] Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2010 Volume 6363, Pages 163-171, 2010
* Gordon Kindlmann, Raúl San José Estépar, Stephen M. Smith, Carl-Fredrik Westin. Sampling and Visualizing Creases with Scale-Space Particles. IEEE Transactions on Visualization and Computer Graphics. 2009; 15(6):1415-1424.
* San José Estépar, R. et al., 2012. Computational Vascular Morphometry for the Assessment of Pulmonary Vascular Disease based on Scale-Space Particles. In Proceedings of the 9th IEEE International Symposium on Biomedical Imaging (ISBI) 2012. Barcelona, pp. 1479–1482.

2013 Summer Project Week:Airway Inspector Porting

2013-06-13T15:57:06Z

Rharmo:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Rola Harmouche,Demian Wassermann, Raul San Jose (BWH)

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<h3>Objective</h3>

We have developed a library of tools for the processing and the analysis of chest images. The main objective is to make the tools available to the public by incorporating them into SLicer as command line extension modules and through a nipype work flow.

</div>

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

<h3>Approach, Plan</h3>

The library contains a mix of tools for image processing, segmentation and airway generation and inspection using particles. These tools are described in the works by Ross et al. and Kindlmann et. al. Our plan for the project week is to port most of these tools.
</div>

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

<h3>Progress</h3>

The tools have been developed using C++ and ITK and have been validated and used in the works described previously.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension -- commandline

==References==
* James C. Ross, R. San Jose Estepar, G. Kindlmann, Alejandro Diaz, C.-F. Westin, Edwin K. Silverman, George R. Washko, [Automatic Lung Lobe Segmentation Using Particles, Thin Plate Splines, and Maximum a Posteriori Estimation] Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2010 Volume 6363, Pages 163-171, 2010

* Gordon Kindlmann, Raúl San José Estépar, Stephen M. Smith, Carl-Fredrik Westin. Sampling and Visualizing Creases with Scale-Space Particles. IEEE Transactions on Visualization and Computer Graphics. 2009; 15(6):1415-1424.