https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=KanglinNAMIC Wiki - User contributions [en]2026-08-13T21:47:14ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=870522014 Summer Project Week:Atlas Selection2014-06-27T14:22:13Z<p>Kanglin: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (MGH)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single image atlas is<br />
not stable. To improve the segmentation, we can select multiple images, which are suitable for image segmentation. After registration we <br />
can merge the segmentations to a final one. An idea to improve atlas selection process lies on that we take advantage of using an average atlas.<br />
The procedure of atlas selection using an average atlas for image segmentation is defined as follows:<br />
* Construct an average atlas based on a database<br />
* Every image of the database is aligned to the average atlas after the atlas construction.<br />
* Register the average atlas to a new image and transfer the database and their segmentations to the new image.<br />
* Compare the transformed database with the new image in the ROI and select some well-matched images with respected to some distance measure, e.g. MI, CC, NGF.<br />
* Merge the segmentations of these well-matched images to a final one based on e.g. weighted voting or STAPLE algorithm. <br />
The crucial step of atlas selection is the average atlas construction. The focus of this project lies on the construction of an average atlas using 3D datasets and validate the average atlas with the inspection of segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
The modeling and algorithm of the average atlas construction are based on non-linear image registration and reconstruction. <br />
The algorithm does not depend on selecting a particular image as the template and the solution is optimal with respect to a minimization problem.<br />
In this project we want to construct the average atlas using a database with segmentations and validate the average atlas by the visual inspection of merged segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* We developed algorithms for the average atlas construction, finished programming in Matlab.<br />
* We constructed the average atlas of 20 datasets for H&N and merged segmentations into the average atlas.<br />
* We visualized the average atlas and its probability maps of segmentations in Slicer.<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lungs and chests. For example<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We selected the ROI of every data excluding lung and chest. For each data there exist the segmentations of brain stem, left and right parotids. For example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* We constructed the average atlas of 20 datasets of ROI, and merged the segmentations into the average atlas. These segmentations are the probability maps of<br />
brain stem, left and right parotids. <br />
<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867352014 Summer Project Week:Atlas Selection2014-06-26T20:27:00Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single image atlas is<br />
not stable. To improve the segmentation, we can select multiple images, which are suitable for image segmentation. After registration we <br />
can merge the segmentations to a final one. An idea to improve atlas selection process lies on that we take advantage of using an average atlas.<br />
The procedure of atlas selection using an average atlas for image segmentation is defined as follows:<br />
* Construct an average atlas based on a database<br />
* Every image of the database is aligned to the average atlas after the atlas construction.<br />
* Register the average atlas to a new image and transfer the database and their segmentations to the new image.<br />
* Compare the transformed database with the new image in the ROI and select some well-matched images with respected to some distance measure, e.g. MI, CC, NGF.<br />
* Merge the segmentations of these well-matched images to a final one based on e.g. weighted voting or STAPLE algorithm. <br />
The crucial step of atlas selection is the average atlas construction. The focus of this project lies on the construction of an average atlas using 3D datasets and validate the average atlas with the inspection of segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
The modeling and algorithm of the average atlas construction are based on non-linear image registration and reconstruction. <br />
The algorithm does not depend on selecting a particular image as the template and the solution is optimal with respect to a minimization problem.<br />
In this project we want to construct the average atlas using a database with segmentations and validate the average atlas by the visual inspection of merged segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* We developed algorithms for the average atlas construction, finished programming in Matlab.<br />
* We constructed the average atlas of 20 datasets for H&N and merged segmentations into the average atlas.<br />
* We visualized the average atlas and its probability maps of segmentations in Slicer.<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lungs and chests. For example<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We selected the ROI of every data excluding lung and chest. For each data there exist the segmentations of brain stem, left and right parotids. For example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* We constructed the average atlas of 20 datasets of ROI, and merged the segmentations into the average atlas. These segmentations are the probability maps of<br />
brain stem, left and right parotids. <br />
<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867342014 Summer Project Week:Atlas Selection2014-06-26T20:25:53Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single image atlas is<br />
not stable. To improve the segmentation, we can select multiple images, which are suitable for image segmentation. After registration we <br />
can merge the segmentations to a final one. An idea to improve atlas selection process lies on that we take advantage of using an average atlas.<br />
The procedure of atlas selection using an average atlas for image segmentation is defined as follows:<br />
* Construct an average atlas based on a database<br />
* Every image of the database is aligned to the average atlas after the atlas construction.<br />
* Register the average atlas to a new image and transfer the database and their segmentations to the new image.<br />
* Compare the transformed database with the new image in the ROI and select some well-matched images with respected to some distance measure, e.g. MI, CC, NGF.<br />
* Merge the segmentations of these well-matched images to a final one based on e.g. weighted voting or STAPLE algorithm. <br />
The crucial step of atlas selection is the average atlas construction. The focus of this project lies on the construction of an average atlas using 3D datasets and validate the average atlas with the inspection of segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
The modeling and algorithm of the average atlas construction are based on non-linear image registration and reconstruction. <br />
The algorithm does not depend on selecting a particular image as the template and the solution is optimal with respect to a minimization problem.<br />
In this project we want to construct the average atlas using a database with segmentations and validate the average atlas by the visual inspection of merged segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* We developed algorithms for the average atlas construction, finished programming in Matlab.<br />
* We constructed the average atlas of 20 datasets for H&N and merged segmentations into the average atlas.<br />
* We visualized the average atlas and its probability maps of segmentations in Slicer.<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lung and chest. For example<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We select the ROI of every data excluding lung and chest. For each data there exist the segmentations of brain stem, left and right parotids. For example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* We constructed the average atlas of 20 datasets of ROI, and merged the segmentations into the average atlas. These segmentations are the probability maps of<br />
brain stem, left and right parotids. <br />
<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867332014 Summer Project Week:Atlas Selection2014-06-26T20:16:44Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single image atlas is<br />
not stable. To improve the segmentation, we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. An idea to improve the atlas selection process is that we take advantage of using an average atlas.<br />
The procedure of atlas selection used for image segmentation is defined as follows:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after the average atlas construction.<br />
* Register the average atlas to a new image and transfer the database and their segmentations to the new image.<br />
* Compare the transformed database with the new image in the ROI and select some well-matched images with respected to some distance measure, e.g. MI, CC, NGF.<br />
* Merge the segmentations of these well-matched images to a final one based on e.g. weighted voting or STAPLE algorithm. <br />
The crucial step of atlas selection is the average atlas construction. The focus of this project lies on the construction of an average atlas using 3D datasets and validate the average atlas with the inspection of segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
The average atlas construction modeling and algorithm are based on non-linear image registration and reconstruction. <br />
The algorithm does not depend on selecting a particular image as the template and the solution is optimal with respect to a minimization problem.<br />
In this project we want to construct an atlas using a database with segmentations and validate the average atlas by the visual inspection of merged segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* We developed algorithms for the average atlas construction, finished programming in Matlab. and visualization in Slicer.<br />
* We constructed the average atlas of 20 datasets for H&N and merged segmentations into the average atlas.<br />
* We visualized the average atlas and its probability maps of segmentations in the Slicer.<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lung and chest. For example<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We select the ROI of every data excluding lung and chest. For each data there exist the segmentations of brain stem, left and right parotids. For example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* We constructed the average atlas of 20 datasets of ROI, and merged the segmentations into the average atlas. These segmentations are the probability maps of<br />
brain stem, left and right parotids. <br />
<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867322014 Summer Project Week:Atlas Selection2014-06-26T20:15:45Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single image atlas is<br />
not stable. To improve the segmentation, we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. An idea to improve the atlas selection process is that we take advantage of using an average atlas.<br />
The procedure of atlas selection used for image segmentation is defined as follows:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after the average atlas construction.<br />
* Register the average atlas to a new image and transfer the database and their segmentations to the new image.<br />
* Compare the transformed database with the new image in the ROI and select some well-matched images with respected to some distance measure, e.g. MI, CC, NGF.<br />
* Merge the segmentations of these well-matched images to a final one based on e.g. weighted voting or STAPLE algorithm. <br />
The crucial step of atlas selection is the average atlas construction. The focus of this project lies on the construction of an average atlas using 3D datasets and validate the average atlas with the inspection of segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
The average atlas construction modeling and algorithm are based on non-linear image registration and reconstruction. <br />
The algorithm does not depend on selecting a particular image as the template and the solution is optimal with respect to a minimization problem.<br />
In this project we want to construct an atlas using a database with segmentations and validate the average atlas by the visual inspection of merged segmentations.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* We developed algorithms for the average atlas construction, finished programming in Matlab. and visualization in Slicer.<br />
* We constructed the average atlas of 20 datasets for H&N and merged segmentations into the average atlas.<br />
* We visualized the average atlas and its probability maps of segmentations in the Slicer.<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lung and chest. For example<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We select the ROI of every data excluding lung and chest. For each data there exist the segmentations of brain stem, left and right parotids. For example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* We constructed an atlas from 20 datasets of ROI, and merged the segmentations. These segmentations are probability maps of<br />
brain stem, left and right parotids. <br />
<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867302014 Summer Project Week:Atlas Selection2014-06-26T19:57:10Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* We developed algorithms for atlas construction, programming in Matlab and visualization in Slicer.<br />
* We constructed an atlas of 40 datasets for H&N and merged segmentations into the atlas.<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lung and chest. For example<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We select the ROI of every data excluding lung and chest. For each data there exist the segmentations of brain stem, left and right parotids. For example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* We constructed an atlas from 20 datasets of ROI, and merged the segmentations. These segmentations are probability maps of<br />
brain stem, left and right parotids. <br />
<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867292014 Summer Project Week:Atlas Selection2014-06-26T19:54:37Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lung and chest. For example<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We select the ROI of every data excluding lung and chest. For each data there exist the segmentations of brain stem, left and right parotids. For example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* We constructed an atlas from 20 datasets of ROI, and merged the segmentations. These segmentations are probability maps of<br />
brain stem, left and right parotids. <br />
<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867282014 Summer Project Week:Atlas Selection2014-06-26T19:51:39Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lung and chest. For example<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We select the ROI of every data excluding lung and chest. For each data there exist the segmentations of brain stem, left and right parotids. For example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* We constructed an atlas from 20 datasets of ROI, and merged the segmentations. These segmentations are probability maps of<br />
brain stem, left and right parotids. <br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867272014 Summer Project Week:Atlas Selection2014-06-26T19:48:05Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* We have 20 datasets for H&N including lung and chest. Example:<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* We select the ROI of every data excluding lung and chest. Example<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* Constructed atlas<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867222014 Summer Project Week:Atlas Selection2014-06-26T19:18:06Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* Datasets<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* ROI of datasets<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* Constructed atlas<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867212014 Summer Project Week:Atlas Selection2014-06-26T19:17:39Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets<br />
[[File:Axial_orig_image.png]]<br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* Datasets<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* ROI of datasets<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]<br />
* Constructed atlas<br />
[[File:Axial_atlas_image.png|||400px|||]] [[File:Coronal_atlas_image.png|||400px|||]] [[File:Sagittal_atlas_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867202014 Summer Project Week:Atlas Selection2014-06-26T19:16:44Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets<br />
[[File:Axial_orig_image.png]]<br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* Datasets<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]<br />
* ROI of datasets<br />
[[File:Axial_roi_image.png|||400px|||]] [[File:Coronal_roi_image.png|||400px|||]] [[File:Sagittal_roi_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867192014 Summer Project Week:Atlas Selection2014-06-26T19:15:59Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets<br />
[[File:Axial_orig_image.png]]<br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* Datasets<br />
[[File:Axial_orig_image.png|||400px|||]] [[File:Coronal_orig_image.png|||400px|||]] [[File:Sagittal_orig_image.png|||400px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867182014 Summer Project Week:Atlas Selection2014-06-26T19:15:26Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets<br />
[[File:Axial_orig_image.png]]<br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* Datasets<br />
[[File:Axial_orig_image.png|||330px|||]] [[File:Coronal_orig_image.png|||330px|||]] [[File:Sagittal_orig_image.png|||330px|||]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867162014 Summer Project Week:Atlas Selection2014-06-26T19:09:07Z<p>Kanglin: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets<br />
[[File:Axial_orig_image.png]]<br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* Datasets<br />
[[Image:Axial_orig_image.png|||100]] [[File:Coronal_orig_image.png]] [[File:Sagittal_orig_image.png]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867092014 Summer Project Week:Atlas Selection2014-06-26T19:01:02Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets<br />
[[File:Axial_orig_image.png]]<br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
* Datasets<br />
[[File:Axial_orig_image.png]] [[File:Coronal_orig_image.png]] [[File:Sagittal_orig_image.png]]</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=867072014 Summer Project Week:Atlas Selection2014-06-26T18:59:37Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets<br />
[[File:Axial_orig_image.png]]<br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Sagittal_roi_image.png&diff=86705File:Sagittal roi image.png2014-06-26T18:56:02Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Sagittal_orig_image.png&diff=86704File:Sagittal orig image.png2014-06-26T18:55:46Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Sagittal_atlas_image.png&diff=86703File:Sagittal atlas image.png2014-06-26T18:55:34Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Coronal_roi_image.png&diff=86702File:Coronal roi image.png2014-06-26T18:55:15Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Coronal_orig_image.png&diff=86701File:Coronal orig image.png2014-06-26T18:54:58Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Coronal_atlas_image.png&diff=86700File:Coronal atlas image.png2014-06-26T18:54:42Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Axial_roi_image.png&diff=86699File:Axial roi image.png2014-06-26T18:54:04Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Axial_orig_image.png&diff=86698File:Axial orig image.png2014-06-26T18:53:36Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=File:Axial_atlas_image.png&diff=86697File:Axial atlas image.png2014-06-26T18:52:34Z<p>Kanglin: </p>
<hr />
<div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866952014 Summer Project Week:Atlas Selection2014-06-26T18:48:28Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets<br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866912014 Summer Project Week:Atlas Selection2014-06-26T17:44:16Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Datasets <br />
* Features of the algorithm of atlas construction<br />
* Results of atlas construction<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866902014 Summer Project Week:Atlas Selection2014-06-26T17:43:11Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Results of atlas construction<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866892014 Summer Project Week:Atlas Selection2014-06-26T17:41:59Z<p>Kanglin: /* Atlas construction and its validation */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=866882014 Summer Project Week2014-06-26T17:40:21Z<p>Kanglin: /* Additional Brain Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
[[image:Projectweek-2014-06-23-IMG 0837.JPG|800px|opening session]]<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|<br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<br><br />
|'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata, Tina Kapur)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias, Andras)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
*[[2014_Summer_Project_Week:EM-tracked_prostate_US_calibration_with_Plus|Calibration of EM-tracked US acquisition using Plus]] (Andrey Fedorov, Tamas Ungi, Andras Lasso, Jay Jagadeesan)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)<br />
*[[2014_Summer_Prioject_Week:AgatstonScoring | Cardiac Agatston Scoring Extension]] (Jessica Forbes, Hans Johnson)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[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})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week: Quantitative image feature extraction | Quantitative image feature extraction in Non-Small Cell Lung Cancer]] (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[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)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistan, Sonia Pujol)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Tammy Riklin Raviv, Ben-Gurion University, rrtammy@ee.bgu.ac.il<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866872014 Summer Project Week:Atlas Selection2014-06-26T17:39:11Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
The crucial step of atlas selection is atlas construction and the focus of this project is to construct an atlas and validate the atlas using segmentation.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div><br />
<br />
==Atlas construction and its validation==<br />
* Datasets<br />
We have 20 datasets<br />
* Algorithm for atlas construction<br />
* Results</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866862014 Summer Project Week:Atlas Selection2014-06-26T17:36:49Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, image segmentation based on single atlas is<br />
not stable. To improve the segmentation we can select multiple images, which are suitable for image segmentation and after registration we <br />
can merge the segmentations to a final one. The selection of these images can be based on an atlas. The procedure defines in the following steps:<br />
* Construct an atlas based on a database<br />
* Every image of the database is aligned to the atlas after atlas construction<br />
* Register the atlas to a new image and transfer the database to the new image<br />
* Compare the transformed database to the new image and select some well-matched images<br />
* Merge the segmentations of these images to a final one based on e.g. "weighted voting" or STAPLE algorithms <br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div><br />
<br />
==Atlas construction and its validation==<br />
* Datasets<br />
We have 20 datasets<br />
* Algorithm for atlas construction<br />
* Results</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866852014 Summer Project Week:Atlas Selection2014-06-26T17:27:08Z<p>Kanglin: /* Atlas construction and its validation */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div><br />
<br />
==Atlas construction and its validation==<br />
* Datasets<br />
We have 20 datasets<br />
* Algorithm for atlas construction<br />
* Results</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866842014 Summer Project Week:Atlas Selection2014-06-26T17:25:27Z<p>Kanglin: /* Atlas construction and its validation */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div><br />
<br />
==Atlas construction and its validation==<br />
* Datasets<br />
* Algorithm for atlas construction:</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=866832014 Summer Project Week:Atlas Selection2014-06-26T17:22:57Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div><br />
<br />
==Atlas construction and its validation==</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=866812014 Summer Project Week2014-06-26T17:17:54Z<p>Kanglin: /* Additional Brain Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
[[image:Projectweek-2014-06-23-IMG 0837.JPG|800px|opening session]]<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|<br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<br><br />
|'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata, Tina Kapur)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias, Andras)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
*[[2014_Summer_Project_Week:EM-tracked_prostate_US_calibration_with_Plus|Calibration of EM-tracked US acquisition using Plus]] (Andrey Fedorov, Tamas Ungi, Andras Lasso, Jay Jagadeesan)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)<br />
*[[2014_Summer_Prioject_Week:AgatstonScoring | Cardiac Agatston Scoring Extension]] (Jessica Forbes, Hans Johnson)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[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})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week: Quantitative image feature extraction | Quantitative image feature extraction in Non-Small Cell Lung Cancer]] (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Construction]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[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)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistan, Sonia Pujol)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Tammy Riklin Raviv, Ben-Gurion University, rrtammy@ee.bgu.ac.il<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=866792014 Summer Project Week2014-06-26T17:17:29Z<p>Kanglin: /* Additional Brain Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
[[image:Projectweek-2014-06-23-IMG 0837.JPG|800px|opening session]]<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|<br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<br><br />
|'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata, Tina Kapur)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias, Andras)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
*[[2014_Summer_Project_Week:EM-tracked_prostate_US_calibration_with_Plus|Calibration of EM-tracked US acquisition using Plus]] (Andrey Fedorov, Tamas Ungi, Andras Lasso, Jay Jagadeesan)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)<br />
*[[2014_Summer_Prioject_Week:AgatstonScoring | Cardiac Agatston Scoring Extension]] (Jessica Forbes, Hans Johnson)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[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})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week: Quantitative image feature extraction | Quantitative image feature extraction in Non-Small Cell Lung Cancer]] (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Construction | Atlas Selection]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[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)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistan, Sonia Pujol)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Tammy Riklin Raviv, Ben-Gurion University, rrtammy@ee.bgu.ac.il<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=866772014 Summer Project Week2014-06-26T17:13:04Z<p>Kanglin: /* Additional Brain Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
[[image:Projectweek-2014-06-23-IMG 0837.JPG|800px|opening session]]<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|<br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<br><br />
|'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata, Tina Kapur)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias, Andras)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
*[[2014_Summer_Project_Week:EM-tracked_prostate_US_calibration_with_Plus|Calibration of EM-tracked US acquisition using Plus]] (Andrey Fedorov, Tamas Ungi, Andras Lasso, Jay Jagadeesan)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)<br />
*[[2014_Summer_Prioject_Week:AgatstonScoring | Cardiac Agatston Scoring Extension]] (Jessica Forbes, Hans Johnson)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[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})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week: Quantitative image feature extraction | Quantitative image feature extraction in Non-Small Cell Lung Cancer]] (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[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)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistan, Sonia Pujol)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Tammy Riklin Raviv, Ben-Gurion University, rrtammy@ee.bgu.ac.il<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week&diff=866762014 Summer Project Week2014-06-26T17:12:11Z<p>Kanglin: /* Additional Brain Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2014.png|300px]]<br />
[[image:Projectweek-2014-06-23-IMG 0837.JPG|800px|opening session]]<br />
<br />
Dates: June 23-27, 2014.<br />
<br />
Location: MIT, Cambridge, MA.<br />
<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 23<br />
!style="width:18%" |Tuesday, June 24<br />
!style="width:18%" |Wednesday, June 25<br />
!style="width:18%" |Thursday, June 26<br />
!style="width:18%" |Friday, June 27<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations'''<br />
|bgcolor="#6494ec"|'''NA-MIC Update Day'''<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|<br />
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)<br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|<br />
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)<br />
<br><br />
|'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<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><br />
[[MIT_Project_Week_Rooms#Star|Star]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br><br />
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]<br />
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''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)<br />
[[MIT_Project_Week_Rooms#Star|Star]] <br />
<br>----------------------------------------<br><br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<br />
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. <br />
<br />
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.<br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
=Projects=<br />
* [[2014_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
<br />
* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata, Tina Kapur)<br />
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)<br />
*[[2014_Summer_Project_Week:Visual_Guidance_for_Neurosurgery_US_Recording |Visual Guidance for Neurosurgery US Data Recording<br />
]] (Alireza, Isaiah, Rahul, Matthew, Tina, Steve, Sandy, Alex Golby)<br />
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias, Andras)<br />
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)<br />
* [[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)<br />
* [[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)<br />
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)<br />
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)<br />
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)<br />
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)<br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Pressure_Sensor| Focused Ultrasound Pressure Sensor ]] (Robin Kouver, Nassim Alikacem) <br />
*[[2014_Summer_Project_Week:Focused_Ultrasound_Positioner| Focused Ultrasound Positioner ]] (Nassim Alikacem, Robin Kouver) <br />
*[[2014_Summer_Project_Week:Software_Platform_for_Robotic_Surgery|Searching for Software Platform for Robotic Surgery]] (Yangming Li)<br />
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)<br />
*[[2014_Summer_Project_Week:Ventriculostomy_Guidance_Transcranial_Ultrasound |Ventriculostomy Guidance with Transcranial Ultrasound<br />
]] (Jason White, Kirby Vosburgh, Can Meral, Alex Golby)<br />
*[[2014_Summer_Project_Week:EM-tracked_prostate_US_calibration_with_Plus|Calibration of EM-tracked US acquisition using Plus]] (Andrey Fedorov, Tamas Ungi, Andras Lasso, Jay Jagadeesan)<br />
<br />
==Huntington's Disease==<br />
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)<br />
*[[2014_Summer_Project_Week:LongitudinalSeg| 4D Segmentation for Longitudinal Consistency ]] (Regina Kim, James Fishbaugh, Guido Gerig, Hans Johnson)<br />
*[[2014_Summer_Project_Week:AutomatedSegmentationQA | Automated Prior-driven Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:ManualSegmentationQA | Manual Segmentation QA]] (Dave Welch, Hans Johnson)<br />
*[[2014_Summer_Project_Week:UpdateBRAINSTools | Update BRAINSTools (BRAINSFit and DWIConvert) in Slicer]] (Hans Johnson, Dave Welch, Kent Williams, JC, Brad)<br />
*[[2014_Summer_Prioject_Week:AgatstonScoring | Cardiac Agatston Scoring Extension]] (Jessica Forbes, Hans Johnson)<br />
<br />
==TBI==<br />
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)<br />
<br />
==Stroke==<br />
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)<br />
<br />
==Cardiac==<br />
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)<br />
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)<br />
*[[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, Raul San Jose)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)<br />
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)<br />
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)<br />
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)<br />
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)<br />
<br />
==[http://qiicr.org QIICR]==<br />
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)<br />
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})<br />
* [[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})<br />
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)<br />
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)<br />
<br />
==Feature Extraction==<br />
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)<br />
*[[2014_Summer_Project_Week: Quantitative image feature extraction | Quantitative image feature extraction in Non-Small Cell Lung Cancer]] (Hugo Aerts)<br />
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Atlas Construction | Atlas Construction]] (Kanglin Chen, Gregory Sharp)<br />
*[[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)<br />
*[[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)<br />
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)<br />
<br />
==Slicer4 Extensions==<br />
<br />
*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)<br />
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)<br />
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)<br />
*[[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)<br />
<br />
==Infrastructure==<br />
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)<br />
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)<br />
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)<br />
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)<br />
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)<br />
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)<br />
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)<br />
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)<br />
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)<br />
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistan, Sonia Pujol)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 23-27, 2014.<br />
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]]. <br />
*'''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.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
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.])<br />
<br />
#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu<br />
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com<br />
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu<br />
#Peter Anderson, retired, traneus@verizon.net<br />
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu<br />
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org<br />
#Francois Budin, NIRAL-UNC, fbudin@unc.edu<br />
#Saskia Camps, SPL, saskiacamps@gmail.com<br />
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu<br />
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu<br />
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de<br />
#Adrian Dalca, MIT CSAIL, adalca@mit.edu<br />
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de<br />
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it<br />
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com<br />
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com<br />
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu<br />
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com<br />
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com<br />
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu<br />
#Polina Golland, MIT CSAIL, polina@csail.mit.edu<br />
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu<br />
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com<br />
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu<br />
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu<br />
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu<br />
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu<br />
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu<br />
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu<br />
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu<br />
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu<br />
#Franklin King, Queen's University, franklin.king@queensu.ca<br />
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu<br />
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu<br />
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com<br />
#Robin Kouver, BWH/SPL, r.kouver@gmail.com<br />
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca<br />
#Yangming Li, University of Washington, ymli81@uw.edu<br />
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu<br />
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au<br />
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov<br />
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu<br />
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu<br />
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu<br />
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu<br />
#Jim Miller, GE Research, millerjv@ge.com<br />
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org<br />
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com<br />
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu<br />
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com<br />
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com<br />
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu<br />
#Danielle Pace, MIT CSAIL, dfpace@mit.edu<br />
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org<br />
#Nirav Patel, WPI, napatel@wpi.edu<br />
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu<br />
#Steve Pieper, Isomics Inc, pieper@isomics.com<br />
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca<br />
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com<br />
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu<br />
#Adam Rankin, Queen's University, rankin@queensu.ca<br />
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu<br />
#Tammy Riklin Raviv, Ben-Gurion University, rrtammy@ee.bgu.ac.il<br />
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu<br />
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu<br />
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu<br />
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com<br />
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu<br />
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu<br />
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu<br />
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu<br />
#Tamas Ungi, Queen's University, ungi@queensu.ca<br />
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca<br />
#David Welch, University of Iowa, david-welch@uiowa.edu<br />
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu<br />
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu<br />
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu<br />
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org<br />
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it<br />
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn<br />
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au</div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=863792014 Summer Project Week:Atlas Selection2014-06-23T17:01:45Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction is based on image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=863722014 Summer Project Week:Atlas Selection2014-06-23T17:00:01Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transferred to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction using image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=863712014 Summer Project Week:Atlas Selection2014-06-23T16:59:50Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transfered to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction using image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=863702014 Summer Project Week:Atlas Selection2014-06-23T16:59:09Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image segmentation. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transformed to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction using image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=863682014 Summer Project Week:Atlas Selection2014-06-23T16:58:49Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image registration. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transformed to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction using image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average atlas construction is finished. We have the datasets.<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=863672014 Summer Project Week:Atlas Selection2014-06-23T16:58:26Z<p>Kanglin: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
Atlas selection is used for image registration. Normally, a single image is chosen as an atlas and the structures are segmented manually.<br />
The segmentation is transformed to patient data using non-linear image registration. However, the choice of single atlas is difficult.<br />
We will develop an average atlas using image registration and reconstruction. The average atlas makes the registration to patient data more robust.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
An average atlas construction using image registration and reconstruction. We plan to construct the average atlas with merged segmentation<br />
using real 3D datasets and validate them.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
The algorithms for average construction is finished. We have the datasets.<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=856682014 Summer Project Week:Atlas Selection2014-06-05T15:09:13Z<p>Kanglin: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kanglin Chen (Fraunhofer MEVIS Germany)<br />
* Gregory Sharp (Harvard Medical School)<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=856672014 Summer Project Week:Atlas Selection2014-06-05T15:02:12Z<p>Kanglin: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
<br />
<br />
==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=Talk:2014_Summer_Project_Week:Atlas_Selection&diff=85666Talk:2014 Summer Project Week:Atlas Selection2014-06-05T14:59:30Z<p>Kanglin: Created page with '==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; pa…'</p>
<hr />
<div>==Project Description==<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Kanglinhttps://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:Atlas_Selection&diff=856652014 Summer Project Week:Atlas Selection2014-06-05T14:58:24Z<p>Kanglin: Created page with '==Key Investigators=='</p>
<hr />
<div>==Key Investigators==</div>Kanglin