https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=AtrivegNAMIC Wiki - User contributions [en]2026-04-08T20:18:06ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=69228Summer project week 2011 Finsler Streamlines2011-06-24T13:12:13Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:screen1.png | Step 1 - You can start by loading a DWI image (should be HARDI) and a mask (not necessary, but very convenient to accelerate computations).<br />
Image:screen2.png | Step 2 - Use the segmentation editor (or load any other label map at your convenience). This method requires target regions as well as seeding regions.<br />
Image:screen3.png | Step 3 - With the Finsler tractography module, generate a cost map ("Output scalar volume" in the picture) and a map of arrival directions ("Output directions volume").<br />
Image:screen4.png | Step 4 - This is how the costs map looks like. Now, you can switch to the Finsler Backtracing module using as input the costs and directions generated in Step 3. Choose a target region different from the seeding region.<br />
Image:screen5.png | Step 5 - The fiber bundles are drawn in Slicer's 3-D view.<br />
Image:screen6.png | Some other examples. Fibers are always saved to disk in RAS, and colored according to the value of the Finsler cost at the points they go through.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data [http://www.nitrc.org/snapshots.php?group_id=464].<br />
* A first version of the backtracing algorithm is ready [http://www.nitrc.org/snapshots.php?group_id=464].<br />
<br />
To do:<br />
<br />
* Add testing.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=69059Summer project week 2011 Finsler Streamlines2011-06-23T19:21:57Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:screen1.png | Step 1 - You can start by loading a DWI image and a mask (not necessary, but very convenient to accelerate computations).<br />
Image:screen2.png | Step 2 - Use the segmentation editor (or load any other label map at your convenience). This method requires target regions as well as seeding regions.<br />
Image:screen3.png | Step 3 - With the Finsler tractography module, generate a cost map ("Output scalar volume" in the picture) and a map of arrival directions ("Output directions volume").<br />
Image:screen4.png | Step 4 - This is how the costs map looks like. Now, you can switch to the Finsler Backtracing module using as input the costs and directions generated in Step 3. Choose a target region different from the seeding region.<br />
Image:screen5.png | Step 5 - The fiber bundles are drawn in Slicer's 3-D view.<br />
Image:screen6.png | Some other examples. Fibers are always saved to disk in RAS, and colored according to the value of the Finsler cost at the points they go through.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data [http://www.nitrc.org/snapshots.php?group_id=464].<br />
* A first version of the backtracing algorithm is ready [http://www.nitrc.org/snapshots.php?group_id=464].<br />
<br />
To do:<br />
<br />
* Add testing.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=69018Summer project week 2011 Finsler Streamlines2011-06-23T17:04:26Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:screen1.png | Step 1 - You can start by loading a DWI image and a mask (not necessary, but very convenient to accelerate computations).<br />
Image:screen2.png | Step 2 - Use the segmentation editor (or load any other label map at your convenience). This method requires target regions as well as seeding regions.<br />
Image:screen3.png | Step 3 - With the Finsler tractography module, generate a cost map ("Output scalar volume" in the picture) and a map of arrival directions ("Output directions volume").<br />
Image:screen4.png | Step 4 - This is how the costs map looks like. Now, you can switch to the Finsler Backtracing module using as input the costs and directions generated in Step 3. Choose a target region different from the seeding region.<br />
Image:screen5.png | Step 5 - The fiber bundles are drawn in Slicer's 3-D view.<br />
Image:screen6.png | Some other examples. Fibers are always saved to disk in RAS, and colored according to the value of the Finsler cost at the points they go through.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data [http://www.nitrc.org/snapshots.php?group_id=464].<br />
* A first version of the backtracing algorithm is ready.<br />
<br />
To do:<br />
<br />
* Add testing.<br />
* Upload code to nitrc.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=69017Summer project week 2011 Finsler Streamlines2011-06-23T16:59:17Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:screen1.png | Step 1 - You can start by loading a DWI image and a mask (not necessary, but very convenient to accelerate computations).<br />
Image:screen2.png | Step 2 - Use the segmentation editor (or load any other label map at your convenience). This method requires target regions as well as seeding regions.<br />
Image:screen3.png | Step 3 - With the Finsler tractography module, generate a cost map ("Output scalar volume" in the picture) and a map of arrival directions ("Output directions volume").<br />
Image:screen4.png | Step 4 - This is how the costs map looks like. Now, you can switch to the Finsler Backtracing module using as input the costs and directions generated in Step 3. Choose a target region different from the seeding region.<br />
Image:screen5.png | Step 5 - The fiber bundles are drawn in Slicer's 3-D view.<br />
Image:screen6.png | Some other examples<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data [http://www.nitrc.org/snapshots.php?group_id=464].<br />
* A first version of the backtracing algorithm is ready.<br />
<br />
To do:<br />
<br />
* Add testing.<br />
* Upload code to nitrc.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=69016Summer project week 2011 Finsler Streamlines2011-06-23T16:56:59Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:screen1.png | Step 1 - You can start by loading a DWI image and a mask (not necessary, but very convenient to accelerate computations).<br />
Image:screen2.png | Step 2 - Use the segmentation editor (or load any other label map at your convenience). This method requires target regions as well as seeding regions.<br />
Image:screen3.png | Step 3 - With the Finsler tractography module, generate a cost map ("Output scalar volume" in the picture) and a map of arrival directions ("Output directions volume").<br />
Image:screen4.png | Step 4 - This is how the costs map looks like. Now, you can switch to the Finsler Backtracing module using as input the costs and directions generated in Step 3. Choose a target region different from the seeding region.<br />
Image:screen5.png | Step 5 - The fiber bundles are drawn in Slicer's 3-D view.<br />
Image:screen6.png | Some other examples<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data [http://www.nitrc.org/snapshots.php?group_id=464].<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=69015Summer project week 2011 Finsler Streamlines2011-06-23T16:55:44Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:screen1.png | You can start by loading a DWI image and a mask (not necessary, but very convenient to accelerate computations).<br />
Image:screen2.png | Use the segmentation editor (or load any other label map at your convenience). This method requires target regions as well as seeding regions.<br />
Image:screen3.png | With the Finsler tractography module, generate a cost map ("Output scalar volume" in the picture) and a map of arrival directions ("Output directions volume").<br />
Image:screen4.png | This is how the costs map looks like. Now, you can switch to the Finsler Backtracing module using as input the costs and directions generated before. Choose a target region different from the seeding region.<br />
Image:screen5.png | The fiber bundles are drawn in Slicer's 3-D view.<br />
Image:screen6.png | Some other examples<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data [http://www.nitrc.org/snapshots.php?group_id=464].<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=69014Summer project week 2011 Finsler Streamlines2011-06-23T16:54:38Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:screen1.png | You can start by loading a DWI image and a mask (not necessary, but very convenient to accelerate computations).<br />
Image:screen2.png | Use the segmentation editor (or load any other label map at your convenience). This method requires seeding regions and target regions.<br />
Image:screen3.png | With the Finsler tractography module, generate a cost map ("Output scalar volume" in the picture) and a map of arrival directions ("Output directions volume").<br />
Image:screen4.png | This is how the costs map looks like. Now, you can switch to the Finsler Backtracing module using as input the costs and directions generated before. Choose a target region different from the seeding region.<br />
Image:screen5.png | The fiber bundles are drawn in Slicer's 3-D view.<br />
Image:screen6.png | Some other examples<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data [http://www.nitrc.org/snapshots.php?group_id=464].<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Screen6.png&diff=69012File:Screen6.png2011-06-23T16:47:37Z<p>Atriveg: </p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Screen5.png&diff=69011File:Screen5.png2011-06-23T16:47:21Z<p>Atriveg: </p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Screen4.png&diff=69010File:Screen4.png2011-06-23T16:47:07Z<p>Atriveg: </p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Screen3.png&diff=69009File:Screen3.png2011-06-23T16:45:47Z<p>Atriveg: </p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Screen2.png&diff=69008File:Screen2.png2011-06-23T16:45:22Z<p>Atriveg: </p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Screen1.png&diff=69006File:Screen1.png2011-06-23T16:45:01Z<p>Atriveg: </p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Slicerfinslermethod.png&diff=68329File:Slicerfinslermethod.png2011-06-16T21:48:53Z<p>Atriveg: Screenshot of the Slicer module for Finsler tractography.</p>
<hr />
<div>Screenshot of the Slicer module for Finsler tractography.</div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=68326Summer project week 2011 Finsler Streamlines2011-06-16T21:32:15Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicerfinslermethod.png | The Finsler tractography module in Slicer, with an example of the costs map obtained.<br />
Image:ss1.png | Example of a streamline computed with the Finsler method.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data [http://www.nitrc.org/snapshots.php?group_id=464].<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=68325Summer project week 2011 Finsler Streamlines2011-06-16T21:31:30Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicerfinslermethod.png | The Finsler tractography module in Slicer, with an example of the costs map obtained.<br />
Image:ss1.png | Example of a streamline computed with the Finsler method.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data: [[http://www.nitrc.org/snapshots.php?group_id=464]]<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=68324Summer project week 2011 Finsler Streamlines2011-06-16T21:30:27Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicerfinslermethod.png | The Finsler tractography module in Slicer, with an example of the costs map obtained.<br />
Image:ss1.png | Example of a streamline computed with the Finsler method.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=68323Summer project week 2011 Finsler Streamlines2011-06-16T21:28:59Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:ss1.png | Example of a streamline computed with the Finsler method<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=68322Summer project week 2011 Finsler Streamlines2011-06-16T21:27:26Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Demian Wasserman<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Project_Week/Template&diff=68321Project Week/Template2011-06-16T21:25:45Z<p>Atriveg: Undo revision 68314 by Atriveg (Talk)</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig<br />
* Utah: Tom Fletcher, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.<br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify)<br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Project_Week/Template&diff=68320Project Week/Template2011-06-16T21:25:22Z<p>Atriveg: Undo revision 68315 by Atriveg (Talk)</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* BWH: Antonio Tristán-Vega, Demian Wasserman, Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method <br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Project_Week/Template&diff=68319Project Week/Template2011-06-16T21:24:53Z<p>Atriveg: Undo revision 68316 by Atriveg (Talk)</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* BWH: Antonio Tristán-Vega, Demian Wasserman, Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the reference below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=68318Summer project week 2011 Finsler Streamlines2011-06-16T21:24:31Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* BWH: Antonio Tristán-Vega, Demian Wasserman, Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Project_Week/Template&diff=68316Project Week/Template2011-06-16T21:23:06Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* BWH: Antonio Tristán-Vega, Demian Wasserman, Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the references below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
By this time the following code available in C++/ITK:<br />
<br />
* HARDI estimation based on Spherical Harmonics (to compute Finsler local costs).<br />
* Parallel fast sweeping algorithm (to compute the globally optimal costs).<br />
* Slicer module implementing the computation of the costs map and arrival directions from input DWI data.<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Project_Week/Template&diff=68315Project Week/Template2011-06-16T21:18:33Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* BWH: Antonio Tristán-Vega, Demian Wasserman, Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method is described in detail in the reference below. To compute the costs map we use the Fast Sweeping algorithm: upon convergence, this method provides the minimum cost at each image voxel together with the direction such cost was reached from. Thus, the "backtracing" of these directions from a given point to the seeding point/region provides the minimum cost path.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Project_Week/Template&diff=68314Project Week/Template2011-06-16T21:15:41Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* BWH: Antonio Tristán-Vega, Demian Wasserman, Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
In the last project week we delivered an implementation of the Finsler method to compute the connectivity among regions in the white matter through High Angular Resolution Diffusion Imaging. Such method provides a costs map from a given seeding point/region to any other point within the brain. The aim in this project is tracing the minimum cost paths between two given regions in the white matter, which will in turn provide the desired streamlines.<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
The method <br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a Slicer Module<br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=Summer_project_week_2011_Finsler_Streamlines&diff=68313Summer project week 2011 Finsler Streamlines2011-06-16T21:09:15Z<p>Atriveg: Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig<br />
* Utah: Tom Fletcher, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.<br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify)<br />
<br />
==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=2011_Summer_Project_Week&diff=683122011 Summer Project Week2011-06-16T21:08:29Z<p>Atriveg: </p>
<hr />
<div> Back to [[Events]]<br />
<br />
[[image:PW-MIT2011.png|right|200px]]<br />
<br />
<br />
*'''Dates:''' June 20-24, 2011<br />
*'''Location:''' MIT<br />
<br />
==Preliminary Agenda==<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 20<br />
!style="width:18%" |Tuesday, June 21<br />
!style="width:18%" |Wednesday, June 22<br />
!style="width:18%" |Thursday, June 23<br />
!style="width:18%" |Friday, June 24<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 />
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]<br />
<br>----------------------------------------<br><br />
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br><br />
[[MIT_Project_Week_Rooms#Star|Star Room]]<br />
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)<br />
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]<br />
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<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 />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
<br>----------------------------------------<br><br />
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]<br />
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]<br />
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]] <br />
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]<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 />
==Projects==<br />
<br />
* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]<br />
<br />
#[[2011_Summer_Project_Week_Slicer_DICOM_RT_Brachytherapy|Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer]](Tina Kapur, Greg Sharp, Jan Egger, Firdaus Janoos)<br />
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)<br />
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)<br />
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)<br />
#[[2011_Summer_Project_Week_Dicom2Nrrd|DicomToNrrdConverter refactoring]] ( Xiaodong Tao, Mark Scully)<br />
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)<br />
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner<br />
#Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)<br />
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)<br />
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)<br />
#[[Multimodality Image Registration for TBI]] (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)<br />
#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)<br />
#Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)<br />
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)<br />
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)<br />
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)<br />
#Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)<br />
#Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)<br />
#Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Mark Scully)<br />
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)<br />
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )<br />
#The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper) <br />
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)<br />
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)<br />
#ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)<br />
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)<br />
#[[2011_Summer_Project__Week_Live_Tracked_Ultrasound|Live Tracked Ultrasound with Slicer4 (Tamas Heffter)]]<br />
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]<br />
#[[2011_Summer_Project_Week_DTIPrep|DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation]] - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)<br />
#[[2011_Summer_Project_Week_DTI_PairWise_Registration|DTI pair-wise registration module]] - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)<br />
#Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Mark Scully, Jim Miller)<br />
#Nifti Support for Diffusion Tensor Images (Demian)<br />
#Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)<br />
#Refactoring of the tractography display widget (Isaiah)<br />
#Laterality (Lauren)<br />
#Selection for models and bundles post-clustering (Lauren)<br />
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)<br />
#[[Summer_project_week_2011_Finsler_Streamlines|Adding streamlined tractography to the Finsler front propagation tractography toolkit]] (Antonio Tristán-Vega)<br />
#[[Summer_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions]] (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)<br />
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)<br />
#Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)<br />
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)<br />
#Slicer module for building an average population HARDI Atlas (Ryan Eckbo)<br />
#4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)<br />
#EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)<br />
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)<br />
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]<br />
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]<br />
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp)<br />
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)<br />
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)<br />
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)<br />
#Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)<br />
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)<br />
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)<br />
#[[2011_Summer_Project_Week_ODF_though_Fiber_Counting | ODF computation through fiber counting]] (Yinpeng Li, Ipek Oguz, Martin Styner)<br />
#[[2011_Summer_Project_Week_Intraoperative_Brain_Shift_Monitor|Intraoperative Brain Shift Monitor]] (Jason White, Alex Golby, Steve Pieper)<br />
#[[2011_Summer_Project_Week_DTI_Volumetric_Segmentation_for_Group_studies | DTI Volumetric Segmentation for Group studies]] (Gopal Veni, Ross Whitaker)<br />
#[[2011_Summer_Project_Week_Segementation_Reconstruction_Pericardial_Sac]] (Mohasen)<br />
<br />
==Background==<br />
<br />
We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].<br />
<br />
<br />
Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. 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 coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and 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 will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 20-24, 2011<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). <br />
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!<br />
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects<br />
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
<br />
<br />
==Registrants==<br />
<br />
Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)<br />
# Nicole Aucoin , Brigham and Women's Hospital<br />
# Dominique Belhachemi , University of Pennsylvania<br />
# Anthony Blumfiled , Radnostics<br />
# Lucile Bompard , UNC NIRAL<br />
# Sylvain Bouix , Brigham and Women's Hospital<br />
# Francois Budin , UNC NIRAL<br />
# Steve Callahan , University of Utah<br />
# Joshua Cates , University of Utah<br />
# Laurent Chauvin , Brigham and Women's Hospital<br />
# Adrian Dalca , MIT CSAIL<br />
# Manasi Datar , University of Utah<br />
# Colin Davey , <br />
# Ryan Eckbo , Brigham and Women's Hospital<br />
# Jan Egger , University Hospital of Marburg<br />
# Luping Fang , Zhejiang University of Technology, China<br />
# mahshid farzinfar , UNC<br />
# Andriy Fedorov , Brigham and Women's Hospital<br />
# Julien Finet , Kitware Inc.<br />
# James Fishbaugh , University of Utah<br />
# Greg Gardner , University of Utah<br />
# Ronen Globinsky , Yale University<br />
# Maged Goubran , Robarts Research Institute<br />
# Daniel Haehn , University of Pennsylvania<br />
# Mike Halle , Brigham and Women's Hospital<br />
# Noby Hata , Brigham and Women's Hospital<br />
# Tamas Heffter , Queen's University<br />
# Andrei Irimia , University of California, Los Angeles<br />
# Hans Johnson , University of Iowa<br />
# Ilknur Kabul , Kitware<br />
# Tina Kapur , Brigham and Women's Hospital<br />
# Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School<br />
# Regina Kim , University of Iowa<br />
# Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL<br />
# Dillon Lee , University of Utah<br />
# Yinpeng Li , UNC-NIRAL<br />
# Yifei Lou , Georgia Institute of Technology<br />
# mohsen mahvash , Harvard Medical School (BWH and VA)<br />
# Katie Mastrogiacomo , Brigham and Women's Hospital<br />
# Joy Matsui , University of Iowa<br />
# Dominik Meier , BWH<br />
# Mikhail Milchenko , Washington University in St. Louis<br />
# James Miller , GE Research<br />
# Isaiah Norton , Brigham and Women's Hospital<br />
# Danielle Pace , Kitware<br />
# Beatriz Paniagua , University of North Carolina at Chapel Hill<br />
# Xenophon Papademetris , Yale University<br />
# Kedar Patwardhan , GE Global Research<br />
# Steve Pieper , Isomics, Inc.<br />
# Csaba Pinter , Queen's University<br />
# Wendy Plesniak , Brigham and Women's Hospital<br />
# Kilian Pohl , UPenn<br />
# Marcel Prastawa , University of Utah<br />
# Sonia Pujol , Brigham and Women's Hospital<br />
# Martin Rajchl , Robarts Research Institute<br />
# Petter Risholm , Brigham and Women's Hospital<br />
# Peter Savadjiev , Brigham and Women's Hospital<br />
# Andreas Schuh , University of Pennsylvania<br />
# Mark Scully , University of Iowa<br />
# Gregory Sharp , MGH<br />
# Yundi Shi , UNC-Chapel Hill<br />
# Nadya Shusharina , MGH<br />
# Ramesh Sridharan , MIT CSAIL<br />
# Hao Su , WPI<br />
# Suarez Tamekue , Brigham and Women's Hospital<br />
# Xiaodong Tao , GE Research<br />
# Clement Vachet , UNC Chapel Hill<br />
# Antonio Vega , Brigham and Women's Hospital<br />
# Gopal Veni , University of Utah<br />
# Bo Wang , University of Utah<br />
# Demian Wasserman , Brigham and Women's Hospital<br />
# Sandy Wells , Brigham and Women's Hospital<br />
# Jason White , Brigham and Women's Hospital<br />
# Atsushi Yamada , Brigham and Women's Hospital<br />
# Alexander Yarmarkovich , Isomics<br />
# Alexander Zaitsev , Brigham and Women's Hospital</div>Atriveghttps://www.na-mic.org/w/index.php?title=2011_Summer_Project_Week&diff=683102011 Summer Project Week2011-06-16T20:31:45Z<p>Atriveg: </p>
<hr />
<div> Back to [[Events]]<br />
<br />
[[image:PW-MIT2011.png|right|200px]]<br />
<br />
<br />
*'''Dates:''' June 20-24, 2011<br />
*'''Location:''' MIT<br />
<br />
==Preliminary Agenda==<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, June 20<br />
!style="width:18%" |Tuesday, June 21<br />
!style="width:18%" |Wednesday, June 22<br />
!style="width:18%" |Thursday, June 23<br />
!style="width:18%" |Friday, June 24<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 />
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]<br />
<br>----------------------------------------<br><br />
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br><br />
[[MIT_Project_Week_Rooms#Star|Star Room]]<br />
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)<br />
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]<br />
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]<br />
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]<br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<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 />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
<br>----------------------------------------<br><br />
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]<br />
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]<br />
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]<br />
<br>----------------------------------------<br><br />
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]<br />
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]<br />
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]] <br />
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]<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 />
==Projects==<br />
<br />
* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]<br />
<br />
#[[2011_Summer_Project_Week_Slicer_DICOM_RT_Brachytherapy|Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer]](Tina Kapur, Greg Sharp, Jan Egger, Firdaus Janoos)<br />
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)<br />
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)<br />
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)<br />
#[[2011_Summer_Project_Week_Dicom2Nrrd|DicomToNrrdConverter refactoring]] ( Xiaodong Tao, Mark Scully)<br />
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)<br />
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner<br />
#Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)<br />
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)<br />
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)<br />
#[[Multimodality Image Registration for TBI]] (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)<br />
#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)<br />
#Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)<br />
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)<br />
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)<br />
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)<br />
#Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)<br />
#Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)<br />
#Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Mark Scully)<br />
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)<br />
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )<br />
#The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper) <br />
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)<br />
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)<br />
#ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)<br />
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)<br />
#[[2011_Summer_Project__Week_Live_Tracked_Ultrasound|Live Tracked Ultrasound with Slicer4 (Tamas Heffter)]]<br />
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]<br />
#[[2011_Summer_Project_Week_DTIPrep|DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation]] - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)<br />
#[[2011_Summer_Project_Week_DTI_PairWise_Registration|DTI pair-wise registration module]] - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)<br />
#Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Mark Scully, Jim Miller)<br />
#Nifti Support for Diffusion Tensor Images (Demian)<br />
#Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)<br />
#Refactoring of the tractography display widget (Isaiah)<br />
#Laterality (Lauren)<br />
#Selection for models and bundles post-clustering (Lauren)<br />
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)<br />
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)<br />
#[[Summer_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions]] (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)<br />
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)<br />
#Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)<br />
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)<br />
#Slicer module for building an average population HARDI Atlas (Ryan Eckbo)<br />
#4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)<br />
#EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)<br />
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)<br />
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]<br />
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]<br />
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp)<br />
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)<br />
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)<br />
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)<br />
#Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)<br />
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)<br />
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)<br />
#[[2011_Summer_Project_Week_ODF_though_Fiber_Counting | ODF computation through fiber counting]] (Yinpeng Li, Ipek Oguz, Martin Styner)<br />
#[[2011_Summer_Project_Week_Intraoperative_Brain_Shift_Monitor|Intraoperative Brain Shift Monitor]] (Jason White, Alex Golby, Steve Pieper)<br />
#[[2011_Summer_Project_Week_DTI_Volumetric_Segmentation_for_Group_studies | DTI Volumetric Segmentation for Group studies]] (Gopal Veni, Ross Whitaker)<br />
#[[2011_Summer_Project_Week_Segementation_Reconstruction_Pericardial_Sac]] (Mohasen)<br />
<br />
==Background==<br />
<br />
We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].<br />
<br />
<br />
Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. 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 coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and 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 will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br />
<br />
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br />
<br />
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
== Logistics ==<br />
*'''Dates:''' June 20-24, 2011<br />
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br />
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.<br />
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). <br />
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''<br />
<br />
== Preparation ==<br />
<br />
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br />
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!<br />
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects<br />
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
# People doing Slicer related projects should come to project week with slicer built on your laptop.<br />
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).<br />
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br />
<br />
<br />
<br />
==Registrants==<br />
<br />
Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)<br />
# Nicole Aucoin , Brigham and Women's Hospital<br />
# Dominique Belhachemi , University of Pennsylvania<br />
# Anthony Blumfiled , Radnostics<br />
# Lucile Bompard , UNC NIRAL<br />
# Sylvain Bouix , Brigham and Women's Hospital<br />
# Francois Budin , UNC NIRAL<br />
# Steve Callahan , University of Utah<br />
# Joshua Cates , University of Utah<br />
# Laurent Chauvin , Brigham and Women's Hospital<br />
# Adrian Dalca , MIT CSAIL<br />
# Manasi Datar , University of Utah<br />
# Colin Davey , <br />
# Ryan Eckbo , Brigham and Women's Hospital<br />
# Jan Egger , University Hospital of Marburg<br />
# Luping Fang , Zhejiang University of Technology, China<br />
# mahshid farzinfar , UNC<br />
# Andriy Fedorov , Brigham and Women's Hospital<br />
# Julien Finet , Kitware Inc.<br />
# James Fishbaugh , University of Utah<br />
# Greg Gardner , University of Utah<br />
# Ronen Globinsky , Yale University<br />
# Maged Goubran , Robarts Research Institute<br />
# Daniel Haehn , University of Pennsylvania<br />
# Mike Halle , Brigham and Women's Hospital<br />
# Noby Hata , Brigham and Women's Hospital<br />
# Tamas Heffter , Queen's University<br />
# Andrei Irimia , University of California, Los Angeles<br />
# Hans Johnson , University of Iowa<br />
# Ilknur Kabul , Kitware<br />
# Tina Kapur , Brigham and Women's Hospital<br />
# Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School<br />
# Regina Kim , University of Iowa<br />
# Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL<br />
# Dillon Lee , University of Utah<br />
# Yinpeng Li , UNC-NIRAL<br />
# Yifei Lou , Georgia Institute of Technology<br />
# mohsen mahvash , Harvard Medical School (BWH and VA)<br />
# Katie Mastrogiacomo , Brigham and Women's Hospital<br />
# Joy Matsui , University of Iowa<br />
# Dominik Meier , BWH<br />
# Mikhail Milchenko , Washington University in St. Louis<br />
# James Miller , GE Research<br />
# Isaiah Norton , Brigham and Women's Hospital<br />
# Danielle Pace , Kitware<br />
# Beatriz Paniagua , University of North Carolina at Chapel Hill<br />
# Xenophon Papademetris , Yale University<br />
# Kedar Patwardhan , GE Global Research<br />
# Steve Pieper , Isomics, Inc.<br />
# Csaba Pinter , Queen's University<br />
# Wendy Plesniak , Brigham and Women's Hospital<br />
# Kilian Pohl , UPenn<br />
# Marcel Prastawa , University of Utah<br />
# Sonia Pujol , Brigham and Women's Hospital<br />
# Martin Rajchl , Robarts Research Institute<br />
# Petter Risholm , Brigham and Women's Hospital<br />
# Peter Savadjiev , Brigham and Women's Hospital<br />
# Andreas Schuh , University of Pennsylvania<br />
# Mark Scully , University of Iowa<br />
# Gregory Sharp , MGH<br />
# Yundi Shi , UNC-Chapel Hill<br />
# Nadya Shusharina , MGH<br />
# Ramesh Sridharan , MIT CSAIL<br />
# Hao Su , WPI<br />
# Suarez Tamekue , Brigham and Women's Hospital<br />
# Xiaodong Tao , GE Research<br />
# Clement Vachet , UNC Chapel Hill<br />
# Antonio Vega , Brigham and Women's Hospital<br />
# Gopal Veni , University of Utah<br />
# Bo Wang , University of Utah<br />
# Demian Wasserman , Brigham and Women's Hospital<br />
# Sandy Wells , Brigham and Women's Hospital<br />
# Jason White , Brigham and Women's Hospital<br />
# Atsushi Yamada , Brigham and Women's Hospital<br />
# Alexander Yarmarkovich , Isomics<br />
# Alexander Zaitsev , Brigham and Women's Hospital</div>Atriveghttps://www.na-mic.org/w/index.php?title=2011_Winter_Project_Week:FinslerTractography&diff=630732011 Winter Project Week:FinslerTractography2011-01-07T15:52:24Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:ss1.png | Examples of the segmented cingulum using Finsler tractography<br />
Image:ss2.png | Examples of the segmented cingulum using Finsler tractography<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are coding in ITK the method for fiber bindle segmentation by John Melonako, which is currently written only in MatLab.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The approach is as described in the references:<br />
* Create anchor tract by minimizing Finsler length using fast sweeping.<br />
* Volumetric segmentation of fiber bundles starting from anchor tract.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
For the development of the method, we start with:<br />
* ITK directional iterators for fast sweeping (complete).<br />
* itk::FastSweeping class (incomplete).<br />
* itk::FinslerTractography class (incomplete).<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a ITK Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=2011_Winter_Project_Week:FinslerTractography&diff=630722011 Winter Project Week:FinslerTractography2011-01-07T15:51:33Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:ss1.png<br />
[[File:ss2.png]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are coding in ITK the method for fiber bindle segmentation by John Melonako, which is currently written only in MatLab.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The approach is as described in the references:<br />
* Create anchor tract by minimizing Finsler length using fast sweeping.<br />
* Volumetric segmentation of fiber bundles starting from anchor tract.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
For the development of the method, we start with:<br />
* ITK directional iterators for fast sweeping (complete).<br />
* itk::FastSweeping class (incomplete).<br />
* itk::FinslerTractography class (incomplete).<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a ITK Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=2011_Winter_Project_Week:FinslerTractography&diff=630702011 Winter Project Week:FinslerTractography2011-01-07T15:50:45Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
[[File:ss1.png]]<br />
[[File:ss2.png]]<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are coding in ITK the method for fiber bindle segmentation by John Melonako, which is currently written only in MatLab.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The approach is as described in the references:<br />
* Create anchor tract by minimizing Finsler length using fast sweeping.<br />
* Volumetric segmentation of fiber bundles starting from anchor tract.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
For the development of the method, we start with:<br />
* ITK directional iterators for fast sweeping (complete).<br />
* itk::FastSweeping class (incomplete).<br />
* itk::FinslerTractography class (incomplete).<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a ITK Module<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=2011_Winter_Project_Week:FinslerTractography&diff=630682011 Winter Project Week:FinslerTractography2011-01-07T15:47:23Z<p>Atriveg: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
[[File:ss1.png]]<br />
[[File:ss2.png]]<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are coding in ITK the method for fiber bindle segmentation by John Melonako, which is currently written only in MatLab.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify)<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonnakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Ss2.png&diff=63067File:Ss2.png2011-01-07T15:46:12Z<p>Atriveg: </p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=File:Ss1.png&diff=63066File:Ss1.png2011-01-07T15:45:45Z<p>Atriveg: </p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=2011_Winter_Project_Week:FinslerTractography&diff=630652011 Winter Project Week:FinslerTractography2011-01-07T15:40:16Z<p>Atriveg: Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* LMI: Antonio Tristán-Vega<br />
* LMI: Carl-Fredrik Westin<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are coding in ITK the method for fiber bindle segmentation by John Melonako, which is currently written only in MatLab.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
<br />
Our plan for the project week is to first try out <bar>,...<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
<br />
#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify)<br />
<br />
==References==<br />
* Melonakos, J.; Pichon, E.; Angenent, S.; Tannenbaum, A.; "Finsler active contours." IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3): 412-423, 2008.<br />
* Melonnakos, J.; Mohan, V.; Niethammer, M.; Smith, K.; Kubicki M.; Tannenbaum, A.; "Finsler tractography for white matter connectivity analysis of the cingulum bundle", Procs. MICCAI 2007, LNCS 4791, pp. 36-43.<br />
<br />
</div></div>Atriveghttps://www.na-mic.org/w/index.php?title=2011_Winter_Project_Week&diff=630642011 Winter Project Week2011-01-07T15:32:43Z<p>Atriveg: /* Diffusion */</p>
<hr />
<div> Back to [[Project Events]], [[Events]]<br />
Back to [[Project Events]], [[AHM_2011]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2011.png|300px]]<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
Please [[AHM_2011#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
== Agenda==<br />
<br />
Please [[AHM_2011#Agenda|click here for the agenda for AHM 2011 and Project Week]].<br />
<br />
==Background==<br />
<br />
From January 10-14, 2011, the twelfth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions. <br />
<br />
Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project. <br />
<br />
On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
<br />
<br />
<br />
==Projects==<br />
<br />
=== Segmentation ===<br />
* [[2011_Winter_Project_Week:Extension of ABC to detect pathology categories|Extension of ABC (Atlas-Based Classification) to detect pathology categories, with tests on TBI images]] (Bo Wang, Jack Van Horn, Marcel Prastawa, Guido Gerig).<br />
* [[2011_Winter_Project_Week:Atrial_Fibrillation|Segmentation of the left atrial wall for atrial fibrillation ablation therapy]] (Behnood Gholami, Yi Gao, and Allen Tannenbaum)<br />
* [[2011_Winter_Project_Week:The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)<br />
* [[2011_Winter_Project_Week:TubeTK_VascularImageSegmentationAndAnalysis|TubeTK for vascular image segmentation and analysis]] (Stephen Aylward, Danielle Pace, Steve Pieper)<br />
* [[2011_Winter_Project_Week:StenosisDetector|A stenosis detector in Slicer4 using VMTK ]](Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)<br />
* [[2011_Winter_Project_Week:MeshCurvolver|Surface Region Segmentation for Surgical Planning and Mapping ]] (Peter Karasev, Karol Chudy, Allen Tannenbaum)<br />
* [[2011_Winter_Project_Week:SPECTRE_Integration|Integration of SPECTRE into Slicer]] (Nicole Aucoin, Min Chen)<br />
* [[2011_Winter_Project_Week:NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ehud Schmidt, Polina Golland)<br />
<br />
=== Registration ===<br />
*[[2011_Winter_Project_Week:RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier,Ron Kikinis)<br />
*[[2011_Winter_Project_Week:RegistrationAnisotropy|Voxel Anisotropy and Bias Field Effects on Slicer Image Registration]] (Dominik Meier, Andriy Fedorov, William Wells) (tentative)<br />
* [[2011_Winter_Project_Week:DTIRegistrationWizard|DTI registration & resampling wizard]] (Dominik Meier, Hans Johnson, Francois Budin, Mark Scully)<br />
* [[2011_Winter_Project_Week:Efficient co-registration of multiple MR modalities using the ABC|Efficient co-registration of multiple MR modalities using the ABC (atlas-based classification) framework, joint visualization of multiple co-registered modalities]] (Bo Wang, Jack Van Horn, Marcel Prastawa, Guido Gerig).<br />
* [[2011_Winter_Project_Week:DTI_MRI_Registration|DTI MRI Registration- Evaluation of registration schemes]] (Anuja Sharma, Guido Gerig)<br />
* [[2011_Winter_Project_Week:Atlas_Registration_in_Slicer3|Atlas Registration in Slicer3]] (Daniel Haehn, Dominik Meier, Kilian Pohl, Ryan Eckbo)<br />
* [[2011_Winter_Project_Week:RegistrationInPresenceOfAnatomicVariation|Registration in the presence of anatomic variation (sliding organ registration)]] (Danielle Pace, Marc Niethammer, Petter Risholm, Tina Kapur, Sandy Wells, Stephen Aylward)<br />
* [[2011_Winter_Project_Week:UncertaintyVisualization|Visualizing registration uncertainty in Slicer3]] (Peter Risholm, William Wells)<br />
* [[2011_Winter_Project_Week:LandmarkRegularization|Landmark-based registration with analytic regularization]] (Nadya Shusharina, Gregory Sharp)<br />
* [[2011_Winter_Project_Week:DTIPipeline|DTI registration/processing pipeline in Slicer3]] (Francois Budin, Clement Vachet)<br />
<br />
=== IGT ===<br />
*[[2011_Winter_Project_Week:OpenIGTLink| OpenIGTLink 2.0]] (Junichi Tokuda, Nobuhiko Hata) <br />
*[[2011_Winter_Project_Week:Osteomark|Osteormark, navigation tool for Osteotomy]] (Laurent Chauvin, Nobuhiko Hata)<br />
*[[2011_Winter_Project_Week:Intra-ProceduralProstateMotion|Detection and compensation for prostate motion during MR-guided prostate biopsy]] (A.Fedorov, Andras Lasso)<br />
*[[2011_Winter_Project_Week:ThinClientQtInterfaceForIGT|Thin Client QT Interface for IGT]] (Nicholas Herlambang, Steve Pieper, Julien Finet, JC)<br />
*[[2011_Winter_Project_Week:TransformRecorderAndProcedureAnnotation|Transform recorder and (surgical) procedure annotation module]] (Tamas Ungi, Junichi Tokuda)<br />
*[[2011_Winter_Project_Week:SurgicalToolsTracking|Surgical Tools Tracking]] (Martin Rajchl, Feng Li)<br />
*[[2011_Winter_Project_Week:Slicer IGT Looking Forward| Slicer IGT Looking forward]] (Nobuhiko Hata, Junichi Tokuda, Andriy Fedorov, Sandy Wells, Danielle Pace)<br />
<br />
=== Radiotherapy ===<br />
* [[2011_Winter_Project_Week:SegEye|Segmentation of the eye structures for Adaptive Radiotherapy]] (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)<br />
* [[2011_Winter_Project_Week:DicomRtExport|DICOM-RT export]] (Greg Sharp, Steve Pieper)<br />
<br />
=== Analysis ===<br />
* [[2011_Winter_Project_Week:GAMBITCorticalThicknessAnalysis |GAMBIT - Cortical thickness analysis]] - Clement Vachet, Martin Styner<br />
* [[2011_Winter_Project_Week:ParticleShapeAnalysis|Particle shape analysis incorporating surface normals ]] - Beatriz Paniagua, Martin Styner<br />
* [[2011_Winter_Project_Week:NAMICShapeAnalysis |NAMIC shape analysis pipeline in Slicer 3]] - Lucile Bompard, Martin Styner, Clement Vachet, Chris Gloschat<br />
* [[2011_Winter_Project_Week:ParticleShapeEngineering|Particle Systems for Shape Analysis]] - Josh Cates, Manasi Datar, Ross Whitaker<br />
* [[2011_Winter_Project_Week:MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] - Bjoern Menze, Jason Crane, Beck Olson, Polina Golland<br />
<br />
=== Informatics ===<br />
* [[2011_Winter_Project_Week:UIowaTHPDTIData|Share all UIowa Traveling Human Phantom DTI data with NAMIC]] - Mark Scully, Hans Johnson, Zack M.<br />
* [[2011_Winter_Project_Week:FetchMIAPI|Recode FetchMI API to work with XNAT 1.5 API]] - Dan Marcus, Misha Milchenko<br />
* [[2011_Winter_Project_Week:XNATSceneSupport|Engineer XNAT infrastructure for handling slicer scene files]] - Dan Marcus, Misha Milchenko<br />
<br />
=== Diffusion ===<br />
* [[2011_Winter_Project_Week:DicomToNrrdTestSuite |Test suite for DicomToNrrdConverter]] - Mark Scully, Zach Mullen, Xiaodong Tao, Hans Johnson <br />
* [[2011_Winter_Project_Week:DicomToNrrdRefactoring |Requirements gathering for refactoring DicomToNrrdConverter]] - Mark Scully, Xiaodong Tao, Hans Johnson <br />
* [[2011_Winter_Project_Week:DTIPrepDocumentation |Documentation and 1st Draft Tutorial for DTIPrep]] - Clement Vachet, Mark Scully, Hans Johnson<br />
* [[2011_Winter_Project_Week:VoxelwizeFiberDistributionFromTractography |Voxelwise fiber distribution from tractography]] - Yinpeng Li, Martin Styner<br />
* [[2011_Winter_Project_Week:TwoTensorTracts |Two-tensor full brain tractography pipeline]] - Lauren O'Donnell, Yogesh Rathi, C-F Westin<br />
* [[2011_Winter_Project_Week:FreeWaterElimination |Free-water elimination]] - Ofer Pasternak, Demian Wassermann, C-F Westin<br />
* [[2011_Winter_Project_Week:FinslerTractography |Finsler tractography in ITK]] - Antonio Tristan-Vega, C-F Westin<br />
* [[Statistical analysis of WM tracts generated by Tractography and Volumetric framework]] - Gopal Veni, Ross Whitaker<br />
<br />
=== NA-MIC Kit Internals ===<br />
<br />
* [[2011_Winter_Project_Week:Command_line_module_logic_redesign|Command line module logic redesign]] (passing paramenters, tie into workflows) - Jim, Steve<br />
* 64bit Windows Builds - Dave P<br />
* Dashboards: Factory machine, subprojects, and CDash@Home - Dave P, Zack M, Steve, and Stephen<br />
* [[2011_Winter_Project_Week:MIDAS_for_data_hosting|MIDAS for data hosting]] - Zach M and Hans<br />
* [[2011_Winter_Project_Week:VTK_Widgets|vtkWidgets]] JC and Will, Nicole Aucoin<br />
* [[2011_Winter_Project_Week:Annotation_module_in_Slicer4_Display_widget_intersections|Annotation module in Slicer4: Display widget intersections]] (Daniel Haehn, Nicole Aucoin, Steve Pieper)<br />
* [[2011_Winter_Project_Week: Python and Slicer4| Python and Slicer4]]: Workflows, Scripting, and Porting - JC, Jim, Steve, and Danielle<br />
* [[2011_Winter_Project_Week: Slice View Performance| Improve Performance of Slice Rendering in slicer3 and slicer4]] (Steve, Will, Jc, J2, Jim, Luca)<br />
* [[2011_NAMIC_Project_week:_Real-Time_Volume_Rendering_for_Virtual_Colonoscopy| Real-Time Volume Rendering for Virtual Colonoscopy]] (Steve, Alex)<br />
* [[2011_Winter_Project_Week:_Slicer4-ITK4_Continuous_Integration| Slicer4 - ITK4 Integration]] (Bill, Luis)<br />
<br />
=== Execution Model ===<br />
* [[2011_Winter_Project_Week::ExtractSEM|Extract SlicerExecutionModel (SEM) into separate entity]]. SEM is the only component needed to build modules compatible with Slicer3D, so it should be easy incorporate into external applications without all of Slicer3D. Jim, Hans<br />
* [[2011_Winter_Project_Week:ExtendSEMXml|Extend SEM xml]] to include sections for explicit grant acknowledgements, pointers to documentation, and pointers to examples. - Hans, Andriy<br />
* [[2011_Winter_Project_Week:SEMXMLSchema|Create a formal schema for the SEM xml so that eternal tools (i.e. nipype) can validate the xml.]] - Hans Johnson, Jim Miller, Tim Olsen<br />
* [[2011_Winter_Project_Week:XMLToMediaWiki|Improve documentation extractor script that converts XML to MediaWiki format so that it can directly push this information into the Slicer3D MediaWiki.]] - (Wiki Systems Admin), Hans Johnson, Steve Pieper, Stephen Aylward<br />
* [[2011_Winter_Project_Week:ExternalToolsMergingStrategies | Improve merging strategies between software that is part of externals tools and part of Slicer.]] - Mark Scully, Hans Johnson<br />
<br />
=== Workflows and Integration ===<br />
# [[Winter_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)<br />
<br />
=== Preparation ===<br />
<br />
#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list] <br />
#Starting Thursday, October 28th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:<br />
#*October 28: Engineering Infrastructure Projects<br />
#*November 4: Engineering Infrastructure Projects<br />
#*November 11: DPB Projects: Iowa, Outcomes from Alg Core Retreat <br />
#*November 18: DPB Projects: MGH <br />
#*November 25: DBP Projects, Funded External Collaborations<br />
#*December 2: Funded External Collaborations<br />
#*December 9: Other External Collaborations<br />
#*December 16:Finalize Engineering Projects <br />
#*January 6: Loose Ends<br />
#By December 16, 2010: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
#By December 16, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
##Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...</div>Atriveghttps://www.na-mic.org/w/index.php?title=User:Atriveg&diff=63063User:Atriveg2011-01-07T15:30:26Z<p>Atriveg: Blanked the page</p>
<hr />
<div></div>Atriveghttps://www.na-mic.org/w/index.php?title=User:Atriveg&diff=63062User:Atriveg2011-01-07T15:28:27Z<p>Atriveg: Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.<br />
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.<br />
</gallery><br />
<br />
==Instructions for Use of this Template==<br />
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name><br />
#Copy the entire text of this page into the page created above<br />
#Link the created page into the list of projects for the project event<br />
#Delete this section from the created page<br />
#Send an email to tkapur at bwh.harvard.edu if you are stuck<br />
<br />
==Key Investigators==<br />
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig<br />
* Utah: Tom Fletcher, Ross Whitaker<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.<br />
<br />
<br />
<br />
<br />
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<h3>Approach, Plan</h3><br />
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Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.<br />
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Our plan for the project week is to first try out <bar>,...<br />
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<h3>Progress</h3><br />
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.<br />
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==Delivery Mechanism==<br />
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This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)<br />
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#ITK Module<br />
#Slicer Module<br />
##Built-in<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
#Other (Please specify)<br />
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==References==<br />
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.<br />
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.<br />
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.<br />
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .<br />
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</div></div>Atriveg