NAMIC Wiki - User contributions [en]

2010 Winter Project Week Spine Segmentation Module in Slicer3

2010-02-24T15:59:29Z

MartinLoepprich: /* Key Investigators */

__NOTOC__
<gallery>
Image:Martin_Loepprich_back_pain_animation_Feb_2010.gif|Rendering of segmentation results showing a disk herniation. This subject suffers from recurrent pain in the lower back.
Image:Loepprich_Jaume_vertebra_Slicer_Jan2010.png|MRI slice and 3D rendering showing spine segmentation results for surgical treatment of disk herniation. [http://www.youtube.com/watch?v=kkAuP80kE8E (video)]
Image:Martin_Loepprich_vertebrae_animation_Jan2010.gif|3D rendering of L3, L4 and L5 vertebrae (brown - top to bottom), inter-vertebral disks (blue) and bundles of spinal nerves (red).
Image:PW-SLC2010.png|3D Slicer's Spine Segmentation module was presented at the [[2010_Winter_Project_Week#Projects|NA-MIC Project Week]] in Salt Lake City, Jan 4-10, 2010.
</gallery>

==Key Investigators==
* Sylvain Jaume (MIT)
* Martin Loepprich (University of Heidelberg)
* Ron Kikinis, Steve Pieper (BWH)
* Polina Golland (MIT), Ehud Schmidt (BWH)

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

<h3>Goal</h3>
We are developing a Slicer module to segment the region within the thecal sac in MRI images of the spine.
Our objective is to provide a segmentation and visualization tool to improve the treatment of disc herniation.
The structures of interests are the cerebro-spinal fluid (CSF), the discs, the vertebrae and the spinal nerves.

</div>

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

<h3>Approach</h3>

Our plan for the project week is to integrate our code into Slicer 3.5.
Our code analyzes the intensity profile of different regions in the MRI and automatically defines the optimum region for the CSF.

</div>

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

<h3>Results</h3>
The algorithm has been implemented in Slicer 3.5 as an extension module.
This volumetric pattern recognition algorithm is fully implemented as a Slicer module using ITK and VTK.
The module has been tested on data sets acquired at Brigham and Women's Hospital.
</div>
</div>

<div style="width: 97%; float: left;">
===Method===

{|
|[[Image:Martin_Loepprich_back_pain_animation_Feb_2010.gif|thumb|200px|Segmentation of a 3D MRI dataset showing a disk herniation. This subject suffers from recurrent pain in the lower back.]]
|[[Image:Netter_atlas_of_anatomy_4th_edition_spinal_cord.png|thumb|200px|Anatomy of the back showing the spinal cord and the lumbar nerves (Courtesy of Netter Atlas of Anatomy 4th Edition)]]
|[[Image:Sylvain_Jaume_vertebrae_and_discs_Jan2010.png|thumb|200px|The nerve bundles (red) are surrounded with cerebro-spinal fluid (CSF) as they traverse the L3 to L5 vertebral canal.]]
|}

{|
|
The cause of back pain is the pressure of the herniated disc onto the spinal nerves. The herniated disc pushes the canal for the cerebro-spinal fluid (CSF). The resulting pressure on the nerve bundles can cause severe discomfort and even permanent disability if not treated.
The right image shows a disc that protrudes into the vertebral foramen and pinches the nerve bundles as they exit the spine.
|
{|
|[[Image:Sylvain_Jaume_disc_herniation_Jan2010.png|thumb|200px|Clinical application]]
|}
|}

{|
|
The CSF has a double role: it acts as a lubricant between the vertebrae and as a mechanical insulation to protect the nerves from outside shocks. The main challenge is to perform the segmentation in a fully automated way.
The image on the right shows the spine overlaid on the MRI image.
|
{|
|[[Image:spine_segmentation_module_in_slicer_001.png|thumb|200px|3D Slicer software]]
|}
|}
{|
|
This patient-specific illustration can help the surgeon during a minimally invasive intervention on the herniated disc.
The image on the right shows an herniated disc that protrudes into the vertebral foramen and reduces the opening for the nerve bundles and the cerebro-spinal fluid (CSF).
|
{|
|[[Image:spine_segmentation_module_in_slicer_002.png|thumb|200px|Disc herniation]]
|}
|}
{|
|[[Image:spine_segmentation_in_slicer_004.png|thumb|340px|Surface meshes and volumetric meshes of our automatically created model of the CSF. The paths where the nerves exit the spine appear as two roots descending on each side of the spinal column.]]
|[[Image:Sylvain_Jaume_nerve_segmentation_rendering_2009.png|thumb|260px|Results of our automated nerve segmentation algorithm. The 3D rendering shows the nerves exiting the spinal cord and the ganglia.]]
|}

{|
|[[Image:spine_segmentation_module_in_slicer_000.png|thumb|300px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:spine_segmentation_module_in_slicer_003.png|thumb|300px|Results of the SpineSegmentation module in Slicer 3.5]]
|}

{|
|[[Image:spine-segmentation-slicer-cylinder.png|thumb|280px|Double cylinder used for our model-based.]]
|[[Image:Jaume_Loepprich_vertebrae_3D_rendering.png|thumb|300px|A complex model of a lumbar vertebrae has been created to drive our shape-based segmentation algorithm in a robust and accurate recognition]]
|}

{|
|[[Image:Sylvain_Jaume_nerve_segmentation_intensity_profile_2009.png|thumb|560px|Intensity profile for the cross-section of a nerve. The MRI image was acquired using the wideband steady-state free-precession (WB-SSFP) protocol.]]
|}

{|
|[[Image:jaume_loepprich_graph_spine_segmentation_module_2010.png|thumb|800px|Organization of the source code for the SpineSegmentation module. This module is available as an extension module for Slicer 3.5.]]
|}

<div style="width: 97%; float: left;">

===Video===
The following video shows the segmentation of a herniated disc from MRI using 3D Slicer

[[Media:Herniated_disc_segmentation_using_3DSlicer.ogg]]

==References==
*Expectation-Maximization segmentation: [http://www.na-mic.org/Wiki/index.php/EMSegment EMSegment] module in Slicer
*Creation of a statistical atlas: [http://www.slicer.org/slicerWiki/index.php/Modules:AtlasCreator-Documentation-3.5 AtlasCreator] module in Slicer
*MRI bias field correction: [http://www.slicer.org/slicerWiki/index.php/Modules:MRIBiasFieldCorrection-Documentation-3.5 MRIBiasFieldCorrection] module in Slicer
*More references: [http://people.csail.mit.edu/sylvain Sylvain Jaume] at MIT CSAIL
</div>

File:Martin Loepprich back pain animation Feb 2010.gif

2010-02-24T15:58:15Z

MartinLoepprich: uploaded a new version of "File:Martin Loepprich back pain animation Feb 2010.gif": Reverted to version as of 15:57, 24 February 2010

Gif animation showing a 3D rendering for spine segmentation results. The pinched nerve due to the disk herniation is highlighted by the flashing concentric circles.

File:Martin Loepprich back pain animation Feb 2010.gif

2010-02-24T15:57:20Z

MartinLoepprich: uploaded a new version of "File:Martin Loepprich back pain animation Feb 2010.gif": Reverted to version as of 15:55, 24 February 2010

Gif animation showing a 3D rendering for spine segmentation results. The pinched nerve due to the disk herniation is highlighted by the flashing concentric circles.

File:Martin Loepprich back pain animation Feb 2010.gif

2010-02-24T15:57:01Z

MartinLoepprich: uploaded a new version of "File:Martin Loepprich back pain animation Feb 2010.gif"

Gif animation showing a 3D rendering for spine segmentation results. The pinched nerve due to the disk herniation is highlighted by the flashing concentric circles.

File:Martin Loepprich back pain animation Feb 2010.gif

2010-02-24T15:55:56Z

MartinLoepprich: uploaded a new version of "File:Martin Loepprich back pain animation Feb 2010.gif"

Gif animation showing a 3D rendering for spine segmentation results. The pinched nerve due to the disk herniation is highlighted by the flashing concentric circles.

2010 Winter Project Week Spine Segmentation Module in Slicer3

2010-01-26T16:56:18Z

MartinLoepprich: /* Video */

__NOTOC__
<gallery>
Image:Loepprich_Jaume_vertebra_Slicer_Jan2010.png|Our 3DSlicer module provides an automated segmentation of the spine in view of the treatment of disc herniation. [http://www.youtube.com/watch?v=kkAuP80kE8E (video)]
Image:Sylvain_Jaume_vertebrae_and_discs_Jan2010.png|This 3D rendering shows the nerve bundles surrounded by the cerebro-spinal fluid as they traverse the vertebrae.
Image:Sylvain_Jaume_disc_herniation_Jan2010.png|Back pain is caused by a disc that protrudes into the vertebral foramen and pinches the nerve bundles as they exit the spine.
Image:PW-SLC2010.png|Our 3DSlicer module for automated segmentation was presented at the [[2010_Winter_Project_Week#Projects|NA-MIC Project Week]] in Salt Lake City, Jan 2010.
</gallery>

==Key Investigators==
* Sylvain Jaume (MIT)
* Martin Löpprich (University of Heidelberg)
* Ron Kikinis, Steve Pieper (BWH)
* Polina Golland (MIT), Ehud Schmidt (BWH)

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

<h3>Objective</h3>
We are developing a Slicer module to segment the region within the thecal sac in MRI images of the spine.
Our objective is to provide a segmentation and visualization tool to improve the treatment of disc herniation.
The structures of interests are the cerebro-spinal fluid (CSF), the discs, the vertebrae and the spinal nerves.

</div>

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

<h3>Approach, Plan</h3>

Our plan for the project week is to integrate our code into Slicer 3.5.
Our code analyzes the intensity profile of different regions in the MRI and automatically defines the optimum region for the CSF.

</div>

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

<h3>Progress</h3>
The algorithm has been implemented in Slicer 3.5 as an extension module.
This volumetric pattern recognition algorithm is fully implemented as a Slicer module using ITK and VTK.
The module has been tested on data sets acquired at Brigham and Women's Hospital.
</div>
</div>

<div style="width: 97%; float: left;">
===Illustrations===

The cause of back pain is the pressure of the herniated disc onto the spinal nerves. The herniated disc pushes the canal for the cerebro-spinal fluid (CSF). The resulting pressure on the nerve bundles can cause severe discomfort and even permanent disability if not treated.

{|
|[[Image:spine_segmentation_module_in_slicer_001.png|thumb|300px|The segmentation the spine overlaid on the MRI image can help the surgeon during a minimally invasive intervention on the herniated disc.]]
|[[Image:spine_segmentation_module_in_slicer_002.png|thumb|300px|This Slicer rendering shows an herniated disc that protrudes into the vertebral foramen and reduces the opening for the nerve bundles and the cerebro-spinal fluid (CSF).]]
|}

The CSF has a double role: it acts as a lubricant between the vertebrae and as a mechanical insulation to protect the nerves from outside shocks. The main challenge is to perform the segmentation in a fully automated way.

{|
|[[Image:spine_segmentation_in_slicer_004.png|thumb|300px|Surface meshes and volumetric meshes of our automatically created model of the CSF. The paths where the nerves exit the spine appear as two roots descending on each side of the spinal column.]]
|[[Image:Sylvain_Jaume_nerve_segmentation_rendering_2009.png|thumb|280px|Results of our automated nerve segmentation algorithm. The 3D rendering shows the nerves exiting the spinal cord and the ganglia.]]
|}

{|
|[[Image:spine_segmentation_module_in_slicer_000.png|thumb|300px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:spine_segmentation_module_in_slicer_003.png|thumb|300px|Results of the SpineSegmentation module in Slicer 3.5]]
|}

{|
|[[Image:spine-segmentation-slicer-cylinder.png|thumb|280px|Double cylinder used for our model-based.]]
|[[Image:Jaume_Loepprich_vertebrae_3D_rendering.png|thumb|300px|A complex model of a lumbar vertebrae has been created to drive our shape-based segmentation algorithm in a robust and accurate recognition]]
|}

{|
|[[Image:Sylvain_Jaume_nerve_segmentation_intensity_profile_2009.png|thumb|560px|Intensity profile for the cross-section of a nerve. The MRI image was acquired using the wideband steady-state free-precession (WB-SSFP) protocol.]]
|}

{|
|[[Image:jaume_loepprich_graph_spine_segmentation_module_2010.png|thumb|800px|Organization of the source code for the SpineSegmentation module. This module is available as an extension module for Slicer 3.5.]]
|}

<div style="width: 97%; float: left;">
===Video===
The following video shows the segmentation of a herniated disc from MRI using 3D Slicer

[[Media:Herniated_disc_segmentation_using_3DSlicer.ogg]]

==References==
*Segmentation using Slicer 3.5, [http://www.na-mic.org/Wiki/index.php/EMSegment EMSegment] module

</div>

2010 Winter Project Week Spine Segmentation Module in Slicer3

2010-01-26T16:56:03Z

MartinLoepprich: /* Key Investigators */

__NOTOC__
<gallery>
Image:Loepprich_Jaume_vertebra_Slicer_Jan2010.png|Our 3DSlicer module provides an automated segmentation of the spine in view of the treatment of disc herniation. [http://www.youtube.com/watch?v=kkAuP80kE8E (video)]
Image:Sylvain_Jaume_vertebrae_and_discs_Jan2010.png|This 3D rendering shows the nerve bundles surrounded by the cerebro-spinal fluid as they traverse the vertebrae.
Image:Sylvain_Jaume_disc_herniation_Jan2010.png|Back pain is caused by a disc that protrudes into the vertebral foramen and pinches the nerve bundles as they exit the spine.
Image:PW-SLC2010.png|Our 3DSlicer module for automated segmentation was presented at the [[2010_Winter_Project_Week#Projects|NA-MIC Project Week]] in Salt Lake City, Jan 2010.
</gallery>

==Key Investigators==
* Sylvain Jaume (MIT)
* Martin Löpprich (University of Heidelberg)
* Ron Kikinis, Steve Pieper (BWH)
* Polina Golland (MIT), Ehud Schmidt (BWH)

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

<h3>Objective</h3>
We are developing a Slicer module to segment the region within the thecal sac in MRI images of the spine.
Our objective is to provide a segmentation and visualization tool to improve the treatment of disc herniation.
The structures of interests are the cerebro-spinal fluid (CSF), the discs, the vertebrae and the spinal nerves.

</div>

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

<h3>Approach, Plan</h3>

Our plan for the project week is to integrate our code into Slicer 3.5.
Our code analyzes the intensity profile of different regions in the MRI and automatically defines the optimum region for the CSF.

</div>

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

<h3>Progress</h3>
The algorithm has been implemented in Slicer 3.5 as an extension module.
This volumetric pattern recognition algorithm is fully implemented as a Slicer module using ITK and VTK.
The module has been tested on data sets acquired at Brigham and Women's Hospital.
</div>
</div>

<div style="width: 97%; float: left;">
===Illustrations===

The cause of back pain is the pressure of the herniated disc onto the spinal nerves. The herniated disc pushes the canal for the cerebro-spinal fluid (CSF). The resulting pressure on the nerve bundles can cause severe discomfort and even permanent disability if not treated.

{|
|[[Image:spine_segmentation_module_in_slicer_001.png|thumb|300px|The segmentation the spine overlaid on the MRI image can help the surgeon during a minimally invasive intervention on the herniated disc.]]
|[[Image:spine_segmentation_module_in_slicer_002.png|thumb|300px|This Slicer rendering shows an herniated disc that protrudes into the vertebral foramen and reduces the opening for the nerve bundles and the cerebro-spinal fluid (CSF).]]
|}

The CSF has a double role: it acts as a lubricant between the vertebrae and as a mechanical insulation to protect the nerves from outside shocks. The main challenge is to perform the segmentation in a fully automated way.

{|
|[[Image:spine_segmentation_in_slicer_004.png|thumb|300px|Surface meshes and volumetric meshes of our automatically created model of the CSF. The paths where the nerves exit the spine appear as two roots descending on each side of the spinal column.]]
|[[Image:Sylvain_Jaume_nerve_segmentation_rendering_2009.png|thumb|280px|Results of our automated nerve segmentation algorithm. The 3D rendering shows the nerves exiting the spinal cord and the ganglia.]]
|}

{|
|[[Image:spine_segmentation_module_in_slicer_000.png|thumb|300px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:spine_segmentation_module_in_slicer_003.png|thumb|300px|Results of the SpineSegmentation module in Slicer 3.5]]
|}

{|
|[[Image:spine-segmentation-slicer-cylinder.png|thumb|280px|Double cylinder used for our model-based.]]
|[[Image:Jaume_Loepprich_vertebrae_3D_rendering.png|thumb|300px|A complex model of a lumbar vertebrae has been created to drive our shape-based segmentation algorithm in a robust and accurate recognition]]
|}

{|
|[[Image:Sylvain_Jaume_nerve_segmentation_intensity_profile_2009.png|thumb|560px|Intensity profile for the cross-section of a nerve. The MRI image was acquired using the wideband steady-state free-precession (WB-SSFP) protocol.]]
|}

{|
|[[Image:jaume_loepprich_graph_spine_segmentation_module_2010.png|thumb|800px|Organization of the source code for the SpineSegmentation module. This module is available as an extension module for Slicer 3.5.]]
|}

<div style="width: 97%; float: left;">
===Video===
The following video shows the segmentation of a herniated disc from MRI using 3D Slicer
[[Media:Herniated_disc_segmentation_using_3DSlicer.ogg]]

==References==
*Segmentation using Slicer 3.5, [http://www.na-mic.org/Wiki/index.php/EMSegment EMSegment] module

</div>

File:Herniated disc segmentation using 3DSlicer.ogg

2010-01-26T16:48:56Z

MartinLoepprich: Segmentation of a Disc Herniation from MRI using 3D Slicer

Segmentation of a Disc Herniation from MRI using 3D Slicer

2010 Winter Project Week Spine Segmentation Module in Slicer3

2010-01-18T23:08:24Z

MartinLoepprich:

__NOTOC__
<gallery>
Image:spine_segmentation_module_in_slicer_001.png|Interface of the SpineSegmentation module in Slicer 3.5
Image:spine_segmentation_module_in_slicer_002.png|Results of the SpineSegmentation module in Slicer 3.5
Image:spine_segmentation_in_slicer_004.png|3D meshes of our automated segmentation results
Image:spine-segmentation-slicer-cylinder.png|Double cylinder used for our model-based ([http://www.youtube.com/watch?v=kkAuP80kE8E segmentation])
</gallery>

==Key Investigators==
* Sylvain Jaume (MIT)
* Martin Loepprich (University of Heidelberg)
* Ron Kikinis, Steve Pieper (BWH)
* Polina Golland (MIT)

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

<h3>Objective</h3>
We are developing a Slicer module to segment the region within the thecal sac in MRI images of the spine.
Our objective is to provide a segmentation and visualization tool to improve the treatment of disc herniation.
The structures of interests are the cerebro-spinal fluid (CSF), the discs, the vertebrae and the spinal nerves.
The main challenge is to perform the segmentation in a fully automated way.

</div>

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

<h3>Approach, Plan</h3>

Our plan for the project week is to integrate our code into Slicer 3.5.
Our code analyzes the intensity profile of different regions in the MRI and automatically defines the optimum region for the CSF.

</div>

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

<h3>Progress</h3>
The algorithm has been implemented in Slicer 3.5 as an extension module.
The code is organized as ITK and VTK classes.
No interaction is required.
The module has been tested on data sets acquired at Brigham and Women's Hospital using the Wideband Steady-State Free-Precession (WB-SSFP) MRI protocol [Krishna Nayak 2007].

</div>
</div>

<div style="width: 97%; float: left;">
===Screenshots===

{|
|[[Image:spine_segmentation_module_in_slicer_000.png|thumb|280px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:spine_segmentation_module_in_slicer_003.png|thumb|280px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:Sylvain_Jaume_nerve_segmentation_rendering_2009.png|thumb|280px|Results of our automated nerve segmentation algorithm. The 3D rendering shows the nerves exiting the spinal cord and the ganglia]]
|}

{|
|[[Image:Sylvain_Jaume_nerve_segmentation_intensity_profile_2009.png|thumb|560px|Intensity profile for the cross-section of a nerve. The MRI image was acquired using the wideband steady-state free-precession (WB-SSFP) protocol.]]
|[[Image:jaume_loepprich_graph_spine_segmentation_module_2010.png|thumb|320px|Organization of the source code for the SpineSegmentation module. This module is available as an extension module for Slicer 3.5.]]
|}

{|
|[[Image:PW-SLC2010.png|thumb|280px|[[2010_Winter_Project_Week#Projects|Projects List]]]]
|}

==References==
*Segmentation using Slicer 3.5, [http://www.na-mic.org/Wiki/index.php/EMSegment EMSegment] module

</div>

2010 Winter Project Week Spine Segmentation Module in Slicer3

2010-01-18T22:14:32Z

MartinLoepprich: /* Video of the Segmentation */

__NOTOC__
<gallery>
Image:spine_segmentation_module_in_slicer_001.png|Interface of the SpineSegmentation module in Slicer 3.5
Image:spine_segmentation_module_in_slicer_002.png|Results of the SpineSegmentation module in Slicer 3.5
Image:spine_segmentation_in_slicer_004.png|3D meshes of our automated segmentation results
Image:spine-segmentation-slicer-cylinder.png|Double cylinder used for our model-based ([http://www.youtube.com/watch?v=kkAuP80kE8E segmentation])
</gallery>

==Key Investigators==
* Sylvain Jaume (MIT)
* Martin Loepprich (University of Heidelberg)
* Ron Kikinis, Steve Pieper (BWH)
* Polina Golland (MIT)

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

<h3>Objective</h3>
We are developing a Slicer module to segment the region within the thecal sac in MRI images of the spine.
Our objective is to provide a segmentation and visualization tool to improve the treatment of disc herniation.
The structures of interests are the cerebro-spinal fluid (CSF), the discs, the vertebrae and the spinal nerves.
The main challenge is to perform the segmentation in a fully automated way.

</div>

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

<h3>Approach, Plan</h3>

Our plan for the project week is to integrate our code into Slicer 3.5.
Our code analyzes the intensity profile of different regions in the MRI and automatically defines the optimum region for the CSF.

</div>

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

<h3>Progress</h3>
The algorithm has been implemented in Slicer 3.5 as an extension module.
The code is organized as ITK and VTK classes.
No interaction is required.
The module has been tested on data sets acquired at Brigham and Women's Hospital using the Wideband Steady-State Free-Precession (WB-SSFP) MRI protocol [Krishna Nayak 2007].

</div>
</div>

<div style="width: 97%; float: left;">
===Screenshots===

{|
|[[Image:spine_segmentation_module_in_slicer_000.png|thumb|280px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:spine_segmentation_module_in_slicer_003.png|thumb|280px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:Sylvain_Jaume_nerve_segmentation_rendering_2009.png|thumb|280px|Results of our automated nerve segmentation algorithm. The 3D rendering shows the nerves exiting the spinal cord and the ganglia]]
|}

{|
|[[Image:Sylvain_Jaume_nerve_segmentation_intensity_profile_2009.png|thumb|560px|Intensity profile for the cross-section of a nerve. The MRI image was acquired using the wideband steady-state free-precession (WB-SSFP) protocol.]]
|[[Image:jaume_loepprich_graph_spine_segmentation_module_2010.png|thumb|320px|Organization of the source code for the SpineSegmentation module. This module is available as an extension module for Slicer 3.5.]]
|}

{|
|[[Image:PW-SLC2010.png|thumb|280px|[[2010_Winter_Project_Week#Projects|Projects List]]]]
|}

<div style="width: 97%; float: left;">
===Video of the Segmentation===
<object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/kkAuP80kE8E&hl=de_DE&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/kkAuP80kE8E&hl=de_DE&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object>

==References==
*Segmentation using Slicer 3.5, [http://www.na-mic.org/Wiki/index.php/EMSegment EMSegment] module

</div>

2010 Winter Project Week Spine Segmentation Module in Slicer3

2010-01-18T22:13:48Z

MartinLoepprich: /* Key Investigators */

__NOTOC__
<gallery>
Image:spine_segmentation_module_in_slicer_001.png|Interface of the SpineSegmentation module in Slicer 3.5
Image:spine_segmentation_module_in_slicer_002.png|Results of the SpineSegmentation module in Slicer 3.5
Image:spine_segmentation_in_slicer_004.png|3D meshes of our automated segmentation results
Image:spine-segmentation-slicer-cylinder.png|Double cylinder used for our model-based ([http://www.youtube.com/watch?v=kkAuP80kE8E segmentation])
</gallery>

==Key Investigators==
* Sylvain Jaume (MIT)
* Martin Loepprich (University of Heidelberg)
* Ron Kikinis, Steve Pieper (BWH)
* Polina Golland (MIT)

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

<h3>Objective</h3>
We are developing a Slicer module to segment the region within the thecal sac in MRI images of the spine.
Our objective is to provide a segmentation and visualization tool to improve the treatment of disc herniation.
The structures of interests are the cerebro-spinal fluid (CSF), the discs, the vertebrae and the spinal nerves.
The main challenge is to perform the segmentation in a fully automated way.

</div>

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

<h3>Approach, Plan</h3>

Our plan for the project week is to integrate our code into Slicer 3.5.
Our code analyzes the intensity profile of different regions in the MRI and automatically defines the optimum region for the CSF.

</div>

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

<h3>Progress</h3>
The algorithm has been implemented in Slicer 3.5 as an extension module.
The code is organized as ITK and VTK classes.
No interaction is required.
The module has been tested on data sets acquired at Brigham and Women's Hospital using the Wideband Steady-State Free-Precession (WB-SSFP) MRI protocol [Krishna Nayak 2007].

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===Screenshots===

{|
|[[Image:spine_segmentation_module_in_slicer_000.png|thumb|280px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:spine_segmentation_module_in_slicer_003.png|thumb|280px|Results of the SpineSegmentation module in Slicer 3.5]]
|[[Image:Sylvain_Jaume_nerve_segmentation_rendering_2009.png|thumb|280px|Results of our automated nerve segmentation algorithm. The 3D rendering shows the nerves exiting the spinal cord and the ganglia]]
|}

{|
|[[Image:Sylvain_Jaume_nerve_segmentation_intensity_profile_2009.png|thumb|560px|Intensity profile for the cross-section of a nerve. The MRI image was acquired using the wideband steady-state free-precession (WB-SSFP) protocol.]]
|[[Image:jaume_loepprich_graph_spine_segmentation_module_2010.png|thumb|320px|Organization of the source code for the SpineSegmentation module. This module is available as an extension module for Slicer 3.5.]]
|}

{|
|[[Image:PW-SLC2010.png|thumb|280px|[[2010_Winter_Project_Week#Projects|Projects List]]]]
|}

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===Video of the Segmentation===

==References==
*Segmentation using Slicer 3.5, [http://www.na-mic.org/Wiki/index.php/EMSegment EMSegment] module

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File:Spine-segmentation-slicer-cylinder.png

2010-01-18T21:22:34Z

MartinLoepprich: uploaded a new version of "File:Spine-segmentation-slicer-cylinder.png"

Add drawing to illustrate the model used for segmentation of the CSF in spine MRI