2009 Summer Project Week Skull Stripping - Revision history

Medcomparts: /* Key Investigators */

2009-07-20T10:43:39Z

Key Investigators

Taox at 13:22, 26 June 2009

2009-06-26T13:22:08Z

Taox at 13:14, 26 June 2009

2009-06-26T13:14:07Z

Snehashis at 02:11, 26 June 2009

2009-06-26T02:11:08Z

Snehashis: update for the week

2009-06-26T02:08:02Z

update for the week

Tkapur at 01:57, 22 June 2009

2009-06-22T01:57:44Z

Naucoin at 18:13, 4 June 2009

2009-06-04T18:13:48Z

Taox at 02:26, 4 June 2009

2009-06-04T02:26:42Z

Taox: Created page with 'NOTOC Image:PW2009-v3.png|Project Week Main Page Image:GESkullStripping.png|Deformble surface modle for skull stripping. Image:JHUSkull...'

2009-06-04T02:20:29Z

Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:GESkullStripping.png|Deformble surface modle for skull stripping. Image:JHUSkull...'

New page

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:GESkullStripping.png|Deformble surface modle for skull stripping.
Image:JHUSkullStripping.png|Skull stripping using joint registration and segmentation.
</gallery>

==Key Investigators==
* JHU: Snehashis Roy
* GE : Xiaodong Tao

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

<h3>Objective</h3>
We will discuss the possibility of combining the skull stripping algorithm developed at JHU (a joint registration and segmentation approach) and the one developed at GE (a deformable surface model) into a single skull stripping algorithm to be included in NA-MIC kit.

</div>

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

<h3>Approach, Plan</h3>
To understand each approach and discuss the best way to combining the effort. Develop a plan for implementation as a Slicer module.

</div>

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

<h3>Progress</h3>
The deformable surface based approach is similar to Brain Extraction Tool (BET). The algorithm has been tested on 300+ T1 weighted images from OASIS database and shows a DICE score of 0.94 with the brain masks provided in the OASIS database. This algorithm may be modified to work on images with other contrast mechanisms. The joint registration and segmentation algorithm also works on T! weighted images, and has been tested on a few hundreds of images with good accuracy.

</div>
</div>

==References==
* Aaron Carass, M. Bryan Wheeler, Jennifer Cuzzocreo, Pierre-Louis Bazin, Susan S. Bassett and Jerry L. Prince, A JOINT REGISTRATION AND SEGMENTATION APPROACH TO SKULL STRIPPING, ISBI 2007.

@@ Line 28: / Line 28: @@
 <h3>Approach, Plan</h3>
-To understand each approach and discuss the best way to combining the effort. Develop a plan for implementation as a Slicer module.
+To understand each approach and discuss the best way to combine these efforts. Develop a plan for implementation as a Slicer module.
 </div>
@@ Line 35: / Line 35: @@
 <h3>Progress</h3>
-The deformable surface based approach is similar to Brain Extraction Tool (BET). The algorithm has been tested on 300+ T1 weighted images from OASIS database and shows a DICE score of 0.94 with the brain masks provided in the OASIS database. This algorithm may be modified to work on images with other contrast mechanisms. The joint registration and segmentation algorithm also works on T1 weighted images, and has been tested on a few hundreds of images with good accuracy.
+The deformable surface-based approach is similar to the Brain Extraction Tool (BET). The algorithm has been tested on 300+ T1 weighted images from OASIS database and shows a DICE score of 0.94 with the brain masks provided in the OASIS database. This algorithm may be modified to work on images with other contrast mechanisms. The joint registration and segmentation algorithm also works on T1 weighted images, and has been tested on several hundred images with good accuracy.
-* '''Update #1''': We have successfully compiled the skull stripping algorithm, Simple Paradigm for Extra-Cranial Tissue Removal (SPECTRE) as a Slicer3.4 plugin. The following images show an OASIS brain skull-stripped with the plugin. The method requires a registration. The Affine Registration module of Slicer3.4 does not provide desired result. So we will include Deformable BSpline registration and provide a plugin.
+* '''Update #1''': We have successfully compiled the skull stripping algorithm, Simple Paradigm for Extra-Cranial Tissue Removal (SPECTRE) as a Slicer3.4 plugin. The following images show an OASIS brain skull-stripped with the plugin. The method requires a registration. The Affine Registration module of Slicer3.4 does not provide the desired result. Therefore, we will include Deformable BSpline registration and provide a plugin.
 </div>
 </div>

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
 Image:GESkullStripping.png | Deformble surface modle for skull stripping.
 Image:JHUSkullStripping.png | Skull stripping using joint registration and segmentation.
 </gallery>

@@ Line 4: / Line 4: @@
 Image:GESkullStripping.png | Deformble surface modle for skull stripping.
 Image:JHUSkullStripping.png | Skull stripping using joint registration and segmentation.
 </gallery>

@@ Line 33: / Line 33: @@
 The deformable surface based approach is similar to Brain Extraction Tool (BET). The algorithm has been tested on 300+ T1 weighted images from OASIS database and shows a DICE score of 0.94 with the brain masks provided in the OASIS database. This algorithm may be modified to work on images with other contrast mechanisms. The joint registration and segmentation algorithm also works on T1 weighted images, and has been tested on a few hundreds of images with good accuracy.
-'''Update #1''': We have successfully compiled the skull stripping algorithm, Simple Paradigm for Extra-Cranial Tissue Removal (SPECTRE) as a Slicer3.4 plugin. The following images show an OASIS brain skull-stripped with the plugin. The method requires a registration. The Affine Transformation module of Slicer3.4 does not provide desired result. So we will include Deformable BSpline registration and provide a plugin.
+* '''Update #1''': We have successfully compiled the skull stripping algorithm, Simple Paradigm for Extra-Cranial Tissue Removal (SPECTRE) as a Slicer3.4 plugin. The following images show an OASIS brain skull-stripped with the plugin. The method requires a registration. The Affine Registration module of Slicer3.4 does not provide desired result. So we will include Deformable BSpline registration and provide a plugin.
 </div>
 </div>

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:PW2009-v3.png | .
+Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
 Image:GESkullStripping.png | Deformble surface modle for skull stripping.
 Image:JHUSkullStripping.png | Skull stripping using joint registration and segmentation.
 </gallery>
 ==Key Investigators==

@@ Line 31: / Line 31: @@
 <h3>Progress</h3>
-The deformable surface based approach is similar to Brain Extraction Tool (BET). The algorithm has been tested on 300+ T1 weighted images from OASIS database and shows a DICE score of 0.94 with the brain masks provided in the OASIS database. This algorithm may be modified to work on images with other contrast mechanisms. The joint registration and segmentation algorithm also works on T! weighted images, and has been tested on a few hundreds of images with good accuracy.
+The deformable surface based approach is similar to Brain Extraction Tool (BET). The algorithm has been tested on 300+ T1 weighted images from OASIS database and shows a DICE score of 0.94 with the brain masks provided in the OASIS database. This algorithm may be modified to work on images with other contrast mechanisms. The joint registration and segmentation algorithm also works on T1 weighted images, and has been tested on a few hundreds of images with good accuracy.
 </div>
 </div>
 ==References==
 * Aaron Carass, M. Bryan Wheeler, Jennifer Cuzzocreo, Pierre-Louis Bazin, Susan S. Bassett and Jerry L. Prince, A JOINT REGISTRATION AND SEGMENTATION APPROACH TO SKULL STRIPPING, ISBI 2007.

@@ Line 9: / Line 9: @@
 * JHU: Snehashis Roy
 * GE : Xiaodong Tao
 <div style="margin: 20px;">