2017 Winter Project Week/MeningiomaSegmentation - Revision history

Jakubk at 21:20, 13 January 2017

2017-01-13T21:20:41Z

Jakubk: fixed formatting

2017-01-13T21:09:09Z

fixed formatting

Jakubk: Added examples

2017-01-13T21:02:38Z

Added examples

Jakubk at 01:44, 13 January 2017

2017-01-13T01:44:31Z

Jakubk at 01:32, 13 January 2017

2017-01-13T01:32:38Z

Jakubk at 01:25, 13 January 2017

2017-01-13T01:25:42Z

Jakubk at 01:21, 13 January 2017

2017-01-13T01:21:50Z

Jakubk at 01:20, 13 January 2017

2017-01-13T01:20:46Z

Jakubk: added progress and next steps

2017-01-13T01:11:56Z

added progress and next steps

Jakubk: Created page

2017-01-04T16:38:58Z

Created page

New page

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==

* Satrajit Ghosh, MIT
* Omar Arnaout, Brigham and Women's Hospital

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Segment meningiomas in structural MR images.
* Assess state of brain after surgical removal of meningioma.
|

* Evaluate performance of existing segmentation methods.
|

*
|}

==Background and References==

MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].

@@ Line 47: / Line 47: @@
 [[File:Case_001_ants_brain_failure.png|thumbnail|Sometimes, ANTs failed to remove parts of the skull close to the tumor or wrongly removed part of the brain.]]
 [[File:Case_052_ants_brain.png|thumbnail|Other times, ANTs extracted the brain well.]]
-[[File:Case_052_ants_brain_seg.png|thumbnail|Automatic segmentation with ANTs usually classified as CSF or it classified different parts of the tumor as different types of tissue.]]
+[[File:Case_052_ants_brain_seg.png|thumbnail|Automatic segmentation with ANTs usually could not distinguish the tumor from the rest of the brain.]]
 [[File:Case_052_2_slicer_seg.png|thumbnail|Semi-automatic segmentation with Slicer was relatively successful. Sometimes the segmentation would bleed outside of the tumor into voxels with similar intensities.]]
+|

@@ Line 44: / Line 44: @@
 ==Examples==
 {| class="wikitable"
 |Sometimes, ANTs failed to remove parts of the skull close to the tumor or wrongly removed part of the brain.
-[[File:Case_001_ants_brain_failure.png|thumbnail|ANTs brain extraction failure]]
+[[File:Case_001_ants_brain_failure.png|thumbnail|Sometimes, ANTs failed to remove parts of the skull close to the tumor or wrongly removed part of the brain.]]
-But other times, ANTs extracted the brain very well.
+[[File:Case_052_ants_brain.png|thumbnail|Other times, ANTs extracted the brain well.]]
-[[File:Case_052_ants_brain.png|thumbnail|Ants brain extraction success]]
+[[File:Case_052_ants_brain_seg.png|thumbnail|Automatic segmentation with ANTs usually classified as CSF or it classified different parts of the tumor as different types of tissue.]]
-Automatic segmentation with ANTs usually classified as CSF or it classified different parts of the tumor as different types of tissue.
+[[File:Case_052_2_slicer_seg.png|thumbnail|Semi-automatic segmentation with Slicer was relatively successful. Sometimes the segmentation would bleed outside of the tumor into voxels with similar intensities.]]
+|
 We tried FSL's FAST with different numbers of classes. None of these methods could identify the entire tumor mass as one type of tissue in this scan.
@@ Line 58: / Line 55: @@
 [[File:Case_052_fast_5classes.png|thumbnail|FAST brain segmentation with 5 classes]]
 |}

@@ Line 36: / Line 36: @@
 * Continue testing existing segmentation methods.
 * Try Slicer in a Nipype workflow.
-* Apply manifold learning (a method of dimensionality reduction).
+* Apply feature engineering techniques, like manifold learning.
 * Get more data, and potentially train a neural network.
 |}

@@ Line 3: / Line 3: @@
 Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]
 <!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" -->
-Image:Jk_meningioma_seg.png|link=http://www.na-mic.org/Wiki/images/5/5b/Jk_meningioma_seg.png | [http://www.na-mic.org/Wiki/images/5/5b/Jk_meningioma_seg.png Meningioma Segmentation]
+Image:Jk_meningioma_seg.png|link=http://www.na-mic.org/Wiki/images/5/5b/Jk_meningioma_seg.png | [http://www.na-mic.org/Wiki/index.php/File:Jk_meningioma_seg.png Meningioma Segmentation]
 </gallery>

@@ Line 37: / Line 37: @@
 * Try Slicer in a Nipype workflow.
 * Apply manifold learning (a method of dimensionality reduction).
 |}

@@ Line 8: / Line 8: @@
 ==Key Investigators==
 <!-- Add a bulleted list of investigators and their institutions here -->
 * Satrajit Ghosh, MIT
 * Omar Arnaout, Brigham and Women's Hospital
@@ Line 39: / Line 40: @@
 * Get more data, and potentially train a neural network.
 |}
 ==Background and References==
 <!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data -->
 MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]
+Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]
 <!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" -->
-Image:Jk_meningioma_seg.png|link=http://www.na-mic.org/Wiki/images/5/5b/Jk_meningioma_seg.png|[http://www.na-mic.org/Wiki/images/5/5b/Jk_meningioma_seg.png Meningioma Segmentation]
+Image:Jk_meningioma_seg.png|link=http://www.na-mic.org/Wiki/images/5/5b/Jk_meningioma_seg.png | [http://www.na-mic.org/Wiki/images/5/5b/Jk_meningioma_seg.png Meningioma Segmentation]
 </gallery>