View source for 2017 Winter Project Week/MeningiomaSegmentation

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Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]
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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]
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==Key Investigators==
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* Jakub Kaczmarzyk, MIT
* 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;"
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* Segment meningiomas in structural MR images.
* Assess state of brain after surgical removal of meningioma.
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<!-- Approach and Plan bullet points -->
* Evaluate performance of existing segmentation methods.
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Progress
* Segmented with ANTs and FSL.
* Learned about Slicer segmentation tools, and segmented semi-automatically.
* Put in contact with people who have segmented meningiomas.

Next steps
* Continue learning about what has been done in the past.
* Improve brain-extraction.
* Continue testing existing segmentation methods.
* Try Slicer in a Nipype workflow.
* Apply feature engineering techniques, like manifold learning.
* Get more data, and potentially train a neural network.
|}


==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]]
But other times, ANTs extracted the brain very well.
[[File:Case_052_ants_brain.png|thumbnail|Ants brain extraction success]]
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|Brain segmentation with ANTs]]
Semi-automatic segmentation with Slicer was relatively successful. Sometimes the segmentation would bleed outside of the tumor into voxels with similar intensities.
[[File:Case_052_2_slicer_seg.png|thumbnail|Semi-automatic segmentation with Slicer]]
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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.
[[File:Case_052_fast_3classes.png|thumbnail|FAST brain segmentation with 3 classes]]
[[File:Case_052_fast_4classes.png|thumbnail|FAST brain segmentation with 4 classes]]
[[File:Case_052_fast_5classes.png|thumbnail|FAST brain segmentation with 5 classes]]
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==Background and References==
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MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].