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	<id>https://www.na-mic.org/w/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Jakubk</id>
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	<updated>2026-05-05T09:30:05Z</updated>
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	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=95190</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=95190"/>
		<updated>2017-01-13T21:20:41Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
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]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Jakub Kaczmarzyk, MIT&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply feature engineering techniques, like manifold learning.&lt;br /&gt;
* Get more data, and potentially train a neural network.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Examples==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
[[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.]]&lt;br /&gt;
[[File:Case_052_ants_brain.png|thumbnail|Other times, ANTs extracted the brain well.]]&lt;br /&gt;
[[File:Case_052_ants_brain_seg.png|thumbnail|Automatic segmentation with ANTs usually could not distinguish the tumor from the rest of the brain.]]&lt;br /&gt;
[[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.]]&lt;br /&gt;
|&lt;br /&gt;
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.&lt;br /&gt;
[[File:Case_052_fast_3classes.png|thumbnail|FAST brain segmentation with 3 classes]]&lt;br /&gt;
[[File:Case_052_fast_4classes.png|thumbnail|FAST brain segmentation with 4 classes]]&lt;br /&gt;
[[File:Case_052_fast_5classes.png|thumbnail|FAST brain segmentation with 5 classes]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=95189</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=95189"/>
		<updated>2017-01-13T21:09:09Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: fixed formatting&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
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]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Jakub Kaczmarzyk, MIT&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply feature engineering techniques, like manifold learning.&lt;br /&gt;
* Get more data, and potentially train a neural network.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Examples==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
[[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.]]&lt;br /&gt;
[[File:Case_052_ants_brain.png|thumbnail|Other times, ANTs extracted the brain well.]]&lt;br /&gt;
[[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.]]&lt;br /&gt;
[[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.]]&lt;br /&gt;
|&lt;br /&gt;
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.&lt;br /&gt;
[[File:Case_052_fast_3classes.png|thumbnail|FAST brain segmentation with 3 classes]]&lt;br /&gt;
[[File:Case_052_fast_4classes.png|thumbnail|FAST brain segmentation with 4 classes]]&lt;br /&gt;
[[File:Case_052_fast_5classes.png|thumbnail|FAST brain segmentation with 5 classes]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=95188</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=95188"/>
		<updated>2017-01-13T21:02:38Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: Added examples&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
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]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Jakub Kaczmarzyk, MIT&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply feature engineering techniques, like manifold learning.&lt;br /&gt;
* Get more data, and potentially train a neural network.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Examples==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|Sometimes, ANTs failed to remove parts of the skull close to the tumor or wrongly removed part of the brain.&lt;br /&gt;
[[File:Case_001_ants_brain_failure.png|thumbnail|ANTs brain extraction failure]]&lt;br /&gt;
But other times, ANTs extracted the brain very well.&lt;br /&gt;
[[File:Case_052_ants_brain.png|thumbnail|Ants brain extraction success]]&lt;br /&gt;
Automatic segmentation with ANTs usually classified as CSF or it classified different parts of the tumor as different types of tissue.&lt;br /&gt;
[[File:Case_052_ants_brain_seg.png|thumbnail|Brain segmentation with ANTs]]&lt;br /&gt;
Semi-automatic segmentation with Slicer was relatively successful. Sometimes the segmentation would bleed outside of the tumor into voxels with similar intensities.&lt;br /&gt;
[[File:Case_052_2_slicer_seg.png|thumbnail|Semi-automatic segmentation with Slicer]]&lt;br /&gt;
|&lt;br /&gt;
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.&lt;br /&gt;
[[File:Case_052_fast_3classes.png|thumbnail|FAST brain segmentation with 3 classes]]&lt;br /&gt;
[[File:Case_052_fast_4classes.png|thumbnail|FAST brain segmentation with 4 classes]]&lt;br /&gt;
[[File:Case_052_fast_5classes.png|thumbnail|FAST brain segmentation with 5 classes]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=File:Case_052_fast_5classes.png&amp;diff=95187</id>
		<title>File:Case 052 fast 5classes.png</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=File:Case_052_fast_5classes.png&amp;diff=95187"/>
		<updated>2017-01-13T20:45:47Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: Segmentation of brain with FAST (4 classes).&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Segmentation of brain with FAST (4 classes).&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=File:Case_052_fast_4classes.png&amp;diff=95186</id>
		<title>File:Case 052 fast 4classes.png</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=File:Case_052_fast_4classes.png&amp;diff=95186"/>
		<updated>2017-01-13T20:45:33Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: Segmentation of brain with FAST (4 classes).&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Segmentation of brain with FAST (4 classes).&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=File:Case_052_fast_3classes.png&amp;diff=95185</id>
		<title>File:Case 052 fast 3classes.png</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=File:Case_052_fast_3classes.png&amp;diff=95185"/>
		<updated>2017-01-13T20:45:22Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: Segmentation of brain with FAST (3 classes).&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Segmentation of brain with FAST (3 classes).&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=File:Case_052_ants_brain.png&amp;diff=95184</id>
		<title>File:Case 052 ants brain.png</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=File:Case_052_ants_brain.png&amp;diff=95184"/>
		<updated>2017-01-13T20:44:53Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: Successful brain extraction with ANTs.&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Successful brain extraction with ANTs.&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=File:Case_052_ants_brain_seg.png&amp;diff=95183</id>
		<title>File:Case 052 ants brain seg.png</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=File:Case_052_ants_brain_seg.png&amp;diff=95183"/>
		<updated>2017-01-13T20:44:05Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: ANTs segmentation of brain with meningioma.&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;ANTs segmentation of brain with meningioma.&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=File:Case_052_2_slicer_seg.png&amp;diff=95182</id>
		<title>File:Case 052 2 slicer seg.png</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=File:Case_052_2_slicer_seg.png&amp;diff=95182"/>
		<updated>2017-01-13T20:43:24Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: Semi-automatic meningioma segmentation with Slicer's Segmentation Editor module.&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Semi-automatic meningioma segmentation with Slicer's Segmentation Editor module.&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=File:Case_001_ants_brain_failure.png&amp;diff=95181</id>
		<title>File:Case 001 ants brain failure.png</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=File:Case_001_ants_brain_failure.png&amp;diff=95181"/>
		<updated>2017-01-13T20:42:30Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: ANTs segmentation fails on this brain with a meningioma.&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;ANTs segmentation fails on this brain with a meningioma.&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94943</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94943"/>
		<updated>2017-01-13T01:44:31Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
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]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply feature engineering techniques, like manifold learning.&lt;br /&gt;
* Get more data, and potentially train a neural network.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94942</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94942"/>
		<updated>2017-01-13T01:32:38Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
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]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply manifold learning (a method of dimensionality reduction).&lt;br /&gt;
* Get more data, and potentially train a neural network.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94941</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94941"/>
		<updated>2017-01-13T01:25:42Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
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]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply manifold learning (a method of dimensionality reduction).&lt;br /&gt;
* Get more data, and potentially train a neural network.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94940</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94940"/>
		<updated>2017-01-13T01:21:50Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects | [[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
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]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply manifold learning (a method of dimensionality reduction).&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94939</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94939"/>
		<updated>2017-01-13T01:20:46Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
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]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply manifold learning (a method of dimensionality reduction).&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94938</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94938"/>
		<updated>2017-01-13T01:11:56Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: added progress and next steps&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
Image:Jk_meningioma_seg.png|link=File:Jk_meningioma_seg.png|[[Jk_meningioma_seg.png|Meningioma Segmentation]]&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
Progress&lt;br /&gt;
* Segmented with ANTs and FSL.&lt;br /&gt;
* Learned about Slicer segmentation tools, and segmented semi-automatically.&lt;br /&gt;
* Put in contact with people who have segmented meningiomas.&lt;br /&gt;
&lt;br /&gt;
Next steps&lt;br /&gt;
* Continue learning about what has been done in the past.&lt;br /&gt;
* Improve brain-extraction.&lt;br /&gt;
* Continue testing existing segmentation methods.&lt;br /&gt;
* Try Slicer in a Nipype workflow.&lt;br /&gt;
* Apply manifold learning (a method of dimensionality reduction).&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=File:Jk_meningioma_seg.png&amp;diff=94937</id>
		<title>File:Jk meningioma seg.png</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=File:Jk_meningioma_seg.png&amp;diff=94937"/>
		<updated>2017-01-13T00:33:20Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: Semi-automatic segmentation of meningioma using Slicer&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Semi-automatic segmentation of meningioma using Slicer&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&amp;diff=94312</id>
		<title>2017 Winter Project Week</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&amp;diff=94312"/>
		<updated>2017-01-04T16:41:41Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: /* IGT: Navigation, Robotics, Surgical Planning */ Added link to new project (meningioma segmentation)&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
[[image:PW-Winter2017.png|300px]]&lt;br /&gt;
&lt;br /&gt;
=Welcome to the web page for the 24th Project Week!=&lt;br /&gt;
&lt;br /&gt;
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].&lt;br /&gt;
&lt;br /&gt;
==Logistics==&lt;br /&gt;
&lt;br /&gt;
*'''Dates:''' January 9-13, 2017.&lt;br /&gt;
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&amp;amp;D)&lt;br /&gt;
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.&lt;br /&gt;
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.&lt;br /&gt;
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], enhancements to the underlying building blocks [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an open source hackathon event called Project Week.&lt;br /&gt;
&lt;br /&gt;
[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. &lt;br /&gt;
&lt;br /&gt;
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.&lt;br /&gt;
&lt;br /&gt;
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. &lt;br /&gt;
&lt;br /&gt;
A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].&lt;br /&gt;
&lt;br /&gt;
Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]&lt;br /&gt;
&lt;br /&gt;
==Conference Calls for Preparation==&lt;br /&gt;
&lt;br /&gt;
Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].&lt;br /&gt;
&lt;br /&gt;
==Calendar==&lt;br /&gt;
&lt;br /&gt;
'''''&amp;lt;font color=&amp;quot;maroon&amp;quot;&amp;gt;The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.&amp;lt;/font&amp;gt;'''''&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{{#widget:Google Calendar&lt;br /&gt;
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com&lt;br /&gt;
|timezone=America/New_York&amp;amp;dates=20170108%2F20170114&lt;br /&gt;
|title=NAMIC Winter Project Week&lt;br /&gt;
|view=WEEK&lt;br /&gt;
|dates=20170108/20170114&lt;br /&gt;
}}&lt;br /&gt;
&lt;br /&gt;
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics&lt;br /&gt;
&lt;br /&gt;
='''Projects'''=&lt;br /&gt;
&lt;br /&gt;
*Use this [[2017_Project_Week_Template | Updated Template for project pages]]&lt;br /&gt;
&lt;br /&gt;
== Learning and GPUs ==&lt;br /&gt;
&lt;br /&gt;
* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Tina Kapur)&lt;br /&gt;
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei &amp;quot;Ada&amp;quot; Wang)&lt;br /&gt;
* [[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)&lt;br /&gt;
&lt;br /&gt;
== Web Technologies ==&lt;br /&gt;
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]]  (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)&lt;br /&gt;
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]]  (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)&lt;br /&gt;
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]]  (Erich Bremer, Steve Pieper)&lt;br /&gt;
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)&lt;br /&gt;
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)&lt;br /&gt;
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)&lt;br /&gt;
&lt;br /&gt;
== Visualization ==&lt;br /&gt;
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer &amp;amp; HoloLens]]  (Adam Rankin, Andras Lasso)&lt;br /&gt;
&lt;br /&gt;
== IGT: Navigation, Robotics, Surgical Planning ==&lt;br /&gt;
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]]  (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)&lt;br /&gt;
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]]  (Tobias Frank, Junichi Tokuda, Longquan Chen)&lt;br /&gt;
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]]  (Peter Traneus Anderson)&lt;br /&gt;
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]]  (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )&lt;br /&gt;
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)&lt;br /&gt;
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)&lt;br /&gt;
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)&lt;br /&gt;
* [[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)&lt;br /&gt;
&lt;br /&gt;
==dMRI==&lt;br /&gt;
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]]  (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)&lt;br /&gt;
* [[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Frederik Westin)&lt;br /&gt;
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]]  (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)&lt;br /&gt;
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)&lt;br /&gt;
* [[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)&lt;br /&gt;
&lt;br /&gt;
== Infrastructure ==&lt;br /&gt;
&lt;br /&gt;
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)&lt;br /&gt;
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)&lt;br /&gt;
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)&lt;br /&gt;
&lt;br /&gt;
==To be Categorized==&lt;br /&gt;
&lt;br /&gt;
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)&lt;br /&gt;
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)&lt;br /&gt;
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)&lt;br /&gt;
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)&lt;br /&gt;
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)&lt;br /&gt;
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)&lt;br /&gt;
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)&lt;br /&gt;
&lt;br /&gt;
= '''Registrants''' =&lt;br /&gt;
&lt;br /&gt;
Do not add your name to this list - it is maintained by the organizers based on your paid registration.  To register, visit this [https://www.regonline.com/2017projectweek registration site].&lt;br /&gt;
&lt;br /&gt;
# A, Zeina :: SHBOUL&lt;br /&gt;
# Aerts, Hugo :: DFCI-Harvard&lt;br /&gt;
# Alam, Mahbubul :: Old Dominion University&lt;br /&gt;
# Anderson, Peter :: Retired&lt;br /&gt;
# Andruejol, Johan  :: Kitware, Inc.&lt;br /&gt;
# Bakeng, Janne Beate  :: SINTEF&lt;br /&gt;
# Beers, Andrew :: Massachusetts General Hospital&lt;br /&gt;
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital&lt;br /&gt;
# Bremer, Erich :: Stony Brook University&lt;br /&gt;
# Burke, Brice :: American University of Antigua College of Medicine&lt;br /&gt;
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital&lt;br /&gt;
# Chae, Michael :: Monash University&lt;br /&gt;
# Chauvin, Laurent :: ETS&lt;br /&gt;
# Dalca, Adrian :: Massachusetts Institute of Technology&lt;br /&gt;
# Fedorov, Andriy :: Brigham and Women's Hospital&lt;br /&gt;
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.&lt;br /&gt;
# Fishbaugh, James :: New York University&lt;br /&gt;
# Frank, Tobias :: Leibniz Universität Hannover&lt;br /&gt;
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid&lt;br /&gt;
# Girault, Alexis :: Kitware, Inc.&lt;br /&gt;
# Golland, Polina :: Massachusetts Institute of Technology&lt;br /&gt;
# Gollub, Randy :: Massachusetts General Hospital&lt;br /&gt;
# Gong, Shun :: Brigham and Women's Hospital&lt;br /&gt;
# Guerrier de Dumast, Priscille :: University of Michigan&lt;br /&gt;
# Harris, Gordon :: Massachusetts General Hospital&lt;br /&gt;
# Herz, Christian :: Brigham and Women's Hospital&lt;br /&gt;
# Hong, Sungmin :: New York University&lt;br /&gt;
# Hosny, Ahmed :: Dana-Farber&lt;br /&gt;
# Jagadeesan, Jayender :: Brigham and Women's Hospital&lt;br /&gt;
# Jensen, Henrik G. :: University of Copenhagen&lt;br /&gt;
# Kapur, Tina :: Brigham and Women's Hospital&lt;br /&gt;
# Kikinis, Ron :: Brigham and Women's Hospital&lt;br /&gt;
# Lasso, Andras :: PerkLab, Queen's University&lt;br /&gt;
# Lauer, Rebekka :: Humboldt University Berlin&lt;br /&gt;
# Lisle, Curtis :: KnowledgeVis, LLC&lt;br /&gt;
# Mastrogiacomo, Katie :: Brigham and Women's Hospital&lt;br /&gt;
# Mateus, D. :: TUM&lt;br /&gt;
# Mehrtash, Alireza :: Brigham and Women's Hospital&lt;br /&gt;
# Meine, Hans :: University of Bremen&lt;br /&gt;
# Meyer, Anneke :: University of Magdeburg&lt;br /&gt;
# Miller, James :: GE Research&lt;br /&gt;
# Mirabel, Clement :: University of Michigan&lt;br /&gt;
# Nitsch, Jennifer :: University of Bremen&lt;br /&gt;
# Norton, Isaiah :: Brigham and Women's Hospital&lt;br /&gt;
# O'Donnell, Lauren :: Brigham and Women's Hospital&lt;br /&gt;
# Oram, Louise :: The Intervention Centre-Oslo University Hospital&lt;br /&gt;
# Paniagua, Beatriz :: Kitware, Inc.&lt;br /&gt;
# Parmar, Chintan :: DFCI-Harvard Medical School&lt;br /&gt;
# Peled, Sharon :: Brigham and Women's Hospital&lt;br /&gt;
# Pieper, Steve :: Isomics, Inc.&lt;br /&gt;
# Pinter, Csaba :: Queen's University&lt;br /&gt;
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School&lt;br /&gt;
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School&lt;br /&gt;
# Rankin, Adam :: Robarts Research Institute&lt;br /&gt;
# Rheault, Francois :: Université de Sherbrooke&lt;br /&gt;
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin&lt;br /&gt;
# Sharp, Gregory :: Massachusetts General Hospital&lt;br /&gt;
# Sridharan, Patmaa :: University of Pennsylvania-CBICA&lt;br /&gt;
# Vidyaratne, Lasitha :: Old Dominion University&lt;br /&gt;
# Wang, Yaofei :: Brigham and Women's Hospital&lt;br /&gt;
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School&lt;br /&gt;
# Yang, Yixin :: Brigham and Women's Hospital&lt;br /&gt;
# Ye, Wu :: Brigham and Women's Hospital&lt;br /&gt;
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy&lt;br /&gt;
# Zeleznik, Roman :: DFCI&lt;br /&gt;
# Zhang, Fan :: Brigham and Women's Hospital&lt;br /&gt;
# Zhang, Miaomiao :: Massachusetts Institute of Technology&lt;br /&gt;
# Zhang, Yuqian :: Brigham and Women's Hospital&lt;br /&gt;
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
	<entry>
		<id>https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94311</id>
		<title>2017 Winter Project Week/MeningiomaSegmentation</title>
		<link rel="alternate" type="text/html" href="https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/MeningiomaSegmentation&amp;diff=94311"/>
		<updated>2017-01-04T16:38:58Z</updated>

		<summary type="html">&lt;p&gt;Jakubk: Created page&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]&lt;br /&gt;
&amp;lt;!-- Use the &amp;quot;Upload file&amp;quot; link on the left and then add a line to this list like &amp;quot;File:MyAlgorithmScreenshot.png&amp;quot; --&amp;gt;&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Key Investigators==&lt;br /&gt;
&amp;lt;!-- Add a bulleted list of investigators and their institutions here --&amp;gt;&lt;br /&gt;
* Satrajit Ghosh, MIT&lt;br /&gt;
* Omar Arnaout, Brigham and Women's Hospital&lt;br /&gt;
&lt;br /&gt;
==Project Description==&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Objective&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Approach and Plan&lt;br /&gt;
! style=&amp;quot;text-align: left; width:27%&amp;quot; |   Progress and Next Steps&lt;br /&gt;
|- style=&amp;quot;vertical-align:top;&amp;quot;&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Objective bullet points --&amp;gt;&lt;br /&gt;
* Segment meningiomas in structural MR images.&lt;br /&gt;
* Assess state of brain after surgical removal of meningioma.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Approach and Plan bullet points --&amp;gt;&lt;br /&gt;
* Evaluate performance of existing segmentation methods.&lt;br /&gt;
|&lt;br /&gt;
&amp;lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&amp;gt;&lt;br /&gt;
*&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Background and References==&lt;br /&gt;
&amp;lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&amp;gt;&lt;br /&gt;
MR images of meningiomas that will be used in this project are available at [http://openneu.ro/metasearch/ OpenNeu.ro].&lt;/div&gt;</summary>
		<author><name>Jakubk</name></author>
		
	</entry>
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