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			<div class="slides">
				<section data-background="#000066">
					<h1>Design Team 0 Slides</h1>
					<h2><NAME>, <NAME>, <NAME></h2>
				</section>

				<section data-background="#000066">
					<h1>F2G pipeline leg overview</h1>
					<h2>Eric Bridgeford</h2>
				</section>
				
				<section data-background="#000066">
					<h2>Steps to Analysis</h2>
					<ul>
						<li>Raw Data</li>
						<li>Distortion Correction</li>
						<li>Motion Correction</li>
						<li>Slice Timing Correction</li>
						<li>Spatial Smoothing</li>
						<li>Registration</li>
						<li>Statistical Analysis</li>
					</ul>
				</section>

				<section data-background="#000066">					
					<h2>Implemented Pipeline</h2>
					<ul>
						<li>Raw Data</li>
						<li>Motion Correction</li>
						<li>Registration</li>
						<li>Timeseries Extraction</li>
						<li>Graph Generation</li>
					</ul>
				</section>
			
				<section data-background="#000066">
					<h2>Raw Data</h2>
					<ul>
						<li>fMRI functional data</li>
						<li>MPRAGE anatomical data</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Challenges that came up along the way</h2>
					<ul>
						<li>motion correction failures</li>
						<li>making image comparisons before and after operations</li>
						<li>deciding on metric for making image comparisons</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Motion Correction Issues</h2>
					<ul>
						<li>Recap: Motion correction corrects blurring from subjects moving their heads</li>
						<li>Goal: to use existing corrective scripts for DTI graphs</li>
						<li>Problem: Eddy correct fails for the scan type with fMRI graphs</li>
						<li>Solution: Easy, use mcFLIRT!</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Image Comparison Issues</h2>
					<ul>
						<li>Recap: QC requires image comparisons before and after a step takes place</li>
						<li>Goal: just take what goes in and compare to what comes out</li>
						<li>Problem: resolution related issues</li>
						<li>Solution: resample before performing a step</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Metric for Image Comparisons</h2>
					<ul>
						<li>Recap: need a metric that determines similarity between two arrays</li>
						<li>Goal: use the DICE comparison metric</li>
						<li>Problem: DICE comparison just checks overlap of values (exactness of overlap); does nothing for similarity of values</li>
						<li>Solution: not the best solution, but so far using MSE helps</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Quality Control Example of Results</h2>
					<ul>
						<li>Left: image before Registration</li>
						<li>Right: image after registration</li>
						<li>Note: very good overlap with template; low MSE</li>
					</ul>
					<img src="images/week_612/registration.png" height="400">
				</section>


				<!-- TODO: add your content here Eric and Albert -->
				<section data-background="#000066">
					<h1>Visualization using Javascript - D3 and ThreeJS</h1>
					<h2><NAME></h2>
				</section>

				<section data-background="#000066">
					<h2>What is Javascript?</h2>
					<ul>
						<li>With HTML and CSS form the trifecta of WWW content production</li>
						<li>Whereas HTML and CSS provide structure/functionality and aesthetics respectively, Javascript provides interactivity</li>
						<li>High-level language and dynamic</li>
						<li>While sharing many syntax similarities with Java, very different languages by design</li>
						<li>Increasingly used in server-side web applications, largely sparked by Node.js</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Why use Javascript for large scale web visualization?</h2>
					<ul>
						<li>Extremely powerful</li>
						<li>Largely automatically supported by web browsers - no pesky packages or libraries necessary</li>
						<li>Can host to make visualization "snappy"</li><commit_msg>added last slide<commit_after><!doctype html>
<html>
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		<meta charset="utf-8">
		<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">

		<title>Design Team 0 6/12</title>

		<link rel="stylesheet" href="css/reveal.css">
		<link rel="stylesheet" href="css/theme/black.css">

		<!-- Theme used for syntax highlighting of code -->
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	</head>
	<body>
		<div class="reveal">
			<div class="slides">
				<section data-background="#000066">
					<h1>Design Team 0 Slides</h1>
					<h2><NAME>, <NAME>, <NAME></h2>
				</section>

				<section data-background="#000066">
					<h1>F2G pipeline leg overview</h1>
					<h2><NAME></h2>
				</section>
				
				<section data-background="#000066">
					<h2>Steps to Analysis</h2>
					<ul>
						<li>Raw Data</li>
						<li>Distortion Correction</li>
						<li>Motion Correction</li>
						<li>Slice Timing Correction</li>
						<li>Spatial Smoothing</li>
						<li>Registration</li>
						<li>Statistical Analysis</li>
					</ul>
				</section>

				<section data-background="#000066">					
					<h2>Implemented Pipeline</h2>
					<ul>
						<li>Raw Data</li>
						<li>Motion Correction</li>
						<li>Registration</li>
						<li>Timeseries Extraction</li>
						<li>Graph Generation</li>
					</ul>
				</section>
			
				<section data-background="#000066">
					<h2>Raw Data</h2>
					<ul>
						<li>fMRI functional data</li>
						<li>MPRAGE anatomical data</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Challenges that came up along the way</h2>
					<ul>
						<li>motion correction failures</li>
						<li>making image comparisons before and after operations</li>
						<li>deciding on metric for making image comparisons</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Motion Correction Issues</h2>
					<ul>
						<li>Recap: Motion correction corrects blurring from subjects moving their heads</li>
						<li>Goal: to use existing corrective scripts for DTI graphs</li>
						<li>Problem: Eddy correct fails for the scan type with fMRI graphs</li>
						<li>Solution: Easy, use mcFLIRT!</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Image Comparison Issues</h2>
					<ul>
						<li>Recap: QC requires image comparisons before and after a step takes place</li>
						<li>Goal: just take what goes in and compare to what comes out</li>
						<li>Problem: resolution related issues</li>
						<li>Solution: resample before performing a step</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Metric for Image Comparisons</h2>
					<ul>
						<li>Recap: need a metric that determines similarity between two arrays</li>
						<li>Goal: use the DICE comparison metric</li>
						<li>Problem: DICE comparison just checks overlap of values (exactness of overlap); does nothing for similarity of values</li>
						<li>Solution: not the best solution, but so far using MSE helps</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Quality Control Example of Results</h2>
					<ul>
						<li>Left: image before Registration</li>
						<li>Right: image after registration</li>
						<li>Note: very good overlap with template; low MSE</li>
					</ul>
					<img src="images/week_612/registration.png" height="400">
				</section>

				<section data-background="#000066">
					<h2>Timeline</h2>
					<ul>
						<li>End of Summer: have pipeline complete and process lots of data</li>
						<li>End of first semester: have upload service completely integrated</li>
						<li>End of second semester: have visualization tools completely built and summarize project</li>
					</ul>
				</section>


				<!-- TODO: add your content here Eric and Albert -->
				<section data-background="#000066">
					<h1>Visualization using Javascript - D3 and ThreeJS</h1>
					<h2><NAME></h2>
				</section>

				<section data-background="#000066">
					<h2>What is Javascript?</h2>
					<ul>
						<li>With HTML and CSS form the trifecta of WWW content production</li>
						<li>Whereas HTML and CSS provide structure/functionality and aesthetics respectively, Javascript provides interactivity</li>
						<li>High-level language and dynamic</li>
						<li>While sharing many syntax similarities with Java, very different languages by design</li>
						<li>Increasingly used in server-side web applications, largely sparked by Node.js</li>
					</ul>
				</section>

				<section data-background="#000066">
					<h2>Why use Javascript for large scale web visualization?</h2>
					<ul>
						<li>Extremely powerful</li>
						<li>Largely automatically supported by web browsers - no pesky packages or libraries necessary</li>
						<li>Can host to make visualization "snappy"</li>
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