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README.html
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<!DOCTYPE html><html><head><meta charset="utf-8"><style>body
{
font-size:15px;
line-height:1.7;
overflow-x:hidden;
background-color: white;
border-radius: 3px;
border: 3px solid #EEE;
box-shadow: inset 0 0 0 1px #CECECE;
font-family: Helvetica, arial, freesans, clean, sans-serif;
max-width: 912px;
padding: 30px;
margin: 2em auto;
color:#333333;
}
.body-classic{
color:#444;
font-family:Georgia, Palatino, 'Palatino Linotype', Times, 'Times New Roman', "Hiragino Sans GB", "STXihei", "微软雅黑", serif;
font-size:16px;
line-height:1.5em;
background:#fefefe;
width: 45em;
margin: 10px auto;
padding: 1em;
outline: 1300px solid #FAFAFA;
}
body>:first-child
{
margin-top:0!important;
}
body>:last-child
{
margin-bottom:0!important;
}
blockquote,dl,ol,p,pre,table,ul {
border: 0;
margin: 15px 0;
padding: 0;
}
body a {
color: #4183c4;
text-decoration: none;
}
body a:hover {
text-decoration: underline;
}
body a.absent
{
color:#c00;
}
body a.anchor
{
display:block;
padding-left:30px;
margin-left:-30px;
cursor:pointer;
position:absolute;
top:0;
left:0;
bottom:0
}
/*h4,h5,h6{ font-weight: bold; }*/
.octicon{
font:normal normal 16px sans-serif;
width: 1em;
height: 1em;
line-height:1;
display:inline-block;
text-decoration:none;
-webkit-font-smoothing:antialiased
}
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background: url("data:image/svg+xml;utf8,<?xml version='1.0' standalone='no'?> <!DOCTYPE svg PUBLIC '-//W3C//DTD SVG 1.1//EN' 'http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd'> <svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 1024 832'> <metadata>Copyright (C) 2013 by GitHub</metadata> <!-- scale(0.01565557729941) --> <path transform='' d='M768 64h-192s-254 0-256 256c0 22 3 43 8 64h137c-11-19-18-41-18-64 0-128 128-128 128-128h192s128 0 128 128-128 128-128 128 0 64-64 128h64s256 0 256-256-256-256-256-256z m-72 192h-137c11 19 18 41 18 64 0 128-128 128-128 128h-192s-128 0-128-128 128-128 128-128-4-65 66-128h-66s-256 0-256 256 256 256 256 256h192s256 0 256-256c0-22-4-44-8-64z'/> </svg>");
background-size: contain;
background-repeat: no-repeat;
background-position: bottom;
}
.octicon-link:before{
content:'\a0';
}
body h1,body h2,body h3,body h4,body h5,body h6{
margin:1em 0 15px;
padding:0;
font-weight:bold;
line-height:1.7;
cursor:text;
position:relative
}
body h1 .octicon-link,body h2 .octicon-link,body h3 .octicon-link,body h4 .octicon-link,body h5 .octicon-link,body h6 .octicon-link{
display:none;
color:#000
}
body h1:hover a.anchor,body h2:hover a.anchor,body h3:hover a.anchor,body h4:hover a.anchor,body h5:hover a.anchor,body h6:hover a.anchor{
text-decoration:none;
line-height:1;
padding-left:0;
margin-left:-22px;
top:15%
}
body h1:hover a.anchor .octicon-link,body h2:hover a.anchor .octicon-link,body h3:hover a.anchor .octicon-link,body h4:hover a.anchor .octicon-link,body h5:hover a.anchor .octicon-link,body h6:hover a.anchor .octicon-link{
display:inline-block
}
body h1 tt,body h1 code,body h2 tt,body h2 code,body h3 tt,body h3 code,body h4 tt,body h4 code,body h5 tt,body h5 code,body h6 tt,body h6 code{
font-size:inherit
}
body h1{
font-size:2.5em;
border-bottom:1px solid #ddd
}
body h2{
font-size:2em;
border-bottom:1px solid #eee
}
body h3{
font-size:1.5em
}
body h4{
font-size:1.2em
}
body h5{
font-size:1em
}
body h6{
color:#777;
font-size:1em
}
body p,body blockquote,body ul,body ol,body dl,body table,body pre{
margin:15px 0
}
body h1 tt,body h1 code,body h2 tt,body h2 code,body h3 tt,body h3 code,body h4 tt,body h4 code,body h5 tt,body h5 code,body h6 tt,body h6 code
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background-repeat: repeat-x;
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background-color: transparent;
background-position: 0;
border:0 none;
color:#ccc;
height:4px;
margin:15px 0;
padding:0;
}
body li p.first
{
display:inline-block;
}
body ul,body ol
{
padding-left:30px;
}
body ul.no-list,body ol.no-list
{
list-style-type:none;
padding:0;
}
body ul ul,body ul ol,body ol ol,body ol ul
{
margin-bottom:0;
margin-top:0;
}
body dl
{
padding:0;
}
body dl dt
{
font-size:14px;
font-style:italic;
font-weight:700;
margin-top:15px;
padding:0;
}
body dl dd
{
margin-bottom:15px;
padding:0 15px;
}
body blockquote
{
border-left:4px solid #DDD;
color:#777;
padding:0 15px;
}
body blockquote>:first-child
{
margin-top:0;
}
body blockquote>:last-child
{
margin-bottom:0;
}
body table
{
display:block;
overflow:auto;
width:100%;
border-collapse: collapse;
border-spacing: 0;
padding: 0;
}
body table th
{
font-weight:700;
}
body table th,body table td
{
border:1px solid #ddd;
padding:6px 13px;
}
body table tr
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background-color:#fff;
border-top:1px solid #ccc;
}
body table tr:nth-child(2n)
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background-color:#f8f8f8;
}
body img
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-moz-box-sizing:border-box;
box-sizing:border-box;
max-width:100%;
}
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display:block;
overflow:hidden;
}
body span.frame>span
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border:1px solid #ddd;
display:block;
float:left;
margin:13px 0 0;
overflow:hidden;
padding:7px;
width:auto;
}
body span.frame span img
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display:block;
float:left;
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body span.frame span span
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clear:both;
color:#333;
display:block;
padding:5px 0 0;
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body span.align-center
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clear:both;
display:block;
overflow:hidden;
}
body span.align-center>span
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display:block;
margin:13px auto 0;
overflow:hidden;
text-align:center;
}
body span.align-center span img
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margin:0 auto;
text-align:center;
}
body span.align-right
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clear:both;
display:block;
overflow:hidden;
}
body span.align-right>span
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display:block;
margin:13px 0 0;
overflow:hidden;
text-align:right;
}
body span.align-right span img
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margin:0;
text-align:right;
}
body span.float-left
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display:block;
float:left;
margin-right:13px;
overflow:hidden;
}
body span.float-left span
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margin:13px 0 0;
}
body span.float-right
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display:block;
float:right;
margin-left:13px;
overflow:hidden;
}
body span.float-right>span
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display:block;
margin:13px auto 0;
overflow:hidden;
text-align:right;
}
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background-color:#f8f8f8;
border:1px solid #ddd;
border-radius:3px;
margin:0 2px;
padding:0 5px;
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white-space:nowrap;
}
code,pre{
font-family:Consolas, "Liberation Mono", Courier, monospace;
font-size:12px
}
body pre>code
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background:transparent;
border:none;
margin:0;
padding:0;
white-space:pre;
}
body .highlight pre,body pre
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background-color:#f8f8f8;
border:1px solid #ddd;
font-size:13px;
line-height:19px;
overflow:auto;
padding:6px 10px;
border-radius:3px
}
body pre code,body pre tt
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background-color:transparent;
border:none;
margin:0;
padding:0;
}
body .task-list{
list-style-type:none;
padding-left:10px
}
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padding-left:20px
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font-weight:normal
}
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cursor:pointer
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margin-top:5px
}
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float:left;
margin-left:-20px;
margin-top:7px
}
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background:#ffffff
}
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color:#999988;
font-style:italic
}
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color:#a61717;
background-color:#e3d2d2
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font-weight:bold
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font-weight:bold
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font-style:italic
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font-weight:bold
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font-style:italic
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font-weight:bold;
font-style:italic
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color:#000000;
background-color:#ffdddd
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background-color:#ffaaaa
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font-style:italic
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color:#aa0000
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color:#000000;
background-color:#ddffdd
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color:#000000;
background-color:#aaffaa
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color:#888888
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font-weight:bold
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font-weight:bold
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font-weight:bold
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font-weight:bold
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font-weight:bold
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color:#000000;
font-weight:normal
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color:#2B91AF
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</style><title>README</title></head><body><h1>
<a name="user-content-utilities" class="anchor" href="#utilities" aria-hidden="true"><span class="octicon octicon-link"></span></a>Utilities</h1>
<p>This project contains scripts and programs related primarily to the processing of experimental functional Magnetic Resonance Imaging studies involving language processing within the brain. It also houses programs and scripts used for other lab projects not related to fMRI processing. The primary intention of this repository is as a resource for research staff to contribute to, learn from, and assist in fMRI processing and coding/scripting in general. </p>
<p>Many of the fMRI specific scripts use <a href="http://afni.nimh.nih.gov/">AFNI</a> as the primary tool for fMRI analysis and preprocessing. However, there are some examples which make use of <a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/">FSL</a> as well. </p>
<p>Please dont expect examples of mind numbingly beautiful code or examples of how it is done right. You might find that here but you're just as likely to find the opposite as well. This repository is a collection of the work Ive done over the last 6 years, ala 2008 - 2014. </p>
<h2>
<a name="user-content-directory-layout" class="anchor" href="#directory-layout" aria-hidden="true"><span class="octicon octicon-link"></span></a>Directory layout</h2>
<ul>
<li>
<p><strong>AttnMem</strong></p>
<blockquote>
<p>Scripts for a published experiment investigating attention and memory in spoken language.</p>
<p><a href="file:///opt/local/Utilities/./AttnMem/NewHope.tcsh"><strong>NewHope.tcsh</strong></a> is the script you really want to check out. Makes extensive use of AFNI. </p>
<p>Otherwise there is a lot of junk in here that Ive kept primarily mostly for personal reasons, and a few provide examples of how to do things that I have referred back to a few times in the past. </p>
<p>Check out our paper! <a href="http://www.hindawi.com/journals/ijbi/2012/579786/">Modulating the Focus of Attention for Spoken Words at Encoding Affects Frontoparietal Activation for Incidental Verbal Memory</a></p>
</blockquote>
</li>
<li>
<p><strong>Dichotic</strong></p>
<blockquote>
<p>Pilot study that never took off.</p>
</blockquote>
</li>
<li>
<p><strong>Iceword</strong></p>
<blockquote>
<p>fMRI experiment examining language features. Scripts designed to process and analyze data collected. Currently on-going. Everything in here served a purpose. </p>
</blockquote>
</li>
<li>
<p><strong>Mouse</strong></p>
<blockquote>
<p>Pilot fMRI experiment examining Mice's response to induced hunger in the brain. </p>
<p><a href="file:///opt/local/Utilities/./Mouse/mouse.reg.sh"><strong>mouse.reg.sh</strong></a> is probably the most interesting as far as processing and analysis goes. Uses AFNI exclusively</p>
</blockquote>
</li>
<li>
<p><strong>NBack</strong></p>
<blockquote>
<p>Scripts for constructing an game/experiment examining 4yr olds attention</p>
</blockquote>
</li>
<li>
<p><strong>Rat</strong></p>
<blockquote>
<p>A pilot project involving the analysis of rat brains</p>
</blockquote>
</li>
<li>
<p><strong>Russian</strong></p>
<blockquote>
<p>fMRI experiment examining language features. Scripts designed to process and analysis data collected. Currently on-going.</p>
</blockquote>
</li>
<li>
<p><strong>Stroop</strong></p>
<blockquote>
<p>Scripts for a published project investigating the "Stroop Effect" in the auditory domain. Our paper for proof! <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020403/">Neural Substrates of Attentive Listening Assessed with a Novel Auditory Stroop Task</a></p>
</blockquote>
</li>
<li>
<p><strong>SustainedAttention</strong></p>
<blockquote>
<p>A project similar to the NBack, investigating Sustained Attention in 4yr olds. Scripts for constructing the game and experiment.</p>
</blockquote>
</li>
<li>
<p><strong>Tap</strong></p>
<blockquote>
<p>A project investigating Transfer-appropriate processing, rejected</p>
</blockquote>
</li>
<li>
<p><strong>WordBoundary</strong></p>
<blockquote>
<p>fMRI experiment examining language features. Scripts designed to process and analysis data collected.</p>
</blockquote>
</li>
<li>
<p><strong>WordBoundary2</strong></p>
<blockquote>
<p>Part two of the WordBoundary Experiment. Currently on-going.</p>
</blockquote>
</li>
<li>
<p><strong>WorkShop</strong></p>
<blockquote>
<p>Work-in-Progress scripts and makeshift testing ground. There are some real gems of learning in here. It's also a complete mess in terms of its organization...be careful in there</p>
</blockquote>
</li>
<li>
<p><strong>NiftiViewer</strong></p>
<blockquote>
<p>A long term project that doesnt really have a presence in here. For more details on this project, check out the dedicated github papge <a href="https://github.com/CreativeCodingLab/aluminum/tree/master/osx/examples/niftiViewer"><strong>here</strong></a></p>
</blockquote>
</li>
<li>
<p><strong>tillsprojectpythoncode</strong></p>
<blockquote>
<p>Scripts for </p>
</blockquote>
</li>
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