ENH: delets ANTs example and resizes short example graph

Author: miykael

index.ipynb

@@ -239,6 +239,15 @@
     "</p>\n",
     "To inspect the html code of this page, click: <form action=\"javascript:code_toggle()\"><input type=\"submit\" value=\"Show HTML code\"></form>"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

notebooks/introduction_nipype.ipynb

@@ -77,7 +77,7 @@
     "deletable": true,
     "editable": true,
     "slideshow": {
-     "slide_type": "slide"
+     "slide_type": "subslide"
     }
    },
    "source": [
@@ -131,7 +131,9 @@
     "\n",
     "You and your problems with fMRI data. I'm perfectly happy with FreeSurfer's command line interface. It gives me all I need to do surface based analyses.\n",
     "\n",
-    "<img src=\"../static/images/example_Freesurfer.png\"  width=\"600\">"
+    "<img src=\"../static/images/example_Freesurfer.png\"  width=\"600\">\n",
+    "\n",
+    "Of course, you can run your sequential FreeSurfer scripts as you want. But wouldn't it be nice to optimize computation time by using parallel computation?"
    ]
   },
   {
@@ -144,8 +146,6 @@
     }
    },
    "source": [
-    "Of course, you can run your sequential FreeSurfer scripts as you want. But wouldn't it be nice to optimize computation time by using parallel computation?\n",
-    "\n",
     "Let's imagine you want to do smoothing on the surface, with **two different FWHM** values, on **both hemispheres** and this on **six subjects**, all in **parallel**? With Nipype this is as simple as that:\n",
     "\n",
     "```python\n",
@@ -161,47 +161,6 @@
     "```"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "deletable": true,
-    "editable": true,
-    "slideshow": {
-     "slide_type": "subslide"
-    }
-   },
-   "source": [
-    "# If you want to have good normalization, you need ANTs!\n",
-    "\n",
-    "I agree, but there's just a difference between this:\n",
-    "\n",
-    "<img src=\"../static/images/example_ANTs.png\"  width=\"600\">"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "deletable": true,
-    "editable": true,
-    "slideshow": {
-     "slide_type": "fragment"
-    }
-   },
-   "source": [
-    "and this:\n",
-    "\n",
-    "```python\n",
-    "from nipype.interfaces.ants import Registration\n",
-    "regist = Registration(fixed_image='MNI152_T1_2mm.nii.gz', \n",
-    "                      moving_image='functional.nii', \n",
-    "                      transforms=['Rigid', 'Affine', 'SyN'], \n",
-    "                      metric=['MI', 'MI', 'CC'], \n",
-    "                      metric_weight=[1.0] * 3, \n",
-    "                      shrink_factors=[[8, 4, 2, 1]] * 3, \n",
-    "                      smoothing_sigmas=[[3, 2, 1, 0]] * 3)\n",
-    "```"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -231,11 +190,9 @@
    "source": [
     "# A short Example\n",
     "\n",
-    "Let's assume we want to do preprocessing that uses **SPM** for *motion correction*, **FreeSurfer** for *coregistration*, **ANTS** for *normalization* and **FSL** for *smoothing*. Normally this would be a hell of a mess. It would mean switching between multiple scripts in different programming languages with a lot of manual intervention.\n",
-    "\n",
-    "**Nipype does all that for you! In parallel and in a very intuitive way!**\n",
+    "Let's assume we want to do preprocessing that uses **SPM** for *motion correction*, **FreeSurfer** for *coregistration*, **ANTS** for *normalization* and **FSL** for *smoothing*. Normally this would be a hell of a mess. It would mean switching between multiple scripts in different programming languages with a lot of manual intervention. **Nipype comes to the rescue!**\n",
     "\n",
-    "<img src=\"../static/images/nipype_example_graph.png\"  width=\"750\">"
+    "<img src=\"../static/images/nipype_example_graph.png\"  width=\"650\">"
    ]
   },
   {

notebooks/introduction_nipype.slides.html

@@ -67,8 +67,8 @@
 *
 */
 /*!
- * Bootstrap v3.3.6 (http://getbootstrap.com)
- * Copyright 2011-2015 Twitter, Inc.
+ * Bootstrap v3.3.7 (http://getbootstrap.com)
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  */
 /*! normalize.css v3.0.3 | MIT License | github.com/necolas/normalize.css */
@@ -1163,7 +1163,6 @@
   text-decoration: underline;
 }
 a:focus {
-  outline: thin dotted;
   outline: 5px auto -webkit-focus-ring-color;
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@@ -2592,7 +2591,6 @@
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@@ -3083,7 +3081,6 @@
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   outline-offset: -2px;
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@@ -8814,6 +8811,9 @@
     margin-left: 10px;
   }
 }
+[dir="rtl"] #ipython_notebook {
+  float: right !important;
+}
 #noscript {
   width: auto;
   padding-top: 16px;
@@ -9016,9 +9016,15 @@
  *
  * Author: Jupyter Development Team
  */
+[dir="rtl"] #tabs li {
+  float: right;
+}
 ul#tabs {
   margin-bottom: 4px;
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+[dir="rtl"] ul#tabs {
+  margin-right: 0px;
+}
 ul#tabs a {
   padding-top: 6px;
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@@ -9041,6 +9047,16 @@
 .list_toolbar .tree-buttons {
   padding-top: 1px;
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+[dir="rtl"] .list_toolbar .tree-buttons {
+  float: left !important;
+}
+[dir="rtl"] .list_toolbar .pull-right {
+  padding-top: 1px;
+  float: left !important;
+}
+[dir="rtl"] .list_toolbar .pull-left {
+  float: right !important;
+}
 .dynamic-buttons {
   padding-top: 3px;
   display: inline-block;
@@ -9176,6 +9192,9 @@
 #tree-selector {
   padding-right: 0px;
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+[dir="rtl"] #tree-selector a {
+  float: right;
+}
 #button-select-all {
   min-width: 50px;
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@@ -9265,6 +9284,9 @@
   left: auto;
   right: 0;
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+[dir="rtl"] #new-menu {
+  text-align: right;
+}
 .kernel-menu-icon {
   padding-right: 12px;
   width: 24px;
@@ -9310,6 +9332,9 @@
 #running .panel-group .panel .panel-body .list_container .list_item:last-child {
   border-bottom: 0px;
 }
+[dir="rtl"] #running .col-sm-8 {
+  float: right !important;
+}
 .delete-button {
   display: none;
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@@ -9605,6 +9630,7 @@
   }
 }
 div.inner_cell {
+  min-width: 0;
   /* Old browsers */
   display: -webkit-box;
   -webkit-box-orient: vertical;
@@ -9626,11 +9652,6 @@
   /* Modern browsers */
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@@ -11300,7 +11321,7 @@
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+  width: 21ex;
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@@ -11612,6 +11633,7 @@
   box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
 }
 .terminal-app .terminal {
+  width: 100%;
   float: left;
   font-family: monospace;
   color: white;
@@ -11626,6 +11648,9 @@
   line-height: 1em;
   font-size: 14px;
 }
+.terminal-app .terminal .xterm-rows {
+  padding: 10px;
+}
 .terminal-app .terminal-cursor {
   color: black;
   background: white;
@@ -11877,7 +11902,7 @@ <h1 id="I-don't-need-that,-I'm-happy-with-SPM12!">I don't need that, I'm happy w
 
 </div>
 </div>
-</div></section></section><section><section>
+</div></section><section>
 <div class="cell border-box-sizing text_cell rendered">
 <div class="prompt input_prompt">
 </div>
@@ -11916,6 +11941,7 @@ <h1 id="I-don't-need-that,-I'm-happy-with-FSL!">I don't need that, I'm happy wit
 <div class="text_cell_render border-box-sizing rendered_html">
 <h1 id="I-don't-need-that,-I'm-happy-with-FreeSurfer!">I don't need that, I'm happy with FreeSurfer!<a class="anchor-link" href="#I-don't-need-that,-I'm-happy-with-FreeSurfer!">&#182;</a></h1><p>You and your problems with fMRI data. I'm perfectly happy with FreeSurfer's command line interface. It gives me all I need to do surface based analyses.</p>
 <p><img src="../static/images/example_Freesurfer.png"  width="600"></p>
+<p>Of course, you can run your sequential FreeSurfer scripts as you want. But wouldn't it be nice to optimize computation time by using parallel computation?</p>
 
 </div>
 </div>
@@ -11925,7 +11951,6 @@ <h1 id="I-don't-need-that,-I'm-happy-with-FreeSurfer!">I don't need that, I'm ha
 </div>
 <div class="inner_cell">
 <div class="text_cell_render border-box-sizing rendered_html">
-<p>Of course, you can run your sequential FreeSurfer scripts as you want. But wouldn't it be nice to optimize computation time by using parallel computation?</p>
 <p>Let's imagine you want to do smoothing on the surface, with <strong>two different FWHM</strong> values, on <strong>both hemispheres</strong> and this on <strong>six subjects</strong>, all in <strong>parallel</strong>? With Nipype this is as simple as that:</p>
 <div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">nipype.interfaces.freesurfer</span> <span class="kn">import</span> <span class="n">SurfaceSmooth</span>
 <span class="n">smoother</span> <span class="o">=</span> <span class="n">SurfaceSmooth</span><span class="p">()</span>
@@ -11946,36 +11971,6 @@ <h1 id="I-don't-need-that,-I'm-happy-with-FreeSurfer!">I don't need that, I'm ha
 </div>
 <div class="inner_cell">
 <div class="text_cell_render border-box-sizing rendered_html">
-<h1 id="If-you-want-to-have-good-normalization,-you-need-ANTs!">If you want to have good normalization, you need ANTs!<a class="anchor-link" href="#If-you-want-to-have-good-normalization,-you-need-ANTs!">&#182;</a></h1><p>I agree, but there's just a difference between this:</p>
-<p><img src="../static/images/example_ANTs.png"  width="600"></p>
-
-</div>
-</div>
-</div><div class="fragment">
-<div class="cell border-box-sizing text_cell rendered">
-<div class="prompt input_prompt">
-</div>
-<div class="inner_cell">
-<div class="text_cell_render border-box-sizing rendered_html">
-<p>and this:</p>
-<div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">nipype.interfaces.ants</span> <span class="kn">import</span> <span class="n">Registration</span>
-<span class="n">regist</span> <span class="o">=</span> <span class="n">Registration</span><span class="p">(</span><span class="n">fixed_image</span><span class="o">=</span><span class="s1">&#39;MNI152_T1_2mm.nii.gz&#39;</span><span class="p">,</span> 
-                      <span class="n">moving_image</span><span class="o">=</span><span class="s1">&#39;functional.nii&#39;</span><span class="p">,</span> 
-                      <span class="n">transforms</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;Rigid&#39;</span><span class="p">,</span> <span class="s1">&#39;Affine&#39;</span><span class="p">,</span> <span class="s1">&#39;SyN&#39;</span><span class="p">],</span> 
-                      <span class="n">metric</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;MI&#39;</span><span class="p">,</span> <span class="s1">&#39;MI&#39;</span><span class="p">,</span> <span class="s1">&#39;CC&#39;</span><span class="p">],</span> 
-                      <span class="n">metric_weight</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0</span><span class="p">]</span> <span class="o">*</span> <span class="mi">3</span><span class="p">,</span> 
-                      <span class="n">shrink_factors</span><span class="o">=</span><span class="p">[[</span><span class="mi">8</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">]]</span> <span class="o">*</span> <span class="mi">3</span><span class="p">,</span> 
-                      <span class="n">smoothing_sigmas</span><span class="o">=</span><span class="p">[[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]]</span> <span class="o">*</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-
-</div>
-</div>
-</div></div></section><section>
-<div class="cell border-box-sizing text_cell rendered">
-<div class="prompt input_prompt">
-</div>
-<div class="inner_cell">
-<div class="text_cell_render border-box-sizing rendered_html">
 <h1 id="But-I-like-my-neuorimaging-toolbox">But I like my neuorimaging toolbox<a class="anchor-link" href="#But-I-like-my-neuorimaging-toolbox">&#182;</a></h1><ul>
 <li>You can keep it! But instead of being stuck in MATLAB with SPM, or having scripting issues with FreeSurfer, ANTs or FSL,..</li>
 <li><strong>Nipype</strong> gives you the possibility to cherry-pick the algorithms that you prefer from many different sofware packages.</li>
@@ -11990,9 +11985,8 @@ <h1 id="But-I-like-my-neuorimaging-toolbox">But I like my neuorimaging toolbox<a
 </div>
 <div class="inner_cell">
 <div class="text_cell_render border-box-sizing rendered_html">
-<h1 id="A-short-Example">A short Example<a class="anchor-link" href="#A-short-Example">&#182;</a></h1><p>Let's assume we want to do preprocessing that uses <strong>SPM</strong> for <em>motion correction</em>, <strong>FreeSurfer</strong> for <em>coregistration</em>, <strong>ANTS</strong> for <em>normalization</em> and <strong>FSL</strong> for <em>smoothing</em>. Normally this would be a hell of a mess. It would mean switching between multiple scripts in different programming languages with a lot of manual intervention.</p>
-<p><strong>Nipype does all that for you! In parallel and in a very intuitive way!</strong></p>
-<p><img src="../static/images/nipype_example_graph.png"  width="750"></p>
+<h1 id="A-short-Example">A short Example<a class="anchor-link" href="#A-short-Example">&#182;</a></h1><p>Let's assume we want to do preprocessing that uses <strong>SPM</strong> for <em>motion correction</em>, <strong>FreeSurfer</strong> for <em>coregistration</em>, <strong>ANTS</strong> for <em>normalization</em> and <strong>FSL</strong> for <em>smoothing</em>. Normally this would be a hell of a mess. It would mean switching between multiple scripts in different programming languages with a lot of manual intervention. <strong>Nipype comes to the rescue!</strong></p>
+<p><img src="../static/images/nipype_example_graph.png"  width="650"></p>
 
 </div>
 </div>