BrainMapper-help/index.html at master · FabienRech/BrainMapper-help · GitHub

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<!DOCTYPE html>
<html>
  <head>
    <title>User manual</title>
	<link rel="stylesheet" type="text/css" href="style.css">
  <link rel="icon" href="imgs/logo.png">
  </head>
  <body>

  <header class="w3-container w3-center w3-padding-32">
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          <img src="imgs/logo.png" style="width:8%">
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      <div class="column-h">
        <h1><b>USER MANUAL</b></h1>
    	  <p>Welcome to the user manual for the <span class="w3-tag">BrainMapper</span> software.</p>
      </div>
    </div>
	</header>
<div class="row">
  <div class="column-left">
    <div class="w3-card w3-margin w3-margin-top">
      <div id="toc_container">
    	<p class="toc_title">Contents</p>
    	<ul class="toc_list">
    	   <li><a href="#Global_presentation">1 Global presentation</a></li>
    	   <li><a href="NIfTI_handling.html">2 NIfTI Handling</a></li>
         <ul>
           <li>2.1 Set</li>
           <ul>
             <li>2.1.1 Create a new set</li>
             <li>2.1.2 Rename a set</li>
             <li>2.1.3 Add a sub set</li>
           </ul>
         <li>2.2 Collection</li>
           <ul>
           <li>2.2.1 Create a new collection</li>
           <ul>
             <li>2.2.1.1 From an Excel file</li>
             <li>2.2.1.2 From a NIfTI file</li>
           </ul>
           <li>2.2.2 Select collections</li>
           </ul>
         <li>2.3 Edit Collections</li>
          <ul>
             <li>2.3.1 Select the collection to edit</li>
             <li>2.3.2 Rename a Collection</li>
             <li>2.3.3 Add images to a Collection</li>
             <li>2.3.4 Remove images</li>
             <li>2.3.5 Show one image</li>
             <li>2.3.6 Delete one collection</li>
           </ul>
          </ul>
            <li><a href="clustering.html">3 Clustering</a></li>
            <li><a href="calculations.html">4 Calculations</a></li>
            <li><a href="import_export.html">5 Import/Export</a></li>
        	</ul>
    	</div>
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  <div class="column-right">
    <div id="Global_presentation">
      <h1> Global presentation </h1>
      Brain-Mapper is the product of a 5-month collaboration between the Central Hospital of Nancy, France (CHRU in french) and Computer Science and Engineering students at TELECOM Nancy<br/><br/>

      The aim of this project was to simplify the treatment chain of neurosurgeon Dr. Fabien Rech, who had to use several librairies, software and methods to extract interesting data from NIfTI files.<br/>
      The workchain of NIfTI processing and information extraction carried out by Dr. Rech for his thesis work was the following one :
      <br/><br/><br/>
       <img src="imgs/chaine.jpg" style="width:50%">
      <br/><br/><br/>
      Our aim was to simplify this work chain and offer the possibility to manage NIfTI, extract the interesting data from them to use it for calculations and clustering algorithms
      <br/><br/>

      <h2> The NIfTI format </h2>

      Our software can open compressed NIfTI formats ('.nii.gz')

      <h2> Install <h2>
        <h3> Dependencies </h3>


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	<footer class="w3-container w3-dark-grey w3-padding-32 w3-margin-top">
	  <p>Source code available on <a href="https://github.com/TELECOMNancy/brainMapper" target="_blank">GitHub repository</a></p>
	</footer>
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