<h1>HCP Pipeline Tools</h1>

<p>The HCP Pipeline Tools product is a set tools (primarily, but not exclusively,
shell scripts) for processing MRI images for the <a href="http://www.humanconnectome.org">Human Connectome Project</a>. 
Among other things, these tools implement the Minimal Preprocessing Pipeline 
(MPP) described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/23668970">Glasser et al. 2013</a></p>

<h2>Prerequisites</h2>

<p>The HCP Pipelines Tools have the following software requirements:</p>

<ol>
<li>A 64-bit Linux Operating System</li>
<li>The <a href="http://fsl.fmrib.ox.ac.uk">FMRIB Software Library</a> (a.k.a. <a href="http://fsl.fmrib.ox.ac.uk">FSL</a>) version 
5.0.6 or greater installed and config properly sourced</li>
<li><a href="http://freesurfer.net">FreeSurfer</a> version <a href="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/">5.3.0-HCP</a> installed and 
config properly sourced</li>
<li>${HCPPIPEDIR}/src/gradient_unwarping installed with dependancies (source
code located in this folder) if using gradient distortion correction</li>
</ol>

<h2>Notes</h2>

<ol>
<li><p>You will need to define an environment variable named <code>HCPPIPEDIR</code> which 
should hold the path to the root folder in which the HCP Pipelines Tools 
reside.</p>

<p>For example, you might set HCPPIPEDIR in a manner similar to one of the
following.</p>

<pre>
<code>
   export HCPPIPEDIR=/home/NRG/tbrown01/projects/Pipelines
   export HCPPIPEDIR=/media/2TBB/Connectome_Project/Pipelines
   export HCPPIPEDIR=/nrgpackages/tools/hcp-pipeline-tools
</code>
</pre></li>
<li><p>An example setup script is provided in 
<code>${HCPPIPEDIR}/Examples/Scripts/SetUpHCPPipeline.sh</code>.</p>

<p>That setup script will need to be edited to set the absolute path to the 
HCP Pipelines Tools root installation folder on your system.  Your modified
setup script will need to be sourced before running an HCP pipeline.</p></li>
<li><p>To test that the pipelines work, there is example data located in:
<code>${HCPPIPEDIR}/Examples/792564</code></p></li>
<li><p>There are example batch scripts to call the pipelines on this data 
located in: <code>${HCPPIPEDIR}/Examples/Scripts</code></p></li>
<li><p>In all example batch scripts, the following variables will need to be 
modified or checked prior to use:</p>

<pre>
<code>
   Subjlist="792564" #Space delimited list of subject IDs
   StudyFolder="/media/myelin/brainmappers/Connectome_Project/TestStudyFolder" #Path to subject's data folder
   EnvironmentScript="/media/2TBB/Connectome_Project/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script
</code>
</pre>

<ul>
<li><code>SubjList</code> needs to be changed to the list of subjects to process</li>
<li><code>StudyFolder</code> needs to be changed to the location of the data that 
will be processed.</li>
<li><code>EnvironmentScript</code> needs to be changed to the location of your 
setup script (your modified version of <code>SetUpHCPPipeline.sh</code></li>
</ul></li>
</ol>

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