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  <div class="section" id="what-is-unix-tcsh-and-afni">
<span id="u-misc-bg0"></span><h1>1. What is ... ?  Unix, tcsh and AFNI<a class="headerlink" href="#what-is-unix-tcsh-and-afni" title="Permalink to this headline">¶</a></h1>
<p>A brief overview of Unix, tcsh and AFNI</p>
<blockquote>
<div>Descriptions, examples, comments, sample commands, syntax and getting help...</div></blockquote>
<div class="section" id="what-is-unix">
<span id="u-mb0-unix"></span><h2>1.1. What is Unix?<a class="headerlink" href="#what-is-unix" title="Permalink to this headline">¶</a></h2>
<p>Unix is a type of operating system (a standard), first developed in 1969</p>
<p>Examples of Unix operating systems:</p>
<blockquote>
<div>Solaris, OpenSolaris, Irix, AIX, HP-UX, OS X, Linux, FreeBSD
(actually, Linux and FreeBSD are not formally Unix, but are very similar)</div></blockquote>
<p>Comments:</p>
<blockquote>
<div><ul class="simple">
<li>has graphical environment, but strength is in command-line capabilities</li>
<li>hundreds or more usually thousands of programs come with systems
(not just a handful that have screen icons)</li>
</ul>
</div></blockquote>
<div class="section" id="sample-commands">
<h3>1.1.1. Sample commands<a class="headerlink" href="#sample-commands" title="Permalink to this headline">¶</a></h3>
<p>A Unix system often has thousands of programs, including:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">ls</span><span class="p">,</span> <span class="n">cat</span><span class="p">,</span> <span class="n">less</span><span class="p">,</span> <span class="n">mv</span><span class="p">,</span> <span class="n">cp</span><span class="p">,</span> <span class="n">date</span><span class="p">,</span> <span class="n">ssh</span><span class="p">,</span> <span class="n">vi</span><span class="p">,</span> <span class="n">rm</span>
</pre></div>
</div>
</div>
<div class="section" id="syntax">
<h3>1.1.2. Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h3>
<p>Many characters special meanings on a Unix system, depending on the shell:</p>
<div class="highlight-python"><pre>variables ($), quotes (', ", `), wildcards (\*, ?, []), pipes (|), redirection (&gt;)</pre>
</div>
</div>
<div class="section" id="getting-help">
<h3>1.1.3. Getting help<a class="headerlink" href="#getting-help" title="Permalink to this headline">¶</a></h3>
<p>There are many places to get help...</p>
<blockquote>
<div><ul>
<li><p class="first">&#8216;man&#8217; is short for manual, the on-line manual for unix commands:</p>
<div class="highlight-python"><pre>man ls
man less
man man</pre>
</div>
</li>
<li><p class="first">&#8216;info&#8217; is a newer help system</p>
</li>
<li><p class="first">books, having one that also covers shell programming can be helpful
(in our case, the focus is on tcsh rather than bash)</p>
</li>
<li><p class="first">our on-line tutorials</p>
</li>
<li><p class="first">examples with the class data</p>
</li>
<li><p class="first">our message board</p>
</li>
<li><p class="first">asking neighbors</p>
</li>
</ul>
</div></blockquote>
</div>
</div>
<div class="section" id="what-is-tcsh">
<span id="u-mb0-tcsh"></span><h2>1.2. What is tcsh?<a class="headerlink" href="#what-is-tcsh" title="Permalink to this headline">¶</a></h2>
<p>T-shell is a Unix shell: a command-line interpreter</p>
<blockquote>
<div><p>When the user types a command and hits &lt;Enter&gt;, the shell
processes that command and decides what to do:</p>
<blockquote>
<div><ul class="simple">
<li>processes special characters</li>
<li>decides what program to run, if any</li>
<li>runs the program, passing along any options and parameters</li>
</ul>
</div></blockquote>
</div></blockquote>
<p>Examples of similar shell programs:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">sh</span><span class="p">,</span> <span class="n">bash</span><span class="p">,</span> <span class="n">csh</span><span class="p">,</span> <span class="n">tcsh</span><span class="p">,</span> <span class="n">ksh</span><span class="p">,</span> <span class="n">zsh</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p>regarding <strong class="command">tcsh</strong></p>
<ul class="last simple">
<li>it is just one of many common Unix programs</li>
<li>the actual program (a file on disk) is generally /bin/tcsh</li>
<li>it has its own syntax</li>
<li>it has its own sub-commands (cd, echo, set, ...)</li>
<li>it is not has powerful as bash, but is more simple and readable</li>
</ul>
</div>
<div class="section" id="id1">
<h3>1.2.1. Sample commands<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
<p>tcsh has many sub-commands: commands that do not exist on the system,
but are just part of the shell, e.g.:</p>
<div class="highlight-python"><pre>cd, echo, set, setenv, alias, foreach, while, bg, exit, ...</pre>
</div>
<p>For example, &#8216;cd&#8217; is not a program, it just tells the shell that you want
to be &#8220;sitting in a new location&#8221;.</p>
<p>Syntax (characters that mean something special):</p>
<div class="highlight-python"><pre>home directories (~), history (!), jobs (%), redirecting stderr (&amp;gt;&amp;amp;)</pre>
</div>
</div>
<div class="section" id="id2">
<h3>1.2.2. Getting help<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
<p>Since &#8216;tcsh&#8217; is just a Unix program, &#8220;man tcsh&#8221; is one way to get help.:</p>
<div class="highlight-python"><pre>man tcsh</pre>
</div>
<p>Again, consider getting a book that covers tcsh.</p>
</div>
</div>
<div class="section" id="what-is-afni">
<span id="u-mb0-afni"></span><h2>1.3. What is AFNI?<a class="headerlink" href="#what-is-afni" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><ul class="simple">
<li>AFNI is a suite of data analysis and viewing tools</li>
<li>well over 500 programs, scripts and plugins</li>
</ul>
</div></blockquote>
<p>Examples of similar packages (there are many):</p>
<blockquote>
<div><ul class="simple">
<li>AFNI, FSL, SPM, BrainVoyager</li>
</ul>
</div></blockquote>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p>regarding <strong>AFNI</strong></p>
<ul class="last simple">
<li>it is good for viewing (and hopefully understanding) data</li>
<li>it is written on top of X11 and for Unix systems</li>
<li>it does not work directly on Windows (but there are options)</li>
<li>it is free (costs nothing)</li>
<li>it is open source (one can see and modify the code)</li>
</ul>
</div>
<div class="section" id="id3">
<h3>1.3.1. Sample commands<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><p>afni, suma, 3dcalc, afni_proc.py, 3dDeconvolve</p>
<p>Syntax (characters that mean something special):</p>
<div class="highlight-python"><pre>- sub-brick selection ([$,..]), range (&lt;&gt;), index ({}), transposition (')
- many programs have their own special syntax</pre>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The special syntax characters overlap with those of the shell,
meaning they need to be hidden from the shell if they are to be
passed on to an AFNI program.</p>
</div>
</div></blockquote>
</div>
<div class="section" id="id4">
<h3>1.3.2. Getting help<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><p>Virtually every AFNI program provides help using the -help option, as in
these examples:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">afni_proc</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">help</span>
<span class="n">afni_proc</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">help</span> <span class="o">|</span> <span class="n">less</span>
<span class="n">afni_proc</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">h_view</span>
</pre></div>
</div>
<ul class="simple">
<li>this output is also available at: <a class="reference external" href="http://afni.nimh.nih.gov/pub/dist/doc/program_help">help: all AFNI programs</a></li>
<li>course material is available at: <a class="reference external" href="http://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts">help: course handouts</a></li>
<li>class data is available at: <a class="reference external" href="http://afni.nimh.nih.gov/pub/dist/edu/data">AFNI data packages</a></li>
</ul>
</div></blockquote>
</div>
</div>
</div>


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  <h3><a href="../index.html">Table Of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">1. What is ... ?  Unix, tcsh and AFNI</a><ul>
<li><a class="reference internal" href="#what-is-unix">1.1. What is Unix?</a><ul>
<li><a class="reference internal" href="#sample-commands">1.1.1. Sample commands</a></li>
<li><a class="reference internal" href="#syntax">1.1.2. Syntax</a></li>
<li><a class="reference internal" href="#getting-help">1.1.3. Getting help</a></li>
</ul>
</li>
<li><a class="reference internal" href="#what-is-tcsh">1.2. What is tcsh?</a><ul>
<li><a class="reference internal" href="#id1">1.2.1. Sample commands</a></li>
<li><a class="reference internal" href="#id2">1.2.2. Getting help</a></li>
</ul>
</li>
<li><a class="reference internal" href="#what-is-afni">1.3. What is AFNI?</a><ul>
<li><a class="reference internal" href="#id3">1.3.1. Sample commands</a></li>
<li><a class="reference internal" href="#id4">1.3.2. Getting help</a></li>
</ul>
</li>
</ul>
</li>
</ul>

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