diff --git a/examples/FIR_design.jl b/examples/FIR_design.jl
index 1efb82e..2a49c0d 100644
--- a/examples/FIR_design.jl
+++ b/examples/FIR_design.jl
@@ -51,17 +51,11 @@ end
 
 #' Designing a lowpass FIR filter is very simple to do with DSP.jl, all you
 #' need to do is to define the window length, cut off frequency and the
-#' window.
-
-#' We will define a lowpass filter with cut off frequency at 5Hz for a signal
+#' window. We will define a lowpass filter with cut off frequency at 5Hz for a signal
 #' sampled at 20 Hz.
-
-#' The Hamming window is defined as:
+#' We will use the Hamming window, which is defined as:
 #' $w(n) = \alpha - \beta\cos\frac{2\pi n}{N-1}$, where $\alpha=0.54$ and $\beta=0.46$
 
-#' The next code chunk is executed in term mode, see the [script](FIR_design.jl) for syntax.
-#+ term=true
-
 
 fs = 20
 f = digitalfilter(Lowpass(5, fs = fs), FIRWindow(hamming(61)))
@@ -70,11 +64,16 @@ h = FIRfreqz(f, w)
 
 #' ## Plot the frequency and impulse response
 
+#' The next code chunk is executed in term mode, see the [script](FIR_design.jl) for syntax.
+#+ term=true
+
 h_db = log10(abs(h))
 ws = w/pi*(fs/2)
 plot(y = h_db, x = ws, Geom.line,
       Guide.xlabel("Frequency (Hz)"), Guide.ylabel("Magnitude (db)"))
 
+#' And again with default options
+
 h_phase = unwrap(-atan2(imag(h),real(h)))
 plot(y = h_phase, x = ws, Geom.line,
     Guide.xlabel("Frequency (Hz)"), Guide.ylabel("Phase (radians)"))
diff --git a/src/pandoc.jl b/src/pandoc.jl
index 3db7e7e..a04c18e 100644
--- a/src/pandoc.jl
+++ b/src/pandoc.jl
@@ -23,7 +23,7 @@ function pandoc2html(formatted::AbstractString, doc::WeaveDoc)
   try
   #html = @compat readstring(
   run(pipeline(`echo $formatted` ,
-   `pandoc -R -s --mathjax --self-contained --highlight-style=tango
+   `pandoc -R -s --mathjax="" --self-contained --highlight-style=tango
    --template $html_template --include-in-header=$css_template
     -V wversion=$wversion -V wtime=$wtime -V wsource=$wsource
     -o $outname`))
@@ -58,7 +58,7 @@ function pandoc2pdf(formatted::AbstractString, doc::WeaveDoc)
   info("Done executing code. Running xelatex")
   try
     run(pipeline(`echo $formatted` ,
-     `pandoc -R -s --self-contained --latex-engine=xelatex --highlight-style=tango
+     `pandoc -R -s  --latex-engine=xelatex --highlight-style=tango
       --include-in-header=$header_template
       -V fontsize=12pt
       -o $outname`))
diff --git a/src/readers.jl b/src/readers.jl
index be62321..0f77bb7 100644
--- a/src/readers.jl
+++ b/src/readers.jl
@@ -183,10 +183,8 @@ function parse_doc(document::AbstractString, format::ScriptInput)
       haskey(options, :name) || (options[:name] = nothing)
 
       state = "code"
-
       continue
-
-    elseif state == "doc" #&& strip(line) != "" && strip(read) != ""
+    elseif state == "doc" && strip(line) != "" && strip(read) != ""
       state = "code"
       (docno > 1) && (read = "\n" * read) # Add whitespace to doc chunk. Needed for markdown output
       chunk = DocChunk(read, docno, start_line)
diff --git a/templates/pandoc_skeleton.css b/templates/pandoc_skeleton.css
index 90379cd..769534a 100644
--- a/templates/pandoc_skeleton.css
+++ b/templates/pandoc_skeleton.css
@@ -1,3 +1,12 @@
+
+
+<script type="text/javascript">
+  var fileref=document.createElement('script')
+  fileref.setAttribute("type","text/javascript")
+  fileref.setAttribute("src", "http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML")
+  document.getElementsByTagName("head")[0].appendChild(fileref)
+</script>
+
 <style type="text/css">
 @font-face {
   font-family: 'Raleway';
diff --git a/templates/pandoc_skeleton.html b/templates/pandoc_skeleton.html
index 83bb548..ca2c9b7 100644
--- a/templates/pandoc_skeleton.html
+++ b/templates/pandoc_skeleton.html
@@ -15,6 +15,7 @@ $if(keywords)$
 $endif$
   <title>$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$</title>
 
+
 $if(math)$
   $math$
 $endif$