From e86c3a5e0003e661e1d256100183cabced7a2165 Mon Sep 17 00:00:00 2001
From: Georg Oeltzschner <schorschinho@users.noreply.github.com>
Date: Mon, 25 Nov 2024 12:40:09 -0500
Subject: [PATCH] Fix typo in documentation #789

---
 docs/404.html                          |  16 +-
 docs/faqs.html                         |  12 +-
 docs/getting-started.html              |  60 +-
 docs/index.html                        |  16 +-
 docs/osprey-basis-set-tools.html       |  36 +-
 docs/osprey-command-line-tutorial.html |  36 +-
 docs/osprey-gui-tutorial.html          |  48 +-
 docs/reference-keys.txt                |   2 +
 docs/the-osprey-job-file.html          | 976 +++++++++++++------------
 docs/the-osprey-workflow.html          |  14 +-
 10 files changed, 627 insertions(+), 589 deletions(-)

diff --git a/docs/404.html b/docs/404.html
index 5f2c1f56..bc58e53c 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Page not found | Osprey Documentation</title>
   <meta name="description" content="Osprey is an all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data." />
-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Page not found | Osprey Documentation" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -92,7 +92,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -105,7 +105,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
@@ -119,6 +119,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="css/style.css" type="text/css" />
 </head>
@@ -165,13 +169,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
diff --git a/docs/faqs.html b/docs/faqs.html
index ed371a56..5dad91be 100644
--- a/docs/faqs.html
+++ b/docs/faqs.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Chapter 1 FAQs | Osprey Documentation</title>
   <meta name="description" content="Osprey is an all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data." />
-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Chapter 1 FAQs | Osprey Documentation" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -55,6 +55,10 @@
 
 
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="css/style.css" type="text/css" />
 </head>
@@ -101,13 +105,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
diff --git a/docs/getting-started.html b/docs/getting-started.html
index d2996df6..fbdd2603 100644
--- a/docs/getting-started.html
+++ b/docs/getting-started.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Chapter 2 Getting started | Osprey Documentation</title>
   <meta name="description" content="Osprey is an all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data." />
-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Chapter 2 Getting started | Osprey Documentation" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -92,7 +92,7 @@
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
@@ -105,7 +105,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
@@ -119,6 +119,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="css/style.css" type="text/css" />
 </head>
@@ -165,13 +169,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
@@ -244,26 +248,26 @@ <h2><span class="header-section-number">2.1</span> System requirements<a href="g
 You may need to ask your system administrator for a separate license for missing toolboxes.
 </div>
 <p>You can check your current MATLAB version and the available toolboxes with the following command at the MATLAB prompt:</p>
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-<span id="cb2-3"><a href="getting-started.html#cb2-3" aria-hidden="true" tabindex="-1"></a>MATLAB License Number<span class="op">:</span> <span class="fl">703789</span></span>
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-<span id="cb2-5"><a href="getting-started.html#cb2-5" aria-hidden="true" tabindex="-1"></a>Java Version<span class="op">:</span> Java <span class="fl">1.8.0</span>_<span class="fl">144</span><span class="op">-</span>b01 with Oracle Corporation Java HotSpot(TM) <span class="fl">64</span><span class="op">-</span>Bit Server VM mixed <span class="fu">mode</span></span>
-<span id="cb2-6"><a href="getting-started.html#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="op">-----------------------------------------------------------------------------------------------------</span></span>
-<span id="cb2-7"><a href="getting-started.html#cb2-7" aria-hidden="true" tabindex="-1"></a>MATLAB                                                Version <span class="fl">9.4</span>         (R2018a)</span>
-<span id="cb2-8"><a href="getting-started.html#cb2-8" aria-hidden="true" tabindex="-1"></a>Curve Fitting Toolbox                                 Version <span class="fl">3.5.7</span>       (R2018a)</span>
-<span id="cb2-9"><a href="getting-started.html#cb2-9" aria-hidden="true" tabindex="-1"></a>GUI Layout Toolbox                                    Version <span class="fl">2.3.4</span>       (R2018b)</span>
-<span id="cb2-10"><a href="getting-started.html#cb2-10" aria-hidden="true" tabindex="-1"></a>Global Optimization Toolbox                           Version <span class="fl">3.4.4</span>       (R2018a)</span>
-<span id="cb2-11"><a href="getting-started.html#cb2-11" aria-hidden="true" tabindex="-1"></a>Image Processing Toolbox                              Version <span class="fl">10.2</span>        (R2018a)</span>
-<span id="cb2-12"><a href="getting-started.html#cb2-12" aria-hidden="true" tabindex="-1"></a>Neural Network Toolbox                                Version <span class="fl">11.1</span>        (R2018a)</span>
-<span id="cb2-13"><a href="getting-started.html#cb2-13" aria-hidden="true" tabindex="-1"></a>Optimization Toolbox                                  Version <span class="fl">8.1</span>         (R2018a)</span>
-<span id="cb2-14"><a href="getting-started.html#cb2-14" aria-hidden="true" tabindex="-1"></a>Parallel Computing Toolbox                            Version <span class="fl">6.12</span>        (R2018a)</span>
-<span id="cb2-15"><a href="getting-started.html#cb2-15" aria-hidden="true" tabindex="-1"></a>Signal Processing Toolbox                             Version <span class="fl">8.0</span>         (R2018a)</span>
-<span id="cb2-16"><a href="getting-started.html#cb2-16" aria-hidden="true" tabindex="-1"></a>Statistics <span class="fu">and</span> Machine Learning Toolbox               Version <span class="fl">11.3</span>        (R2018a)</span>
-<span id="cb2-17"><a href="getting-started.html#cb2-17" aria-hidden="true" tabindex="-1"></a>Symbolic Math Toolbox                                 Version <span class="fl">8.1</span>         (R2018a)</span>
-<span id="cb2-18"><a href="getting-started.html#cb2-18" aria-hidden="true" tabindex="-1"></a>Wavelet Toolbox                                       Version <span class="fl">5.0</span>         (R2018a)</span>
-<span id="cb2-19"><a href="getting-started.html#cb2-19" aria-hidden="true" tabindex="-1"></a>Widgets Toolbox                                       Version <span class="fl">1.3.330</span>     (R2019a)</span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="getting-started.html#cb1-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> <span class="fu">ver</span></span></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="getting-started.html#cb2-1" tabindex="-1"></a><span class="op">-----------------------------------------------------------------------------------------------------</span></span>
+<span id="cb2-2"><a href="getting-started.html#cb2-2" tabindex="-1"></a>MATLAB Version<span class="op">:</span> <span class="fl">9.4.0.949201</span> (R2018a) Update <span class="fl">6</span></span>
+<span id="cb2-3"><a href="getting-started.html#cb2-3" tabindex="-1"></a>MATLAB License Number<span class="op">:</span> <span class="fl">703789</span></span>
+<span id="cb2-4"><a href="getting-started.html#cb2-4" tabindex="-1"></a>Operating System<span class="op">:</span> Mac OS X  Version<span class="op">:</span> <span class="fl">10.14.6</span> Build<span class="op">:</span> <span class="fl">18</span>G4032</span>
+<span id="cb2-5"><a href="getting-started.html#cb2-5" tabindex="-1"></a>Java Version<span class="op">:</span> Java <span class="fl">1.8.0</span>_<span class="fl">144</span><span class="op">-</span>b01 with Oracle Corporation Java HotSpot(TM) <span class="fl">64</span><span class="op">-</span>Bit Server VM mixed <span class="fu">mode</span></span>
+<span id="cb2-6"><a href="getting-started.html#cb2-6" tabindex="-1"></a><span class="op">-----------------------------------------------------------------------------------------------------</span></span>
+<span id="cb2-7"><a href="getting-started.html#cb2-7" tabindex="-1"></a>MATLAB                                                Version <span class="fl">9.4</span>         (R2018a)</span>
+<span id="cb2-8"><a href="getting-started.html#cb2-8" tabindex="-1"></a>Curve Fitting Toolbox                                 Version <span class="fl">3.5.7</span>       (R2018a)</span>
+<span id="cb2-9"><a href="getting-started.html#cb2-9" tabindex="-1"></a>GUI Layout Toolbox                                    Version <span class="fl">2.3.4</span>       (R2018b)</span>
+<span id="cb2-10"><a href="getting-started.html#cb2-10" tabindex="-1"></a>Global Optimization Toolbox                           Version <span class="fl">3.4.4</span>       (R2018a)</span>
+<span id="cb2-11"><a href="getting-started.html#cb2-11" tabindex="-1"></a>Image Processing Toolbox                              Version <span class="fl">10.2</span>        (R2018a)</span>
+<span id="cb2-12"><a href="getting-started.html#cb2-12" tabindex="-1"></a>Neural Network Toolbox                                Version <span class="fl">11.1</span>        (R2018a)</span>
+<span id="cb2-13"><a href="getting-started.html#cb2-13" tabindex="-1"></a>Optimization Toolbox                                  Version <span class="fl">8.1</span>         (R2018a)</span>
+<span id="cb2-14"><a href="getting-started.html#cb2-14" tabindex="-1"></a>Parallel Computing Toolbox                            Version <span class="fl">6.12</span>        (R2018a)</span>
+<span id="cb2-15"><a href="getting-started.html#cb2-15" tabindex="-1"></a>Signal Processing Toolbox                             Version <span class="fl">8.0</span>         (R2018a)</span>
+<span id="cb2-16"><a href="getting-started.html#cb2-16" tabindex="-1"></a>Statistics <span class="fu">and</span> Machine Learning Toolbox               Version <span class="fl">11.3</span>        (R2018a)</span>
+<span id="cb2-17"><a href="getting-started.html#cb2-17" tabindex="-1"></a>Symbolic Math Toolbox                                 Version <span class="fl">8.1</span>         (R2018a)</span>
+<span id="cb2-18"><a href="getting-started.html#cb2-18" tabindex="-1"></a>Wavelet Toolbox                                       Version <span class="fl">5.0</span>         (R2018a)</span>
+<span id="cb2-19"><a href="getting-started.html#cb2-19" tabindex="-1"></a>Widgets Toolbox                                       Version <span class="fl">1.3.330</span>     (R2019a)</span></code></pre></div>
 
 <div class="rmdnote">
 The available toolboxes (including SPM) are checked at the initial call of the Osprey GUI, and missing toolboxes are reported back to the user.
@@ -275,7 +279,7 @@ <h2><span class="header-section-number">2.2</span> Installing Osprey<a href="get
 <ul>
 <li><p>Clone the repository, or download and extract the contents of the .ZIP file to a directory on your drive.</p>
 <div class="figure"><span style="display:block;" id="fig:installOsprey"></span>
-<img src="img/02-installing-osprey-download-clone.png" alt="Cloning Osprey from GitHub." width="358" />
+<img src="img/02-installing-osprey-download-clone.png" alt="Cloning Osprey from GitHub."  />
 <p class="caption">
 Figure 2.1: Cloning Osprey from GitHub.
 </p>
@@ -288,7 +292,7 @@ <h2><span class="header-section-number">2.2</span> Installing Osprey<a href="get
 <li>Extract the downloaded archive so that the <code>spm12</code> folder is on the same directory level as the <code>osprey</code> folder:</li>
 </ul>
 <div class="figure"><span style="display:block;" id="fig:spmFolder"></span>
-<img src="img/02-installing-osprey-spm-folder.png" alt="Make sure that the SPM12 and Osprey folders are in the same directory." width="694" />
+<img src="img/02-installing-osprey-spm-folder.png" alt="Make sure that the SPM12 and Osprey folders are in the same directory."  />
 <p class="caption">
 Figure 2.2: Make sure that the SPM12 and Osprey folders are in the same directory.
 </p>
diff --git a/docs/index.html b/docs/index.html
index cf990fa4..5212e0b7 100644
--- a/docs/index.html
+++ b/docs/index.html
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-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
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@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
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 </head>
@@ -101,13 +105,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
@@ -167,11 +171,11 @@ <h1>
 <div id="header">
 <h1 class="title">Osprey Documentation</h1>
 <p class="author"><em>Georg Oeltzschner</em></p>
-<p class="date"><em>2023-04-28</em></p>
+<p class="date"><em>2024-11-25</em></p>
 </div>
 <div id="osprey" class="section level1 unnumbered hasAnchor">
 <h1>Osprey<a href="index.html#osprey" class="anchor-section" aria-label="Anchor link to header"></a></h1>
-<p><img src="img/osprey.png" width="512" /></p>
+<p><img src="img/osprey.png" /><!-- --></p>
 <p>Osprey is an all-in-one software suite for state-of-the art processing and
 quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data.</p>
 <div id="contact-feedback-suggestions" class="section level2 unnumbered hasAnchor">
diff --git a/docs/osprey-basis-set-tools.html b/docs/osprey-basis-set-tools.html
index 854e216b..0fdaf63c 100644
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-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
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@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
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 </head>
@@ -165,13 +169,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
@@ -240,29 +244,29 @@ <h1><span class="header-section-number">Chapter 7</span> Osprey basis set tools<
 <div id="io_lcmbasis" class="section level2 hasAnchor" number="7.1">
 <h2><span class="header-section-number">7.1</span> io_LCMBasis<a href="osprey-basis-set-tools.html#io_lcmbasis" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>If you have an existing LCModel basis set (<code>.BASIS</code>), you can import it into <strong>Osprey</strong>. Assuming the basis set is located at <code>/Users/Georg/LCModelBasissets/GE/press144</code>, you can execute the following command at the MATLAB prompt after you have run <code>OspreyJob</code>:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="osprey-basis-set-tools.html#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;</span> file <span class="op">=</span> <span class="st">&#39;/Users/Georg/LCModelBasissets/GE/press144&#39;</span><span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="osprey-basis-set-tools.html#cb1-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> file <span class="op">=</span> <span class="st">&#39;/Users/Georg/LCModelBasissets/GE/press144&#39;</span><span class="op">;</span></span></code></pre></div>
 <p>You can then call <strong>Osprey</strong>’s <code>io_LCMBasis</code> function to create a basis set:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="osprey-basis-set-tools.html#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;</span> [BASIS] <span class="op">=</span> io_LCMBasis(file<span class="op">,</span> <span class="fl">1</span><span class="op">,</span> <span class="st">&#39;unedited&#39;</span><span class="op">,</span> <span class="st">&#39;none&#39;</span>)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="osprey-basis-set-tools.html#cb2-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> [BASIS] <span class="op">=</span> io_LCMBasis(file<span class="op">,</span> <span class="fl">1</span><span class="op">,</span> <span class="st">&#39;unedited&#39;</span><span class="op">,</span> <span class="st">&#39;none&#39;</span>)<span class="op">;</span></span></code></pre></div>
 <p>Follow the instructions in the MATLAB prompt, and from then on, OspreyFit will automatically pick this basis set, but only if there is no internal existing <strong>Osprey</strong> basis set with matching parameters. We will soon provide the option to specify an individual basis set in the job file.</p>
 </div>
 <div id="fit_makebasis" class="section level2 hasAnchor" number="7.2">
 <h2><span class="header-section-number">7.2</span> fit_makeBasis<a href="osprey-basis-set-tools.html#fit_makebasis" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>For the purpose of this tutorial, we will assume that you have a set of FID-A simulations saved in a folder on your hard drive. Your folder may look like this:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyFIDASims"></span>
-<img src="img/05-fid-a-folder.png" alt="A folder full of FID-A simulations." width="300" />
+<img src="img/05-fid-a-folder.png" alt="A folder full of FID-A simulations."  />
 <p class="caption">
 Figure 7.1: A folder full of FID-A simulations.
 </p>
 </div>
 <p>In this case, we have simulated a bunch of metabolites for the GE PRESS sequence at an echo time of 144 ms.</p>
 <p>If this folder is located at, say, <code>/Users/Georg/MRS_Simulations/GE/press144</code>, you can create a variable called <code>folder</code> at the MATLAB prompt:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb3-1"><a href="osprey-basis-set-tools.html#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;</span> folder <span class="op">=</span> <span class="st">&#39;/Users/Georg/MRS_Simulations/GE/press144&#39;</span><span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb3-1"><a href="osprey-basis-set-tools.html#cb3-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> folder <span class="op">=</span> <span class="st">&#39;/Users/Georg/MRS_Simulations/GE/press144&#39;</span><span class="op">;</span></span></code></pre></div>
 <p>You can then call <strong>Osprey</strong>’s <code>fit_makeBasis</code> function to create a basis set:</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb4-1"><a href="osprey-basis-set-tools.html#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;</span> [BASIS] <span class="op">=</span> fit_makeBasis(folder<span class="op">,</span> <span class="fl">1</span><span class="op">,</span> <span class="st">&#39;unedited&#39;</span>)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb4-1"><a href="osprey-basis-set-tools.html#cb4-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> [BASIS] <span class="op">=</span> fit_makeBasis(folder<span class="op">,</span> <span class="fl">1</span><span class="op">,</span> <span class="st">&#39;unedited&#39;</span>)<span class="op">;</span></span></code></pre></div>
 <p>This will generate a struct array called <code>BASIS</code> in the MATLAB workspace, and also save it to the current MATLAB working directory. This file is your new <strong>Osprey</strong> basis set. If the <code>addMMFlag</code> argument (see below) is set to <code>1</code>, the filename of the basis set is going to be <code>BASIS_MM.mat</code>; if it is set to <code>0</code>, the filename will be <code>BASIS_noMM.mat</code>.</p>
 <div id="complete-syntax" class="section level3 hasAnchor" number="7.2.1">
 <h3><span class="header-section-number">7.2.1</span> Complete syntax<a href="osprey-basis-set-tools.html#complete-syntax" class="anchor-section" aria-label="Anchor link to header"></a></h3>
-<div class="sourceCode" id="cb5"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb5-1"><a href="osprey-basis-set-tools.html#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;</span> [BASIS] <span class="op">=</span> fit_makeBasis(folder<span class="op">,</span> addMMFlag<span class="op">,</span> sequence<span class="op">,</span> editTarget)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb5-1"><a href="osprey-basis-set-tools.html#cb5-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> [BASIS] <span class="op">=</span> fit_makeBasis(folder<span class="op">,</span> addMMFlag<span class="op">,</span> sequence<span class="op">,</span> editTarget)<span class="op">;</span></span></code></pre></div>
 <div id="inputs" class="section level4 unnumbered hasAnchor">
 <h4>Inputs<a href="osprey-basis-set-tools.html#inputs" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <table>
@@ -351,23 +355,23 @@ <h2><span class="header-section-number">7.3</span> fit_plotBasis<a href="osprey-
 <p>Once you have generated the basis set, you may want to plot the basis functions and inspect that they look like you expect them to. For this purpose, <strong>Osprey</strong> includes a function called <code>fit_plotBasis</code>.</p>
 <p><code>fit_plotBasis</code> acts on the contents of an <strong>Osprey</strong> <code>.MAT</code> basis set file. If you load any basis set into MATLAB by double-clicking on it, you will see the struct <code>BASIS</code> in the MATLAB workspace:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyBasisInWorkspace"></span>
-<img src="img/05-basis-in-workspace.png" alt="An Osprey basis set after loading into MATLAB." width="549" />
+<img src="img/05-basis-in-workspace.png" alt="An Osprey basis set after loading into MATLAB."  />
 <p class="caption">
 Figure 7.2: An Osprey basis set after loading into MATLAB.
 </p>
 </div>
 <p>You can then call <code>fit_plotBasis</code> to create a plot overview of the basis set:</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb6-1"><a href="osprey-basis-set-tools.html#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;</span> fit_plotBasis(BASIS<span class="op">,</span> <span class="fl">1</span><span class="op">,</span> <span class="fl">1</span>)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb6-1"><a href="osprey-basis-set-tools.html#cb6-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> fit_plotBasis(BASIS<span class="op">,</span> <span class="fl">1</span><span class="op">,</span> <span class="fl">1</span>)<span class="op">;</span></span></code></pre></div>
 <p>This command will generate a stack plot of all basis functions (including macromolecules and lipids, if you have chosen to include them in the basis set) along with a ppm axis:</p>
 <div class="figure">
-<img src="img/05-plot-basis.png" alt="Output from fit_plotBasis." width="699" />
+<img src="img/05-plot-basis.png" alt="Output from fit_plotBasis."  />
 <p class="caption">
 (#fig:ospreyFit_plotBasis)Output from fit_plotBasis.
 </p>
 </div>
 <div id="complete-syntax-1" class="section level3 hasAnchor" number="7.3.1">
 <h3><span class="header-section-number">7.3.1</span> Complete syntax<a href="osprey-basis-set-tools.html#complete-syntax-1" class="anchor-section" aria-label="Anchor link to header"></a></h3>
-<div class="sourceCode" id="cb7"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb7-1"><a href="osprey-basis-set-tools.html#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;</span> out <span class="op">=</span> fit_plotBasis(basisSet<span class="op">,</span> dim<span class="op">,</span> stagFlag<span class="op">,</span> ppmmin<span class="op">,</span> ppmmax<span class="op">,</span> xlab<span class="op">,</span> ylab<span class="op">,</span> figTitle)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb7-1"><a href="osprey-basis-set-tools.html#cb7-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> out <span class="op">=</span> fit_plotBasis(basisSet<span class="op">,</span> dim<span class="op">,</span> stagFlag<span class="op">,</span> ppmmin<span class="op">,</span> ppmmax<span class="op">,</span> xlab<span class="op">,</span> ylab<span class="op">,</span> figTitle)<span class="op">;</span></span></code></pre></div>
 <div id="inputs-1" class="section level4 unnumbered hasAnchor">
 <h4>Inputs<a href="osprey-basis-set-tools.html#inputs-1" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <table>
diff --git a/docs/osprey-command-line-tutorial.html b/docs/osprey-command-line-tutorial.html
index be102ed7..d4e86266 100644
--- a/docs/osprey-command-line-tutorial.html
+++ b/docs/osprey-command-line-tutorial.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Chapter 6 Osprey command line tutorial | Osprey Documentation</title>
   <meta name="description" content="Osprey is an all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data." />
-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
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@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
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+code span.bu { color: #008000; } /* BuiltIn */
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@@ -105,7 +105,7 @@
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+code span.im { color: #008000; font-weight: bold; } /* Import */
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@@ -119,6 +119,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="css/style.css" type="text/css" />
 </head>
@@ -165,13 +169,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
@@ -231,26 +235,26 @@ <h1>
 <div id="osprey-command-line-tutorial" class="section level1 hasAnchor" number="6">
 <h1><span class="header-section-number">Chapter 6</span> Osprey command line tutorial<a href="osprey-command-line-tutorial.html#osprey-command-line-tutorial" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>All <strong>Osprey</strong> functions descibed in the GUI section can alternatively be called directly using a series of commands in the Matlab terminal. The function RunOspreyJob.m is a one-stop-shop wrapper for all of these commands, running the full analysis without interruption:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="osprey-command-line-tutorial.html#cb1-1" aria-hidden="true" tabindex="-1"></a>MRSCont <span class="op">=</span> RunOspreyJob(<span class="st">&#39;Path/To/Job/File&#39;</span>)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="osprey-command-line-tutorial.html#cb1-1" tabindex="-1"></a>MRSCont <span class="op">=</span> RunOspreyJob(<span class="st">&#39;Path/To/Job/File&#39;</span>)<span class="op">;</span></span></code></pre></div>
 <p>It may be preferable to view your analysis at each step by calling each command in turn. After setting up the job file, either as a Matlab .m file, .json, or .csv, the <strong>Osprey</strong> job is initialized as follows:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="osprey-command-line-tutorial.html#cb2-1" aria-hidden="true" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyJob(<span class="st">&#39;Path/To/Job/File&#39;</span>)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="osprey-command-line-tutorial.html#cb2-1" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyJob(<span class="st">&#39;Path/To/Job/File&#39;</span>)<span class="op">;</span></span></code></pre></div>
 <p>MRSCont will now contain the options and file locations for your data, as specified in the job file. Next, the data can be loaded:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb3-1"><a href="osprey-command-line-tutorial.html#cb3-1" aria-hidden="true" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyLoad(MRScont)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb3-1"><a href="osprey-command-line-tutorial.html#cb3-1" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyLoad(MRSCont)<span class="op">;</span></span></code></pre></div>
 <p>The substructure, MRSCont.raw, now contains the raw MRS data, as extracted from their native format. We may now preprocess these data:</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb4-1"><a href="osprey-command-line-tutorial.html#cb4-1" aria-hidden="true" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyProcess(MRSCont)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb4-1"><a href="osprey-command-line-tutorial.html#cb4-1" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyProcess(MRSCont)<span class="op">;</span></span></code></pre></div>
 <p>The MRSCont.processed will now contain the processed data, as well as some quality control measures in MRSCont.QM for your inspection. If all is well, we may now fit the data:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb5-1"><a href="osprey-command-line-tutorial.html#cb5-1" aria-hidden="true" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyFit(MRSCont)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb5-1"><a href="osprey-command-line-tutorial.html#cb5-1" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyFit(MRSCont)<span class="op">;</span></span></code></pre></div>
 <p>Modeling results are added to the MRSCont.fit, including results tables. If we have structural data, we can coregister our voxels, and perform tissue segmentation:</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb6-1"><a href="osprey-command-line-tutorial.html#cb6-1" aria-hidden="true" tabindex="-1"></a>MRScont <span class="op">=</span> OspreyCoreg(MRSCont)<span class="op">;</span></span>
-<span id="cb6-2"><a href="osprey-command-line-tutorial.html#cb6-2" aria-hidden="true" tabindex="-1"></a>MRScont <span class="op">=</span> OspreySeg(MRSCont)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb6-1"><a href="osprey-command-line-tutorial.html#cb6-1" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyCoreg(MRSCont)<span class="op">;</span></span>
+<span id="cb6-2"><a href="osprey-command-line-tutorial.html#cb6-2" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreySeg(MRSCont)<span class="op">;</span></span></code></pre></div>
 <p>MRSCont now has sub-structures relating to voxel masks and volumes, MRSCont.coreg, and tissue segmentation results in MRSCont.seg.</p>
 <p>Whether we had structural images or not, we may now quantify our spectra to produce some numerical results:</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb7-1"><a href="osprey-command-line-tutorial.html#cb7-1" aria-hidden="true" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyQuantify(MRSCont)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb7-1"><a href="osprey-command-line-tutorial.html#cb7-1" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyQuantify(MRSCont)<span class="op">;</span></span></code></pre></div>
 <p>Finally, we may run the OspreyOverview function:</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb8-1"><a href="osprey-command-line-tutorial.html#cb8-1" aria-hidden="true" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyOverview(MRSCont)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb8"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb8-1"><a href="osprey-command-line-tutorial.html#cb8-1" tabindex="-1"></a>MRSCont <span class="op">=</span> OspreyOverview(MRSCont)<span class="op">;</span></span></code></pre></div>
 <p>This final function adds group measures, if we have a stat.csv file, and performs some statistics necesary for some of the plotting functions and GUI windows.</p>
 <p>At any point during a command-line analysis, it is possible to visualize the data using the plot functions found in <strong>Osprey/plot</strong>, or even by switching to the GUI mid-analysis using:</p>
-<div class="sourceCode" id="cb9"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb9-1"><a href="osprey-command-line-tutorial.html#cb9-1" aria-hidden="true" tabindex="-1"></a>OspreyGUI(MRSCont)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb9"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb9-1"><a href="osprey-command-line-tutorial.html#cb9-1" tabindex="-1"></a>OspreyGUI(MRSCont)<span class="op">;</span></span></code></pre></div>
 
 </div>
             </section>
diff --git a/docs/osprey-gui-tutorial.html b/docs/osprey-gui-tutorial.html
index 94401b10..856a535f 100644
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-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
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@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
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+</style>
 
 <link rel="stylesheet" href="css/style.css" type="text/css" />
 </head>
@@ -165,13 +169,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
@@ -239,10 +243,10 @@ <h1><span class="header-section-number">Chapter 5</span> Osprey GUI tutorial<a h
 <div id="starting-osprey" class="section level2 hasAnchor" number="5.1">
 <h2><span class="header-section-number">5.1</span> Starting Osprey<a href="osprey-gui-tutorial.html#starting-osprey" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>At the MATLAB prompt, enter</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="osprey-gui-tutorial.html#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;</span> Osprey</span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="osprey-gui-tutorial.html#cb1-1" tabindex="-1"></a><span class="op">&gt;&gt;</span> Osprey</span></code></pre></div>
 <p>This will initiate the <strong>Osprey</strong> GUI application and the underlying processing modules. Once the startup is complete, you will see the <strong>Osprey</strong> startup menu box:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyStartupMenu"></span>
-<img src="img/04-osprey-startup-menu.png" alt="The Osprey Startup Menu." width="181" />
+<img src="img/04-osprey-startup-menu.png" alt="The Osprey Startup Menu."  />
 <p class="caption">
 Figure 5.1: The Osprey Startup Menu.
 </p>
@@ -252,21 +256,21 @@ <h2><span class="header-section-number">5.1</span> Starting Osprey<a href="ospre
 <h2><span class="header-section-number">5.2</span> Loading a job file<a href="osprey-gui-tutorial.html#loading-a-job-file" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>Click the <code>Load Job file</code> button, navigate to the <code>exampledata/twix</code> directory, and add the file <code>jobTwix.m</code> to the right column:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreySelectJobFile"></span>
-<img src="img/04-osprey-select-job-file.png" alt="Selecting a job file." width="510" />
+<img src="img/04-osprey-select-job-file.png" alt="Selecting a job file."  />
 <p class="caption">
 Figure 5.2: Selecting a job file.
 </p>
 </div>
 <p>Click <code>Done</code>. If you have run an <strong>Osprey</strong> analysis previously with the same output folder specified in the job file, you will be shown a warning:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyOverwriteWarning"></span>
-<img src="img/04-warning-overwrite.png" alt="Warning when you are about to overwrite a previous analysis." width="270" />
+<img src="img/04-warning-overwrite.png" alt="Warning when you are about to overwrite a previous analysis."  />
 <p class="caption">
 Figure 5.3: Warning when you are about to overwrite a previous analysis.
 </p>
 </div>
 <p>Click <code>Yes</code>. <strong>Osprey</strong> will now extract all necessary information from the job file you selected by running the <code>OspreyJob</code> module in the background. The next window you see is the main GUI:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyJob"></span>
-<img src="img/04-osprey-gui-job.png" alt="The Osprey GUI after OspreyJob." width="742" />
+<img src="img/04-osprey-gui-job.png" alt="The Osprey GUI after OspreyJob."  />
 <p class="caption">
 Figure 5.4: The Osprey GUI after OspreyJob.
 </p>
@@ -338,7 +342,7 @@ <h2><span class="header-section-number">5.4</span> Processing the raw data<a hre
 <p>Click the (now available!) <code>Process data</code> button to initiate the post-processing. <strong>Osprey</strong> will now perform all appropriate processing steps (depending on the available data: eddy-current correction, frequency-and-phase alignment, water removal, frequency referencing, initial phasing) by running the <code>OspreyProcess</code> module in the background. This process may take several seconds per dataset. You can monitor the progress through the wait bar.</p>
 <p>Once the post-processing is complete, the <code>Processed</code> tab becomes active, showing four different panels:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyProcess"></span>
-<img src="img/04-process-mets.png" alt="The Osprey GUI after OspreyProcess." width="694" />
+<img src="img/04-process-mets.png" alt="The Osprey GUI after OspreyProcess."  />
 <p class="caption">
 Figure 5.5: The Osprey GUI after OspreyProcess.
 </p>
@@ -346,7 +350,7 @@ <h2><span class="header-section-number">5.4</span> Processing the raw data<a hre
 <p>The top left panel shows the individual averages prior to frequency-and-phase alignment. The bottom left panel shows them after frequency-and-phase alignment.
 The top right panel shows a scatter plot of the maximum of the 3.02 ppm Cr/PCr signal over the course of the acquisition for both pre- and post-alignment. Finally, the bottom right panel shows the aligned, averaged and referenced spectrum after eddy-current correction and residual water removal. This spectrum will be passed on to the <code>Fit</code> module for modeling.</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyProcess2"></span>
-<img src="img/04-process-mets-subspec.png" alt="Different sub-spectra can be visualized by cycling through the &quot;Spec&quot; windows." width="672" />
+<img src="img/04-process-mets-subspec.png" alt="Different sub-spectra can be visualized by cycling through the &quot;Spec&quot; windows."  />
 <p class="caption">
 Figure 5.6: Different sub-spectra can be visualized by cycling through the “Spec” windows.
 </p>
@@ -371,7 +375,7 @@ <h2><span class="header-section-number">5.5</span> Fitting the spectra<a href="o
 <p>Click the (now available!) <code>Fit data</code> button to initiate the post-processing. <strong>Osprey</strong> will now model the processed metabolite and water spectra by running the <code>OspreyFit</code> module in the background. This process may take a few seconds, or up to a minute or more per dataset, depending on the complexity of the data and model. You can monitor the progress through the wait bar.</p>
 <p>Once the modeling is complete, the <code>Fit</code> tab becomes active:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyFit"></span>
-<img src="img/04-fit-mets.png" alt="The Osprey GUI after OspreyFit." width="694" />
+<img src="img/04-fit-mets.png" alt="The Osprey GUI after OspreyFit."  />
 <p class="caption">
 Figure 5.7: The Osprey GUI after OspreyFit.
 </p>
@@ -402,7 +406,7 @@ <h2><span class="header-section-number">5.6</span> Co-registering to an anatomic
 </div>
 <p>Once the co-registration is complete, the <code>Cor/Seg</code> tab becomes active:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyCoreg"></span>
-<img src="img/04-coreg.png" alt="The Osprey GUI after OspreyCoReg." width="645" />
+<img src="img/04-coreg.png" alt="The Osprey GUI after OspreyCoReg."  />
 <p class="caption">
 Figure 5.8: The Osprey GUI after OspreyCoReg.
 </p>
@@ -426,7 +430,7 @@ <h2><span class="header-section-number">5.7</span> Segmentation and tissue fract
 </div>
 <p>Once the segmentation is complete, the <code>Cor/Seg</code> tab features another figure:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreySeg"></span>
-<img src="img/04-seg.png" alt="The Osprey GUI after OspreySeg." width="645" />
+<img src="img/04-seg.png" alt="The Osprey GUI after OspreySeg."  />
 <p class="caption">
 Figure 5.9: The Osprey GUI after OspreySeg.
 </p>
@@ -442,7 +446,7 @@ <h2><span class="header-section-number">5.8</span> Quantification<a href="osprey
 <p>Click the <code>Quantify</code> button to have <strong>Osprey</strong> run the <code>OspreyQuantify</code> module in the background. This should take less than a second per dataset. During this process, several quantitative metabolite estimates are calculated, such as tCr ratios and water-scaled estimates with different degrees of sophistication. Please refer to the <strong>Osprey</strong> manuscript for details on the implementation of these quantification routines.</p>
 <p>Once the quantification is complete, the <code>Quantify</code> tab becomes active:</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyQuantify"></span>
-<img src="img/04-quantify.png" alt="The Osprey GUI after OspreyQuantify." width="645" />
+<img src="img/04-quantify.png" alt="The Osprey GUI after OspreyQuantify."  />
 <p class="caption">
 Figure 5.10: The Osprey GUI after OspreyQuantify.
 </p>
@@ -462,7 +466,7 @@ <h2><span class="header-section-number">5.9</span> Overview<a href="osprey-gui-t
 You can select the data or complete fits for the metabolite and water data by using the dropdown menu at the top of the window.
 </div>
 <div class="figure"><span style="display:block;" id="fig:ospreyOverviewSpectra"></span>
-<img src="img/04-overview-spectra.png" alt="The Overview Spectra tab in the Osprey GUI." width="645" />
+<img src="img/04-overview-spectra.png" alt="The Overview Spectra tab in the Osprey GUI."  />
 <p class="caption">
 Figure 5.11: The Overview Spectra tab in the Osprey GUI.
 </p>
@@ -475,7 +479,7 @@ <h2><span class="header-section-number">5.9</span> Overview<a href="osprey-gui-t
 You can select the metabolite and water data by using the dropdown menu at the top of the window.
 </div>
 <div class="figure"><span style="display:block;" id="fig:ospreyOverviewMeanSpectra"></span>
-<img src="img/04-overview-mean-spectra.png" alt="The Overview Mean Spectra tab in the Osprey GUI." width="645" />
+<img src="img/04-overview-mean-spectra.png" alt="The Overview Mean Spectra tab in the Osprey GUI."  />
 <p class="caption">
 Figure 5.12: The Overview Mean Spectra tab in the Osprey GUI.
 </p>
@@ -495,7 +499,7 @@ <h2><span class="header-section-number">5.9</span> Overview<a href="osprey-gui-t
 You can select the quantification routine to be displayed (tCr ratios, raw water-scaled, CSF-corrected water-scaled, tissue-corrected water-scaled) by using the dropdown menu at the top of the window.
 </div>
 <div class="figure"><span style="display:block;" id="fig:ospreyQuantifyTable"></span>
-<img src="img/04-overview-quantify-table.png" alt="The Overview Quantify Table tab in the Osprey GUI." width="645" />
+<img src="img/04-overview-quantify-table.png" alt="The Overview Quantify Table tab in the Osprey GUI."  />
 <p class="caption">
 Figure 5.13: The Overview Quantify Table tab in the Osprey GUI.
 </p>
@@ -509,7 +513,7 @@ <h2><span class="header-section-number">5.9</span> Overview<a href="osprey-gui-t
 </div>
 <p>By default, the <code>Distribution</code> tab is set to display the tCr ratios of tNAA.</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyOverviewDistribution"></span>
-<img src="img/04-overview-distribution.png" alt="The Overview Distribution tab in the Osprey GUI." width="645" />
+<img src="img/04-overview-distribution.png" alt="The Overview Distribution tab in the Osprey GUI."  />
 <p class="caption">
 Figure 5.14: The Overview Distribution tab in the Osprey GUI.
 </p>
@@ -523,7 +527,7 @@ <h2><span class="header-section-number">5.9</span> Overview<a href="osprey-gui-t
 </div>
 <p>By default, the <code>Correlation</code> tab is set to display the correlation of tNAA/tCr to SNR.</p>
 <div class="figure"><span style="display:block;" id="fig:ospreyOverviewCorrelation"></span>
-<img src="img/04-overview-correlation.png" alt="The Overview Correlation tab in the Osprey GUI." width="645" />
+<img src="img/04-overview-correlation.png" alt="The Overview Correlation tab in the Osprey GUI."  />
 <p class="caption">
 Figure 5.15: The Overview Correlation tab in the Osprey GUI.
 </p>
diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt
index 1d75315d..b834e5ca 100644
--- a/docs/reference-keys.txt
+++ b/docs/reference-keys.txt
@@ -79,3 +79,5 @@ specifying-stat-file
 explicit-vs-automated-file
 osprey-command-line-tutorial
 fig:ospreyProcess2
+metabolites-included-in-the-basis-set
+co-edited-macromolecules
diff --git a/docs/the-osprey-job-file.html b/docs/the-osprey-job-file.html
index 28cd8cf7..a9f63066 100644
--- a/docs/the-osprey-job-file.html
+++ b/docs/the-osprey-job-file.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Chapter 4 The Osprey job file | Osprey Documentation</title>
   <meta name="description" content="Osprey is an all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data." />
-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Chapter 4 The Osprey job file | Osprey Documentation" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -92,7 +92,7 @@
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 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
-code span.bu { } /* BuiltIn */
+code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
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@@ -105,7 +105,7 @@
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
-code span.im { } /* Import */
+code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
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@@ -119,6 +119,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
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+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="css/style.css" type="text/css" />
 </head>
@@ -165,13 +169,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
@@ -236,333 +240,333 @@ <h1><span class="header-section-number">Chapter 4</span> The Osprey job file<a h
 <h2><span class="header-section-number">4.1</span> Example job file<a href="the-osprey-job-file.html#example-job-file" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>The following box contains the <a href="https://github.com/schorschinho/osprey/blob/develop/exampledata/sdat/UnEdited/jobSDAT.m">example job file <code>jobSDAT.m</code></a>, defining a batched analysis of the two Philips PRESS (TE = 30 ms) datasets that are included in the <code>exampledata/sdat/</code> directory of the <a href="https://github.com/schorschinho/osprey"><strong>Osprey</strong> repository</a>. You can click on the dropdown arrow on the right to take a look through the file, and then read on for a detailed description of each job file item.</p>
 <p>Example job file <code>jobSDAT.m</code>:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="the-osprey-job-file.html#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co">%% jobSDAT.m</span></span>
-<span id="cb1-2"><a href="the-osprey-job-file.html#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">%   This function describes an Osprey job defined in a MATLAB script.</span></span>
-<span id="cb1-3"><a href="the-osprey-job-file.html#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">%</span></span>
-<span id="cb1-4"><a href="the-osprey-job-file.html#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">%   A valid Osprey job contains four distinct classes of items:</span></span>
-<span id="cb1-5"><a href="the-osprey-job-file.html#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">%       1. basic information on the MRS sequence used</span></span>
-<span id="cb1-6"><a href="the-osprey-job-file.html#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">%       2. several settings for data handling and modeling</span></span>
-<span id="cb1-7"><a href="the-osprey-job-file.html#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">%       3. a list of MRS (and, optionally, structural imaging) data files</span></span>
-<span id="cb1-8"><a href="the-osprey-job-file.html#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="co">%          to be loaded</span></span>
-<span id="cb1-9"><a href="the-osprey-job-file.html#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="co">%       4. an output folder to store the results and exported files</span></span>
-<span id="cb1-10"><a href="the-osprey-job-file.html#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">%</span></span>
-<span id="cb1-11"><a href="the-osprey-job-file.html#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co">%   The list of MRS and structural imaging files is provided in the form of</span></span>
-<span id="cb1-12"><a href="the-osprey-job-file.html#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">%   cell arrays. They can simply be provided explicitly, or from a more</span></span>
-<span id="cb1-13"><a href="the-osprey-job-file.html#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">%   complex script that automatically determines file names from a given</span></span>
-<span id="cb1-14"><a href="the-osprey-job-file.html#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="co">%   folder structure.</span></span>
-<span id="cb1-15"><a href="the-osprey-job-file.html#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="co">%</span></span>
-<span id="cb1-16"><a href="the-osprey-job-file.html#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="co">%   Osprey distinguishes between four sets of data:</span></span>
-<span id="cb1-17"><a href="the-osprey-job-file.html#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="co">%       - metabolite (water-suppressed) data</span></span>
-<span id="cb1-18"><a href="the-osprey-job-file.html#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="co">%           (MANDATORY)</span></span>
-<span id="cb1-19"><a href="the-osprey-job-file.html#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files&quot;</span></span>
-<span id="cb1-20"><a href="the-osprey-job-file.html#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="co">%       - water reference data acquired with the SAME sequence as the</span></span>
-<span id="cb1-21"><a href="the-osprey-job-file.html#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="co">%           metabolite data, just without water suppression RF pulses. This</span></span>
-<span id="cb1-22"><a href="the-osprey-job-file.html#cb1-22" aria-hidden="true" tabindex="-1"></a><span class="co">%           data is used to determine complex coil combination</span></span>
-<span id="cb1-23"><a href="the-osprey-job-file.html#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="co">%           coefficients, and perform eddy current correction.</span></span>
-<span id="cb1-24"><a href="the-osprey-job-file.html#cb1-24" aria-hidden="true" tabindex="-1"></a><span class="co">%           (OPTIONAL)</span></span>
-<span id="cb1-25"><a href="the-osprey-job-file.html#cb1-25" aria-hidden="true" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files_ref&quot;</span></span>
-<span id="cb1-26"><a href="the-osprey-job-file.html#cb1-26" aria-hidden="true" tabindex="-1"></a><span class="co">%       - additional water data used for water-scaled quantification,</span></span>
-<span id="cb1-27"><a href="the-osprey-job-file.html#cb1-27" aria-hidden="true" tabindex="-1"></a><span class="co">%           usually from short-TE acquisitions due to reduced T2-weighting</span></span>
-<span id="cb1-28"><a href="the-osprey-job-file.html#cb1-28" aria-hidden="true" tabindex="-1"></a><span class="co">%           (OPTIONAL)</span></span>
-<span id="cb1-29"><a href="the-osprey-job-file.html#cb1-29" aria-hidden="true" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files_w&quot;</span></span>
-<span id="cb1-30"><a href="the-osprey-job-file.html#cb1-30" aria-hidden="true" tabindex="-1"></a><span class="co">%       - Structural image data used for co-registration and tissue class</span></span>
-<span id="cb1-31"><a href="the-osprey-job-file.html#cb1-31" aria-hidden="true" tabindex="-1"></a><span class="co">%           segmentation (usually a T1 MPRAGE). These files need to be</span></span>
-<span id="cb1-32"><a href="the-osprey-job-file.html#cb1-32" aria-hidden="true" tabindex="-1"></a><span class="co">%           provided in the NIfTI format (*.nii or *.nii.gz) or, for GE data, as a</span></span>
-<span id="cb1-33"><a href="the-osprey-job-file.html#cb1-33" aria-hidden="true" tabindex="-1"></a><span class="co">%           folder containing DICOM Files (*.dcm).</span></span>
-<span id="cb1-34"><a href="the-osprey-job-file.html#cb1-34" aria-hidden="true" tabindex="-1"></a><span class="co">%           (OPTIONAL)</span></span>
-<span id="cb1-35"><a href="the-osprey-job-file.html#cb1-35" aria-hidden="true" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files_nii&quot;</span></span>
-<span id="cb1-36"><a href="the-osprey-job-file.html#cb1-36" aria-hidden="true" tabindex="-1"></a><span class="co">%       - External segmentation results. These files need to be</span></span>
-<span id="cb1-37"><a href="the-osprey-job-file.html#cb1-37" aria-hidden="true" tabindex="-1"></a><span class="co">%           provided in the NIfTI format (*.nii or *.nii.gz).</span></span>
-<span id="cb1-38"><a href="the-osprey-job-file.html#cb1-38" aria-hidden="true" tabindex="-1"></a><span class="co">%           (OPTIONAL)</span></span>
-<span id="cb1-39"><a href="the-osprey-job-file.html#cb1-39" aria-hidden="true" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files_seg&quot; with 1 x 3 cell for each</span></span>
-<span id="cb1-40"><a href="the-osprey-job-file.html#cb1-40" aria-hidden="true" tabindex="-1"></a><span class="co">%           subject or 1 x 1 cell if a single 4D NIfTI is supplied.</span></span>
-<span id="cb1-41"><a href="the-osprey-job-file.html#cb1-41" aria-hidden="true" tabindex="-1"></a><span class="co">%</span></span>
-<span id="cb1-42"><a href="the-osprey-job-file.html#cb1-42" aria-hidden="true" tabindex="-1"></a><span class="co">%   Files in the formats</span></span>
-<span id="cb1-43"><a href="the-osprey-job-file.html#cb1-43" aria-hidden="true" tabindex="-1"></a><span class="co">%       - .7 (GE)</span></span>
-<span id="cb1-44"><a href="the-osprey-job-file.html#cb1-44" aria-hidden="true" tabindex="-1"></a><span class="co">%       - .SDAT, .DATA/.LIST, .RAW/.SIN/.LAB (Philips)</span></span>
-<span id="cb1-45"><a href="the-osprey-job-file.html#cb1-45" aria-hidden="true" tabindex="-1"></a><span class="co">%       - .DAT (Siemens)</span></span>
-<span id="cb1-46"><a href="the-osprey-job-file.html#cb1-46" aria-hidden="true" tabindex="-1"></a><span class="co">%       - .nii, .nii.gz (NIfTI-MRS)</span></span>
-<span id="cb1-47"><a href="the-osprey-job-file.html#cb1-47" aria-hidden="true" tabindex="-1"></a><span class="co">%   usually contain all of the acquired data in a single file per scan. GE</span></span>
-<span id="cb1-48"><a href="the-osprey-job-file.html#cb1-48" aria-hidden="true" tabindex="-1"></a><span class="co">%   systems store water reference data in the same .7 file, so there is no</span></span>
-<span id="cb1-49"><a href="the-osprey-job-file.html#cb1-49" aria-hidden="true" tabindex="-1"></a><span class="co">%   need to specify it separately under files_ref.</span></span>
-<span id="cb1-50"><a href="the-osprey-job-file.html#cb1-50" aria-hidden="true" tabindex="-1"></a><span class="co">%</span></span>
-<span id="cb1-51"><a href="the-osprey-job-file.html#cb1-51" aria-hidden="true" tabindex="-1"></a><span class="co">%   Files in the formats</span></span>
-<span id="cb1-52"><a href="the-osprey-job-file.html#cb1-52" aria-hidden="true" tabindex="-1"></a><span class="co">%       - .DCM (any)</span></span>
-<span id="cb1-53"><a href="the-osprey-job-file.html#cb1-53" aria-hidden="true" tabindex="-1"></a><span class="co">%       - .IMA, .RDA (Siemens)</span></span>
-<span id="cb1-54"><a href="the-osprey-job-file.html#cb1-54" aria-hidden="true" tabindex="-1"></a><span class="co">%   may contain separate files for each average. Instead of providing</span></span>
-<span id="cb1-55"><a href="the-osprey-job-file.html#cb1-55" aria-hidden="true" tabindex="-1"></a><span class="co">%   individual file names, please specify folders. Metabolite data, water</span></span>
-<span id="cb1-56"><a href="the-osprey-job-file.html#cb1-56" aria-hidden="true" tabindex="-1"></a><span class="co">%   reference data, and water data need to be located in separate folders.</span></span>
-<span id="cb1-57"><a href="the-osprey-job-file.html#cb1-57" aria-hidden="true" tabindex="-1"></a><span class="co">%</span></span>
-<span id="cb1-58"><a href="the-osprey-job-file.html#cb1-58" aria-hidden="true" tabindex="-1"></a><span class="co">%   In the example script at hand the MATLAB functions strrep and which are</span></span>
-<span id="cb1-59"><a href="the-osprey-job-file.html#cb1-59" aria-hidden="true" tabindex="-1"></a><span class="co">%   used to generate a relative path, which allows you to run the examples</span></span>
-<span id="cb1-60"><a href="the-osprey-job-file.html#cb1-60" aria-hidden="true" tabindex="-1"></a><span class="co">%   on your machine directly. To set up your own Osprey job supply the</span></span>
-<span id="cb1-61"><a href="the-osprey-job-file.html#cb1-61" aria-hidden="true" tabindex="-1"></a><span class="co">%   specific locations as described above.</span></span>
-<span id="cb1-62"><a href="the-osprey-job-file.html#cb1-62" aria-hidden="true" tabindex="-1"></a><span class="co">%</span></span>
-<span id="cb1-63"><a href="the-osprey-job-file.html#cb1-63" aria-hidden="true" tabindex="-1"></a><span class="co">%   AUTHOR:</span></span>
-<span id="cb1-64"><a href="the-osprey-job-file.html#cb1-64" aria-hidden="true" tabindex="-1"></a><span class="co">%       Dr. Georg Oeltzschner (Johns Hopkins University, 2019-07-15)</span></span>
-<span id="cb1-65"><a href="the-osprey-job-file.html#cb1-65" aria-hidden="true" tabindex="-1"></a><span class="co">%       goeltzs1@jhmi.edu</span></span>
-<span id="cb1-66"><a href="the-osprey-job-file.html#cb1-66" aria-hidden="true" tabindex="-1"></a><span class="co">%</span></span>
-<span id="cb1-67"><a href="the-osprey-job-file.html#cb1-67" aria-hidden="true" tabindex="-1"></a><span class="co">%   HISTORY:</span></span>
-<span id="cb1-68"><a href="the-osprey-job-file.html#cb1-68" aria-hidden="true" tabindex="-1"></a><span class="co">%       2019-07-15: First version of the code.</span></span>
-<span id="cb1-69"><a href="the-osprey-job-file.html#cb1-69" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-70"><a href="the-osprey-job-file.html#cb1-70" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-71"><a href="the-osprey-job-file.html#cb1-71" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-72"><a href="the-osprey-job-file.html#cb1-72" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
-<span id="cb1-73"><a href="the-osprey-job-file.html#cb1-73" aria-hidden="true" tabindex="-1"></a><span class="co">%%% 1. SPECIFY SEQUENCE INFORMATION %%%</span></span>
-<span id="cb1-74"><a href="the-osprey-job-file.html#cb1-74" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-75"><a href="the-osprey-job-file.html#cb1-75" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify sequence type</span></span>
-<span id="cb1-76"><a href="the-osprey-job-file.html#cb1-76" aria-hidden="true" tabindex="-1"></a>seqType <span class="op">=</span> <span class="st">&#39;unedited&#39;</span><span class="op">;</span>           <span class="co">% OPTIONS:    - &#39;unedited&#39; (default)</span></span>
-<span id="cb1-77"><a href="the-osprey-job-file.html#cb1-77" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;MEGA&#39;</span></span>
-<span id="cb1-78"><a href="the-osprey-job-file.html#cb1-78" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;HERMES&#39;</span></span>
-<span id="cb1-79"><a href="the-osprey-job-file.html#cb1-79" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;HERCULES&#39;</span></span>
-<span id="cb1-80"><a href="the-osprey-job-file.html#cb1-80" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-81"><a href="the-osprey-job-file.html#cb1-81" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify editing targets</span></span>
-<span id="cb1-82"><a href="the-osprey-job-file.html#cb1-82" aria-hidden="true" tabindex="-1"></a>editTarget <span class="op">=</span> {<span class="st">&#39;none&#39;</span>}<span class="op">;</span>          <span class="co">% OPTIONS:    - {&#39;none&#39;} (default if &#39;unedited&#39;)</span></span>
-<span id="cb1-83"><a href="the-osprey-job-file.html#cb1-83" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - {&#39;GABA&#39;}, {&#39;GSH&#39;}, {&#39;Lac&#39;}, {&#39;PE322&#39;}, {&#39;PE398&#39;}  (for &#39;MEGA&#39;)</span></span>
-<span id="cb1-84"><a href="the-osprey-job-file.html#cb1-84" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - {&#39;GABA&#39;, &#39;GSH&#39;}, {&#39;GABA&#39;, &#39;Lac&#39;}, {&#39;NAA&#39;, &#39;NAAG&#39;} (for &#39;HERMES&#39;and &#39;HERCULES&#39;)</span></span>
-<span id="cb1-85"><a href="the-osprey-job-file.html#cb1-85" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-86"><a href="the-osprey-job-file.html#cb1-86" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-87"><a href="the-osprey-job-file.html#cb1-87" aria-hidden="true" tabindex="-1"></a>                                <span class="co">% Specify data scenario</span></span>
-<span id="cb1-88"><a href="the-osprey-job-file.html#cb1-88" aria-hidden="true" tabindex="-1"></a>dataScenario <span class="op">=</span> <span class="st">&#39;invivo&#39;</span><span class="op">;</span>        <span class="co">% OPTIONS:    - &#39;invivo&#39; (default)</span></span>
-<span id="cb1-89"><a href="the-osprey-job-file.html#cb1-89" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;phantom&#39;</span></span>
-<span id="cb1-90"><a href="the-osprey-job-file.html#cb1-90" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;PRIAM&#39;</span></span>
-<span id="cb1-91"><a href="the-osprey-job-file.html#cb1-91" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;MRSI&#39;</span></span>
-<span id="cb1-92"><a href="the-osprey-job-file.html#cb1-92" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
-<span id="cb1-93"><a href="the-osprey-job-file.html#cb1-93" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-94"><a href="the-osprey-job-file.html#cb1-94" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-95"><a href="the-osprey-job-file.html#cb1-95" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-96"><a href="the-osprey-job-file.html#cb1-96" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
-<span id="cb1-97"><a href="the-osprey-job-file.html#cb1-97" aria-hidden="true" tabindex="-1"></a><span class="co">%%% 2. SPECIFY DATA HANDLING AND MODELING OPTIONS %%%</span></span>
-<span id="cb1-98"><a href="the-osprey-job-file.html#cb1-98" aria-hidden="true" tabindex="-1"></a><span class="co">% Which spectral registration method should be used? Robust spectral</span></span>
-<span id="cb1-99"><a href="the-osprey-job-file.html#cb1-99" aria-hidden="true" tabindex="-1"></a><span class="co">% registration is default, a frequency restricted spectral registration</span></span>
-<span id="cb1-100"><a href="the-osprey-job-file.html#cb1-100" aria-hidden="true" tabindex="-1"></a><span class="co">% method is also availaible and is linked to the fit range.</span></span>
-<span id="cb1-101"><a href="the-osprey-job-file.html#cb1-101" aria-hidden="true" tabindex="-1"></a>opts.SpecReg <span class="op">=</span> <span class="st">&#39;RobSpecReg&#39;</span><span class="op">;</span>                  <span class="co">% OPTIONS:    - &#39;RobSpecReg&#39; (default) Spectral aligment with Water/Lipid removal, using simialrity meric, and weighted averaging</span></span>
-<span id="cb1-102"><a href="the-osprey-job-file.html#cb1-102" aria-hidden="true" tabindex="-1"></a>                                              <span class="co">%             - &#39;ProbSpecReg&#39; Probabilistic spectral aligment to median target and weighted averaging</span></span>
-<span id="cb1-103"><a href="the-osprey-job-file.html#cb1-103" aria-hidden="true" tabindex="-1"></a>                                              <span class="co">%             - &#39;RestrSpecReg&#39; Frequency restricted (fit range) spectral aligment, using simialrity meric, and weighted averaging</span></span>
-<span id="cb1-104"><a href="the-osprey-job-file.html#cb1-104" aria-hidden="true" tabindex="-1"></a>                                              <span class="co">%             - &#39;none&#39;</span></span>
-<span id="cb1-105"><a href="the-osprey-job-file.html#cb1-105" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-106"><a href="the-osprey-job-file.html#cb1-106" aria-hidden="true" tabindex="-1"></a><span class="co">% Which algorithm do you want to align the sub spectra? L2 norm</span></span>
-<span id="cb1-107"><a href="the-osprey-job-file.html#cb1-107" aria-hidden="true" tabindex="-1"></a><span class="co">% optimization is the default. This is only used for edited MRS!</span></span>
-<span id="cb1-108"><a href="the-osprey-job-file.html#cb1-108" aria-hidden="true" tabindex="-1"></a><span class="co">%Perform correction on the metabolite data (raw) or metabolite</span></span>
-<span id="cb1-109"><a href="the-osprey-job-file.html#cb1-109" aria-hidden="true" tabindex="-1"></a><span class="co">%-nulled data (mm).</span></span>
-<span id="cb1-110"><a href="the-osprey-job-file.html#cb1-110" aria-hidden="true" tabindex="-1"></a>opts.SubSpecAlignment.mets <span class="op">=</span> <span class="st">&#39;L2Norm&#39;</span><span class="op">;</span>          <span class="co">% OPTIONS:    - &#39;L2Norm&#39; (default)</span></span>
-<span id="cb1-111"><a href="the-osprey-job-file.html#cb1-111" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - &#39;L1Norm&#39;</span></span>
-<span id="cb1-112"><a href="the-osprey-job-file.html#cb1-112" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - &#39;none&#39;</span></span>
-<span id="cb1-113"><a href="the-osprey-job-file.html#cb1-113" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-114"><a href="the-osprey-job-file.html#cb1-114" aria-hidden="true" tabindex="-1"></a><span class="co">%Perform eddy-current correction on the metabolite data (raw) or metabolite</span></span>
-<span id="cb1-115"><a href="the-osprey-job-file.html#cb1-115" aria-hidden="true" tabindex="-1"></a><span class="co">%-nulled data (mm). This can either be done similar for all data sets by</span></span>
-<span id="cb1-116"><a href="the-osprey-job-file.html#cb1-116" aria-hidden="true" tabindex="-1"></a><span class="co">%supplying a single value or specified for each dataset individually by supplying</span></span>
-<span id="cb1-117"><a href="the-osprey-job-file.html#cb1-117" aria-hidden="true" tabindex="-1"></a><span class="co">% multiple entries (number has to match the number of datasets) e.g. to perform ECC</span></span>
-<span id="cb1-118"><a href="the-osprey-job-file.html#cb1-118" aria-hidden="true" tabindex="-1"></a><span class="co">% for the second dataset only:</span></span>
-<span id="cb1-119"><a href="the-osprey-job-file.html#cb1-119" aria-hidden="true" tabindex="-1"></a><span class="co">% opts.ECC.raw               = [0 1];</span></span>
-<span id="cb1-120"><a href="the-osprey-job-file.html#cb1-120" aria-hidden="true" tabindex="-1"></a><span class="co">% opts.ECC.mm                = [0 1];</span></span>
-<span id="cb1-121"><a href="the-osprey-job-file.html#cb1-121" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-122"><a href="the-osprey-job-file.html#cb1-122" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-123"><a href="the-osprey-job-file.html#cb1-123" aria-hidden="true" tabindex="-1"></a>opts.ECC.raw                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - &#39;1&#39; (default)</span></span>
-<span id="cb1-124"><a href="the-osprey-job-file.html#cb1-124" aria-hidden="true" tabindex="-1"></a>opts.ECC.mm                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                 <span class="co">%             - &#39;0&#39; (no)</span></span>
-<span id="cb1-125"><a href="the-osprey-job-file.html#cb1-125" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - [] array</span></span>
-<span id="cb1-126"><a href="the-osprey-job-file.html#cb1-126" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-127"><a href="the-osprey-job-file.html#cb1-127" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-128"><a href="the-osprey-job-file.html#cb1-128" aria-hidden="true" tabindex="-1"></a><span class="co">% Save LCModel-exportable files for each spectrum?</span></span>
-<span id="cb1-129"><a href="the-osprey-job-file.html#cb1-129" aria-hidden="true" tabindex="-1"></a>opts.saveLCM                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb1-130"><a href="the-osprey-job-file.html#cb1-130" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb1-131"><a href="the-osprey-job-file.html#cb1-131" aria-hidden="true" tabindex="-1"></a><span class="co">% Save jMRUI-exportable files for each spectrum?</span></span>
-<span id="cb1-132"><a href="the-osprey-job-file.html#cb1-132" aria-hidden="true" tabindex="-1"></a>opts.savejMRUI              <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb1-133"><a href="the-osprey-job-file.html#cb1-133" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb1-134"><a href="the-osprey-job-file.html#cb1-134" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-135"><a href="the-osprey-job-file.html#cb1-135" aria-hidden="true" tabindex="-1"></a><span class="co">% Save processed spectra in vendor-specific format (SDAT/SPAR, RDA, P)?</span></span>
-<span id="cb1-136"><a href="the-osprey-job-file.html#cb1-136" aria-hidden="true" tabindex="-1"></a>opts.saveVendor             <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb1-137"><a href="the-osprey-job-file.html#cb1-137" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb1-138"><a href="the-osprey-job-file.html#cb1-138" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-139"><a href="the-osprey-job-file.html#cb1-139" aria-hidden="true" tabindex="-1"></a><span class="co">% Save processed spectra in NIfTI-MRS format?</span></span>
-<span id="cb1-140"><a href="the-osprey-job-file.html#cb1-140" aria-hidden="true" tabindex="-1"></a>opts.saveNII                <span class="op">=</span> <span class="fl">0</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb1-141"><a href="the-osprey-job-file.html#cb1-141" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb1-142"><a href="the-osprey-job-file.html#cb1-142" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-143"><a href="the-osprey-job-file.html#cb1-143" aria-hidden="true" tabindex="-1"></a><span class="co">% Save PDF output for all Osprey modules and subjects?</span></span>
-<span id="cb1-144"><a href="the-osprey-job-file.html#cb1-144" aria-hidden="true" tabindex="-1"></a>opts.savePDF                <span class="op">=</span> <span class="fl">0</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb1-145"><a href="the-osprey-job-file.html#cb1-145" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb1-146"><a href="the-osprey-job-file.html#cb1-146" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-147"><a href="the-osprey-job-file.html#cb1-147" aria-hidden="true" tabindex="-1"></a><span class="co">% Select the metabolites to be included in the basis set as a cell array,</span></span>
-<span id="cb1-148"><a href="the-osprey-job-file.html#cb1-148" aria-hidden="true" tabindex="-1"></a><span class="co">% with entries separates by commas.</span></span>
-<span id="cb1-149"><a href="the-osprey-job-file.html#cb1-149" aria-hidden="true" tabindex="-1"></a><span class="co">% With default Osprey basis sets, you can select the following metabolites:</span></span>
-<span id="cb1-150"><a href="the-osprey-job-file.html#cb1-150" aria-hidden="true" tabindex="-1"></a><span class="co">% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,</span></span>
-<span id="cb1-151"><a href="the-osprey-job-file.html#cb1-151" aria-hidden="true" tabindex="-1"></a><span class="co">% Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,</span></span>
-<span id="cb1-152"><a href="the-osprey-job-file.html#cb1-152" aria-hidden="true" tabindex="-1"></a><span class="co">% Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.</span></span>
-<span id="cb1-153"><a href="the-osprey-job-file.html#cb1-153" aria-hidden="true" tabindex="-1"></a><span class="co">% If you enter &#39;default&#39;, the basis set will include all of the above</span></span>
-<span id="cb1-154"><a href="the-osprey-job-file.html#cb1-154" aria-hidden="true" tabindex="-1"></a><span class="co">% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.</span></span>
-<span id="cb1-155"><a href="the-osprey-job-file.html#cb1-155" aria-hidden="true" tabindex="-1"></a>opts.fit.includeMetabs      <span class="op">=</span> {<span class="st">&#39;default&#39;</span>}<span class="op">;</span>      <span class="co">% OPTIONS:    - {&#39;default&#39;}</span></span>
-<span id="cb1-156"><a href="the-osprey-job-file.html#cb1-156" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - {custom}</span></span>
-<span id="cb1-157"><a href="the-osprey-job-file.html#cb1-157" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-158"><a href="the-osprey-job-file.html#cb1-158" aria-hidden="true" tabindex="-1"></a><span class="co">% Choose the fitting algorithm</span></span>
-<span id="cb1-159"><a href="the-osprey-job-file.html#cb1-159" aria-hidden="true" tabindex="-1"></a>opts.fit.method             <span class="op">=</span> <span class="st">&#39;Osprey&#39;</span><span class="op">;</span>         <span class="co">% OPTIONS:    - &#39;Osprey&#39; (default)</span></span>
-<span id="cb1-160"><a href="the-osprey-job-file.html#cb1-160" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%           - &#39;LCModel&#39;</span></span>
-<span id="cb1-161"><a href="the-osprey-job-file.html#cb1-161" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-162"><a href="the-osprey-job-file.html#cb1-162" aria-hidden="true" tabindex="-1"></a><span class="co">% Choose the fitting style for difference-edited datasets (MEGA, HERMES, HERCULES)</span></span>
-<span id="cb1-163"><a href="the-osprey-job-file.html#cb1-163" aria-hidden="true" tabindex="-1"></a><span class="co">% (only available for the Osprey fitting method)</span></span>
-<span id="cb1-164"><a href="the-osprey-job-file.html#cb1-164" aria-hidden="true" tabindex="-1"></a>opts.fit.style              <span class="op">=</span> <span class="st">&#39;Separate&#39;</span><span class="op">;</span>       <span class="co">% OPTIONS:  - &#39;Concatenated&#39; (default) - will fit DIFF and SUM simultaneously)</span></span>
-<span id="cb1-165"><a href="the-osprey-job-file.html#cb1-165" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%           - &#39;Separate&#39; - will fit DIFF and OFF separately</span></span>
-<span id="cb1-166"><a href="the-osprey-job-file.html#cb1-166" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-167"><a href="the-osprey-job-file.html#cb1-167" aria-hidden="true" tabindex="-1"></a><span class="co">% Determine fitting range (in ppm) for the metabolite and water spectra</span></span>
-<span id="cb1-168"><a href="the-osprey-job-file.html#cb1-168" aria-hidden="true" tabindex="-1"></a>opts.fit.range              <span class="op">=</span> [<span class="fl">0.5</span> <span class="fl">4</span>]<span class="op">;</span>          <span class="co">% [ppm] Default: [0.5 4]</span></span>
-<span id="cb1-169"><a href="the-osprey-job-file.html#cb1-169" aria-hidden="true" tabindex="-1"></a>opts.fit.rangeWater         <span class="op">=</span> [<span class="fl">2.0</span> <span class="fl">7.4</span>]<span class="op">;</span>        <span class="co">% [ppm] Default: [2.0 7.4]</span></span>
-<span id="cb1-170"><a href="the-osprey-job-file.html#cb1-170" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-171"><a href="the-osprey-job-file.html#cb1-171" aria-hidden="true" tabindex="-1"></a><span class="co">% Determine the baseline knot spacing (in ppm) for the metabolite spectra</span></span>
-<span id="cb1-172"><a href="the-osprey-job-file.html#cb1-172" aria-hidden="true" tabindex="-1"></a>opts.fit.bLineKnotSpace     <span class="op">=</span> <span class="fl">0.4</span><span class="op">;</span>              <span class="co">% [ppm] Default: 0.4.</span></span>
-<span id="cb1-173"><a href="the-osprey-job-file.html#cb1-173" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-174"><a href="the-osprey-job-file.html#cb1-174" aria-hidden="true" tabindex="-1"></a><span class="co">% Add macromolecule and lipid basis functions to the fit?</span></span>
-<span id="cb1-175"><a href="the-osprey-job-file.html#cb1-175" aria-hidden="true" tabindex="-1"></a>opts.fit.fitMM              <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no)</span></span>
-<span id="cb1-176"><a href="the-osprey-job-file.html#cb1-176" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes, default)</span></span>
-<span id="cb1-177"><a href="the-osprey-job-file.html#cb1-177" aria-hidden="true" tabindex="-1"></a>                                                </span>
-<span id="cb1-178"><a href="the-osprey-job-file.html#cb1-178" aria-hidden="true" tabindex="-1"></a><span class="co">% Optional: In case the automatic basisset picker is not working you can manually</span></span>
-<span id="cb1-179"><a href="the-osprey-job-file.html#cb1-179" aria-hidden="true" tabindex="-1"></a><span class="co">% select the path to the basis set in the osprey/fit/basis, i.e.:</span></span>
-<span id="cb1-180"><a href="the-osprey-job-file.html#cb1-180" aria-hidden="true" tabindex="-1"></a><span class="co">% opts.fit.basisSetFile = &#39;osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat&#39;;</span></span>
-<span id="cb1-181"><a href="the-osprey-job-file.html#cb1-181" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
-<span id="cb1-182"><a href="the-osprey-job-file.html#cb1-182" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-183"><a href="the-osprey-job-file.html#cb1-183" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-184"><a href="the-osprey-job-file.html#cb1-184" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-185"><a href="the-osprey-job-file.html#cb1-185" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
-<span id="cb1-186"><a href="the-osprey-job-file.html#cb1-186" aria-hidden="true" tabindex="-1"></a><span class="co">%%% 3. SPECIFY MRS DATA AND STRUCTURAL IMAGING FILES %%</span></span>
-<span id="cb1-187"><a href="the-osprey-job-file.html#cb1-187" aria-hidden="true" tabindex="-1"></a><span class="co">% When using single-average Siemens RDA or DICOM files, specify their</span></span>
-<span id="cb1-188"><a href="the-osprey-job-file.html#cb1-188" aria-hidden="true" tabindex="-1"></a><span class="co">% folders instead of single files!</span></span>
-<span id="cb1-189"><a href="the-osprey-job-file.html#cb1-189" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-190"><a href="the-osprey-job-file.html#cb1-190" aria-hidden="true" tabindex="-1"></a><span class="co">% Clear existing files</span></span>
-<span id="cb1-191"><a href="the-osprey-job-file.html#cb1-191" aria-hidden="true" tabindex="-1"></a><span class="bu">clear</span> files files_ref files_w files_nii files_mm</span>
-<span id="cb1-192"><a href="the-osprey-job-file.html#cb1-192" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-193"><a href="the-osprey-job-file.html#cb1-193" aria-hidden="true" tabindex="-1"></a><span class="co">% Data folder in BIDS format</span></span>
-<span id="cb1-194"><a href="the-osprey-job-file.html#cb1-194" aria-hidden="true" tabindex="-1"></a><span class="co">% The filparts(which()) comment is needed to find the data on your machine. If you set</span></span>
-<span id="cb1-195"><a href="the-osprey-job-file.html#cb1-195" aria-hidden="true" tabindex="-1"></a><span class="co">% up the jobFile for your own data you can set a direct path to your data</span></span>
-<span id="cb1-196"><a href="the-osprey-job-file.html#cb1-196" aria-hidden="true" tabindex="-1"></a><span class="co">% folder e.g., data_folder = /Volumes/MyProject/data/&#39;</span></span>
-<span id="cb1-197"><a href="the-osprey-job-file.html#cb1-197" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-198"><a href="the-osprey-job-file.html#cb1-198" aria-hidden="true" tabindex="-1"></a>data_folder <span class="op">=</span> <span class="fu">fileparts</span>(<span class="fu">which</span>(<span class="fu">fullfile</span>(<span class="st">&#39;exampledata&#39;</span><span class="op">,</span><span class="st">&#39;sdat&#39;</span><span class="op">,</span><span class="st">&#39;UnEdited&#39;</span><span class="op">,</span><span class="st">&#39;jobSDAT.m&#39;</span>)))<span class="op">;</span></span>
-<span id="cb1-199"><a href="the-osprey-job-file.html#cb1-199" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-200"><a href="the-osprey-job-file.html#cb1-200" aria-hidden="true" tabindex="-1"></a><span class="co">% The following lines perform an automated set-up of the jobFile which</span></span>
-<span id="cb1-201"><a href="the-osprey-job-file.html#cb1-201" aria-hidden="true" tabindex="-1"></a><span class="co">% takes advatage of the BIDS foramt. If you are not using BIDS (highly</span></span>
-<span id="cb1-202"><a href="the-osprey-job-file.html#cb1-202" aria-hidden="true" tabindex="-1"></a><span class="co">% recommended) you can look at the definitions below the loop to see how to</span></span>
-<span id="cb1-203"><a href="the-osprey-job-file.html#cb1-203" aria-hidden="true" tabindex="-1"></a><span class="co">% set up direct path links to your data.</span></span>
-<span id="cb1-204"><a href="the-osprey-job-file.html#cb1-204" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-205"><a href="the-osprey-job-file.html#cb1-205" aria-hidden="true" tabindex="-1"></a>subs       <span class="op">=</span> <span class="fu">dir</span>(data_folder)<span class="op">;</span></span>
-<span id="cb1-206"><a href="the-osprey-job-file.html#cb1-206" aria-hidden="true" tabindex="-1"></a>subs(<span class="fl">1</span><span class="op">:</span><span class="fl">2</span>)  <span class="op">=</span> []<span class="op">;</span></span>
-<span id="cb1-207"><a href="the-osprey-job-file.html#cb1-207" aria-hidden="true" tabindex="-1"></a>subs       <span class="op">=</span> subs([subs.isdir])<span class="op">;</span></span>
-<span id="cb1-208"><a href="the-osprey-job-file.html#cb1-208" aria-hidden="true" tabindex="-1"></a>subs       <span class="op">=</span> subs(contains({subs.name}<span class="op">,</span><span class="st">&#39;sub&#39;</span>))<span class="op">;</span></span>
-<span id="cb1-209"><a href="the-osprey-job-file.html#cb1-209" aria-hidden="true" tabindex="-1"></a>counter    <span class="op">=</span> <span class="fl">1</span><span class="op">;</span></span>
-<span id="cb1-210"><a href="the-osprey-job-file.html#cb1-210" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-211"><a href="the-osprey-job-file.html#cb1-211" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> kk <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu">length</span>(subs)</span>
-<span id="cb1-212"><a href="the-osprey-job-file.html#cb1-212" aria-hidden="true" tabindex="-1"></a>    <span class="co">% Loop over sessions</span></span>
-<span id="cb1-213"><a href="the-osprey-job-file.html#cb1-213" aria-hidden="true" tabindex="-1"></a>    sess        <span class="op">=</span> <span class="fu">dir</span>([subs(kk).folder <span class="fu">filesep</span> subs(kk).name])<span class="op">;</span></span>
-<span id="cb1-214"><a href="the-osprey-job-file.html#cb1-214" aria-hidden="true" tabindex="-1"></a>    sess(<span class="fl">1</span><span class="op">:</span><span class="fl">2</span>)   <span class="op">=</span> []<span class="op">;</span></span>
-<span id="cb1-215"><a href="the-osprey-job-file.html#cb1-215" aria-hidden="true" tabindex="-1"></a>    sess        <span class="op">=</span> sess([sess.isdir])<span class="op">;</span></span>
-<span id="cb1-216"><a href="the-osprey-job-file.html#cb1-216" aria-hidden="true" tabindex="-1"></a>    sess        <span class="op">=</span> sess(contains({sess.name}<span class="op">,</span><span class="st">&#39;ses&#39;</span>))<span class="op">;</span></span>
-<span id="cb1-217"><a href="the-osprey-job-file.html#cb1-217" aria-hidden="true" tabindex="-1"></a>    <span class="cf">for</span> ll <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu">length</span>(sess)</span>
-<span id="cb1-218"><a href="the-osprey-job-file.html#cb1-218" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-219"><a href="the-osprey-job-file.html#cb1-219" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Specify metabolite data</span></span>
-<span id="cb1-220"><a href="the-osprey-job-file.html#cb1-220" aria-hidden="true" tabindex="-1"></a>        <span class="co">% (MANDATORY)</span></span>
-<span id="cb1-221"><a href="the-osprey-job-file.html#cb1-221" aria-hidden="true" tabindex="-1"></a>        dir_metabolite    <span class="op">=</span> <span class="fu">dir</span>([sess(ll).folder <span class="fu">filesep</span> sess(ll).name <span class="fu">filesep</span> <span class="st">&#39;mrs&#39;</span> <span class="fu">filesep</span> subs(kk).name <span class="st">&#39;_&#39;</span> sess(ll).name <span class="st">&#39;_press&#39;</span> <span class="fu">filesep</span> <span class="st">&#39;*.SDAT&#39;</span>])<span class="op">;</span></span>
-<span id="cb1-222"><a href="the-osprey-job-file.html#cb1-222" aria-hidden="true" tabindex="-1"></a>        files(counter)      <span class="op">=</span> {[dir_metabolite(<span class="cf">end</span>).folder <span class="fu">filesep</span> dir_metabolite(<span class="cf">end</span>).name]}<span class="op">;</span></span>
-<span id="cb1-223"><a href="the-osprey-job-file.html#cb1-223" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-224"><a href="the-osprey-job-file.html#cb1-224" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Specify water reference data for eddy-current correction (same sequence as metabolite data!)</span></span>
-<span id="cb1-225"><a href="the-osprey-job-file.html#cb1-225" aria-hidden="true" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-226"><a href="the-osprey-job-file.html#cb1-226" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Leave empty for GE P-files (.7) - these include water reference data by</span></span>
-<span id="cb1-227"><a href="the-osprey-job-file.html#cb1-227" aria-hidden="true" tabindex="-1"></a>        <span class="co">% default.</span></span>
-<span id="cb1-228"><a href="the-osprey-job-file.html#cb1-228" aria-hidden="true" tabindex="-1"></a>        dir_ref    <span class="op">=</span> <span class="fu">dir</span>([sess(ll).folder <span class="fu">filesep</span> sess(ll).name <span class="fu">filesep</span> <span class="st">&#39;mrs&#39;</span> <span class="fu">filesep</span> subs(kk).name <span class="st">&#39;_&#39;</span> sess(ll).name <span class="st">&#39;_press-ref&#39;</span> <span class="fu">filesep</span> <span class="st">&#39;*.SDAT&#39;</span>])<span class="op">;</span></span>
-<span id="cb1-229"><a href="the-osprey-job-file.html#cb1-229" aria-hidden="true" tabindex="-1"></a>        files_ref(counter)  <span class="op">=</span> {[dir_ref(<span class="cf">end</span>).folder <span class="fu">filesep</span> dir_ref(<span class="cf">end</span>).name]}<span class="op">;</span></span>
-<span id="cb1-230"><a href="the-osprey-job-file.html#cb1-230" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-231"><a href="the-osprey-job-file.html#cb1-231" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Specify water data for quantification (e.g. short-TE water scan)</span></span>
-<span id="cb1-232"><a href="the-osprey-job-file.html#cb1-232" aria-hidden="true" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-233"><a href="the-osprey-job-file.html#cb1-233" aria-hidden="true" tabindex="-1"></a>        files_w     <span class="op">=</span> {}<span class="op">;</span></span>
-<span id="cb1-234"><a href="the-osprey-job-file.html#cb1-234" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-235"><a href="the-osprey-job-file.html#cb1-235" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Specify metabolite-nulled data for quantification</span></span>
-<span id="cb1-236"><a href="the-osprey-job-file.html#cb1-236" aria-hidden="true" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-237"><a href="the-osprey-job-file.html#cb1-237" aria-hidden="true" tabindex="-1"></a>        files_mm     <span class="op">=</span> {}<span class="op">;</span></span>
-<span id="cb1-238"><a href="the-osprey-job-file.html#cb1-238" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-239"><a href="the-osprey-job-file.html#cb1-239" aria-hidden="true" tabindex="-1"></a>       <span class="co">% Specify T1-weighted structural imaging data</span></span>
-<span id="cb1-240"><a href="the-osprey-job-file.html#cb1-240" aria-hidden="true" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-241"><a href="the-osprey-job-file.html#cb1-241" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Link to single NIfTI (*.nii) files for Siemens and Philips data</span></span>
-<span id="cb1-242"><a href="the-osprey-job-file.html#cb1-242" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Link to DICOM (*.dcm) folders for GE data</span></span>
-<span id="cb1-243"><a href="the-osprey-job-file.html#cb1-243" aria-hidden="true" tabindex="-1"></a>        files_nii(counter)  <span class="op">=</span> {[sess(ll).folder <span class="fu">filesep</span> sess(ll).name <span class="fu">filesep</span> <span class="st">&#39;anat&#39;</span> <span class="fu">filesep</span> subs(kk).name <span class="fu">filesep</span> sess(ll).name <span class="st">&#39;_T1w.nii.gz&#39;</span>]}<span class="op">;</span></span>
-<span id="cb1-244"><a href="the-osprey-job-file.html#cb1-244" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-245"><a href="the-osprey-job-file.html#cb1-245" aria-hidden="true" tabindex="-1"></a>        <span class="co">% External segmentation results</span></span>
-<span id="cb1-246"><a href="the-osprey-job-file.html#cb1-246" aria-hidden="true" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-247"><a href="the-osprey-job-file.html#cb1-247" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Link to NIfTI (*.nii or *.nii.gz) files with segmentation results</span></span>
-<span id="cb1-248"><a href="the-osprey-job-file.html#cb1-248" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Add supply gray matter, white matter, and CSF as 1 x 3 cell within a</span></span>
-<span id="cb1-249"><a href="the-osprey-job-file.html#cb1-249" aria-hidden="true" tabindex="-1"></a>        <span class="co">% cell array  or a single 4D file in the same order supplied as 1 x 1 cell;</span></span>
-<span id="cb1-250"><a href="the-osprey-job-file.html#cb1-250" aria-hidden="true" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{[sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c1&#39; sess(ll).name &#39;_T1w.nii.gz&#39;],...</span></span>
-<span id="cb1-251"><a href="the-osprey-job-file.html#cb1-251" aria-hidden="true" tabindex="-1"></a><span class="co">%                                  [sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c2&#39; sess(ll).name &#39;_T1w.nii.gz&#39;],...</span></span>
-<span id="cb1-252"><a href="the-osprey-job-file.html#cb1-252" aria-hidden="true" tabindex="-1"></a><span class="co">%                                  [sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c3&#39; sess(ll).name &#39;_T1w.nii.gz&#39;]}};</span></span>
-<span id="cb1-253"><a href="the-osprey-job-file.html#cb1-253" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-254"><a href="the-osprey-job-file.html#cb1-254" aria-hidden="true" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{[sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;4D&#39; sess(ll).name &#39;_T1w.nii.gz&#39;]}};</span></span>
-<span id="cb1-255"><a href="the-osprey-job-file.html#cb1-255" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-256"><a href="the-osprey-job-file.html#cb1-256" aria-hidden="true" tabindex="-1"></a>        counter             <span class="op">=</span> counter <span class="op">+</span> <span class="fl">1</span><span class="op">;</span></span>
-<span id="cb1-257"><a href="the-osprey-job-file.html#cb1-257" aria-hidden="true" tabindex="-1"></a>    <span class="cf">end</span></span>
-<span id="cb1-258"><a href="the-osprey-job-file.html#cb1-258" aria-hidden="true" tabindex="-1"></a><span class="cf">end</span></span>
-<span id="cb1-259"><a href="the-osprey-job-file.html#cb1-259" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-260"><a href="the-osprey-job-file.html#cb1-260" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
-<span id="cb1-261"><a href="the-osprey-job-file.html#cb1-261" aria-hidden="true" tabindex="-1"></a><span class="co">% Definitions without using BIDS</span></span>
-<span id="cb1-262"><a href="the-osprey-job-file.html#cb1-262" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-263"><a href="the-osprey-job-file.html#cb1-263" aria-hidden="true" tabindex="-1"></a><span class="co">% You can always supply direct path to each of the files within</span></span>
-<span id="cb1-264"><a href="the-osprey-job-file.html#cb1-264" aria-hidden="true" tabindex="-1"></a><span class="co">% the cell array. For example:</span></span>
-<span id="cb1-265"><a href="the-osprey-job-file.html#cb1-265" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-266"><a href="the-osprey-job-file.html#cb1-266" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify metabolite data</span></span>
-<span id="cb1-267"><a href="the-osprey-job-file.html#cb1-267" aria-hidden="true" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
-<span id="cb1-268"><a href="the-osprey-job-file.html#cb1-268" aria-hidden="true" tabindex="-1"></a><span class="co">% files(counter)      = {&#39;/Volumes/MyProject/data/sub-01/mrs/PRESS_act.SDAT&#39;,...</span></span>
-<span id="cb1-269"><a href="the-osprey-job-file.html#cb1-269" aria-hidden="true" tabindex="-1"></a><span class="co">%                        &#39;/Volumes/MyProject/data/sub-02/mrs/PRESS_act.SDAT&#39;};</span></span>
-<span id="cb1-270"><a href="the-osprey-job-file.html#cb1-270" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-271"><a href="the-osprey-job-file.html#cb1-271" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify water reference data for eddy-current correction (same sequence as metabolite data!)</span></span>
-<span id="cb1-272"><a href="the-osprey-job-file.html#cb1-272" aria-hidden="true" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-273"><a href="the-osprey-job-file.html#cb1-273" aria-hidden="true" tabindex="-1"></a><span class="co">% Leave empty for GE P-files (.7) - these include water reference data by</span></span>
-<span id="cb1-274"><a href="the-osprey-job-file.html#cb1-274" aria-hidden="true" tabindex="-1"></a><span class="co">% default.</span></span>
-<span id="cb1-275"><a href="the-osprey-job-file.html#cb1-275" aria-hidden="true" tabindex="-1"></a><span class="co">% files_ref(counter)      = {&#39;/Volumes/MyProject/data/sub-01/mrs/PRESS_ref.SDAT&#39;,...</span></span>
-<span id="cb1-276"><a href="the-osprey-job-file.html#cb1-276" aria-hidden="true" tabindex="-1"></a><span class="co">%                            &#39;/Volumes/MyProject/data/sub-02/mrs/PRESS_ref.SDAT&#39;};</span></span>
-<span id="cb1-277"><a href="the-osprey-job-file.html#cb1-277" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-278"><a href="the-osprey-job-file.html#cb1-278" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify water data for quantification (e.g. short-TE water scan)</span></span>
-<span id="cb1-279"><a href="the-osprey-job-file.html#cb1-279" aria-hidden="true" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-280"><a href="the-osprey-job-file.html#cb1-280" aria-hidden="true" tabindex="-1"></a><span class="co">% files_w     = {};</span></span>
-<span id="cb1-281"><a href="the-osprey-job-file.html#cb1-281" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-282"><a href="the-osprey-job-file.html#cb1-282" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify metabolite-nulled data for quantification</span></span>
-<span id="cb1-283"><a href="the-osprey-job-file.html#cb1-283" aria-hidden="true" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-284"><a href="the-osprey-job-file.html#cb1-284" aria-hidden="true" tabindex="-1"></a><span class="co">% files_mm     = {};</span></span>
-<span id="cb1-285"><a href="the-osprey-job-file.html#cb1-285" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-286"><a href="the-osprey-job-file.html#cb1-286" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify T1-weighted structural imaging data</span></span>
-<span id="cb1-287"><a href="the-osprey-job-file.html#cb1-287" aria-hidden="true" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-288"><a href="the-osprey-job-file.html#cb1-288" aria-hidden="true" tabindex="-1"></a><span class="co">% Link to single NIfTI (*.nii.gz or #.nii) files for GE, Siemens and Philips data</span></span>
-<span id="cb1-289"><a href="the-osprey-job-file.html#cb1-289" aria-hidden="true" tabindex="-1"></a><span class="co">% files_nii  = {&#39;/Volumes/MyProject/data/sub-01/anat/T1w.nii.gz&#39;,...</span></span>
-<span id="cb1-290"><a href="the-osprey-job-file.html#cb1-290" aria-hidden="true" tabindex="-1"></a><span class="co">%               &#39;/Volumes/MyProject/data/sub-02/anat/T1w.nii.gz&#39;};</span></span>
-<span id="cb1-291"><a href="the-osprey-job-file.html#cb1-291" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-292"><a href="the-osprey-job-file.html#cb1-292" aria-hidden="true" tabindex="-1"></a><span class="co">% External segmentation results</span></span>
-<span id="cb1-293"><a href="the-osprey-job-file.html#cb1-293" aria-hidden="true" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
-<span id="cb1-294"><a href="the-osprey-job-file.html#cb1-294" aria-hidden="true" tabindex="-1"></a><span class="co">% Link to NIfTI (*.nii or *.nii.gz) files with segmentation results</span></span>
-<span id="cb1-295"><a href="the-osprey-job-file.html#cb1-295" aria-hidden="true" tabindex="-1"></a><span class="co">% Add supply gray matter, white matter, and CSF as 1 x 3 cell within a</span></span>
-<span id="cb1-296"><a href="the-osprey-job-file.html#cb1-296" aria-hidden="true" tabindex="-1"></a><span class="co">% cell array  or a single 4D file in the same order supplied as 1 x 1 cell;</span></span>
-<span id="cb1-297"><a href="the-osprey-job-file.html#cb1-297" aria-hidden="true" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{&#39;/Volumes/MyProject/data/sub-01/anat/c1T1w.nii.gz&#39;,...</span></span>
-<span id="cb1-298"><a href="the-osprey-job-file.html#cb1-298" aria-hidden="true" tabindex="-1"></a><span class="co">%                                  &#39;/Volumes/MyProject/data/sub-01/anat/c2T1w.nii.gz&#39;,...</span></span>
-<span id="cb1-299"><a href="the-osprey-job-file.html#cb1-299" aria-hidden="true" tabindex="-1"></a><span class="co">%                                  &#39;/Volumes/MyProject/data/sub-01/anat/c3T1w.nii.gz&#39;},...</span></span>
-<span id="cb1-300"><a href="the-osprey-job-file.html#cb1-300" aria-hidden="true" tabindex="-1"></a><span class="co">%                                   {&#39;/Volumes/MyProject/data/sub-02/anat/c1T1w.nii.gz&#39;,...</span></span>
-<span id="cb1-301"><a href="the-osprey-job-file.html#cb1-301" aria-hidden="true" tabindex="-1"></a><span class="co">%                                  &#39;/Volumes/MyProject/data/sub-02/anat/c2T1w.nii.gz&#39;,...</span></span>
-<span id="cb1-302"><a href="the-osprey-job-file.html#cb1-302" aria-hidden="true" tabindex="-1"></a><span class="co">%                                  &#39;/Volumes/MyProject/data/sub-02/anat/c3T1w.nii.gz&#39;}};</span></span>
-<span id="cb1-303"><a href="the-osprey-job-file.html#cb1-303" aria-hidden="true" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{&#39;/Volumes/MyProject/data/sub-01/anat/4DT1w.nii.gz&#39;},...</span></span>
-<span id="cb1-304"><a href="the-osprey-job-file.html#cb1-304" aria-hidden="true" tabindex="-1"></a><span class="co">%                                   {&#39;/Volumes/MyProject/data/sub-02/anat/4DT1w.nii.gz&#39;}};</span></span>
-<span id="cb1-305"><a href="the-osprey-job-file.html#cb1-305" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-306"><a href="the-osprey-job-file.html#cb1-306" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
-<span id="cb1-307"><a href="the-osprey-job-file.html#cb1-307" aria-hidden="true" tabindex="-1"></a><span class="co">%%% 4. SPECIFY STAT FILE %%%</span></span>
-<span id="cb1-308"><a href="the-osprey-job-file.html#cb1-308" aria-hidden="true" tabindex="-1"></a><span class="co">% Supply location of a csv file, which contains possible correlation</span></span>
-<span id="cb1-309"><a href="the-osprey-job-file.html#cb1-309" aria-hidden="true" tabindex="-1"></a><span class="co">% measures and group variables. Each column must start with the name of the</span></span>
-<span id="cb1-310"><a href="the-osprey-job-file.html#cb1-310" aria-hidden="true" tabindex="-1"></a><span class="co">% measure. For the grouping variable use &#39;group&#39; and numbers between 1 and</span></span>
-<span id="cb1-311"><a href="the-osprey-job-file.html#cb1-311" aria-hidden="true" tabindex="-1"></a><span class="co">% the number of included groups. If no group is supplied the data will be</span></span>
-<span id="cb1-312"><a href="the-osprey-job-file.html#cb1-312" aria-hidden="true" tabindex="-1"></a><span class="co">% treated as one group. (You can always use the direct path)</span></span>
-<span id="cb1-313"><a href="the-osprey-job-file.html#cb1-313" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-314"><a href="the-osprey-job-file.html#cb1-314" aria-hidden="true" tabindex="-1"></a><span class="co">% file_stat = fullfile(data_folder, &#39;stat.csv&#39;);</span></span>
-<span id="cb1-315"><a href="the-osprey-job-file.html#cb1-315" aria-hidden="true" tabindex="-1"></a>file_stat <span class="op">=</span> <span class="st">&#39;&#39;</span><span class="op">;</span></span>
-<span id="cb1-316"><a href="the-osprey-job-file.html#cb1-316" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-317"><a href="the-osprey-job-file.html#cb1-317" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
-<span id="cb1-318"><a href="the-osprey-job-file.html#cb1-318" aria-hidden="true" tabindex="-1"></a><span class="co">%%% 5. SPECIFY OUTPUT FOLDER %%</span></span>
-<span id="cb1-319"><a href="the-osprey-job-file.html#cb1-319" aria-hidden="true" tabindex="-1"></a><span class="co">% The Osprey data container will be saved as a *.mat file in the output</span></span>
-<span id="cb1-320"><a href="the-osprey-job-file.html#cb1-320" aria-hidden="true" tabindex="-1"></a><span class="co">% folder that you specify below. In addition, any exported files (for use</span></span>
-<span id="cb1-321"><a href="the-osprey-job-file.html#cb1-321" aria-hidden="true" tabindex="-1"></a><span class="co">% with jMRUI, TARQUIN, or LCModel) will be saved in sub-folders.</span></span>
-<span id="cb1-322"><a href="the-osprey-job-file.html#cb1-322" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-323"><a href="the-osprey-job-file.html#cb1-323" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify output folder (you can always use the direct path)</span></span>
-<span id="cb1-324"><a href="the-osprey-job-file.html#cb1-324" aria-hidden="true" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
-<span id="cb1-325"><a href="the-osprey-job-file.html#cb1-325" aria-hidden="true" tabindex="-1"></a>outputFolder <span class="op">=</span> <span class="fu">fullfile</span>(data_folder<span class="op">,</span> <span class="st">&#39;derivatives&#39;</span>)<span class="op">;</span></span>
-<span id="cb1-326"><a href="the-osprey-job-file.html#cb1-326" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-327"><a href="the-osprey-job-file.html#cb1-327" aria-hidden="true" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="the-osprey-job-file.html#cb1-1" tabindex="-1"></a><span class="co">%% jobSDAT.m</span></span>
+<span id="cb1-2"><a href="the-osprey-job-file.html#cb1-2" tabindex="-1"></a><span class="co">%   This function describes an Osprey job defined in a MATLAB script.</span></span>
+<span id="cb1-3"><a href="the-osprey-job-file.html#cb1-3" tabindex="-1"></a><span class="co">%</span></span>
+<span id="cb1-4"><a href="the-osprey-job-file.html#cb1-4" tabindex="-1"></a><span class="co">%   A valid Osprey job contains four distinct classes of items:</span></span>
+<span id="cb1-5"><a href="the-osprey-job-file.html#cb1-5" tabindex="-1"></a><span class="co">%       1. basic information on the MRS sequence used</span></span>
+<span id="cb1-6"><a href="the-osprey-job-file.html#cb1-6" tabindex="-1"></a><span class="co">%       2. several settings for data handling and modeling</span></span>
+<span id="cb1-7"><a href="the-osprey-job-file.html#cb1-7" tabindex="-1"></a><span class="co">%       3. a list of MRS (and, optionally, structural imaging) data files</span></span>
+<span id="cb1-8"><a href="the-osprey-job-file.html#cb1-8" tabindex="-1"></a><span class="co">%          to be loaded</span></span>
+<span id="cb1-9"><a href="the-osprey-job-file.html#cb1-9" tabindex="-1"></a><span class="co">%       4. an output folder to store the results and exported files</span></span>
+<span id="cb1-10"><a href="the-osprey-job-file.html#cb1-10" tabindex="-1"></a><span class="co">%</span></span>
+<span id="cb1-11"><a href="the-osprey-job-file.html#cb1-11" tabindex="-1"></a><span class="co">%   The list of MRS and structural imaging files is provided in the form of</span></span>
+<span id="cb1-12"><a href="the-osprey-job-file.html#cb1-12" tabindex="-1"></a><span class="co">%   cell arrays. They can simply be provided explicitly, or from a more</span></span>
+<span id="cb1-13"><a href="the-osprey-job-file.html#cb1-13" tabindex="-1"></a><span class="co">%   complex script that automatically determines file names from a given</span></span>
+<span id="cb1-14"><a href="the-osprey-job-file.html#cb1-14" tabindex="-1"></a><span class="co">%   folder structure.</span></span>
+<span id="cb1-15"><a href="the-osprey-job-file.html#cb1-15" tabindex="-1"></a><span class="co">%</span></span>
+<span id="cb1-16"><a href="the-osprey-job-file.html#cb1-16" tabindex="-1"></a><span class="co">%   Osprey distinguishes between four sets of data:</span></span>
+<span id="cb1-17"><a href="the-osprey-job-file.html#cb1-17" tabindex="-1"></a><span class="co">%       - metabolite (water-suppressed) data</span></span>
+<span id="cb1-18"><a href="the-osprey-job-file.html#cb1-18" tabindex="-1"></a><span class="co">%           (MANDATORY)</span></span>
+<span id="cb1-19"><a href="the-osprey-job-file.html#cb1-19" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files&quot;</span></span>
+<span id="cb1-20"><a href="the-osprey-job-file.html#cb1-20" tabindex="-1"></a><span class="co">%       - water reference data acquired with the SAME sequence as the</span></span>
+<span id="cb1-21"><a href="the-osprey-job-file.html#cb1-21" tabindex="-1"></a><span class="co">%           metabolite data, just without water suppression RF pulses. This</span></span>
+<span id="cb1-22"><a href="the-osprey-job-file.html#cb1-22" tabindex="-1"></a><span class="co">%           data is used to determine complex coil combination</span></span>
+<span id="cb1-23"><a href="the-osprey-job-file.html#cb1-23" tabindex="-1"></a><span class="co">%           coefficients, and perform eddy current correction.</span></span>
+<span id="cb1-24"><a href="the-osprey-job-file.html#cb1-24" tabindex="-1"></a><span class="co">%           (OPTIONAL)</span></span>
+<span id="cb1-25"><a href="the-osprey-job-file.html#cb1-25" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files_ref&quot;</span></span>
+<span id="cb1-26"><a href="the-osprey-job-file.html#cb1-26" tabindex="-1"></a><span class="co">%       - additional water data used for water-scaled quantification,</span></span>
+<span id="cb1-27"><a href="the-osprey-job-file.html#cb1-27" tabindex="-1"></a><span class="co">%           usually from short-TE acquisitions due to reduced T2-weighting</span></span>
+<span id="cb1-28"><a href="the-osprey-job-file.html#cb1-28" tabindex="-1"></a><span class="co">%           (OPTIONAL)</span></span>
+<span id="cb1-29"><a href="the-osprey-job-file.html#cb1-29" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files_w&quot;</span></span>
+<span id="cb1-30"><a href="the-osprey-job-file.html#cb1-30" tabindex="-1"></a><span class="co">%       - Structural image data used for co-registration and tissue class</span></span>
+<span id="cb1-31"><a href="the-osprey-job-file.html#cb1-31" tabindex="-1"></a><span class="co">%           segmentation (usually a T1 MPRAGE). These files need to be</span></span>
+<span id="cb1-32"><a href="the-osprey-job-file.html#cb1-32" tabindex="-1"></a><span class="co">%           provided in the NIfTI format (*.nii or *.nii.gz) or, for GE data, as a</span></span>
+<span id="cb1-33"><a href="the-osprey-job-file.html#cb1-33" tabindex="-1"></a><span class="co">%           folder containing DICOM Files (*.dcm).</span></span>
+<span id="cb1-34"><a href="the-osprey-job-file.html#cb1-34" tabindex="-1"></a><span class="co">%           (OPTIONAL)</span></span>
+<span id="cb1-35"><a href="the-osprey-job-file.html#cb1-35" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files_nii&quot;</span></span>
+<span id="cb1-36"><a href="the-osprey-job-file.html#cb1-36" tabindex="-1"></a><span class="co">%       - External segmentation results. These files need to be</span></span>
+<span id="cb1-37"><a href="the-osprey-job-file.html#cb1-37" tabindex="-1"></a><span class="co">%           provided in the NIfTI format (*.nii or *.nii.gz).</span></span>
+<span id="cb1-38"><a href="the-osprey-job-file.html#cb1-38" tabindex="-1"></a><span class="co">%           (OPTIONAL)</span></span>
+<span id="cb1-39"><a href="the-osprey-job-file.html#cb1-39" tabindex="-1"></a><span class="co">%           Defined in cell array &quot;files_seg&quot; with 1 x 3 cell for each</span></span>
+<span id="cb1-40"><a href="the-osprey-job-file.html#cb1-40" tabindex="-1"></a><span class="co">%           subject or 1 x 1 cell if a single 4D NIfTI is supplied.</span></span>
+<span id="cb1-41"><a href="the-osprey-job-file.html#cb1-41" tabindex="-1"></a><span class="co">%</span></span>
+<span id="cb1-42"><a href="the-osprey-job-file.html#cb1-42" tabindex="-1"></a><span class="co">%   Files in the formats</span></span>
+<span id="cb1-43"><a href="the-osprey-job-file.html#cb1-43" tabindex="-1"></a><span class="co">%       - .7 (GE)</span></span>
+<span id="cb1-44"><a href="the-osprey-job-file.html#cb1-44" tabindex="-1"></a><span class="co">%       - .SDAT, .DATA/.LIST, .RAW/.SIN/.LAB (Philips)</span></span>
+<span id="cb1-45"><a href="the-osprey-job-file.html#cb1-45" tabindex="-1"></a><span class="co">%       - .DAT (Siemens)</span></span>
+<span id="cb1-46"><a href="the-osprey-job-file.html#cb1-46" tabindex="-1"></a><span class="co">%       - .nii, .nii.gz (NIfTI-MRS)</span></span>
+<span id="cb1-47"><a href="the-osprey-job-file.html#cb1-47" tabindex="-1"></a><span class="co">%   usually contain all of the acquired data in a single file per scan. GE</span></span>
+<span id="cb1-48"><a href="the-osprey-job-file.html#cb1-48" tabindex="-1"></a><span class="co">%   systems store water reference data in the same .7 file, so there is no</span></span>
+<span id="cb1-49"><a href="the-osprey-job-file.html#cb1-49" tabindex="-1"></a><span class="co">%   need to specify it separately under files_ref.</span></span>
+<span id="cb1-50"><a href="the-osprey-job-file.html#cb1-50" tabindex="-1"></a><span class="co">%</span></span>
+<span id="cb1-51"><a href="the-osprey-job-file.html#cb1-51" tabindex="-1"></a><span class="co">%   Files in the formats</span></span>
+<span id="cb1-52"><a href="the-osprey-job-file.html#cb1-52" tabindex="-1"></a><span class="co">%       - .DCM (any)</span></span>
+<span id="cb1-53"><a href="the-osprey-job-file.html#cb1-53" tabindex="-1"></a><span class="co">%       - .IMA, .RDA (Siemens)</span></span>
+<span id="cb1-54"><a href="the-osprey-job-file.html#cb1-54" tabindex="-1"></a><span class="co">%   may contain separate files for each average. Instead of providing</span></span>
+<span id="cb1-55"><a href="the-osprey-job-file.html#cb1-55" tabindex="-1"></a><span class="co">%   individual file names, please specify folders. Metabolite data, water</span></span>
+<span id="cb1-56"><a href="the-osprey-job-file.html#cb1-56" tabindex="-1"></a><span class="co">%   reference data, and water data need to be located in separate folders.</span></span>
+<span id="cb1-57"><a href="the-osprey-job-file.html#cb1-57" tabindex="-1"></a><span class="co">%</span></span>
+<span id="cb1-58"><a href="the-osprey-job-file.html#cb1-58" tabindex="-1"></a><span class="co">%   In the example script at hand the MATLAB functions strrep and which are</span></span>
+<span id="cb1-59"><a href="the-osprey-job-file.html#cb1-59" tabindex="-1"></a><span class="co">%   used to generate a relative path, which allows you to run the examples</span></span>
+<span id="cb1-60"><a href="the-osprey-job-file.html#cb1-60" tabindex="-1"></a><span class="co">%   on your machine directly. To set up your own Osprey job supply the</span></span>
+<span id="cb1-61"><a href="the-osprey-job-file.html#cb1-61" tabindex="-1"></a><span class="co">%   specific locations as described above.</span></span>
+<span id="cb1-62"><a href="the-osprey-job-file.html#cb1-62" tabindex="-1"></a><span class="co">%</span></span>
+<span id="cb1-63"><a href="the-osprey-job-file.html#cb1-63" tabindex="-1"></a><span class="co">%   AUTHOR:</span></span>
+<span id="cb1-64"><a href="the-osprey-job-file.html#cb1-64" tabindex="-1"></a><span class="co">%       Dr. Georg Oeltzschner (Johns Hopkins University, 2019-07-15)</span></span>
+<span id="cb1-65"><a href="the-osprey-job-file.html#cb1-65" tabindex="-1"></a><span class="co">%       goeltzs1@jhmi.edu</span></span>
+<span id="cb1-66"><a href="the-osprey-job-file.html#cb1-66" tabindex="-1"></a><span class="co">%</span></span>
+<span id="cb1-67"><a href="the-osprey-job-file.html#cb1-67" tabindex="-1"></a><span class="co">%   HISTORY:</span></span>
+<span id="cb1-68"><a href="the-osprey-job-file.html#cb1-68" tabindex="-1"></a><span class="co">%       2019-07-15: First version of the code.</span></span>
+<span id="cb1-69"><a href="the-osprey-job-file.html#cb1-69" tabindex="-1"></a></span>
+<span id="cb1-70"><a href="the-osprey-job-file.html#cb1-70" tabindex="-1"></a></span>
+<span id="cb1-71"><a href="the-osprey-job-file.html#cb1-71" tabindex="-1"></a></span>
+<span id="cb1-72"><a href="the-osprey-job-file.html#cb1-72" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
+<span id="cb1-73"><a href="the-osprey-job-file.html#cb1-73" tabindex="-1"></a><span class="co">%%% 1. SPECIFY SEQUENCE INFORMATION %%%</span></span>
+<span id="cb1-74"><a href="the-osprey-job-file.html#cb1-74" tabindex="-1"></a></span>
+<span id="cb1-75"><a href="the-osprey-job-file.html#cb1-75" tabindex="-1"></a><span class="co">% Specify sequence type</span></span>
+<span id="cb1-76"><a href="the-osprey-job-file.html#cb1-76" tabindex="-1"></a>seqType <span class="op">=</span> <span class="st">&#39;unedited&#39;</span><span class="op">;</span>           <span class="co">% OPTIONS:    - &#39;unedited&#39; (default)</span></span>
+<span id="cb1-77"><a href="the-osprey-job-file.html#cb1-77" tabindex="-1"></a>                                <span class="co">%             - &#39;MEGA&#39;</span></span>
+<span id="cb1-78"><a href="the-osprey-job-file.html#cb1-78" tabindex="-1"></a>                                <span class="co">%             - &#39;HERMES&#39;</span></span>
+<span id="cb1-79"><a href="the-osprey-job-file.html#cb1-79" tabindex="-1"></a>                                <span class="co">%             - &#39;HERCULES&#39;</span></span>
+<span id="cb1-80"><a href="the-osprey-job-file.html#cb1-80" tabindex="-1"></a></span>
+<span id="cb1-81"><a href="the-osprey-job-file.html#cb1-81" tabindex="-1"></a><span class="co">% Specify editing targets</span></span>
+<span id="cb1-82"><a href="the-osprey-job-file.html#cb1-82" tabindex="-1"></a>editTarget <span class="op">=</span> {<span class="st">&#39;none&#39;</span>}<span class="op">;</span>          <span class="co">% OPTIONS:    - {&#39;none&#39;} (default if &#39;unedited&#39;)</span></span>
+<span id="cb1-83"><a href="the-osprey-job-file.html#cb1-83" tabindex="-1"></a>                                <span class="co">%             - {&#39;GABA&#39;}, {&#39;GSH&#39;}, {&#39;Lac&#39;}, {&#39;PE322&#39;}, {&#39;PE398&#39;}  (for &#39;MEGA&#39;)</span></span>
+<span id="cb1-84"><a href="the-osprey-job-file.html#cb1-84" tabindex="-1"></a>                                <span class="co">%             - {&#39;GABA&#39;, &#39;GSH&#39;}, {&#39;GABA&#39;, &#39;Lac&#39;}, {&#39;NAA&#39;, &#39;NAAG&#39;} (for &#39;HERMES&#39;and &#39;HERCULES&#39;)</span></span>
+<span id="cb1-85"><a href="the-osprey-job-file.html#cb1-85" tabindex="-1"></a></span>
+<span id="cb1-86"><a href="the-osprey-job-file.html#cb1-86" tabindex="-1"></a></span>
+<span id="cb1-87"><a href="the-osprey-job-file.html#cb1-87" tabindex="-1"></a>                                <span class="co">% Specify data scenario</span></span>
+<span id="cb1-88"><a href="the-osprey-job-file.html#cb1-88" tabindex="-1"></a>dataScenario <span class="op">=</span> <span class="st">&#39;invivo&#39;</span><span class="op">;</span>        <span class="co">% OPTIONS:    - &#39;invivo&#39; (default)</span></span>
+<span id="cb1-89"><a href="the-osprey-job-file.html#cb1-89" tabindex="-1"></a>                                <span class="co">%             - &#39;phantom&#39;</span></span>
+<span id="cb1-90"><a href="the-osprey-job-file.html#cb1-90" tabindex="-1"></a>                                <span class="co">%             - &#39;PRIAM&#39;</span></span>
+<span id="cb1-91"><a href="the-osprey-job-file.html#cb1-91" tabindex="-1"></a>                                <span class="co">%             - &#39;MRSI&#39;</span></span>
+<span id="cb1-92"><a href="the-osprey-job-file.html#cb1-92" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
+<span id="cb1-93"><a href="the-osprey-job-file.html#cb1-93" tabindex="-1"></a></span>
+<span id="cb1-94"><a href="the-osprey-job-file.html#cb1-94" tabindex="-1"></a></span>
+<span id="cb1-95"><a href="the-osprey-job-file.html#cb1-95" tabindex="-1"></a></span>
+<span id="cb1-96"><a href="the-osprey-job-file.html#cb1-96" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
+<span id="cb1-97"><a href="the-osprey-job-file.html#cb1-97" tabindex="-1"></a><span class="co">%%% 2. SPECIFY DATA HANDLING AND MODELING OPTIONS %%%</span></span>
+<span id="cb1-98"><a href="the-osprey-job-file.html#cb1-98" tabindex="-1"></a><span class="co">% Which spectral registration method should be used? Robust spectral</span></span>
+<span id="cb1-99"><a href="the-osprey-job-file.html#cb1-99" tabindex="-1"></a><span class="co">% registration is default, a frequency restricted spectral registration</span></span>
+<span id="cb1-100"><a href="the-osprey-job-file.html#cb1-100" tabindex="-1"></a><span class="co">% method is also availaible and is linked to the fit range.</span></span>
+<span id="cb1-101"><a href="the-osprey-job-file.html#cb1-101" tabindex="-1"></a>opts.SpecReg <span class="op">=</span> <span class="st">&#39;RobSpecReg&#39;</span><span class="op">;</span>                  <span class="co">% OPTIONS:    - &#39;RobSpecReg&#39; (default) Spectral aligment with Water/Lipid removal, using simialrity meric, and weighted averaging</span></span>
+<span id="cb1-102"><a href="the-osprey-job-file.html#cb1-102" tabindex="-1"></a>                                              <span class="co">%             - &#39;ProbSpecReg&#39; Probabilistic spectral aligment to median target and weighted averaging</span></span>
+<span id="cb1-103"><a href="the-osprey-job-file.html#cb1-103" tabindex="-1"></a>                                              <span class="co">%             - &#39;RestrSpecReg&#39; Frequency restricted (fit range) spectral aligment, using simialrity meric, and weighted averaging</span></span>
+<span id="cb1-104"><a href="the-osprey-job-file.html#cb1-104" tabindex="-1"></a>                                              <span class="co">%             - &#39;none&#39;</span></span>
+<span id="cb1-105"><a href="the-osprey-job-file.html#cb1-105" tabindex="-1"></a></span>
+<span id="cb1-106"><a href="the-osprey-job-file.html#cb1-106" tabindex="-1"></a><span class="co">% Which algorithm do you want to align the sub spectra? L2 norm</span></span>
+<span id="cb1-107"><a href="the-osprey-job-file.html#cb1-107" tabindex="-1"></a><span class="co">% optimization is the default. This is only used for edited MRS!</span></span>
+<span id="cb1-108"><a href="the-osprey-job-file.html#cb1-108" tabindex="-1"></a><span class="co">%Perform correction on the metabolite data (raw) or metabolite</span></span>
+<span id="cb1-109"><a href="the-osprey-job-file.html#cb1-109" tabindex="-1"></a><span class="co">%-nulled data (mm).</span></span>
+<span id="cb1-110"><a href="the-osprey-job-file.html#cb1-110" tabindex="-1"></a>opts.SubSpecAlignment.mets <span class="op">=</span> <span class="st">&#39;L2Norm&#39;</span><span class="op">;</span>          <span class="co">% OPTIONS:    - &#39;L2Norm&#39; (default)</span></span>
+<span id="cb1-111"><a href="the-osprey-job-file.html#cb1-111" tabindex="-1"></a>                                                <span class="co">%             - &#39;L1Norm&#39;</span></span>
+<span id="cb1-112"><a href="the-osprey-job-file.html#cb1-112" tabindex="-1"></a>                                                <span class="co">%             - &#39;none&#39;</span></span>
+<span id="cb1-113"><a href="the-osprey-job-file.html#cb1-113" tabindex="-1"></a></span>
+<span id="cb1-114"><a href="the-osprey-job-file.html#cb1-114" tabindex="-1"></a><span class="co">%Perform eddy-current correction on the metabolite data (raw) or metabolite</span></span>
+<span id="cb1-115"><a href="the-osprey-job-file.html#cb1-115" tabindex="-1"></a><span class="co">%-nulled data (mm). This can either be done similar for all data sets by</span></span>
+<span id="cb1-116"><a href="the-osprey-job-file.html#cb1-116" tabindex="-1"></a><span class="co">%supplying a single value or specified for each dataset individually by supplying</span></span>
+<span id="cb1-117"><a href="the-osprey-job-file.html#cb1-117" tabindex="-1"></a><span class="co">% multiple entries (number has to match the number of datasets) e.g. to perform ECC</span></span>
+<span id="cb1-118"><a href="the-osprey-job-file.html#cb1-118" tabindex="-1"></a><span class="co">% for the second dataset only:</span></span>
+<span id="cb1-119"><a href="the-osprey-job-file.html#cb1-119" tabindex="-1"></a><span class="co">% opts.ECC.raw               = [0 1];</span></span>
+<span id="cb1-120"><a href="the-osprey-job-file.html#cb1-120" tabindex="-1"></a><span class="co">% opts.ECC.mm                = [0 1];</span></span>
+<span id="cb1-121"><a href="the-osprey-job-file.html#cb1-121" tabindex="-1"></a></span>
+<span id="cb1-122"><a href="the-osprey-job-file.html#cb1-122" tabindex="-1"></a></span>
+<span id="cb1-123"><a href="the-osprey-job-file.html#cb1-123" tabindex="-1"></a>opts.ECC.raw                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - &#39;1&#39; (default)</span></span>
+<span id="cb1-124"><a href="the-osprey-job-file.html#cb1-124" tabindex="-1"></a>opts.ECC.mm                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                 <span class="co">%             - &#39;0&#39; (no)</span></span>
+<span id="cb1-125"><a href="the-osprey-job-file.html#cb1-125" tabindex="-1"></a>                                                <span class="co">%             - [] array</span></span>
+<span id="cb1-126"><a href="the-osprey-job-file.html#cb1-126" tabindex="-1"></a></span>
+<span id="cb1-127"><a href="the-osprey-job-file.html#cb1-127" tabindex="-1"></a></span>
+<span id="cb1-128"><a href="the-osprey-job-file.html#cb1-128" tabindex="-1"></a><span class="co">% Save LCModel-exportable files for each spectrum?</span></span>
+<span id="cb1-129"><a href="the-osprey-job-file.html#cb1-129" tabindex="-1"></a>opts.saveLCM                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb1-130"><a href="the-osprey-job-file.html#cb1-130" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb1-131"><a href="the-osprey-job-file.html#cb1-131" tabindex="-1"></a><span class="co">% Save jMRUI-exportable files for each spectrum?</span></span>
+<span id="cb1-132"><a href="the-osprey-job-file.html#cb1-132" tabindex="-1"></a>opts.savejMRUI              <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb1-133"><a href="the-osprey-job-file.html#cb1-133" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb1-134"><a href="the-osprey-job-file.html#cb1-134" tabindex="-1"></a></span>
+<span id="cb1-135"><a href="the-osprey-job-file.html#cb1-135" tabindex="-1"></a><span class="co">% Save processed spectra in vendor-specific format (SDAT/SPAR, RDA, P)?</span></span>
+<span id="cb1-136"><a href="the-osprey-job-file.html#cb1-136" tabindex="-1"></a>opts.saveVendor             <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb1-137"><a href="the-osprey-job-file.html#cb1-137" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb1-138"><a href="the-osprey-job-file.html#cb1-138" tabindex="-1"></a></span>
+<span id="cb1-139"><a href="the-osprey-job-file.html#cb1-139" tabindex="-1"></a><span class="co">% Save processed spectra in NIfTI-MRS format?</span></span>
+<span id="cb1-140"><a href="the-osprey-job-file.html#cb1-140" tabindex="-1"></a>opts.saveNII                <span class="op">=</span> <span class="fl">0</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb1-141"><a href="the-osprey-job-file.html#cb1-141" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb1-142"><a href="the-osprey-job-file.html#cb1-142" tabindex="-1"></a></span>
+<span id="cb1-143"><a href="the-osprey-job-file.html#cb1-143" tabindex="-1"></a><span class="co">% Save PDF output for all Osprey modules and subjects?</span></span>
+<span id="cb1-144"><a href="the-osprey-job-file.html#cb1-144" tabindex="-1"></a>opts.savePDF                <span class="op">=</span> <span class="fl">0</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb1-145"><a href="the-osprey-job-file.html#cb1-145" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb1-146"><a href="the-osprey-job-file.html#cb1-146" tabindex="-1"></a></span>
+<span id="cb1-147"><a href="the-osprey-job-file.html#cb1-147" tabindex="-1"></a><span class="co">% Select the metabolites to be included in the basis set as a cell array,</span></span>
+<span id="cb1-148"><a href="the-osprey-job-file.html#cb1-148" tabindex="-1"></a><span class="co">% with entries separates by commas.</span></span>
+<span id="cb1-149"><a href="the-osprey-job-file.html#cb1-149" tabindex="-1"></a><span class="co">% With default Osprey basis sets, you can select the following metabolites:</span></span>
+<span id="cb1-150"><a href="the-osprey-job-file.html#cb1-150" tabindex="-1"></a><span class="co">% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,</span></span>
+<span id="cb1-151"><a href="the-osprey-job-file.html#cb1-151" tabindex="-1"></a><span class="co">% Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,</span></span>
+<span id="cb1-152"><a href="the-osprey-job-file.html#cb1-152" tabindex="-1"></a><span class="co">% Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.</span></span>
+<span id="cb1-153"><a href="the-osprey-job-file.html#cb1-153" tabindex="-1"></a><span class="co">% If you enter &#39;default&#39;, the basis set will include all of the above</span></span>
+<span id="cb1-154"><a href="the-osprey-job-file.html#cb1-154" tabindex="-1"></a><span class="co">% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.</span></span>
+<span id="cb1-155"><a href="the-osprey-job-file.html#cb1-155" tabindex="-1"></a>opts.fit.includeMetabs      <span class="op">=</span> {<span class="st">&#39;default&#39;</span>}<span class="op">;</span>      <span class="co">% OPTIONS:    - {&#39;default&#39;}</span></span>
+<span id="cb1-156"><a href="the-osprey-job-file.html#cb1-156" tabindex="-1"></a>                                                <span class="co">%             - {custom}</span></span>
+<span id="cb1-157"><a href="the-osprey-job-file.html#cb1-157" tabindex="-1"></a></span>
+<span id="cb1-158"><a href="the-osprey-job-file.html#cb1-158" tabindex="-1"></a><span class="co">% Choose the fitting algorithm</span></span>
+<span id="cb1-159"><a href="the-osprey-job-file.html#cb1-159" tabindex="-1"></a>opts.fit.method             <span class="op">=</span> <span class="st">&#39;Osprey&#39;</span><span class="op">;</span>         <span class="co">% OPTIONS:    - &#39;Osprey&#39; (default)</span></span>
+<span id="cb1-160"><a href="the-osprey-job-file.html#cb1-160" tabindex="-1"></a>                                                <span class="co">%           - &#39;LCModel&#39;</span></span>
+<span id="cb1-161"><a href="the-osprey-job-file.html#cb1-161" tabindex="-1"></a></span>
+<span id="cb1-162"><a href="the-osprey-job-file.html#cb1-162" tabindex="-1"></a><span class="co">% Choose the fitting style for difference-edited datasets (MEGA, HERMES, HERCULES)</span></span>
+<span id="cb1-163"><a href="the-osprey-job-file.html#cb1-163" tabindex="-1"></a><span class="co">% (only available for the Osprey fitting method)</span></span>
+<span id="cb1-164"><a href="the-osprey-job-file.html#cb1-164" tabindex="-1"></a>opts.fit.style              <span class="op">=</span> <span class="st">&#39;Separate&#39;</span><span class="op">;</span>       <span class="co">% OPTIONS:  - &#39;Concatenated&#39; (default) - will fit DIFF and SUM simultaneously)</span></span>
+<span id="cb1-165"><a href="the-osprey-job-file.html#cb1-165" tabindex="-1"></a>                                                <span class="co">%           - &#39;Separate&#39; - will fit DIFF and OFF separately</span></span>
+<span id="cb1-166"><a href="the-osprey-job-file.html#cb1-166" tabindex="-1"></a></span>
+<span id="cb1-167"><a href="the-osprey-job-file.html#cb1-167" tabindex="-1"></a><span class="co">% Determine fitting range (in ppm) for the metabolite and water spectra</span></span>
+<span id="cb1-168"><a href="the-osprey-job-file.html#cb1-168" tabindex="-1"></a>opts.fit.range              <span class="op">=</span> [<span class="fl">0.5</span> <span class="fl">4</span>]<span class="op">;</span>          <span class="co">% [ppm] Default: [0.5 4]</span></span>
+<span id="cb1-169"><a href="the-osprey-job-file.html#cb1-169" tabindex="-1"></a>opts.fit.rangeWater         <span class="op">=</span> [<span class="fl">2.0</span> <span class="fl">7.4</span>]<span class="op">;</span>        <span class="co">% [ppm] Default: [2.0 7.4]</span></span>
+<span id="cb1-170"><a href="the-osprey-job-file.html#cb1-170" tabindex="-1"></a></span>
+<span id="cb1-171"><a href="the-osprey-job-file.html#cb1-171" tabindex="-1"></a><span class="co">% Determine the baseline knot spacing (in ppm) for the metabolite spectra</span></span>
+<span id="cb1-172"><a href="the-osprey-job-file.html#cb1-172" tabindex="-1"></a>opts.fit.bLineKnotSpace     <span class="op">=</span> <span class="fl">0.4</span><span class="op">;</span>              <span class="co">% [ppm] Default: 0.4.</span></span>
+<span id="cb1-173"><a href="the-osprey-job-file.html#cb1-173" tabindex="-1"></a></span>
+<span id="cb1-174"><a href="the-osprey-job-file.html#cb1-174" tabindex="-1"></a><span class="co">% Add macromolecule and lipid basis functions to the fit?</span></span>
+<span id="cb1-175"><a href="the-osprey-job-file.html#cb1-175" tabindex="-1"></a>opts.fit.fitMM              <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no)</span></span>
+<span id="cb1-176"><a href="the-osprey-job-file.html#cb1-176" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes, default)</span></span>
+<span id="cb1-177"><a href="the-osprey-job-file.html#cb1-177" tabindex="-1"></a>                                                </span>
+<span id="cb1-178"><a href="the-osprey-job-file.html#cb1-178" tabindex="-1"></a><span class="co">% Optional: In case the automatic basisset picker is not working you can manually</span></span>
+<span id="cb1-179"><a href="the-osprey-job-file.html#cb1-179" tabindex="-1"></a><span class="co">% select the path to the basis set in the osprey/fit/basis, i.e.:</span></span>
+<span id="cb1-180"><a href="the-osprey-job-file.html#cb1-180" tabindex="-1"></a><span class="co">% opts.fit.basisSetFile = &#39;osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat&#39;;</span></span>
+<span id="cb1-181"><a href="the-osprey-job-file.html#cb1-181" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
+<span id="cb1-182"><a href="the-osprey-job-file.html#cb1-182" tabindex="-1"></a></span>
+<span id="cb1-183"><a href="the-osprey-job-file.html#cb1-183" tabindex="-1"></a></span>
+<span id="cb1-184"><a href="the-osprey-job-file.html#cb1-184" tabindex="-1"></a></span>
+<span id="cb1-185"><a href="the-osprey-job-file.html#cb1-185" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
+<span id="cb1-186"><a href="the-osprey-job-file.html#cb1-186" tabindex="-1"></a><span class="co">%%% 3. SPECIFY MRS DATA AND STRUCTURAL IMAGING FILES %%</span></span>
+<span id="cb1-187"><a href="the-osprey-job-file.html#cb1-187" tabindex="-1"></a><span class="co">% When using single-average Siemens RDA or DICOM files, specify their</span></span>
+<span id="cb1-188"><a href="the-osprey-job-file.html#cb1-188" tabindex="-1"></a><span class="co">% folders instead of single files!</span></span>
+<span id="cb1-189"><a href="the-osprey-job-file.html#cb1-189" tabindex="-1"></a></span>
+<span id="cb1-190"><a href="the-osprey-job-file.html#cb1-190" tabindex="-1"></a><span class="co">% Clear existing files</span></span>
+<span id="cb1-191"><a href="the-osprey-job-file.html#cb1-191" tabindex="-1"></a><span class="bu">clear</span> files files_ref files_w files_nii files_mm</span>
+<span id="cb1-192"><a href="the-osprey-job-file.html#cb1-192" tabindex="-1"></a></span>
+<span id="cb1-193"><a href="the-osprey-job-file.html#cb1-193" tabindex="-1"></a><span class="co">% Data folder in BIDS format</span></span>
+<span id="cb1-194"><a href="the-osprey-job-file.html#cb1-194" tabindex="-1"></a><span class="co">% The filparts(which()) comment is needed to find the data on your machine. If you set</span></span>
+<span id="cb1-195"><a href="the-osprey-job-file.html#cb1-195" tabindex="-1"></a><span class="co">% up the jobFile for your own data you can set a direct path to your data</span></span>
+<span id="cb1-196"><a href="the-osprey-job-file.html#cb1-196" tabindex="-1"></a><span class="co">% folder e.g., data_folder = /Volumes/MyProject/data/&#39;</span></span>
+<span id="cb1-197"><a href="the-osprey-job-file.html#cb1-197" tabindex="-1"></a></span>
+<span id="cb1-198"><a href="the-osprey-job-file.html#cb1-198" tabindex="-1"></a>data_folder <span class="op">=</span> <span class="fu">fileparts</span>(<span class="fu">which</span>(<span class="fu">fullfile</span>(<span class="st">&#39;exampledata&#39;</span><span class="op">,</span><span class="st">&#39;sdat&#39;</span><span class="op">,</span><span class="st">&#39;UnEdited&#39;</span><span class="op">,</span><span class="st">&#39;jobSDAT.m&#39;</span>)))<span class="op">;</span></span>
+<span id="cb1-199"><a href="the-osprey-job-file.html#cb1-199" tabindex="-1"></a></span>
+<span id="cb1-200"><a href="the-osprey-job-file.html#cb1-200" tabindex="-1"></a><span class="co">% The following lines perform an automated set-up of the jobFile which</span></span>
+<span id="cb1-201"><a href="the-osprey-job-file.html#cb1-201" tabindex="-1"></a><span class="co">% takes advatage of the BIDS foramt. If you are not using BIDS (highly</span></span>
+<span id="cb1-202"><a href="the-osprey-job-file.html#cb1-202" tabindex="-1"></a><span class="co">% recommended) you can look at the definitions below the loop to see how to</span></span>
+<span id="cb1-203"><a href="the-osprey-job-file.html#cb1-203" tabindex="-1"></a><span class="co">% set up direct path links to your data.</span></span>
+<span id="cb1-204"><a href="the-osprey-job-file.html#cb1-204" tabindex="-1"></a></span>
+<span id="cb1-205"><a href="the-osprey-job-file.html#cb1-205" tabindex="-1"></a>subs       <span class="op">=</span> <span class="fu">dir</span>(data_folder)<span class="op">;</span></span>
+<span id="cb1-206"><a href="the-osprey-job-file.html#cb1-206" tabindex="-1"></a>subs(<span class="fl">1</span><span class="op">:</span><span class="fl">2</span>)  <span class="op">=</span> []<span class="op">;</span></span>
+<span id="cb1-207"><a href="the-osprey-job-file.html#cb1-207" tabindex="-1"></a>subs       <span class="op">=</span> subs([subs.isdir])<span class="op">;</span></span>
+<span id="cb1-208"><a href="the-osprey-job-file.html#cb1-208" tabindex="-1"></a>subs       <span class="op">=</span> subs(contains({subs.name}<span class="op">,</span><span class="st">&#39;sub&#39;</span>))<span class="op">;</span></span>
+<span id="cb1-209"><a href="the-osprey-job-file.html#cb1-209" tabindex="-1"></a>counter    <span class="op">=</span> <span class="fl">1</span><span class="op">;</span></span>
+<span id="cb1-210"><a href="the-osprey-job-file.html#cb1-210" tabindex="-1"></a></span>
+<span id="cb1-211"><a href="the-osprey-job-file.html#cb1-211" tabindex="-1"></a><span class="cf">for</span> kk <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu">length</span>(subs)</span>
+<span id="cb1-212"><a href="the-osprey-job-file.html#cb1-212" tabindex="-1"></a>    <span class="co">% Loop over sessions</span></span>
+<span id="cb1-213"><a href="the-osprey-job-file.html#cb1-213" tabindex="-1"></a>    sess        <span class="op">=</span> <span class="fu">dir</span>([subs(kk).folder <span class="fu">filesep</span> subs(kk).name])<span class="op">;</span></span>
+<span id="cb1-214"><a href="the-osprey-job-file.html#cb1-214" tabindex="-1"></a>    sess(<span class="fl">1</span><span class="op">:</span><span class="fl">2</span>)   <span class="op">=</span> []<span class="op">;</span></span>
+<span id="cb1-215"><a href="the-osprey-job-file.html#cb1-215" tabindex="-1"></a>    sess        <span class="op">=</span> sess([sess.isdir])<span class="op">;</span></span>
+<span id="cb1-216"><a href="the-osprey-job-file.html#cb1-216" tabindex="-1"></a>    sess        <span class="op">=</span> sess(contains({sess.name}<span class="op">,</span><span class="st">&#39;ses&#39;</span>))<span class="op">;</span></span>
+<span id="cb1-217"><a href="the-osprey-job-file.html#cb1-217" tabindex="-1"></a>    <span class="cf">for</span> ll <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu">length</span>(sess)</span>
+<span id="cb1-218"><a href="the-osprey-job-file.html#cb1-218" tabindex="-1"></a></span>
+<span id="cb1-219"><a href="the-osprey-job-file.html#cb1-219" tabindex="-1"></a>        <span class="co">% Specify metabolite data</span></span>
+<span id="cb1-220"><a href="the-osprey-job-file.html#cb1-220" tabindex="-1"></a>        <span class="co">% (MANDATORY)</span></span>
+<span id="cb1-221"><a href="the-osprey-job-file.html#cb1-221" tabindex="-1"></a>        dir_metabolite    <span class="op">=</span> <span class="fu">dir</span>([sess(ll).folder <span class="fu">filesep</span> sess(ll).name <span class="fu">filesep</span> <span class="st">&#39;mrs&#39;</span> <span class="fu">filesep</span> subs(kk).name <span class="st">&#39;_&#39;</span> sess(ll).name <span class="st">&#39;_press&#39;</span> <span class="fu">filesep</span> <span class="st">&#39;*.SDAT&#39;</span>])<span class="op">;</span></span>
+<span id="cb1-222"><a href="the-osprey-job-file.html#cb1-222" tabindex="-1"></a>        files(counter)      <span class="op">=</span> {[dir_metabolite(<span class="cf">end</span>).folder <span class="fu">filesep</span> dir_metabolite(<span class="cf">end</span>).name]}<span class="op">;</span></span>
+<span id="cb1-223"><a href="the-osprey-job-file.html#cb1-223" tabindex="-1"></a></span>
+<span id="cb1-224"><a href="the-osprey-job-file.html#cb1-224" tabindex="-1"></a>        <span class="co">% Specify water reference data for eddy-current correction (same sequence as metabolite data!)</span></span>
+<span id="cb1-225"><a href="the-osprey-job-file.html#cb1-225" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-226"><a href="the-osprey-job-file.html#cb1-226" tabindex="-1"></a>        <span class="co">% Leave empty for GE P-files (.7) - these include water reference data by</span></span>
+<span id="cb1-227"><a href="the-osprey-job-file.html#cb1-227" tabindex="-1"></a>        <span class="co">% default.</span></span>
+<span id="cb1-228"><a href="the-osprey-job-file.html#cb1-228" tabindex="-1"></a>        dir_ref    <span class="op">=</span> <span class="fu">dir</span>([sess(ll).folder <span class="fu">filesep</span> sess(ll).name <span class="fu">filesep</span> <span class="st">&#39;mrs&#39;</span> <span class="fu">filesep</span> subs(kk).name <span class="st">&#39;_&#39;</span> sess(ll).name <span class="st">&#39;_press-ref&#39;</span> <span class="fu">filesep</span> <span class="st">&#39;*.SDAT&#39;</span>])<span class="op">;</span></span>
+<span id="cb1-229"><a href="the-osprey-job-file.html#cb1-229" tabindex="-1"></a>        files_ref(counter)  <span class="op">=</span> {[dir_ref(<span class="cf">end</span>).folder <span class="fu">filesep</span> dir_ref(<span class="cf">end</span>).name]}<span class="op">;</span></span>
+<span id="cb1-230"><a href="the-osprey-job-file.html#cb1-230" tabindex="-1"></a></span>
+<span id="cb1-231"><a href="the-osprey-job-file.html#cb1-231" tabindex="-1"></a>        <span class="co">% Specify water data for quantification (e.g. short-TE water scan)</span></span>
+<span id="cb1-232"><a href="the-osprey-job-file.html#cb1-232" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-233"><a href="the-osprey-job-file.html#cb1-233" tabindex="-1"></a>        files_w     <span class="op">=</span> {}<span class="op">;</span></span>
+<span id="cb1-234"><a href="the-osprey-job-file.html#cb1-234" tabindex="-1"></a></span>
+<span id="cb1-235"><a href="the-osprey-job-file.html#cb1-235" tabindex="-1"></a>        <span class="co">% Specify metabolite-nulled data for quantification</span></span>
+<span id="cb1-236"><a href="the-osprey-job-file.html#cb1-236" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-237"><a href="the-osprey-job-file.html#cb1-237" tabindex="-1"></a>        files_mm     <span class="op">=</span> {}<span class="op">;</span></span>
+<span id="cb1-238"><a href="the-osprey-job-file.html#cb1-238" tabindex="-1"></a></span>
+<span id="cb1-239"><a href="the-osprey-job-file.html#cb1-239" tabindex="-1"></a>       <span class="co">% Specify T1-weighted structural imaging data</span></span>
+<span id="cb1-240"><a href="the-osprey-job-file.html#cb1-240" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-241"><a href="the-osprey-job-file.html#cb1-241" tabindex="-1"></a>        <span class="co">% Link to single NIfTI (*.nii) files for Siemens and Philips data</span></span>
+<span id="cb1-242"><a href="the-osprey-job-file.html#cb1-242" tabindex="-1"></a>        <span class="co">% Link to DICOM (*.dcm) folders for GE data</span></span>
+<span id="cb1-243"><a href="the-osprey-job-file.html#cb1-243" tabindex="-1"></a>        files_nii(counter)  <span class="op">=</span> {[sess(ll).folder <span class="fu">filesep</span> sess(ll).name <span class="fu">filesep</span> <span class="st">&#39;anat&#39;</span> <span class="fu">filesep</span> subs(kk).name <span class="fu">filesep</span> sess(ll).name <span class="st">&#39;_T1w.nii.gz&#39;</span>]}<span class="op">;</span></span>
+<span id="cb1-244"><a href="the-osprey-job-file.html#cb1-244" tabindex="-1"></a></span>
+<span id="cb1-245"><a href="the-osprey-job-file.html#cb1-245" tabindex="-1"></a>        <span class="co">% External segmentation results</span></span>
+<span id="cb1-246"><a href="the-osprey-job-file.html#cb1-246" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-247"><a href="the-osprey-job-file.html#cb1-247" tabindex="-1"></a>        <span class="co">% Link to NIfTI (*.nii or *.nii.gz) files with segmentation results</span></span>
+<span id="cb1-248"><a href="the-osprey-job-file.html#cb1-248" tabindex="-1"></a>        <span class="co">% Add supply gray matter, white matter, and CSF as 1 x 3 cell within a</span></span>
+<span id="cb1-249"><a href="the-osprey-job-file.html#cb1-249" tabindex="-1"></a>        <span class="co">% cell array  or a single 4D file in the same order supplied as 1 x 1 cell;</span></span>
+<span id="cb1-250"><a href="the-osprey-job-file.html#cb1-250" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{[sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c1&#39; sess(ll).name &#39;_T1w.nii.gz&#39;],...</span></span>
+<span id="cb1-251"><a href="the-osprey-job-file.html#cb1-251" tabindex="-1"></a><span class="co">%                                  [sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c2&#39; sess(ll).name &#39;_T1w.nii.gz&#39;],...</span></span>
+<span id="cb1-252"><a href="the-osprey-job-file.html#cb1-252" tabindex="-1"></a><span class="co">%                                  [sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c3&#39; sess(ll).name &#39;_T1w.nii.gz&#39;]}};</span></span>
+<span id="cb1-253"><a href="the-osprey-job-file.html#cb1-253" tabindex="-1"></a></span>
+<span id="cb1-254"><a href="the-osprey-job-file.html#cb1-254" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{[sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;4D&#39; sess(ll).name &#39;_T1w.nii.gz&#39;]}};</span></span>
+<span id="cb1-255"><a href="the-osprey-job-file.html#cb1-255" tabindex="-1"></a></span>
+<span id="cb1-256"><a href="the-osprey-job-file.html#cb1-256" tabindex="-1"></a>        counter             <span class="op">=</span> counter <span class="op">+</span> <span class="fl">1</span><span class="op">;</span></span>
+<span id="cb1-257"><a href="the-osprey-job-file.html#cb1-257" tabindex="-1"></a>    <span class="cf">end</span></span>
+<span id="cb1-258"><a href="the-osprey-job-file.html#cb1-258" tabindex="-1"></a><span class="cf">end</span></span>
+<span id="cb1-259"><a href="the-osprey-job-file.html#cb1-259" tabindex="-1"></a></span>
+<span id="cb1-260"><a href="the-osprey-job-file.html#cb1-260" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
+<span id="cb1-261"><a href="the-osprey-job-file.html#cb1-261" tabindex="-1"></a><span class="co">% Definitions without using BIDS</span></span>
+<span id="cb1-262"><a href="the-osprey-job-file.html#cb1-262" tabindex="-1"></a></span>
+<span id="cb1-263"><a href="the-osprey-job-file.html#cb1-263" tabindex="-1"></a><span class="co">% You can always supply direct path to each of the files within</span></span>
+<span id="cb1-264"><a href="the-osprey-job-file.html#cb1-264" tabindex="-1"></a><span class="co">% the cell array. For example:</span></span>
+<span id="cb1-265"><a href="the-osprey-job-file.html#cb1-265" tabindex="-1"></a></span>
+<span id="cb1-266"><a href="the-osprey-job-file.html#cb1-266" tabindex="-1"></a><span class="co">% Specify metabolite data</span></span>
+<span id="cb1-267"><a href="the-osprey-job-file.html#cb1-267" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
+<span id="cb1-268"><a href="the-osprey-job-file.html#cb1-268" tabindex="-1"></a><span class="co">% files(counter)      = {&#39;/Volumes/MyProject/data/sub-01/mrs/PRESS_act.SDAT&#39;,...</span></span>
+<span id="cb1-269"><a href="the-osprey-job-file.html#cb1-269" tabindex="-1"></a><span class="co">%                        &#39;/Volumes/MyProject/data/sub-02/mrs/PRESS_act.SDAT&#39;};</span></span>
+<span id="cb1-270"><a href="the-osprey-job-file.html#cb1-270" tabindex="-1"></a></span>
+<span id="cb1-271"><a href="the-osprey-job-file.html#cb1-271" tabindex="-1"></a><span class="co">% Specify water reference data for eddy-current correction (same sequence as metabolite data!)</span></span>
+<span id="cb1-272"><a href="the-osprey-job-file.html#cb1-272" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-273"><a href="the-osprey-job-file.html#cb1-273" tabindex="-1"></a><span class="co">% Leave empty for GE P-files (.7) - these include water reference data by</span></span>
+<span id="cb1-274"><a href="the-osprey-job-file.html#cb1-274" tabindex="-1"></a><span class="co">% default.</span></span>
+<span id="cb1-275"><a href="the-osprey-job-file.html#cb1-275" tabindex="-1"></a><span class="co">% files_ref(counter)      = {&#39;/Volumes/MyProject/data/sub-01/mrs/PRESS_ref.SDAT&#39;,...</span></span>
+<span id="cb1-276"><a href="the-osprey-job-file.html#cb1-276" tabindex="-1"></a><span class="co">%                            &#39;/Volumes/MyProject/data/sub-02/mrs/PRESS_ref.SDAT&#39;};</span></span>
+<span id="cb1-277"><a href="the-osprey-job-file.html#cb1-277" tabindex="-1"></a></span>
+<span id="cb1-278"><a href="the-osprey-job-file.html#cb1-278" tabindex="-1"></a><span class="co">% Specify water data for quantification (e.g. short-TE water scan)</span></span>
+<span id="cb1-279"><a href="the-osprey-job-file.html#cb1-279" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-280"><a href="the-osprey-job-file.html#cb1-280" tabindex="-1"></a><span class="co">% files_w     = {};</span></span>
+<span id="cb1-281"><a href="the-osprey-job-file.html#cb1-281" tabindex="-1"></a></span>
+<span id="cb1-282"><a href="the-osprey-job-file.html#cb1-282" tabindex="-1"></a><span class="co">% Specify metabolite-nulled data for quantification</span></span>
+<span id="cb1-283"><a href="the-osprey-job-file.html#cb1-283" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-284"><a href="the-osprey-job-file.html#cb1-284" tabindex="-1"></a><span class="co">% files_mm     = {};</span></span>
+<span id="cb1-285"><a href="the-osprey-job-file.html#cb1-285" tabindex="-1"></a></span>
+<span id="cb1-286"><a href="the-osprey-job-file.html#cb1-286" tabindex="-1"></a><span class="co">% Specify T1-weighted structural imaging data</span></span>
+<span id="cb1-287"><a href="the-osprey-job-file.html#cb1-287" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-288"><a href="the-osprey-job-file.html#cb1-288" tabindex="-1"></a><span class="co">% Link to single NIfTI (*.nii.gz or #.nii) files for GE, Siemens and Philips data</span></span>
+<span id="cb1-289"><a href="the-osprey-job-file.html#cb1-289" tabindex="-1"></a><span class="co">% files_nii  = {&#39;/Volumes/MyProject/data/sub-01/anat/T1w.nii.gz&#39;,...</span></span>
+<span id="cb1-290"><a href="the-osprey-job-file.html#cb1-290" tabindex="-1"></a><span class="co">%               &#39;/Volumes/MyProject/data/sub-02/anat/T1w.nii.gz&#39;};</span></span>
+<span id="cb1-291"><a href="the-osprey-job-file.html#cb1-291" tabindex="-1"></a></span>
+<span id="cb1-292"><a href="the-osprey-job-file.html#cb1-292" tabindex="-1"></a><span class="co">% External segmentation results</span></span>
+<span id="cb1-293"><a href="the-osprey-job-file.html#cb1-293" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
+<span id="cb1-294"><a href="the-osprey-job-file.html#cb1-294" tabindex="-1"></a><span class="co">% Link to NIfTI (*.nii or *.nii.gz) files with segmentation results</span></span>
+<span id="cb1-295"><a href="the-osprey-job-file.html#cb1-295" tabindex="-1"></a><span class="co">% Add supply gray matter, white matter, and CSF as 1 x 3 cell within a</span></span>
+<span id="cb1-296"><a href="the-osprey-job-file.html#cb1-296" tabindex="-1"></a><span class="co">% cell array  or a single 4D file in the same order supplied as 1 x 1 cell;</span></span>
+<span id="cb1-297"><a href="the-osprey-job-file.html#cb1-297" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{&#39;/Volumes/MyProject/data/sub-01/anat/c1T1w.nii.gz&#39;,...</span></span>
+<span id="cb1-298"><a href="the-osprey-job-file.html#cb1-298" tabindex="-1"></a><span class="co">%                                  &#39;/Volumes/MyProject/data/sub-01/anat/c2T1w.nii.gz&#39;,...</span></span>
+<span id="cb1-299"><a href="the-osprey-job-file.html#cb1-299" tabindex="-1"></a><span class="co">%                                  &#39;/Volumes/MyProject/data/sub-01/anat/c3T1w.nii.gz&#39;},...</span></span>
+<span id="cb1-300"><a href="the-osprey-job-file.html#cb1-300" tabindex="-1"></a><span class="co">%                                   {&#39;/Volumes/MyProject/data/sub-02/anat/c1T1w.nii.gz&#39;,...</span></span>
+<span id="cb1-301"><a href="the-osprey-job-file.html#cb1-301" tabindex="-1"></a><span class="co">%                                  &#39;/Volumes/MyProject/data/sub-02/anat/c2T1w.nii.gz&#39;,...</span></span>
+<span id="cb1-302"><a href="the-osprey-job-file.html#cb1-302" tabindex="-1"></a><span class="co">%                                  &#39;/Volumes/MyProject/data/sub-02/anat/c3T1w.nii.gz&#39;}};</span></span>
+<span id="cb1-303"><a href="the-osprey-job-file.html#cb1-303" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{&#39;/Volumes/MyProject/data/sub-01/anat/4DT1w.nii.gz&#39;},...</span></span>
+<span id="cb1-304"><a href="the-osprey-job-file.html#cb1-304" tabindex="-1"></a><span class="co">%                                   {&#39;/Volumes/MyProject/data/sub-02/anat/4DT1w.nii.gz&#39;}};</span></span>
+<span id="cb1-305"><a href="the-osprey-job-file.html#cb1-305" tabindex="-1"></a></span>
+<span id="cb1-306"><a href="the-osprey-job-file.html#cb1-306" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
+<span id="cb1-307"><a href="the-osprey-job-file.html#cb1-307" tabindex="-1"></a><span class="co">%%% 4. SPECIFY STAT FILE %%%</span></span>
+<span id="cb1-308"><a href="the-osprey-job-file.html#cb1-308" tabindex="-1"></a><span class="co">% Supply location of a csv file, which contains possible correlation</span></span>
+<span id="cb1-309"><a href="the-osprey-job-file.html#cb1-309" tabindex="-1"></a><span class="co">% measures and group variables. Each column must start with the name of the</span></span>
+<span id="cb1-310"><a href="the-osprey-job-file.html#cb1-310" tabindex="-1"></a><span class="co">% measure. For the grouping variable use &#39;group&#39; and numbers between 1 and</span></span>
+<span id="cb1-311"><a href="the-osprey-job-file.html#cb1-311" tabindex="-1"></a><span class="co">% the number of included groups. If no group is supplied the data will be</span></span>
+<span id="cb1-312"><a href="the-osprey-job-file.html#cb1-312" tabindex="-1"></a><span class="co">% treated as one group. (You can always use the direct path)</span></span>
+<span id="cb1-313"><a href="the-osprey-job-file.html#cb1-313" tabindex="-1"></a></span>
+<span id="cb1-314"><a href="the-osprey-job-file.html#cb1-314" tabindex="-1"></a><span class="co">% file_stat = fullfile(data_folder, &#39;stat.csv&#39;);</span></span>
+<span id="cb1-315"><a href="the-osprey-job-file.html#cb1-315" tabindex="-1"></a>file_stat <span class="op">=</span> <span class="st">&#39;&#39;</span><span class="op">;</span></span>
+<span id="cb1-316"><a href="the-osprey-job-file.html#cb1-316" tabindex="-1"></a></span>
+<span id="cb1-317"><a href="the-osprey-job-file.html#cb1-317" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span>
+<span id="cb1-318"><a href="the-osprey-job-file.html#cb1-318" tabindex="-1"></a><span class="co">%%% 5. SPECIFY OUTPUT FOLDER %%</span></span>
+<span id="cb1-319"><a href="the-osprey-job-file.html#cb1-319" tabindex="-1"></a><span class="co">% The Osprey data container will be saved as a *.mat file in the output</span></span>
+<span id="cb1-320"><a href="the-osprey-job-file.html#cb1-320" tabindex="-1"></a><span class="co">% folder that you specify below. In addition, any exported files (for use</span></span>
+<span id="cb1-321"><a href="the-osprey-job-file.html#cb1-321" tabindex="-1"></a><span class="co">% with jMRUI, TARQUIN, or LCModel) will be saved in sub-folders.</span></span>
+<span id="cb1-322"><a href="the-osprey-job-file.html#cb1-322" tabindex="-1"></a></span>
+<span id="cb1-323"><a href="the-osprey-job-file.html#cb1-323" tabindex="-1"></a><span class="co">% Specify output folder (you can always use the direct path)</span></span>
+<span id="cb1-324"><a href="the-osprey-job-file.html#cb1-324" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
+<span id="cb1-325"><a href="the-osprey-job-file.html#cb1-325" tabindex="-1"></a>outputFolder <span class="op">=</span> <span class="fu">fullfile</span>(data_folder<span class="op">,</span> <span class="st">&#39;derivatives&#39;</span>)<span class="op">;</span></span>
+<span id="cb1-326"><a href="the-osprey-job-file.html#cb1-326" tabindex="-1"></a></span>
+<span id="cb1-327"><a href="the-osprey-job-file.html#cb1-327" tabindex="-1"></a><span class="co">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span></span></code></pre></div>
 </div>
 <div id="specifying-sequence-information" class="section level2 hasAnchor" number="4.2">
 <h2><span class="header-section-number">4.2</span> Specifying Sequence Information<a href="the-osprey-job-file.html#specifying-sequence-information" class="anchor-section" aria-label="Anchor link to header"></a></h2>
@@ -570,28 +574,28 @@ <h2><span class="header-section-number">4.2</span> Specifying Sequence Informati
 <div id="sequence-type" class="section level3 hasAnchor" number="4.2.1">
 <h3><span class="header-section-number">4.2.1</span> Sequence Type<a href="the-osprey-job-file.html#sequence-type" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>seqType</code> variable describes the type of sequence used and is a required input in the form of a string.<code>seqType</code> determines whether the supplied datasets have been acquired with spectral editing experiments.</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="the-osprey-job-file.html#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify sequence type</span></span>
-<span id="cb2-2"><a href="the-osprey-job-file.html#cb2-2" aria-hidden="true" tabindex="-1"></a>seqType <span class="op">=</span> <span class="st">&#39;unedited&#39;</span><span class="op">;</span>           <span class="co">% OPTIONS:    - &#39;unedited&#39; (default)</span></span>
-<span id="cb2-3"><a href="the-osprey-job-file.html#cb2-3" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;MEGA&#39;</span></span>
-<span id="cb2-4"><a href="the-osprey-job-file.html#cb2-4" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;HERMES&#39;</span></span>
-<span id="cb2-5"><a href="the-osprey-job-file.html#cb2-5" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;HERCULES&#39;</span></span></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="the-osprey-job-file.html#cb2-1" tabindex="-1"></a><span class="co">% Specify sequence type</span></span>
+<span id="cb2-2"><a href="the-osprey-job-file.html#cb2-2" tabindex="-1"></a>seqType <span class="op">=</span> <span class="st">&#39;unedited&#39;</span><span class="op">;</span>           <span class="co">% OPTIONS:    - &#39;unedited&#39; (default)</span></span>
+<span id="cb2-3"><a href="the-osprey-job-file.html#cb2-3" tabindex="-1"></a>                                <span class="co">%             - &#39;MEGA&#39;</span></span>
+<span id="cb2-4"><a href="the-osprey-job-file.html#cb2-4" tabindex="-1"></a>                                <span class="co">%             - &#39;HERMES&#39;</span></span>
+<span id="cb2-5"><a href="the-osprey-job-file.html#cb2-5" tabindex="-1"></a>                                <span class="co">%             - &#39;HERCULES&#39;</span></span></code></pre></div>
 </div>
 <div id="editing-targets" class="section level3 hasAnchor" number="4.2.2">
 <h3><span class="header-section-number">4.2.2</span> Editing Targets<a href="the-osprey-job-file.html#editing-targets" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>editTarget</code> variable describes the sequence type and is a required input in the form of a cell array. <code>editTarget</code> determines the target spin system(s) of spectral editing experiments. If no spectral editing has been performed, enter <code>{'none'}</code>.</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb3-1"><a href="the-osprey-job-file.html#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify editing targets</span></span>
-<span id="cb3-2"><a href="the-osprey-job-file.html#cb3-2" aria-hidden="true" tabindex="-1"></a>editTarget <span class="op">=</span> {<span class="st">&#39;none&#39;</span>}<span class="op">;</span>          <span class="co">% OPTIONS:    - {&#39;none&#39;} (default if &#39;unedited&#39;)</span></span>
-<span id="cb3-3"><a href="the-osprey-job-file.html#cb3-3" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - {&#39;GABA&#39;}, {&#39;GSH&#39;}, {&#39;Lac&#39;}, {&#39;PE322&#39;}, {&#39;PE398&#39;}  (for &#39;MEGA&#39;)</span></span>
-<span id="cb3-4"><a href="the-osprey-job-file.html#cb3-4" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - {&#39;GABA&#39;, &#39;GSH&#39;}, {&#39;GABA&#39;, &#39;Lac&#39;}, {&#39;NAA&#39;, &#39;NAAG&#39;} (for &#39;HERMES&#39;and &#39;HERCULES&#39;)</span></span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb3-1"><a href="the-osprey-job-file.html#cb3-1" tabindex="-1"></a><span class="co">% Specify editing targets</span></span>
+<span id="cb3-2"><a href="the-osprey-job-file.html#cb3-2" tabindex="-1"></a>editTarget <span class="op">=</span> {<span class="st">&#39;none&#39;</span>}<span class="op">;</span>          <span class="co">% OPTIONS:    - {&#39;none&#39;} (default if &#39;unedited&#39;)</span></span>
+<span id="cb3-3"><a href="the-osprey-job-file.html#cb3-3" tabindex="-1"></a>                                <span class="co">%             - {&#39;GABA&#39;}, {&#39;GSH&#39;}, {&#39;Lac&#39;}, {&#39;PE322&#39;}, {&#39;PE398&#39;}  (for &#39;MEGA&#39;)</span></span>
+<span id="cb3-4"><a href="the-osprey-job-file.html#cb3-4" tabindex="-1"></a>                                <span class="co">%             - {&#39;GABA&#39;, &#39;GSH&#39;}, {&#39;GABA&#39;, &#39;Lac&#39;}, {&#39;NAA&#39;, &#39;NAAG&#39;} (for &#39;HERMES&#39;and &#39;HERCULES&#39;)</span></span></code></pre></div>
 </div>
 <div id="data-scenario" class="section level3 hasAnchor" number="4.2.3">
 <h3><span class="header-section-number">4.2.3</span> Data Scenario<a href="the-osprey-job-file.html#data-scenario" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>datascenario</code> variable specifies the conditions in which the data were acquired.For in-vivo single-voxel MRS, select <code>invivo</code>. Further options are available for data acquired in a phantom, or multi-voxel data acquired with PRIAM or MRSI.</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb4-1"><a href="the-osprey-job-file.html#cb4-1" aria-hidden="true" tabindex="-1"></a>                                <span class="co">% Specify data scenario</span></span>
-<span id="cb4-2"><a href="the-osprey-job-file.html#cb4-2" aria-hidden="true" tabindex="-1"></a>dataScenario <span class="op">=</span> <span class="st">&#39;invivo&#39;</span><span class="op">;</span>        <span class="co">% OPTIONS:    - &#39;invivo&#39; (default)</span></span>
-<span id="cb4-3"><a href="the-osprey-job-file.html#cb4-3" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;phantom&#39;</span></span>
-<span id="cb4-4"><a href="the-osprey-job-file.html#cb4-4" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;PRIAM&#39;</span></span>
-<span id="cb4-5"><a href="the-osprey-job-file.html#cb4-5" aria-hidden="true" tabindex="-1"></a>                                <span class="co">%             - &#39;MRSI&#39;</span></span></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb4-1"><a href="the-osprey-job-file.html#cb4-1" tabindex="-1"></a>                                <span class="co">% Specify data scenario</span></span>
+<span id="cb4-2"><a href="the-osprey-job-file.html#cb4-2" tabindex="-1"></a>dataScenario <span class="op">=</span> <span class="st">&#39;invivo&#39;</span><span class="op">;</span>        <span class="co">% OPTIONS:    - &#39;invivo&#39; (default)</span></span>
+<span id="cb4-3"><a href="the-osprey-job-file.html#cb4-3" tabindex="-1"></a>                                <span class="co">%             - &#39;phantom&#39;</span></span>
+<span id="cb4-4"><a href="the-osprey-job-file.html#cb4-4" tabindex="-1"></a>                                <span class="co">%             - &#39;PRIAM&#39;</span></span>
+<span id="cb4-5"><a href="the-osprey-job-file.html#cb4-5" tabindex="-1"></a>                                <span class="co">%             - &#39;MRSI&#39;</span></span></code></pre></div>
 </div>
 </div>
 <div id="data-handling-and-modeling-options" class="section level2 hasAnchor" number="4.3">
@@ -603,33 +607,33 @@ <h3><span class="header-section-number">4.3.1</span> Spectral registration optio
 <p>By setting <code>opts.SpecReg</code> to <code>RobSpecReg</code>, alignment is performed with lipid/water removal using simialrity meric, and weighted averaging.
 By setting <code>opts.SpecReg</code> to <code>ProbSpecReg</code>, Probabilistic spectral alignment is performed, registering to a median target with weighted averaging.
 By setting <code>opts.SpecReg</code> to <code>RestrSpecReg</code>, Spectral alignment using similarity metric and weighted average over a restricted fit range.</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb5-1"><a href="the-osprey-job-file.html#cb5-1" aria-hidden="true" tabindex="-1"></a>opts.SpecReg <span class="op">=</span> <span class="st">&#39;RobSpecReg&#39;</span><span class="op">;</span>                  <span class="co">% OPTIONS:    - &#39;RobSpecReg&#39; (default) Spectral aligment with Water/Lipid removal, using simialrity meric, and weighted averaging</span></span>
-<span id="cb5-2"><a href="the-osprey-job-file.html#cb5-2" aria-hidden="true" tabindex="-1"></a>                                              <span class="co">%             - &#39;ProbSpecReg&#39; Probabilistic spectral aligment to median target and weighted averaging</span></span>
-<span id="cb5-3"><a href="the-osprey-job-file.html#cb5-3" aria-hidden="true" tabindex="-1"></a>                                              <span class="co">%             - &#39;RestrSpecReg&#39; Frequency restricted (fit range) spectral aligment, using simialrity meric, and weighted averaging</span></span>
-<span id="cb5-4"><a href="the-osprey-job-file.html#cb5-4" aria-hidden="true" tabindex="-1"></a>                                              <span class="co">%             - &#39;none&#39;</span></span></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb5-1"><a href="the-osprey-job-file.html#cb5-1" tabindex="-1"></a>opts.SpecReg <span class="op">=</span> <span class="st">&#39;RobSpecReg&#39;</span><span class="op">;</span>                  <span class="co">% OPTIONS:    - &#39;RobSpecReg&#39; (default) Spectral aligment with Water/Lipid removal, using simialrity meric, and weighted averaging</span></span>
+<span id="cb5-2"><a href="the-osprey-job-file.html#cb5-2" tabindex="-1"></a>                                              <span class="co">%             - &#39;ProbSpecReg&#39; Probabilistic spectral aligment to median target and weighted averaging</span></span>
+<span id="cb5-3"><a href="the-osprey-job-file.html#cb5-3" tabindex="-1"></a>                                              <span class="co">%             - &#39;RestrSpecReg&#39; Frequency restricted (fit range) spectral aligment, using simialrity meric, and weighted averaging</span></span>
+<span id="cb5-4"><a href="the-osprey-job-file.html#cb5-4" tabindex="-1"></a>                                              <span class="co">%             - &#39;none&#39;</span></span></code></pre></div>
 </div>
 <div id="sub-spectral-alignment" class="section level3 hasAnchor" number="4.3.2">
 <h3><span class="header-section-number">4.3.2</span> Sub-spectral alignment<a href="the-osprey-job-file.html#sub-spectral-alignment" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p><code>opts.SubSpecAlignment</code> allows specification of the metric used to optimize sub-spectral alignment. <code>L2Norm</code> is the default, with <code>L1Norm</code> as an alternative option. Choosing <code>none</code> will circumvent sub-spectral alignment altogether.</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb6-1"><a href="the-osprey-job-file.html#cb6-1" aria-hidden="true" tabindex="-1"></a>opts.SubSpecAlignment.mets <span class="op">=</span> <span class="st">&#39;L2Norm&#39;</span><span class="op">;</span>          <span class="co">% OPTIONS:    - &#39;L2Norm&#39; (default)</span></span>
-<span id="cb6-2"><a href="the-osprey-job-file.html#cb6-2" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - &#39;L1Norm&#39;</span></span>
-<span id="cb6-3"><a href="the-osprey-job-file.html#cb6-3" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - &#39;none&#39;</span></span></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb6-1"><a href="the-osprey-job-file.html#cb6-1" tabindex="-1"></a>opts.SubSpecAlignment.mets <span class="op">=</span> <span class="st">&#39;L2Norm&#39;</span><span class="op">;</span>          <span class="co">% OPTIONS:    - &#39;L2Norm&#39; (default)</span></span>
+<span id="cb6-2"><a href="the-osprey-job-file.html#cb6-2" tabindex="-1"></a>                                                <span class="co">%             - &#39;L1Norm&#39;</span></span>
+<span id="cb6-3"><a href="the-osprey-job-file.html#cb6-3" tabindex="-1"></a>                                                <span class="co">%             - &#39;none&#39;</span></span></code></pre></div>
 </div>
 <div id="eddy-current-correction" class="section level3 hasAnchor" number="4.3.3">
 <h3><span class="header-section-number">4.3.3</span> Eddy-current correction<a href="the-osprey-job-file.html#eddy-current-correction" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p><code>opts.ECC</code> specifies the data to be eddy-current corrected using a corresponding water-unsuppressed reference scan (Klose, Magn Reson Med 14:26-30 (1990)). The sub-structures <code>opts.ECC.raw</code> and <code>opts.ECC.mm</code> correspond to the raw metabolite and macromolecule spectra, respectively. <code>opts.ECC.raw</code> and <code>opts.ECC.mm</code> may be specified as 1 to apply ECC to all data, 0 to not apply ECC at all, or as a vector to apply ECC to a sub-set of the data.</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb7-1"><a href="the-osprey-job-file.html#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co">%Perform eddy-current correction on the metabolite data (raw) or metabolite</span></span>
-<span id="cb7-2"><a href="the-osprey-job-file.html#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="co">%-nulled data (mm). This can either be done similar for all data sets by</span></span>
-<span id="cb7-3"><a href="the-osprey-job-file.html#cb7-3" aria-hidden="true" tabindex="-1"></a><span class="co">%supplying a single value or specified for each dataset individually by supplying</span></span>
-<span id="cb7-4"><a href="the-osprey-job-file.html#cb7-4" aria-hidden="true" tabindex="-1"></a><span class="co">% multiple entries (number has to match the number of datasets) e.g. to perform ECC</span></span>
-<span id="cb7-5"><a href="the-osprey-job-file.html#cb7-5" aria-hidden="true" tabindex="-1"></a><span class="co">% for the second dataset only:</span></span>
-<span id="cb7-6"><a href="the-osprey-job-file.html#cb7-6" aria-hidden="true" tabindex="-1"></a><span class="co">% opts.ECC.raw               = [0 1];</span></span>
-<span id="cb7-7"><a href="the-osprey-job-file.html#cb7-7" aria-hidden="true" tabindex="-1"></a><span class="co">% opts.ECC.mm                = [0 1];</span></span>
-<span id="cb7-8"><a href="the-osprey-job-file.html#cb7-8" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb7-9"><a href="the-osprey-job-file.html#cb7-9" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb7-10"><a href="the-osprey-job-file.html#cb7-10" aria-hidden="true" tabindex="-1"></a>opts.ECC.raw                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - &#39;1&#39; (default)</span></span>
-<span id="cb7-11"><a href="the-osprey-job-file.html#cb7-11" aria-hidden="true" tabindex="-1"></a>opts.ECC.mm                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                 <span class="co">%             - &#39;0&#39; (no)</span></span>
-<span id="cb7-12"><a href="the-osprey-job-file.html#cb7-12" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - [] array</span></span></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb7-1"><a href="the-osprey-job-file.html#cb7-1" tabindex="-1"></a><span class="co">%Perform eddy-current correction on the metabolite data (raw) or metabolite</span></span>
+<span id="cb7-2"><a href="the-osprey-job-file.html#cb7-2" tabindex="-1"></a><span class="co">%-nulled data (mm). This can either be done similar for all data sets by</span></span>
+<span id="cb7-3"><a href="the-osprey-job-file.html#cb7-3" tabindex="-1"></a><span class="co">%supplying a single value or specified for each dataset individually by supplying</span></span>
+<span id="cb7-4"><a href="the-osprey-job-file.html#cb7-4" tabindex="-1"></a><span class="co">% multiple entries (number has to match the number of datasets) e.g. to perform ECC</span></span>
+<span id="cb7-5"><a href="the-osprey-job-file.html#cb7-5" tabindex="-1"></a><span class="co">% for the second dataset only:</span></span>
+<span id="cb7-6"><a href="the-osprey-job-file.html#cb7-6" tabindex="-1"></a><span class="co">% opts.ECC.raw               = [0 1];</span></span>
+<span id="cb7-7"><a href="the-osprey-job-file.html#cb7-7" tabindex="-1"></a><span class="co">% opts.ECC.mm                = [0 1];</span></span>
+<span id="cb7-8"><a href="the-osprey-job-file.html#cb7-8" tabindex="-1"></a></span>
+<span id="cb7-9"><a href="the-osprey-job-file.html#cb7-9" tabindex="-1"></a></span>
+<span id="cb7-10"><a href="the-osprey-job-file.html#cb7-10" tabindex="-1"></a>opts.ECC.raw                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - &#39;1&#39; (default)</span></span>
+<span id="cb7-11"><a href="the-osprey-job-file.html#cb7-11" tabindex="-1"></a>opts.ECC.mm                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                 <span class="co">%             - &#39;0&#39; (no)</span></span>
+<span id="cb7-12"><a href="the-osprey-job-file.html#cb7-12" tabindex="-1"></a>                                                <span class="co">%             - [] array</span></span></code></pre></div>
 </div>
 <div id="saving-data-to-external-formats" class="section level3 hasAnchor" number="4.3.4">
 <h3><span class="header-section-number">4.3.4</span> Saving data to external formats<a href="the-osprey-job-file.html#saving-data-to-external-formats" class="anchor-section" aria-label="Anchor link to header"></a></h3>
@@ -639,39 +643,39 @@ <h3><span class="header-section-number">4.3.4</span> Saving data to external for
 By setting <code>opts.saveVendor</code> to <code>1</code>, single vendor-specific files are created, i.e. <code>.SDAT/.SPAR</code> files for Philips data, and <code>.RDA</code> files for Siemens data, regardless of the raw data format.<br />
 By setting <code>opts.saveNII</code> to <code>1</code>, processed spectra are produced in the NIfTI-MRS format.<br />
 By setting <code>opts.savePDF</code> to <code>1</code>, PDF summaries are produced for all subjects after running each module.</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb8-1"><a href="the-osprey-job-file.html#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Save LCModel-exportable files for each spectrum?</span></span>
-<span id="cb8-2"><a href="the-osprey-job-file.html#cb8-2" aria-hidden="true" tabindex="-1"></a>opts.saveLCM                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb8-3"><a href="the-osprey-job-file.html#cb8-3" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb8-4"><a href="the-osprey-job-file.html#cb8-4" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb8-5"><a href="the-osprey-job-file.html#cb8-5" aria-hidden="true" tabindex="-1"></a><span class="co">% Save jMRUI-exportable files for each spectrum?</span></span>
-<span id="cb8-6"><a href="the-osprey-job-file.html#cb8-6" aria-hidden="true" tabindex="-1"></a>opts.savejMRUI              <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb8-7"><a href="the-osprey-job-file.html#cb8-7" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb8-8"><a href="the-osprey-job-file.html#cb8-8" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb8-9"><a href="the-osprey-job-file.html#cb8-9" aria-hidden="true" tabindex="-1"></a><span class="co">% Save processed spectra in vendor-specific format (SDAT/SPAR, RDA, P)?</span></span>
-<span id="cb8-10"><a href="the-osprey-job-file.html#cb8-10" aria-hidden="true" tabindex="-1"></a>opts.saveVendor             <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb8-11"><a href="the-osprey-job-file.html#cb8-11" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb8-12"><a href="the-osprey-job-file.html#cb8-12" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb8-13"><a href="the-osprey-job-file.html#cb8-13" aria-hidden="true" tabindex="-1"></a><span class="co">% Save processed spectra in NIfTI-MRS format?</span></span>
-<span id="cb8-14"><a href="the-osprey-job-file.html#cb8-14" aria-hidden="true" tabindex="-1"></a>opts.saveNII                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb8-15"><a href="the-osprey-job-file.html#cb8-15" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
-<span id="cb8-16"><a href="the-osprey-job-file.html#cb8-16" aria-hidden="true" tabindex="-1"></a>                                                </span>
-<span id="cb8-17"><a href="the-osprey-job-file.html#cb8-17" aria-hidden="true" tabindex="-1"></a><span class="co">% Save PDF output for all Osprey modules and subjects?</span></span>
-<span id="cb8-18"><a href="the-osprey-job-file.html#cb8-18" aria-hidden="true" tabindex="-1"></a>opts.savePDF                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
-<span id="cb8-19"><a href="the-osprey-job-file.html#cb8-19" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span></code></pre></div>
+<div class="sourceCode" id="cb8"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb8-1"><a href="the-osprey-job-file.html#cb8-1" tabindex="-1"></a><span class="co">% Save LCModel-exportable files for each spectrum?</span></span>
+<span id="cb8-2"><a href="the-osprey-job-file.html#cb8-2" tabindex="-1"></a>opts.saveLCM                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb8-3"><a href="the-osprey-job-file.html#cb8-3" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb8-4"><a href="the-osprey-job-file.html#cb8-4" tabindex="-1"></a></span>
+<span id="cb8-5"><a href="the-osprey-job-file.html#cb8-5" tabindex="-1"></a><span class="co">% Save jMRUI-exportable files for each spectrum?</span></span>
+<span id="cb8-6"><a href="the-osprey-job-file.html#cb8-6" tabindex="-1"></a>opts.savejMRUI              <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb8-7"><a href="the-osprey-job-file.html#cb8-7" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb8-8"><a href="the-osprey-job-file.html#cb8-8" tabindex="-1"></a></span>
+<span id="cb8-9"><a href="the-osprey-job-file.html#cb8-9" tabindex="-1"></a><span class="co">% Save processed spectra in vendor-specific format (SDAT/SPAR, RDA, P)?</span></span>
+<span id="cb8-10"><a href="the-osprey-job-file.html#cb8-10" tabindex="-1"></a>opts.saveVendor             <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb8-11"><a href="the-osprey-job-file.html#cb8-11" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb8-12"><a href="the-osprey-job-file.html#cb8-12" tabindex="-1"></a></span>
+<span id="cb8-13"><a href="the-osprey-job-file.html#cb8-13" tabindex="-1"></a><span class="co">% Save processed spectra in NIfTI-MRS format?</span></span>
+<span id="cb8-14"><a href="the-osprey-job-file.html#cb8-14" tabindex="-1"></a>opts.saveNII                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb8-15"><a href="the-osprey-job-file.html#cb8-15" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span>
+<span id="cb8-16"><a href="the-osprey-job-file.html#cb8-16" tabindex="-1"></a>                                                </span>
+<span id="cb8-17"><a href="the-osprey-job-file.html#cb8-17" tabindex="-1"></a><span class="co">% Save PDF output for all Osprey modules and subjects?</span></span>
+<span id="cb8-18"><a href="the-osprey-job-file.html#cb8-18" tabindex="-1"></a>opts.savePDF                <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no, default)</span></span>
+<span id="cb8-19"><a href="the-osprey-job-file.html#cb8-19" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes)</span></span></code></pre></div>
 <p>LCModel <code>.RAW</code> files can be loaded via the <code>Other</code> option in the LCModel file type selection menu.</p>
 <p>Please be aware that LCModel may prompt you to enter the number of FID data points (a positive integer number, e.g. <code>2048</code>), dwell time (in seconds, e.g. <code>0.0005</code>), and the static magnetic field strength in MHz (e.g. <code>123.26</code> for a Siemens 2.89 T magnet).</p>
 <p>In addition to the <code>.RAW</code> files, Osprey also creates the corresponding <code>.CONTROL</code> files. These files can be used for LCModel batch processing.</p>
-<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href="the-osprey-job-file.html#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> file <span class="kw">in</span> /storage/LCModelControlFiles/<span class="pp">*</span><span class="kw">;</span></span>
-<span id="cb9-2"><a href="the-osprey-job-file.html#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="cf">do</span> <span class="ex">/usr/local/.lcmodel/bin/lcmodel</span> <span class="op">&lt;</span> <span class="va">$file</span><span class="kw">;</span></span>
-<span id="cb9-3"><a href="the-osprey-job-file.html#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="cf">done</span> </span></code></pre></div>
+<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href="the-osprey-job-file.html#cb9-1" tabindex="-1"></a><span class="cf">for</span> file <span class="kw">in</span> /storage/LCModelControlFiles/<span class="pp">*</span><span class="kw">;</span></span>
+<span id="cb9-2"><a href="the-osprey-job-file.html#cb9-2" tabindex="-1"></a><span class="cf">do</span> <span class="ex">/usr/local/.lcmodel/bin/lcmodel</span> <span class="op">&lt;</span> <span class="va">$file</span><span class="kw">;</span></span>
+<span id="cb9-3"><a href="the-osprey-job-file.html#cb9-3" tabindex="-1"></a><span class="cf">done</span> </span></code></pre></div>
 
 <div class="rmdimportant">
 To create working <code>.CONTROL</code> files you have to specify the following mandatory variables in the <code>osp_lcmcontrol_params()</code> function located in the process folder: <code>key</code>, <code>FILBAS</code>, <code>FOLDER</code>, and <code>DOECC</code>.
 </div>
-<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="the-osprey-job-file.html#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="ex">key</span> = 0<span class="kw">;</span> <span class="ex">%Your</span> LCM key goes here</span>
-<span id="cb10-2"><a href="the-osprey-job-file.html#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="ex">FILBAS</span> = <span class="st">&#39;/storage/myBasisSet_30ms_PRESS.BASIS&#39;</span><span class="kw">;</span> <span class="ex">%</span> Location of .BASIS file used in LCModel</span>
-<span id="cb10-3"><a href="the-osprey-job-file.html#cb10-3" aria-hidden="true" tabindex="-1"></a><span class="ex">FOLDER</span> = <span class="st">&#39;/storage/LCMoutput&#39;</span><span class="kw">;</span> <span class="ex">%Output</span> folder <span class="er">(</span><span class="ex">Create</span> this on your linux machine first<span class="kw">)</span></span>
-<span id="cb10-4"><a href="the-osprey-job-file.html#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="va">DOECC</span><span class="op">=</span> <span class="st">&#39;F&#39;</span><span class="kw">;</span> <span class="ex">%</span> No eddy current correction in LCModel as this is already performed in Osprey.</span></code></pre></div>
+<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="the-osprey-job-file.html#cb10-1" tabindex="-1"></a><span class="ex">key</span> = 0<span class="kw">;</span> <span class="ex">%Your</span> LCM key goes here</span>
+<span id="cb10-2"><a href="the-osprey-job-file.html#cb10-2" tabindex="-1"></a><span class="ex">FILBAS</span> = <span class="st">&#39;/storage/myBasisSet_30ms_PRESS.BASIS&#39;</span><span class="kw">;</span> <span class="ex">%</span> Location of .BASIS file used in LCModel</span>
+<span id="cb10-3"><a href="the-osprey-job-file.html#cb10-3" tabindex="-1"></a><span class="ex">FOLDER</span> = <span class="st">&#39;/storage/LCMoutput&#39;</span><span class="kw">;</span> <span class="ex">%Output</span> folder <span class="er">(</span><span class="ex">Create</span> this on your linux machine first<span class="kw">)</span></span>
+<span id="cb10-4"><a href="the-osprey-job-file.html#cb10-4" tabindex="-1"></a><span class="va">DOECC</span><span class="op">=</span> <span class="st">&#39;F&#39;</span><span class="kw">;</span> <span class="ex">%</span> No eddy current correction in LCModel as this is already performed in Osprey.</span></code></pre></div>
 
 <div class="rmdnote">
 The other parameters are optional and are described in the <code>osp_lcmcontrol_params()</code> function.
@@ -680,78 +684,78 @@ <h3><span class="header-section-number">4.3.4</span> Saving data to external for
 <p>The <code>opts.saveVendor</code> switch has been introduced to sidestep these problems with <code>.RAW</code> and <code>.TXT</code> files. LCModel, TARQUIN and jMRUI accept the <code>.SDAT/.SPAR</code> and <code>.RDA</code> file formats, and should be able to read the header information correctly.</p>
 <p>All exported third-party format files are stored in sub-directories of the output folder specified further down in the job file.</p>
 </div>
-<div id="matbolites-included-in-the-basis-set" class="section level3 hasAnchor" number="4.3.5">
-<h3><span class="header-section-number">4.3.5</span> Matbolites included in the basis-set<a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set" class="anchor-section" aria-label="Anchor link to header"></a></h3>
+<div id="metabolites-included-in-the-basis-set" class="section level3 hasAnchor" number="4.3.5">
+<h3><span class="header-section-number">4.3.5</span> Metabolites included in the basis-set<a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p><code>opts.fit.includeMetabs</code> can be used to specify a custom set of metabolites to be included in the fitting. By default, all of the metabolites listed below are included, but a subset may be specified as a cell array of strings:
 <code>opts.fit.includeMetabs = {Cr, CrCH2, GABA, PCr,...}</code></p>
-<div class="sourceCode" id="cb11"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb11-1"><a href="the-osprey-job-file.html#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Select the metabolites to be included in the basis set as a cell array,</span></span>
-<span id="cb11-2"><a href="the-osprey-job-file.html#cb11-2" aria-hidden="true" tabindex="-1"></a><span class="co">% with entries separates by commas.</span></span>
-<span id="cb11-3"><a href="the-osprey-job-file.html#cb11-3" aria-hidden="true" tabindex="-1"></a><span class="co">% With default Osprey basis sets, you can select the following metabolites:</span></span>
-<span id="cb11-4"><a href="the-osprey-job-file.html#cb11-4" aria-hidden="true" tabindex="-1"></a><span class="co">% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,</span></span>
-<span id="cb11-5"><a href="the-osprey-job-file.html#cb11-5" aria-hidden="true" tabindex="-1"></a><span class="co">% Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,</span></span>
-<span id="cb11-6"><a href="the-osprey-job-file.html#cb11-6" aria-hidden="true" tabindex="-1"></a><span class="co">% Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.</span></span>
-<span id="cb11-7"><a href="the-osprey-job-file.html#cb11-7" aria-hidden="true" tabindex="-1"></a><span class="co">% If you enter &#39;default&#39;, the basis set will include all of the above</span></span>
-<span id="cb11-8"><a href="the-osprey-job-file.html#cb11-8" aria-hidden="true" tabindex="-1"></a><span class="co">% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.</span></span>
-<span id="cb11-9"><a href="the-osprey-job-file.html#cb11-9" aria-hidden="true" tabindex="-1"></a>opts.fit.includeMetabs      <span class="op">=</span> {<span class="st">&#39;default&#39;</span>}<span class="op">;</span>      <span class="co">% OPTIONS:    - {&#39;default&#39;}</span></span>
-<span id="cb11-10"><a href="the-osprey-job-file.html#cb11-10" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - {custom}</span></span></code></pre></div>
+<div class="sourceCode" id="cb11"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb11-1"><a href="the-osprey-job-file.html#cb11-1" tabindex="-1"></a><span class="co">% Select the metabolites to be included in the basis set as a cell array,</span></span>
+<span id="cb11-2"><a href="the-osprey-job-file.html#cb11-2" tabindex="-1"></a><span class="co">% with entries separates by commas.</span></span>
+<span id="cb11-3"><a href="the-osprey-job-file.html#cb11-3" tabindex="-1"></a><span class="co">% With default Osprey basis sets, you can select the following metabolites:</span></span>
+<span id="cb11-4"><a href="the-osprey-job-file.html#cb11-4" tabindex="-1"></a><span class="co">% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,</span></span>
+<span id="cb11-5"><a href="the-osprey-job-file.html#cb11-5" tabindex="-1"></a><span class="co">% Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,</span></span>
+<span id="cb11-6"><a href="the-osprey-job-file.html#cb11-6" tabindex="-1"></a><span class="co">% Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.</span></span>
+<span id="cb11-7"><a href="the-osprey-job-file.html#cb11-7" tabindex="-1"></a><span class="co">% If you enter &#39;default&#39;, the basis set will include all of the above</span></span>
+<span id="cb11-8"><a href="the-osprey-job-file.html#cb11-8" tabindex="-1"></a><span class="co">% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.</span></span>
+<span id="cb11-9"><a href="the-osprey-job-file.html#cb11-9" tabindex="-1"></a>opts.fit.includeMetabs      <span class="op">=</span> {<span class="st">&#39;default&#39;</span>}<span class="op">;</span>      <span class="co">% OPTIONS:    - {&#39;default&#39;}</span></span>
+<span id="cb11-10"><a href="the-osprey-job-file.html#cb11-10" tabindex="-1"></a>                                                <span class="co">%             - {custom}</span></span></code></pre></div>
 <p><code>opts.fit.basisSetFile</code> may be manually specified to bypass the Osprey automatic selction, or to specify an alternative. <code>opts.fit.basisSetFile</code> is a string specifying the path to the basis set stored in FID-A format.</p>
-<div class="sourceCode" id="cb12"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb12-1"><a href="the-osprey-job-file.html#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Optional: In case the automatic basisset picker is not working you can manually</span></span>
-<span id="cb12-2"><a href="the-osprey-job-file.html#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="co">% select the path to the basis set in the osprey/fit/basis, i.e.:</span></span>
-<span id="cb12-3"><a href="the-osprey-job-file.html#cb12-3" aria-hidden="true" tabindex="-1"></a><span class="co">% opts.fit.basisSetFile = &#39;osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat&#39;;</span></span>
-<span id="cb12-4"><a href="the-osprey-job-file.html#cb12-4" aria-hidden="true" tabindex="-1"></a><span class="co">### Specifying modelling algorithm</span></span></code></pre></div>
+<div class="sourceCode" id="cb12"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb12-1"><a href="the-osprey-job-file.html#cb12-1" tabindex="-1"></a><span class="co">% Optional: In case the automatic basisset picker is not working you can manually</span></span>
+<span id="cb12-2"><a href="the-osprey-job-file.html#cb12-2" tabindex="-1"></a><span class="co">% select the path to the basis set in the osprey/fit/basis, i.e.:</span></span>
+<span id="cb12-3"><a href="the-osprey-job-file.html#cb12-3" tabindex="-1"></a><span class="co">% opts.fit.basisSetFile = &#39;osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat&#39;;</span></span>
+<span id="cb12-4"><a href="the-osprey-job-file.html#cb12-4" tabindex="-1"></a><span class="co">### Specifying modelling algorithm</span></span></code></pre></div>
 <p>The <code>opts.fit.method</code> variable set determines the modeling algorithm used to fit the processed spectra. The default is to use the Osprey method, as described in the <a href="(https://doi.org/10.1016/j.jneumeth.2020.108827)">publication</a>, but Osprey can also utilize LCModel for fitting. If <code>LCModel</code> is specified, Osprey will generate .RAW files of the processed spectra, populate minimal control files, and read the outputs back into the Matlab container.</p>
-<div class="sourceCode" id="cb13"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb13-1"><a href="the-osprey-job-file.html#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Choose the fitting algorithm</span></span>
-<span id="cb13-2"><a href="the-osprey-job-file.html#cb13-2" aria-hidden="true" tabindex="-1"></a>opts.fit.method             <span class="op">=</span> <span class="st">&#39;Osprey&#39;</span><span class="op">;</span>         <span class="co">% OPTIONS:    - &#39;Osprey&#39; (default)</span></span>
-<span id="cb13-3"><a href="the-osprey-job-file.html#cb13-3" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - &#39;LCModel&#39;</span></span></code></pre></div>
+<div class="sourceCode" id="cb13"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb13-1"><a href="the-osprey-job-file.html#cb13-1" tabindex="-1"></a><span class="co">% Choose the fitting algorithm</span></span>
+<span id="cb13-2"><a href="the-osprey-job-file.html#cb13-2" tabindex="-1"></a>opts.fit.method             <span class="op">=</span> <span class="st">&#39;Osprey&#39;</span><span class="op">;</span>         <span class="co">% OPTIONS:    - &#39;Osprey&#39; (default)</span></span>
+<span id="cb13-3"><a href="the-osprey-job-file.html#cb13-3" tabindex="-1"></a>                                                <span class="co">%             - &#39;LCModel&#39;</span></span></code></pre></div>
 </div>
 <div id="lcmodel-specific-options" class="section level3 hasAnchor" number="4.3.6">
 <h3><span class="header-section-number">4.3.6</span> LCModel-specific options<a href="the-osprey-job-file.html#lcmodel-specific-options" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>If LCModel is used as a method, further options may be specified. <code>opts.fit.basisSetFile</code>is a string specifying the path to a basis file. <code>opts.fit.controlFile</code> is a string specifying the path to a control file. File-specific entries of the control file will be populated by Osprey, allowing you to simply specify a generic control file template.</p>
-<div class="sourceCode" id="cb14"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb14-1"><a href="the-osprey-job-file.html#cb14-1" aria-hidden="true" tabindex="-1"></a>opts.fit.basisSetFile   <span class="op">=</span> <span class="st">&#39;/storage/LCModelBasisFiles/MyBasis.basis&#39;</span><span class="op">;</span></span>
-<span id="cb14-2"><a href="the-osprey-job-file.html#cb14-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb14-3"><a href="the-osprey-job-file.html#cb14-3" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify LCModel-type control file (.CONTROL)</span></span>
-<span id="cb14-4"><a href="the-osprey-job-file.html#cb14-4" aria-hidden="true" tabindex="-1"></a><span class="co">% This is optional: If you leave this field blank, Osprey will create a</span></span>
-<span id="cb14-5"><a href="the-osprey-job-file.html#cb14-5" aria-hidden="true" tabindex="-1"></a><span class="co">% minimum control file for you.</span></span>
-<span id="cb14-6"><a href="the-osprey-job-file.html#cb14-6" aria-hidden="true" tabindex="-1"></a>opts.fit.controlFile    <span class="op">=</span> <span class="st">&#39;/storage/LCModelControlFiles/MyControl.control&#39;</span>)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb14"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb14-1"><a href="the-osprey-job-file.html#cb14-1" tabindex="-1"></a>opts.fit.basisSetFile   <span class="op">=</span> <span class="st">&#39;/storage/LCModelBasisFiles/MyBasis.basis&#39;</span><span class="op">;</span></span>
+<span id="cb14-2"><a href="the-osprey-job-file.html#cb14-2" tabindex="-1"></a></span>
+<span id="cb14-3"><a href="the-osprey-job-file.html#cb14-3" tabindex="-1"></a><span class="co">% Specify LCModel-type control file (.CONTROL)</span></span>
+<span id="cb14-4"><a href="the-osprey-job-file.html#cb14-4" tabindex="-1"></a><span class="co">% This is optional: If you leave this field blank, Osprey will create a</span></span>
+<span id="cb14-5"><a href="the-osprey-job-file.html#cb14-5" tabindex="-1"></a><span class="co">% minimum control file for you.</span></span>
+<span id="cb14-6"><a href="the-osprey-job-file.html#cb14-6" tabindex="-1"></a>opts.fit.controlFile    <span class="op">=</span> <span class="st">&#39;/storage/LCModelControlFiles/MyControl.control&#39;</span>)<span class="op">;</span></span></code></pre></div>
 </div>
 <div id="fit-style" class="section level3 hasAnchor" number="4.3.7">
 <h3><span class="header-section-number">4.3.7</span> Fit style<a href="the-osprey-job-file.html#fit-style" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>opts.fit.style</code> variable set determines how difference-edited data are modeled.</p>
 <p>By setting <code>opts.fit.style</code> to <code>Concatenated</code>, the difference and sum spectra in MEGA, HERMES and HERCULES datasets will be modeled simultaneously, i.e. with common metabolite amplitude parameters across these spectra.
 By setting <code>opts.fit.style</code> to <code>Separate</code>, the difference and edit-OFF spectra in MEGA, HERMES and HERCULES datasets will be modeled independently. In this case, the creatine reference signal will be determined from the edit-OFF spectrum.</p>
-<div class="sourceCode" id="cb15"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb15-1"><a href="the-osprey-job-file.html#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Choose the fitting style for difference-edited datasets (MEGA, HERMES, HERCULES)</span></span>
-<span id="cb15-2"><a href="the-osprey-job-file.html#cb15-2" aria-hidden="true" tabindex="-1"></a><span class="co">% (only available for the Osprey fitting method)</span></span>
-<span id="cb15-3"><a href="the-osprey-job-file.html#cb15-3" aria-hidden="true" tabindex="-1"></a>opts.fit.style              <span class="op">=</span> <span class="st">&#39;Concatenated&#39;</span><span class="op">;</span>   <span class="co">% OPTIONS:  - &#39;Concatenated&#39; (default) - will fit DIFF and SUM simultaneously)</span></span>
-<span id="cb15-4"><a href="the-osprey-job-file.html#cb15-4" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%           - &#39;Separate&#39; - will fit DIFF and OFF separately</span></span></code></pre></div>
+<div class="sourceCode" id="cb15"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb15-1"><a href="the-osprey-job-file.html#cb15-1" tabindex="-1"></a><span class="co">% Choose the fitting style for difference-edited datasets (MEGA, HERMES, HERCULES)</span></span>
+<span id="cb15-2"><a href="the-osprey-job-file.html#cb15-2" tabindex="-1"></a><span class="co">% (only available for the Osprey fitting method)</span></span>
+<span id="cb15-3"><a href="the-osprey-job-file.html#cb15-3" tabindex="-1"></a>opts.fit.style              <span class="op">=</span> <span class="st">&#39;Concatenated&#39;</span><span class="op">;</span>   <span class="co">% OPTIONS:  - &#39;Concatenated&#39; (default) - will fit DIFF and SUM simultaneously)</span></span>
+<span id="cb15-4"><a href="the-osprey-job-file.html#cb15-4" tabindex="-1"></a>                                                <span class="co">%           - &#39;Separate&#39; - will fit DIFF and OFF separately</span></span></code></pre></div>
 </div>
 <div id="fitting-range" class="section level3 hasAnchor" number="4.3.8">
 <h3><span class="header-section-number">4.3.8</span> Fitting range<a href="the-osprey-job-file.html#fitting-range" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>opts.fit.range</code> and <code>opts.fit.rangeWater</code> variables determine the fitting range (in ppm) of the metabolite and water spectra, respectively.</p>
-<div class="sourceCode" id="cb16"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb16-1"><a href="the-osprey-job-file.html#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Determine fitting range (in ppm) for the metabolite and water spectra</span></span>
-<span id="cb16-2"><a href="the-osprey-job-file.html#cb16-2" aria-hidden="true" tabindex="-1"></a>opts.fit.range              <span class="op">=</span> [<span class="fl">0.5</span> <span class="fl">4</span>]<span class="op">;</span>          <span class="co">% [ppm] Default: [0.5 4]</span></span>
-<span id="cb16-3"><a href="the-osprey-job-file.html#cb16-3" aria-hidden="true" tabindex="-1"></a>opts.fit.rangeWater         <span class="op">=</span> [<span class="fl">2.0</span> <span class="fl">7.4</span>]<span class="op">;</span>        <span class="co">% [ppm] Default: [2.0 7.4]</span></span></code></pre></div>
+<div class="sourceCode" id="cb16"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb16-1"><a href="the-osprey-job-file.html#cb16-1" tabindex="-1"></a><span class="co">% Determine fitting range (in ppm) for the metabolite and water spectra</span></span>
+<span id="cb16-2"><a href="the-osprey-job-file.html#cb16-2" tabindex="-1"></a>opts.fit.range              <span class="op">=</span> [<span class="fl">0.5</span> <span class="fl">4</span>]<span class="op">;</span>          <span class="co">% [ppm] Default: [0.5 4]</span></span>
+<span id="cb16-3"><a href="the-osprey-job-file.html#cb16-3" tabindex="-1"></a>opts.fit.rangeWater         <span class="op">=</span> [<span class="fl">2.0</span> <span class="fl">7.4</span>]<span class="op">;</span>        <span class="co">% [ppm] Default: [2.0 7.4]</span></span></code></pre></div>
 <p>The <code>opts.fit.GAP</code> option specifies a range (in ppm) to be excluded from the fitting of specified sub-spectra. The input is a vector specifying the upper and lower bounds of the range.</p>
-<div class="sourceCode" id="cb17"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb17-1"><a href="the-osprey-job-file.html#cb17-1" aria-hidden="true" tabindex="-1"></a>opts.fit.GAP.A              <span class="op">=</span> []<span class="op">;</span></span>
-<span id="cb17-2"><a href="the-osprey-job-file.html#cb17-2" aria-hidden="true" tabindex="-1"></a>opts.fit.GAP.diff1          <span class="op">=</span> []<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb17"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb17-1"><a href="the-osprey-job-file.html#cb17-1" tabindex="-1"></a>opts.fit.GAP.A              <span class="op">=</span> []<span class="op">;</span></span>
+<span id="cb17-2"><a href="the-osprey-job-file.html#cb17-2" tabindex="-1"></a>opts.fit.GAP.diff1          <span class="op">=</span> []<span class="op">;</span></span></code></pre></div>
 </div>
 <div id="baseline-knot-spacing" class="section level3 hasAnchor" number="4.3.9">
 <h3><span class="header-section-number">4.3.9</span> Baseline knot spacing<a href="the-osprey-job-file.html#baseline-knot-spacing" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>opts.fit.bLineKnotSpace</code> variable determines the spacing (in ppm) between two adjacent knots of the cubic B-spline baseline. This parameter is equivalent to the <code>DKNTMN</code> parameter in LCModel.</p>
 <p>Higher values correspond to a stiffer baseline, while lower values will produce a larger number of spline knots, allowing for greater flexibility of the baseline.</p>
-<div class="sourceCode" id="cb18"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb18-1"><a href="the-osprey-job-file.html#cb18-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Determine the baseline knot spacing (in ppm) for the metabolite spectra</span></span>
-<span id="cb18-2"><a href="the-osprey-job-file.html#cb18-2" aria-hidden="true" tabindex="-1"></a>opts.fit.bLineKnotSpace     <span class="op">=</span> <span class="fl">0.4</span><span class="op">;</span>              <span class="co">% [ppm] Default: 0.4.</span></span></code></pre></div>
+<div class="sourceCode" id="cb18"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb18-1"><a href="the-osprey-job-file.html#cb18-1" tabindex="-1"></a><span class="co">% Determine the baseline knot spacing (in ppm) for the metabolite spectra</span></span>
+<span id="cb18-2"><a href="the-osprey-job-file.html#cb18-2" tabindex="-1"></a>opts.fit.bLineKnotSpace     <span class="op">=</span> <span class="fl">0.4</span><span class="op">;</span>              <span class="co">% [ppm] Default: 0.4.</span></span></code></pre></div>
 <p>Choosing lower values for the <code>bLineKnotSpace</code> variable will improve the fit quality at the expense of overparametrization of the model. LCModel uses a default knot spacing of <code>DKNTMN = 0.15</code>, i.e. 0.15 ppm, which likely allows too much flexibility. In the absence of baseline regularization in the current stage of the <strong>Osprey</strong> model development, we chose to restrict baseline flexibility by opting for a default value of 0.4 ppm.</p>
 </div>
 <div id="macromolecule-and-lipid-signals" class="section level3 hasAnchor" number="4.3.10">
 <h3><span class="header-section-number">4.3.10</span> Macromolecule and lipid signals<a href="the-osprey-job-file.html#macromolecule-and-lipid-signals" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>opts.fit.fitMM</code> variable determines whether simulated Gaussian signals representing broad macromolecular and lipid signals are included in the basis set.</p>
 <p>By default, <strong>Osprey</strong> includes these basis functions. If you want to use an experimentally measured MM/lipid basis function, or operate at long echo times where the MM and lipid resonances have decayed, you can set <code>opts.fit.fitMM = 0</code> to exclude them.</p>
-<div class="sourceCode" id="cb19"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb19-1"><a href="the-osprey-job-file.html#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Add macromolecule and lipid basis functions to the fit?</span></span>
-<span id="cb19-2"><a href="the-osprey-job-file.html#cb19-2" aria-hidden="true" tabindex="-1"></a>opts.fit.fitMM              <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no)</span></span>
-<span id="cb19-3"><a href="the-osprey-job-file.html#cb19-3" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes, default)</span></span></code></pre></div>
+<div class="sourceCode" id="cb19"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb19-1"><a href="the-osprey-job-file.html#cb19-1" tabindex="-1"></a><span class="co">% Add macromolecule and lipid basis functions to the fit?</span></span>
+<span id="cb19-2"><a href="the-osprey-job-file.html#cb19-2" tabindex="-1"></a>opts.fit.fitMM              <span class="op">=</span> <span class="fl">1</span><span class="op">;</span>                <span class="co">% OPTIONS:    - 0 (no)</span></span>
+<span id="cb19-3"><a href="the-osprey-job-file.html#cb19-3" tabindex="-1"></a>                                                <span class="co">%             - 1 (yes, default)</span></span></code></pre></div>
 </div>
-<div id="co-edited-macrommolecules" class="section level3 hasAnchor" number="4.3.11">
-<h3><span class="header-section-number">4.3.11</span> Co-edited macrommolecules<a href="the-osprey-job-file.html#co-edited-macrommolecules" class="anchor-section" aria-label="Anchor link to header"></a></h3>
+<div id="co-edited-macromolecules" class="section level3 hasAnchor" number="4.3.11">
+<h3><span class="header-section-number">4.3.11</span> Co-edited macromolecules<a href="the-osprey-job-file.html#co-edited-macromolecules" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p><code>opts.fit.coMM3</code> specifies the approach to modeling the co-edited macromolecule resonance at 3ppm for GABA-edited MRS experiments. By default a 14 Hz Gaussian peak is used as basis function. the options are as follows:
 1. <code>3to2MM</code> - uses a fixed 3 to 2 amplitude ratio between the 0.93-ppm-MM peak and the co-edited 3.0-ppm-MM peak by generating a single composite basis function
 2. <code>3to2MMsoft</code> - uses a soft constraints during the modeling to enforce 3 to 2 amplitude ratio between the 0.93-ppm-MM peak and the co-edited 3.0-ppm-MM peak
@@ -760,14 +764,14 @@ <h3><span class="header-section-number">4.3.11</span> Co-edited macrommolecules<
 5. <code>freeGauss</code> - uses a separate basis function for the co-edited 3.0-ppm-MM peak with an initial 14 Hz FWHM of the Gaussian basis function
 6. <code>fixedGauss</code> - uses a separate basis function for the co-edited 3.0-ppm-MM peak, however, the FWHM of the Gaussian basis function is optimized during the modeling process
 7. <code>none</code> - uses no MM basis function for the co-edited 3.0-ppm MM in the difference spectrum.</p>
-<div class="sourceCode" id="cb20"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb20-1"><a href="the-osprey-job-file.html#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="co">% How do you want to model the co-edited macromolecules at 3 ppm for GABA-edited MRS?</span></span>
-<span id="cb20-2"><a href="the-osprey-job-file.html#cb20-2" aria-hidden="true" tabindex="-1"></a>opts.fit.coMM3              <span class="op">=</span> <span class="st">&#39;freeGauss&#39;</span><span class="op">;</span>      <span class="co">% OPTIONS:    - {&#39;3to2MM&#39;} (default)</span></span>
-<span id="cb20-3"><a href="the-osprey-job-file.html#cb20-3" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - {&#39;3to2MMsoft&#39;}</span></span>
-<span id="cb20-4"><a href="the-osprey-job-file.html#cb20-4" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - {&#39;1to1GABA&#39;}</span></span>
-<span id="cb20-5"><a href="the-osprey-job-file.html#cb20-5" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - {&#39;1to1GABAsoft&#39;}</span></span>
-<span id="cb20-6"><a href="the-osprey-job-file.html#cb20-6" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - {&#39;freeGauss&#39;}</span></span>
-<span id="cb20-7"><a href="the-osprey-job-file.html#cb20-7" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - {&#39;fixedGauss&#39;}</span></span>
-<span id="cb20-8"><a href="the-osprey-job-file.html#cb20-8" aria-hidden="true" tabindex="-1"></a>                                                <span class="co">%             - {&#39;none&#39;}</span></span></code></pre></div>
+<div class="sourceCode" id="cb20"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb20-1"><a href="the-osprey-job-file.html#cb20-1" tabindex="-1"></a><span class="co">% How do you want to model the co-edited macromolecules at 3 ppm for GABA-edited MRS?</span></span>
+<span id="cb20-2"><a href="the-osprey-job-file.html#cb20-2" tabindex="-1"></a>opts.fit.coMM3              <span class="op">=</span> <span class="st">&#39;freeGauss&#39;</span><span class="op">;</span>      <span class="co">% OPTIONS:    - {&#39;3to2MM&#39;} (default)</span></span>
+<span id="cb20-3"><a href="the-osprey-job-file.html#cb20-3" tabindex="-1"></a>                                                <span class="co">%             - {&#39;3to2MMsoft&#39;}</span></span>
+<span id="cb20-4"><a href="the-osprey-job-file.html#cb20-4" tabindex="-1"></a>                                                <span class="co">%             - {&#39;1to1GABA&#39;}</span></span>
+<span id="cb20-5"><a href="the-osprey-job-file.html#cb20-5" tabindex="-1"></a>                                                <span class="co">%             - {&#39;1to1GABAsoft&#39;}</span></span>
+<span id="cb20-6"><a href="the-osprey-job-file.html#cb20-6" tabindex="-1"></a>                                                <span class="co">%             - {&#39;freeGauss&#39;}</span></span>
+<span id="cb20-7"><a href="the-osprey-job-file.html#cb20-7" tabindex="-1"></a>                                                <span class="co">%             - {&#39;fixedGauss&#39;}</span></span>
+<span id="cb20-8"><a href="the-osprey-job-file.html#cb20-8" tabindex="-1"></a>                                                <span class="co">%             - {&#39;none&#39;}</span></span></code></pre></div>
 </div>
 </div>
 <div id="specifying-mrs-data-and-structural-imaging-files" class="section level2 hasAnchor" number="4.4">
@@ -782,15 +786,15 @@ <h2><span class="header-section-number">4.4</span> Specifying MRS data and struc
 <div id="metabolite-data" class="section level3 hasAnchor" number="4.4.1">
 <h3><span class="header-section-number">4.4.1</span> Metabolite data<a href="the-osprey-job-file.html#metabolite-data" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>files</code> variable is defined as a cell array of full paths to the raw MRS data files containing your metabolite (water-suppressed) data.</p>
-<div class="sourceCode" id="cb21"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb21-1"><a href="the-osprey-job-file.html#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify metabolite data</span></span>
-<span id="cb21-2"><a href="the-osprey-job-file.html#cb21-2" aria-hidden="true" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
-<span id="cb21-3"><a href="the-osprey-job-file.html#cb21-3" aria-hidden="true" tabindex="-1"></a>files       <span class="op">=</span> {<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-01/mrs/sub-01_press/sub-01_PRESS_35_act.sdat&#39;</span>)<span class="op">,...</span></span>
-<span id="cb21-4"><a href="the-osprey-job-file.html#cb21-4" aria-hidden="true" tabindex="-1"></a>               <span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-02/mrs/sub-02_press/sub-02_PRESS_35_act.sdat&#39;</span>)}<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb21"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb21-1"><a href="the-osprey-job-file.html#cb21-1" tabindex="-1"></a><span class="co">% Specify metabolite data</span></span>
+<span id="cb21-2"><a href="the-osprey-job-file.html#cb21-2" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
+<span id="cb21-3"><a href="the-osprey-job-file.html#cb21-3" tabindex="-1"></a>files       <span class="op">=</span> {<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-01/mrs/sub-01_press/sub-01_PRESS_35_act.sdat&#39;</span>)<span class="op">,...</span></span>
+<span id="cb21-4"><a href="the-osprey-job-file.html#cb21-4" tabindex="-1"></a>               <span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-02/mrs/sub-02_press/sub-02_PRESS_35_act.sdat&#39;</span>)}<span class="op">;</span></span></code></pre></div>
 <p>In the job files in the <code>exampledata</code> folder of the <strong>Osprey</strong> repository, the <code>which</code> function ensures that the paths are correctly defined regardless of where you put your <strong>Osprey</strong> folder. When designing your own job file, you will have to provide the full paths to your raw data, e.g.:</p>
-<div class="sourceCode" id="cb22"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb22-1"><a href="the-osprey-job-file.html#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify metabolite data</span></span>
-<span id="cb22-2"><a href="the-osprey-job-file.html#cb22-2" aria-hidden="true" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
-<span id="cb22-3"><a href="the-osprey-job-file.html#cb22-3" aria-hidden="true" tabindex="-1"></a>files       <span class="op">=</span> {<span class="st">&#39;/Users/Georg/Documents/MRSData/study-01/sub-01/mrs/sub-01_press/sub-01_PRESS_35_act.sdat&#39;</span><span class="op">,...</span></span>
-<span id="cb22-4"><a href="the-osprey-job-file.html#cb22-4" aria-hidden="true" tabindex="-1"></a>               <span class="st">&#39;/Users/Georg/Documents/MRSData/study-01/sub-02/mrs/sub-02_press/sub-02_PRESS_35_act.sdat&#39;</span><span class="op">,</span>}<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb22"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb22-1"><a href="the-osprey-job-file.html#cb22-1" tabindex="-1"></a><span class="co">% Specify metabolite data</span></span>
+<span id="cb22-2"><a href="the-osprey-job-file.html#cb22-2" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
+<span id="cb22-3"><a href="the-osprey-job-file.html#cb22-3" tabindex="-1"></a>files       <span class="op">=</span> {<span class="st">&#39;/Users/Georg/Documents/MRSData/study-01/sub-01/mrs/sub-01_press/sub-01_PRESS_35_act.sdat&#39;</span><span class="op">,...</span></span>
+<span id="cb22-4"><a href="the-osprey-job-file.html#cb22-4" tabindex="-1"></a>               <span class="st">&#39;/Users/Georg/Documents/MRSData/study-01/sub-02/mrs/sub-02_press/sub-02_PRESS_35_act.sdat&#39;</span><span class="op">,</span>}<span class="op">;</span></span></code></pre></div>
 <p>Instead of writing out the full paths explicitly, you can also create a procedure that is tailored to your local file organization, as long as you end up with a <code>files</code> cell array containing an element for each file you want to analyze.</p>
 
 <div class="rmdwarning">
@@ -802,60 +806,60 @@ <h3><span class="header-section-number">4.4.1</span> Metabolite data<a href="the
 <h3><span class="header-section-number">4.4.2</span> Lineshape reference data<a href="the-osprey-job-file.html#lineshape-reference-data" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>files_ref</code> variable is defined as a cell array of full paths to the raw MRS data files to your lineshape (water-unsuppressed) reference data.</p>
 <p>These are an optional input, acquired with the same sequence as the metabolite data, but without water suppression, and used to perform eddy-current correction of the metabolite data.</p>
-<div class="sourceCode" id="cb23"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb23-1"><a href="the-osprey-job-file.html#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify water reference data for eddy-current correction (same sequence as metabolite data!)</span></span>
-<span id="cb23-2"><a href="the-osprey-job-file.html#cb23-2" aria-hidden="true" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
-<span id="cb23-3"><a href="the-osprey-job-file.html#cb23-3" aria-hidden="true" tabindex="-1"></a><span class="co">% Leave empty for GE P-files (.7) - these include water reference data by</span></span>
-<span id="cb23-4"><a href="the-osprey-job-file.html#cb23-4" aria-hidden="true" tabindex="-1"></a><span class="co">% default.</span></span>
-<span id="cb23-5"><a href="the-osprey-job-file.html#cb23-5" aria-hidden="true" tabindex="-1"></a>files_ref   <span class="op">=</span> {<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-01/mrs/sub-01_press-ref/sub-01_PRESS_35_ref.sdat&#39;</span>)<span class="op">,...</span></span>
-<span id="cb23-6"><a href="the-osprey-job-file.html#cb23-6" aria-hidden="true" tabindex="-1"></a>               <span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-02/mrs/sub-02_press-ref/sub-02_PRESS_35_ref.sdat&#39;</span>)}<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb23"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb23-1"><a href="the-osprey-job-file.html#cb23-1" tabindex="-1"></a><span class="co">% Specify water reference data for eddy-current correction (same sequence as metabolite data!)</span></span>
+<span id="cb23-2"><a href="the-osprey-job-file.html#cb23-2" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
+<span id="cb23-3"><a href="the-osprey-job-file.html#cb23-3" tabindex="-1"></a><span class="co">% Leave empty for GE P-files (.7) - these include water reference data by</span></span>
+<span id="cb23-4"><a href="the-osprey-job-file.html#cb23-4" tabindex="-1"></a><span class="co">% default.</span></span>
+<span id="cb23-5"><a href="the-osprey-job-file.html#cb23-5" tabindex="-1"></a>files_ref   <span class="op">=</span> {<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-01/mrs/sub-01_press-ref/sub-01_PRESS_35_ref.sdat&#39;</span>)<span class="op">,...</span></span>
+<span id="cb23-6"><a href="the-osprey-job-file.html#cb23-6" tabindex="-1"></a>               <span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-02/mrs/sub-02_press-ref/sub-02_PRESS_35_ref.sdat&#39;</span>)}<span class="op">;</span></span></code></pre></div>
 <p>If only lineshape reference data are provided, this signal is also used to calculate water-scaled concentration estimates.</p>
 </div>
 <div id="short-te-water-data" class="section level3 hasAnchor" number="4.4.3">
 <h3><span class="header-section-number">4.4.3</span> Short-TE water data<a href="the-osprey-job-file.html#short-te-water-data" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>files_w</code> variable is defined as a cell array of full paths to the raw MRS data files to short-TE water data.</p>
 <p>These are another optional input, and can be used to derive water-scaled concentration estimates (while lineshape reference data are only used for eddy-current correction). Using short-TE water as the concentration reference standard reduces T2-weighting of the water reference signal (and associated correction errors) compared to long-TE water data.</p>
-<div class="sourceCode" id="cb24"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb24-1"><a href="the-osprey-job-file.html#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify water data for quantification (e.g. short-TE water scan)</span></span>
-<span id="cb24-2"><a href="the-osprey-job-file.html#cb24-2" aria-hidden="true" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
-<span id="cb24-3"><a href="the-osprey-job-file.html#cb24-3" aria-hidden="true" tabindex="-1"></a>files_w     <span class="op">=</span> {<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-01/mrs/sub-01_press-ref/sub-01_PRESS_35_ref.sdat&#39;</span>)<span class="op">,...</span></span>
-<span id="cb24-4"><a href="the-osprey-job-file.html#cb24-4" aria-hidden="true" tabindex="-1"></a>               <span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-02/mrs/sub-02_press-ref/sub-02_PRESS_35_ref.sdat&#39;</span>)}<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb24"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb24-1"><a href="the-osprey-job-file.html#cb24-1" tabindex="-1"></a><span class="co">% Specify water data for quantification (e.g. short-TE water scan)</span></span>
+<span id="cb24-2"><a href="the-osprey-job-file.html#cb24-2" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
+<span id="cb24-3"><a href="the-osprey-job-file.html#cb24-3" tabindex="-1"></a>files_w     <span class="op">=</span> {<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-01/mrs/sub-01_press-ref/sub-01_PRESS_35_ref.sdat&#39;</span>)<span class="op">,...</span></span>
+<span id="cb24-4"><a href="the-osprey-job-file.html#cb24-4" tabindex="-1"></a>               <span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-02/mrs/sub-02_press-ref/sub-02_PRESS_35_ref.sdat&#39;</span>)}<span class="op">;</span></span></code></pre></div>
 </div>
 <div id="structural-images" class="section level3 hasAnchor" number="4.4.4">
 <h3><span class="header-section-number">4.4.4</span> Structural images<a href="the-osprey-job-file.html#structural-images" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>The <code>files_nii</code> variable is defined as a cell array of full paths to T1-weighted structural images used for co-registration and segmentation purposes.</p>
 <p><strong>Osprey</strong> requires NIfTI (<code>.nii</code>) files to be supplied. For GE files, you may also provide the full path to a directory containing the DICOM folders corresponding to the T1 acquisition.</p>
-<div class="sourceCode" id="cb25"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb25-1"><a href="the-osprey-job-file.html#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify T1-weighted structural imaging data</span></span>
-<span id="cb25-2"><a href="the-osprey-job-file.html#cb25-2" aria-hidden="true" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
-<span id="cb25-3"><a href="the-osprey-job-file.html#cb25-3" aria-hidden="true" tabindex="-1"></a><span class="co">% Link to single NIfTI (.nii) files for Siemens and Philips data</span></span>
-<span id="cb25-4"><a href="the-osprey-job-file.html#cb25-4" aria-hidden="true" tabindex="-1"></a><span class="co">% Link to DICOM (.dcm) folders for GE data</span></span>
-<span id="cb25-5"><a href="the-osprey-job-file.html#cb25-5" aria-hidden="true" tabindex="-1"></a>files_nii   <span class="op">=</span> {<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-01/anat/sub-01_T1w.nii&#39;</span>)<span class="op">,...</span></span>
-<span id="cb25-6"><a href="the-osprey-job-file.html#cb25-6" aria-hidden="true" tabindex="-1"></a>               <span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-02/anat/sub-02_T1w.nii&#39;</span>)}<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb25"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb25-1"><a href="the-osprey-job-file.html#cb25-1" tabindex="-1"></a><span class="co">% Specify T1-weighted structural imaging data</span></span>
+<span id="cb25-2"><a href="the-osprey-job-file.html#cb25-2" tabindex="-1"></a><span class="co">% (OPTIONAL)</span></span>
+<span id="cb25-3"><a href="the-osprey-job-file.html#cb25-3" tabindex="-1"></a><span class="co">% Link to single NIfTI (.nii) files for Siemens and Philips data</span></span>
+<span id="cb25-4"><a href="the-osprey-job-file.html#cb25-4" tabindex="-1"></a><span class="co">% Link to DICOM (.dcm) folders for GE data</span></span>
+<span id="cb25-5"><a href="the-osprey-job-file.html#cb25-5" tabindex="-1"></a>files_nii   <span class="op">=</span> {<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-01/anat/sub-01_T1w.nii&#39;</span>)<span class="op">,...</span></span>
+<span id="cb25-6"><a href="the-osprey-job-file.html#cb25-6" tabindex="-1"></a>               <span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/sub-02/anat/sub-02_T1w.nii&#39;</span>)}<span class="op">;</span></span></code></pre></div>
 <p><strong>Osprey</strong> uses <strong>SPM12</strong> functions to load and process structural images. Please refer to the <a href="/01-getting-started/02-installing-osprey/">installation instructions</a> for information on how to set up SPM12.</p>
 
 <div class="rmdnote">
 It is now also possible to supply Osprey with extrernally segmented images, bypassing SPM12 segmentation.
 </div>
-<div class="sourceCode" id="cb26"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb26-1"><a href="the-osprey-job-file.html#cb26-1" aria-hidden="true" tabindex="-1"></a>        <span class="co">% External segmentation results</span></span>
-<span id="cb26-2"><a href="the-osprey-job-file.html#cb26-2" aria-hidden="true" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
-<span id="cb26-3"><a href="the-osprey-job-file.html#cb26-3" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Link to NIfTI (*.nii or *.nii.gz) files with segmentation results</span></span>
-<span id="cb26-4"><a href="the-osprey-job-file.html#cb26-4" aria-hidden="true" tabindex="-1"></a>        <span class="co">% Add supply gray matter, white matter, and CSF as 1 x 3 cell within a</span></span>
-<span id="cb26-5"><a href="the-osprey-job-file.html#cb26-5" aria-hidden="true" tabindex="-1"></a>        <span class="co">% cell array  or a single 4D file in the same order supplied as 1 x 1 cell;</span></span>
-<span id="cb26-6"><a href="the-osprey-job-file.html#cb26-6" aria-hidden="true" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{[sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c1&#39; sess(ll).name &#39;_T1w.nii.gz&#39;],...</span></span>
-<span id="cb26-7"><a href="the-osprey-job-file.html#cb26-7" aria-hidden="true" tabindex="-1"></a><span class="co">%                                  [sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c2&#39; sess(ll).name &#39;_T1w.nii.gz&#39;],...</span></span>
-<span id="cb26-8"><a href="the-osprey-job-file.html#cb26-8" aria-hidden="true" tabindex="-1"></a><span class="co">%                                  [sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c3&#39; sess(ll).name &#39;_T1w.nii.gz&#39;]}};</span></span>
-<span id="cb26-9"><a href="the-osprey-job-file.html#cb26-9" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb26-10"><a href="the-osprey-job-file.html#cb26-10" aria-hidden="true" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{[sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;4D&#39; sess(ll).name &#39;_T1w.nii.gz&#39;]}};</span></span></code></pre></div>
+<div class="sourceCode" id="cb26"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb26-1"><a href="the-osprey-job-file.html#cb26-1" tabindex="-1"></a>        <span class="co">% External segmentation results</span></span>
+<span id="cb26-2"><a href="the-osprey-job-file.html#cb26-2" tabindex="-1"></a>        <span class="co">% (OPTIONAL)</span></span>
+<span id="cb26-3"><a href="the-osprey-job-file.html#cb26-3" tabindex="-1"></a>        <span class="co">% Link to NIfTI (*.nii or *.nii.gz) files with segmentation results</span></span>
+<span id="cb26-4"><a href="the-osprey-job-file.html#cb26-4" tabindex="-1"></a>        <span class="co">% Add supply gray matter, white matter, and CSF as 1 x 3 cell within a</span></span>
+<span id="cb26-5"><a href="the-osprey-job-file.html#cb26-5" tabindex="-1"></a>        <span class="co">% cell array  or a single 4D file in the same order supplied as 1 x 1 cell;</span></span>
+<span id="cb26-6"><a href="the-osprey-job-file.html#cb26-6" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{[sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c1&#39; sess(ll).name &#39;_T1w.nii.gz&#39;],...</span></span>
+<span id="cb26-7"><a href="the-osprey-job-file.html#cb26-7" tabindex="-1"></a><span class="co">%                                  [sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c2&#39; sess(ll).name &#39;_T1w.nii.gz&#39;],...</span></span>
+<span id="cb26-8"><a href="the-osprey-job-file.html#cb26-8" tabindex="-1"></a><span class="co">%                                  [sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;c3&#39; sess(ll).name &#39;_T1w.nii.gz&#39;]}};</span></span>
+<span id="cb26-9"><a href="the-osprey-job-file.html#cb26-9" tabindex="-1"></a></span>
+<span id="cb26-10"><a href="the-osprey-job-file.html#cb26-10" tabindex="-1"></a><span class="co">%         files_seg(counter)   = {{[sess(ll).folder filesep sess(ll).name filesep &#39;anat&#39; filesep subs(kk).name filesep &#39;4D&#39; sess(ll).name &#39;_T1w.nii.gz&#39;]}};</span></span></code></pre></div>
 </div>
 <div id="specifying-stat-file" class="section level3 hasAnchor" number="4.4.5">
 <h3><span class="header-section-number">4.4.5</span> Specifying stat file<a href="the-osprey-job-file.html#specifying-stat-file" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>In this section of the job it is possible to specify the location of a csv file containing group variables, and possible correlation measures.</p>
-<div class="sourceCode" id="cb27"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb27-1"><a href="the-osprey-job-file.html#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Supply location of a csv file, which contains possible correlation</span></span>
-<span id="cb27-2"><a href="the-osprey-job-file.html#cb27-2" aria-hidden="true" tabindex="-1"></a><span class="co">% measures and group variables. Each column must start with the name of the</span></span>
-<span id="cb27-3"><a href="the-osprey-job-file.html#cb27-3" aria-hidden="true" tabindex="-1"></a><span class="co">% measure. For the grouping variable use &#39;group&#39; and numbers between 1 and</span></span>
-<span id="cb27-4"><a href="the-osprey-job-file.html#cb27-4" aria-hidden="true" tabindex="-1"></a><span class="co">% the number of included groups. If no group is supplied the data will be</span></span>
-<span id="cb27-5"><a href="the-osprey-job-file.html#cb27-5" aria-hidden="true" tabindex="-1"></a><span class="co">% treated as one group. (You can always use the direct path)</span></span>
-<span id="cb27-6"><a href="the-osprey-job-file.html#cb27-6" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-7"><a href="the-osprey-job-file.html#cb27-7" aria-hidden="true" tabindex="-1"></a><span class="co">% file_stat = fullfile(data_folder, &#39;stat.csv&#39;);</span></span>
-<span id="cb27-8"><a href="the-osprey-job-file.html#cb27-8" aria-hidden="true" tabindex="-1"></a>file_stat <span class="op">=</span> <span class="st">&#39;&#39;</span><span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb27"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb27-1"><a href="the-osprey-job-file.html#cb27-1" tabindex="-1"></a><span class="co">% Supply location of a csv file, which contains possible correlation</span></span>
+<span id="cb27-2"><a href="the-osprey-job-file.html#cb27-2" tabindex="-1"></a><span class="co">% measures and group variables. Each column must start with the name of the</span></span>
+<span id="cb27-3"><a href="the-osprey-job-file.html#cb27-3" tabindex="-1"></a><span class="co">% measure. For the grouping variable use &#39;group&#39; and numbers between 1 and</span></span>
+<span id="cb27-4"><a href="the-osprey-job-file.html#cb27-4" tabindex="-1"></a><span class="co">% the number of included groups. If no group is supplied the data will be</span></span>
+<span id="cb27-5"><a href="the-osprey-job-file.html#cb27-5" tabindex="-1"></a><span class="co">% treated as one group. (You can always use the direct path)</span></span>
+<span id="cb27-6"><a href="the-osprey-job-file.html#cb27-6" tabindex="-1"></a></span>
+<span id="cb27-7"><a href="the-osprey-job-file.html#cb27-7" tabindex="-1"></a><span class="co">% file_stat = fullfile(data_folder, &#39;stat.csv&#39;);</span></span>
+<span id="cb27-8"><a href="the-osprey-job-file.html#cb27-8" tabindex="-1"></a>file_stat <span class="op">=</span> <span class="st">&#39;&#39;</span><span class="op">;</span></span></code></pre></div>
 </div>
 <div id="specifying-the-output-folder" class="section level3 hasAnchor" number="4.4.6">
 <h3><span class="header-section-number">4.4.6</span> Specifying the output folder<a href="the-osprey-job-file.html#specifying-the-output-folder" class="anchor-section" aria-label="Anchor link to header"></a></h3>
@@ -865,9 +869,9 @@ <h3><span class="header-section-number">4.4.6</span> Specifying the output folde
 <p>The <code>outputFolder</code> variable specifies a full path to the output folder.</p>
 If the output folder does not exist yet, it will be created.
 </div>
-<div class="sourceCode" id="cb28"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb28-1"><a href="the-osprey-job-file.html#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="co">% Specify output folder</span></span>
-<span id="cb28-2"><a href="the-osprey-job-file.html#cb28-2" aria-hidden="true" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
-<span id="cb28-3"><a href="the-osprey-job-file.html#cb28-3" aria-hidden="true" tabindex="-1"></a>outputFolder <span class="op">=</span> <span class="fu">strrep</span>(<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/jobSDAT.m&#39;</span>)<span class="op">,</span><span class="st">&#39;jobSDAT.m&#39;</span><span class="op">,</span><span class="st">&#39;derivatives&#39;</span>)<span class="op">;</span></span></code></pre></div>
+<div class="sourceCode" id="cb28"><pre class="sourceCode octave"><code class="sourceCode octave"><span id="cb28-1"><a href="the-osprey-job-file.html#cb28-1" tabindex="-1"></a><span class="co">% Specify output folder</span></span>
+<span id="cb28-2"><a href="the-osprey-job-file.html#cb28-2" tabindex="-1"></a><span class="co">% (MANDATORY)</span></span>
+<span id="cb28-3"><a href="the-osprey-job-file.html#cb28-3" tabindex="-1"></a>outputFolder <span class="op">=</span> <span class="fu">strrep</span>(<span class="fu">which</span>(<span class="st">&#39;exampledata/sdat/jobSDAT.m&#39;</span>)<span class="op">,</span><span class="st">&#39;jobSDAT.m&#39;</span><span class="op">,</span><span class="st">&#39;derivatives&#39;</span>)<span class="op">;</span></span></code></pre></div>
 <p>In the job files in the <code>example</code> folder of the <strong>Osprey</strong> repository, the <code>which</code> and <code>strrep</code> functions ensures that an output folder <code>derivatives</code> in the folder where the job file <code>jobSDAT</code> resides. When designing your own job file, you will have to provide the full path to your desired output folder.</p>
 <p>Note that <strong>Osprey</strong> detects if the output folder already exists and contains data from a previous analysis. In this case, you will be prompted whether you would like to overwrite the existing output.</p>
 
diff --git a/docs/the-osprey-workflow.html b/docs/the-osprey-workflow.html
index 1f15f2df..caa1ba88 100644
--- a/docs/the-osprey-workflow.html
+++ b/docs/the-osprey-workflow.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Chapter 3 The Osprey Workflow | Osprey Documentation</title>
   <meta name="description" content="Osprey is an all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data." />
-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Chapter 3 The Osprey Workflow | Osprey Documentation" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Georg Oeltzschner" />
 
 
-<meta name="date" content="2023-04-28" />
+<meta name="date" content="2024-11-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -55,6 +55,10 @@
 
 
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="css/style.css" type="text/css" />
 </head>
@@ -101,13 +105,13 @@
 <li class="chapter" data-level="4.3.2" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#sub-spectral-alignment"><i class="fa fa-check"></i><b>4.3.2</b> Sub-spectral alignment</a></li>
 <li class="chapter" data-level="4.3.3" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#eddy-current-correction"><i class="fa fa-check"></i><b>4.3.3</b> Eddy-current correction</a></li>
 <li class="chapter" data-level="4.3.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#saving-data-to-external-formats"><i class="fa fa-check"></i><b>4.3.4</b> Saving data to external formats</a></li>
-<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#matbolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Matbolites included in the basis-set</a></li>
+<li class="chapter" data-level="4.3.5" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#metabolites-included-in-the-basis-set"><i class="fa fa-check"></i><b>4.3.5</b> Metabolites included in the basis-set</a></li>
 <li class="chapter" data-level="4.3.6" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#lcmodel-specific-options"><i class="fa fa-check"></i><b>4.3.6</b> LCModel-specific options</a></li>
 <li class="chapter" data-level="4.3.7" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fit-style"><i class="fa fa-check"></i><b>4.3.7</b> Fit style</a></li>
 <li class="chapter" data-level="4.3.8" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#fitting-range"><i class="fa fa-check"></i><b>4.3.8</b> Fitting range</a></li>
 <li class="chapter" data-level="4.3.9" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#baseline-knot-spacing"><i class="fa fa-check"></i><b>4.3.9</b> Baseline knot spacing</a></li>
 <li class="chapter" data-level="4.3.10" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#macromolecule-and-lipid-signals"><i class="fa fa-check"></i><b>4.3.10</b> Macromolecule and lipid signals</a></li>
-<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macrommolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macrommolecules</a></li>
+<li class="chapter" data-level="4.3.11" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#co-edited-macromolecules"><i class="fa fa-check"></i><b>4.3.11</b> Co-edited macromolecules</a></li>
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="the-osprey-job-file.html"><a href="the-osprey-job-file.html#specifying-mrs-data-and-structural-imaging-files"><i class="fa fa-check"></i><b>4.4</b> Specifying MRS data and structural imaging files</a>
 <ul>
@@ -169,7 +173,7 @@ <h1><span class="header-section-number">Chapter 3</span> The Osprey Workflow<a h
 <p><strong>Osprey</strong> was designed to have an easy, linear workflow with as little user input as possible. It has many built-in routines to recognize data formats and sequence types, and will be able to perform most required processing steps automatically.</p>
 <p>Osprey consists of seven separate modules – Job, Load, Proc, Fit, Coreg, Seg, and Quant, all of which are sequentially called in a graphical user interface. Alternatively, users can conduct the entire workflow from the MATLAB command prompt.</p>
 <div class="figure"><span style="display:block;" id="fig:workflowChart"></span>
-<img src="img/osprey-workflow-chart.png" alt="The Osprey workflow." width="2608" />
+<img src="img/osprey-workflow-chart.png" alt="The Osprey workflow."  />
 <p class="caption">
 Figure 3.1: The Osprey workflow.
 </p>