-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathrsfmri.html
180 lines (162 loc) · 10.7 KB
/
rsfmri.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Resting-state BOLD imaging — BrainMRIpipelines 0.1 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script src="_static/jquery.js?v=5d32c60e"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="_static/documentation_options.js?v=2709fde1"></script>
<script src="_static/doctools.js?v=888ff710"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Miscellaneous tips" href="misc.html" />
<link rel="prev" title="Diffusion-weighted imaging (DWI)" href="dwi.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="index.html" class="icon icon-home">
BrainMRIpipelines
</a>
<div class="version">
0.1.0
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<ul class="current">
<li class="toctree-l1 current"><a class="reference internal" href="bmp.html">Welcome to BrainMRIpipelines documentation!</a><ul class="current">
<li class="toctree-l2 current"><a class="reference internal" href="bmp.html#modules">Modules</a><ul class="current">
<li class="toctree-l3"><a class="reference internal" href="io.html">Input/output module</a></li>
<li class="toctree-l3"><a class="reference internal" href="asl.html">Arterial spin labelling (ASL)</a></li>
<li class="toctree-l3"><a class="reference internal" href="dwi.html">Diffusion-weighted imaging (DWI)</a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">Resting-state BOLD imaging</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#data-preparation">Data preparation</a></li>
<li class="toctree-l4"><a class="reference internal" href="#visual-inspection-of-image-quality">Visual inspection of image quality</a></li>
<li class="toctree-l4"><a class="reference internal" href="#generate-lists">Generate lists</a></li>
<li class="toctree-l4"><a class="reference internal" href="#extract-anat-brain">Extract anat brain</a></li>
<li class="toctree-l4"><a class="reference internal" href="#optional-despike-rsfmri-data">[OPTIONAL] Despike rsfMRI data</a></li>
<li class="toctree-l4"><a class="reference internal" href="#remove-existing-func-feat-func-feat-etc-if-any">Remove existing func.feat, func+.feat, etc., if any</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="misc.html">Miscellaneous tips</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="svdd.html">Cerebral Small Vessel Disease Lesion Detectors (SVD Detector)</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">BrainMRIpipelines</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item"><a href="bmp.html">Welcome to BrainMRIpipelines documentation!</a></li>
<li class="breadcrumb-item active">Resting-state BOLD imaging</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/rsfmri.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<section id="resting-state-bold-imaging">
<h1>Resting-state BOLD imaging<a class="headerlink" href="#resting-state-bold-imaging" title="Link to this heading"></a></h1>
<section id="data-preparation">
<h2>Data preparation<a class="headerlink" href="#data-preparation" title="Link to this heading"></a></h2>
<p>To automate the processing steps, imaging files should be named and stored in a predefined way in this pipeline. Specifically, there should be a <em>cohortFolder</em>, which includes multiple <em>studyFolder</em> (<em>studyFolder</em> can be subject ID’s). In each <em>studyFolder</em>, there should exist a T1-weighted scan (named <em>struc.nii</em>), a resting-state BOLD imaging scan (named <em>func.nii</em>), and if images in reverse PE directions for distortion correction were acquired, <em>ap.nii</em> and <em>pa.nii</em> (e.g., MAS2 data).</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cohortFolder</span> <span class="o">---</span> <span class="n">studyFolder_1</span> <span class="p">(</span><span class="n">ie</span><span class="o">.</span> <span class="n">subjID</span><span class="p">)</span> <span class="o">-</span> <span class="n">struc</span><span class="o">.</span><span class="n">nii</span><span class="p">,</span> <span class="n">func</span><span class="o">.</span><span class="n">nii</span><span class="p">,</span> <span class="n">ap</span><span class="o">.</span><span class="n">nii</span><span class="p">,</span> <span class="n">pa</span><span class="o">.</span><span class="n">nii</span>
<span class="o">|</span>
<span class="o">|---</span> <span class="n">studyFolder_2</span> <span class="p">(</span><span class="n">ie</span><span class="o">.</span> <span class="n">subjID</span><span class="p">)</span> <span class="o">-</span> <span class="n">struc</span><span class="o">.</span><span class="n">nii</span> <span class="o">&</span> <span class="n">func</span><span class="o">.</span><span class="n">nii</span>
<span class="o">|</span>
<span class="o">|---</span> <span class="n">studyFolder_3</span> <span class="p">(</span><span class="n">ie</span><span class="o">.</span> <span class="n">subjID</span><span class="p">)</span> <span class="o">-</span> <span class="n">struc</span><span class="o">.</span><span class="n">nii</span> <span class="o">&</span> <span class="n">func</span><span class="o">.</span><span class="n">nii</span>
</pre></div>
</div>
</section>
<section id="visual-inspection-of-image-quality">
<h2>Visual inspection of image quality<a class="headerlink" href="#visual-inspection-of-image-quality" title="Link to this heading"></a></h2>
<p>It is always a good idea to visualise <em>func.nii</em> and <em>struc.nii</em> to identify any defects.</p>
</section>
<section id="generate-lists">
<h2>Generate lists<a class="headerlink" href="#generate-lists" title="Link to this heading"></a></h2>
<p>Generate lists, so that the processing steps can be applied to all subjects. Depending on the following denoising strategy, lists can be generated by:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span># Generate lists
cohortFolder=/srv/scratch/cheba/Imaging/mas2/pilot2_Karina/dnldFromFlywheel/fmri/work/cohortFolder
bmp_fmri_ini_genLists.sh -c ${cohortFolder} -l fix # If FIX denoising will be used
bmp_fmri_ini_genLists.sh -c ${cohortFolder} -l aroma # If AROMA denoising will be used
</pre></div>
</div>
</section>
<section id="extract-anat-brain">
<h2>Extract anat brain<a class="headerlink" href="#extract-anat-brain" title="Link to this heading"></a></h2>
<p>Brain extraction from T1-weighed image:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span># Extract brain from T1
for_each -nthreads 8 $(cat ${cohortFolder}/studyFolder.list) : bmp_fmri_ini_Xbrain.sh IN
</pre></div>
</div>
<p>Visualise <em>struc_brain.nii.gz</em> for the quality of brain extraction.</p>
</section>
<section id="optional-despike-rsfmri-data">
<h2>[OPTIONAL] Despike rsfMRI data<a class="headerlink" href="#optional-despike-rsfmri-data" title="Link to this heading"></a></h2>
<p>Despike rsfMRI data. This calls AFNI’s 3dDespike, and requires AFNI to be installed.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span># Despike
for_each -nthreads 8 $(cat ${cohortFolder}/studyFolder.list) : bmp_fmri_ini_despike.sh IN
</pre></div>
</div>
</section>
<section id="remove-existing-func-feat-func-feat-etc-if-any">
<h2>Remove existing func.feat, func+.feat, etc., if any<a class="headerlink" href="#remove-existing-func-feat-func-feat-etc-if-any" title="Link to this heading"></a></h2>
<p>Removing previous FEAT results. If you want to keep previous results, rename them.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>for_each -nthreads 8 $(cat ${cohortFolder}/studyFolder.list) : rm -fr IN/func*.feat
</pre></div>
</div>
</section>
</section>
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="dwi.html" class="btn btn-neutral float-left" title="Diffusion-weighted imaging (DWI)" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="misc.html" class="btn btn-neutral float-right" title="Miscellaneous tips" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
<hr/>
<div role="contentinfo">
<p>© Copyright 2021, Graziella.</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>