Started fleshing out a bit the MRI section.

build/html/DATASETS.html

@@ -104,7 +104,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="ETHICS.html">Ethics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="PHYSIOLOGY.html">Physiology</a></li>
-<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI sequences</a></li>
+<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI</a></li>
 </ul>
 
 

build/html/ETHICS.html

@@ -90,7 +90,7 @@
 <li class="toctree-l1"><a class="reference internal" href="DATASETS.html">Datasets</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Ethics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="PHYSIOLOGY.html">Physiology</a></li>
-<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI sequences</a></li>
+<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI</a></li>
 </ul>
 
 
@@ -157,7 +157,7 @@
 
   <div class="section" id="ethics">
 <h1>Ethics<a class="headerlink" href="#ethics" title="Permalink to this headline">¶</a></h1>
-<p>The Courtois NeuroMod project has been approved by the institutional research ethics board of the <a class="reference external" href="https://ciusss-centresudmtl.gouv.qc.ca/propos/services-en-anglais">CIUSSS du Centre-Sud-de-l’île-de-Montréal</a>. The CIUSSS is a large governmental health organization, and the core NeuroMod team is based at the Research Centre of the Montreal Geriatric Institute (<a class="reference external" href="http://www.criugm.qc.ca/en.html">CRIUGM</a>), paln of the CIUSSS. The ethics documentation may be useful for research teams to receive ethics approval for secondary analysis by their local institutions, if required.</p>
+<p>The Courtois NeuroMod project has been approved by the institutional research ethics board of the <a class="reference external" href="https://ciusss-centresudmtl.gouv.qc.ca/propos/services-en-anglais">CIUSSS du Centre-Sud-de-l’île-de-Montréal</a>. The CIUSSS is a large governmental health organization, and the core NeuroMod team is based at the Research Centre of the Montreal Geriatric Institute (<a class="reference external" href="http://www.criugm.qc.ca/en.html">CRIUGM</a>), which is a part of the CIUSSS. The ethics documentation may be useful for research teams to receive ethics approval for secondary analysis by their local institutions, if required.</p>
 <ul class="simple">
 <li><p><a class="reference external" href="./_static/ethics/approval_irb_ciusss_french.pdf">approval_irb_ciusss_french.pdf</a>: letter of approval from the institutional review board for the Courtois NeuroMod project (in French).</p></li>
 <li><p><a class="reference external" href="./_static/ethics/courtois_neuromod_project_description.pdf">courtois_neuromod_project_description.pdf</a>: scientific overview of the Courtois NeuroMod project (in English).</p></li>

build/html/MRI.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>MRI sequences &mdash; Courtois NeuroMod 0.0 documentation</title>
+  <title>MRI &mdash; Courtois NeuroMod 0.0 documentation</title>
 
 
 
@@ -89,13 +89,17 @@
 <li class="toctree-l1"><a class="reference internal" href="DATASETS.html">Datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ETHICS.html">Ethics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="PHYSIOLOGY.html">Physiology</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">MRI sequences</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#anatomical-sessions">Anatomical sessions</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#brain-imaging">Brain imaging</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#cervical-spinal-cord-imaging">Cervical spinal cord imaging</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">MRI</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#personalized-head-cases">Personalized head cases</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#auditory-stimuli">Auditory stimuli</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#visual-stimuli">Visual stimuli</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#video-game-controller">Video  game controller</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#functional-acquisitions">Functional acquisitions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#anatomical-acquisitions">Anatomical acquisitions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#brain">Brain</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cervical-spinal-cord">Cervical spinal cord</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#functional-sessions">Functional sessions</a></li>
 </ul>
 </li>
 </ul>
@@ -143,7 +147,7 @@
 
       <li><a href="index.html">Docs</a> &raquo;</li>
 
-      <li>MRI sequences</li>
+      <li>MRI</li>
 
 
       <li class="wy-breadcrumbs-aside">
@@ -162,12 +166,32 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="mri-sequences">
-<h1>MRI sequences<a class="headerlink" href="#mri-sequences" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="anatomical-sessions">
-<h2>Anatomical sessions<a class="headerlink" href="#anatomical-sessions" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="brain-imaging">
-<h3>Brain imaging<a class="headerlink" href="#brain-imaging" title="Permalink to this headline">¶</a></h3>
+  <div class="section" id="mri">
+<h1>MRI<a class="headerlink" href="#mri" title="Permalink to this headline">¶</a></h1>
+<p>Magnetic resonance imaging (MRI) for the Courtois neuromod project is being acquired at the functional neuroimaging unit (<a class="reference external" href="https://unf-montreal.ca/">UNF</a>), located at the “Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal” (<a class="reference external" href="http://www.criugm.qc.ca/">CRIUGM</a>) and affiliated with <a class="reference external" href="https://www.umontreal.ca/">Université de Montréal</a> as well as the <a class="reference external" href="https://ciusss-centresudmtl.gouv.qc.ca/propos/services-en-anglais">CIUSSS du Centre-Sud-de-l’île-de-Montréal</a>. The scanner is a Siemens Prisma fit, with a 64 channels head coil. Most imaging in the Courtois Neuromod project are composed solely of functional MRI runs. Periodically, an entire session is dedicated to anatomical scans. The scanning environment includes a number of stimulation and response equipment, detailed below.</p>
+<div class="section" id="personalized-head-cases">
+<h2>Personalized head cases<a class="headerlink" href="#personalized-head-cases" title="Permalink to this headline">¶</a></h2>
+<p><img src="./_static/mri/headcase.png" alt="head case" width="200" align="right" hspace="10"/> In order to minimize movement during neuroimaging scans, each participant wears a custom-designed, personalized headcase built by a company called <a class="reference external" href="https://caseforge.co">Caseforge</a> during scanning. The headcase are milled based on a scan of each participant’s head generated using a handheld 3D scanner, as well as the shape of the MRI coil. Caseforge  mills the personalized headcases in foam blocks.</p>
+</div>
+<div class="section" id="auditory-stimuli">
+<h2>Auditory stimuli<a class="headerlink" href="#auditory-stimuli" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="visual-stimuli">
+<h2>Visual stimuli<a class="headerlink" href="#visual-stimuli" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="video-game-controller">
+<h2>Video  game controller<a class="headerlink" href="#video-game-controller" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="functional-acquisitions">
+<h2>Functional acquisitions<a class="headerlink" href="#functional-acquisitions" title="Permalink to this headline">¶</a></h2>
+<p>TODO: acq params</p>
+<p>For further information regarding the fMRI data structure and parameters, consult the BIDS dataset and included metadata.
+<a class="reference external" href="https://git.unf-montreal.ca/neuromod/">BIDS dataset</a></p>
+</div>
+<div class="section" id="anatomical-acquisitions">
+<h2>Anatomical acquisitions<a class="headerlink" href="#anatomical-acquisitions" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="brain">
+<h3>Brain<a class="headerlink" href="#brain" title="Permalink to this headline">¶</a></h3>
 <p>Localizer:          ~0:21
 ANA T1W:             6:38
 ANA T2W:             5:57
@@ -179,8 +203,8 @@ <h3>Brain imaging<a class="headerlink" href="#brain-imaging" title="Permalink to
 T1_MPRAGE:           7:26
 T2_SWI_TRA_P2_!5MM:  4:54</p>
 </div>
-<div class="section" id="cervical-spinal-cord-imaging">
-<h3>Cervical spinal cord imaging<a class="headerlink" href="#cervical-spinal-cord-imaging" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="cervical-spinal-cord">
+<h3>Cervical spinal cord<a class="headerlink" href="#cervical-spinal-cord" title="Permalink to this headline">¶</a></h3>
 <p>Localizer:         ~0:21
 T2W:                4:02
 *DWI gated:        ~2:12<br />GRE_MTI:            2:12
@@ -190,12 +214,6 @@ <h3>Cervical spinal cord imaging<a class="headerlink" href="#cervical-spinal-cor
 <p>TODO: acq params, link to osf.io of JCA protocol</p>
 </div>
 </div>
-<div class="section" id="functional-sessions">
-<h2>Functional sessions<a class="headerlink" href="#functional-sessions" title="Permalink to this headline">¶</a></h2>
-<p>TODO: acq params</p>
-<p>For further information regarding the fMRI data structure and parameters, consult the BIDS dataset and included metadata.
-<a class="reference external" href="https://git.unf-montreal.ca/neuromod/">BIDS dataset</a></p>
-</div>
 </div>
 
 

build/html/OVERVIEW.html

@@ -88,7 +88,7 @@
 <li class="toctree-l1"><a class="reference internal" href="DATASETS.html">Datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ETHICS.html">Ethics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="PHYSIOLOGY.html">Physiology</a></li>
-<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI sequences</a></li>
+<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI</a></li>
 </ul>
 
 

build/html/PHYSIOLOGY.html

@@ -37,7 +37,7 @@
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="MRI sequences" href="MRI.html" />
+    <link rel="next" title="MRI" href="MRI.html" />
     <link rel="prev" title="Ethics" href="ETHICS.html" /> 
 </head>
 
@@ -96,7 +96,7 @@
 <li class="toctree-l2"><a class="reference internal" href="#respiration">Respiration</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI sequences</a></li>
+<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI</a></li>
 </ul>
 
 
@@ -190,7 +190,7 @@ <h2>Respiration<a class="headerlink" href="#respiration" title="Permalink to thi
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="MRI.html" class="btn btn-neutral float-right" title="MRI sequences" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="MRI.html" class="btn btn-neutral float-right" title="MRI" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
         <a href="ETHICS.html" class="btn btn-neutral float-left" title="Ethics" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>

build/html/_sources/ETHICS.md.txt

@@ -1,6 +1,6 @@
 # Ethics
 
-The Courtois NeuroMod project has been approved by the institutional research ethics board of the [CIUSSS du Centre-Sud-de-l'île-de-Montréal](https://ciusss-centresudmtl.gouv.qc.ca/propos/services-en-anglais). The CIUSSS is a large governmental health organization, and the core NeuroMod team is based at the Research Centre of the Montreal Geriatric Institute ([CRIUGM](http://www.criugm.qc.ca/en.html)), paln of the CIUSSS. The ethics documentation may be useful for research teams to receive ethics approval for secondary analysis by their local institutions, if required.
+The Courtois NeuroMod project has been approved by the institutional research ethics board of the [CIUSSS du Centre-Sud-de-l'île-de-Montréal](https://ciusss-centresudmtl.gouv.qc.ca/propos/services-en-anglais). The CIUSSS is a large governmental health organization, and the core NeuroMod team is based at the Research Centre of the Montreal Geriatric Institute ([CRIUGM](http://www.criugm.qc.ca/en.html)), which is a part of the CIUSSS. The ethics documentation may be useful for research teams to receive ethics approval for secondary analysis by their local institutions, if required.
   * [approval_irb_ciusss_french.pdf](./_static/ethics/approval_irb_ciusss_french.pdf): letter of approval from the institutional review board for the Courtois NeuroMod project (in French).
   * [courtois_neuromod_project_description.pdf](./_static/ethics/courtois_neuromod_project_description.pdf): scientific overview of the Courtois NeuroMod project (in English).
   * [consent_form_english.pdf](./_static/ethics/consent_form_english.pdf): the informed consent form signed by participants (English version).

build/html/_sources/MRI.md.txt

@@ -1,8 +1,26 @@
-# MRI sequences
+# MRI
 
-## Anatomical sessions
+Magnetic resonance imaging (MRI) for the Courtois neuromod project is being acquired at the functional neuroimaging unit ([UNF](https://unf-montreal.ca/)), located at the "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal" ([CRIUGM](http://www.criugm.qc.ca/)) and affiliated with [Université de Montréal](https://www.umontreal.ca/) as well as the [CIUSSS du Centre-Sud-de-l'île-de-Montréal](https://ciusss-centresudmtl.gouv.qc.ca/propos/services-en-anglais). The scanner is a Siemens Prisma fit, with a 64 channels head coil. Most imaging in the Courtois Neuromod project are composed solely of functional MRI runs. Periodically, an entire session is dedicated to anatomical scans. The scanning environment includes a number of stimulation and response equipment, detailed below.   
 
-### Brain imaging
+## Personalized head cases
+<img src="./_static/mri/headcase.png" alt="head case" width="200" align="right" hspace="10"/> In order to minimize movement during neuroimaging scans, each participant wears a custom-designed, personalized headcase built by a company called [Caseforge](https://caseforge.co) during scanning. The headcase are milled based on a scan of each participant's head generated using a handheld 3D scanner, as well as the shape of the MRI coil. Caseforge  mills the personalized headcases in foam blocks.
+
+## Auditory stimuli
+
+## Visual stimuli
+
+## Video  game controller
+
+## Functional acquisitions
+
+TODO: acq params
+
+For further information regarding the fMRI data structure and parameters, consult the BIDS dataset and included metadata.
+[BIDS dataset](https://git.unf-montreal.ca/neuromod/)
+
+## Anatomical acquisitions
+
+### Brain
 
 Localizer:          ~0:21
 ANA T1W:             6:38
@@ -16,7 +34,7 @@ T1_MPRAGE:           7:26
 T2_SWI_TRA_P2_!5MM:  4:54
 
 
-### Cervical spinal cord imaging
+### Cervical spinal cord
 Localizer:         ~0:21
 T2W:                4:02
 *DWI gated:        ~2:12  
@@ -27,10 +45,3 @@ GRE_ME:             4:45
 
 
 TODO: acq params, link to osf.io of JCA protocol
-
-## Functional sessions
-
-  TODO: acq params
-
-  For further information regarding the fMRI data structure and parameters, consult the BIDS dataset and included metadata.
-  [BIDS dataset](https://git.unf-montreal.ca/neuromod/)

build/html/_sources/OVERVIEW.rst.txt

@@ -1,5 +1,5 @@
 Courtois NeuroMod
-=============
+=================
 
 .. warning:: This site is under construction. The first data release is scheduled for June 2020. Thank you for your patience!
 
@@ -17,7 +17,7 @@ Functional neuroimaging data are collected with several state-of-the-art techniq
 * magnetoencephalography,
 * a variety of sensors (including electrodermal activity and occulometry).
 
-Courtois NeuroMod data are freely shared with the scientific community to advance research at the interface of neuroscience and artificial intelligence. 
+Courtois NeuroMod data are freely shared with the scientific community to advance research at the interface of neuroscience and artificial intelligence.
 
 
 .. image:: img/logo_neuromod_black.png

build/html/genindex.html

@@ -89,7 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="DATASETS.html">Datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ETHICS.html">Ethics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="PHYSIOLOGY.html">Physiology</a></li>
-<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI sequences</a></li>
+<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI</a></li>
 </ul>
 
 

build/html/index.html

@@ -89,7 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="DATASETS.html">Datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ETHICS.html">Ethics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="PHYSIOLOGY.html">Physiology</a></li>
-<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI sequences</a></li>
+<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI</a></li>
 </ul>
 
 
@@ -183,7 +183,7 @@ <h1>Courtois NeuroMod<a class="headerlink" href="#courtois-neuromod" title="Perm
 <li class="toctree-l1"><a class="reference internal" href="DATASETS.html">Datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ETHICS.html">Ethics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="PHYSIOLOGY.html">Physiology</a></li>
-<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI sequences</a></li>
+<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI</a></li>
 </ul>
 </div>
 </div>

build/html/search.html

@@ -89,7 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="DATASETS.html">Datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="ETHICS.html">Ethics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="PHYSIOLOGY.html">Physiology</a></li>
-<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI sequences</a></li>
+<li class="toctree-l1"><a class="reference internal" href="MRI.html">MRI</a></li>
 </ul>