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Expand Up @@ -1502,7 +1502,6 @@ <h2 id="opening-fsl-on-the-bluebear-gui">Opening FSL on the BlueBEAR GUI<a class
<li>Iowa State University also have a <a href="https://www.hpc.iastate.edu/guides/unix-introduction">course</a> introducing users to UNIX.</li>
</ul>
</div>
<p><b>The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 01 workshop materials.</b></p>



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Expand Up @@ -1159,7 +1159,6 @@ <h1 id="workshop-1-introduction-to-bluebear-and-linux">Workshop 1 - Introduction
<p class="admonition-title">Pre-requisites for the workshop</p>
<p>Please ensure that you have completed the '<a href="https://chbh-opensource.github.io/mri-on-bear-edu/setting-up/">Setting Up</a>' section of this course, as you will require access to the BEAR Portal for this workshop.</p>
</div>
<p><b>The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 01 workshop materials.</b></p>



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Expand Up @@ -1163,7 +1163,6 @@ <h1 id="workshop-2-mri-data-formats-data-visualization-and-atlas-tools">Workshop

<p>You have already been given access to the RDS project, <code>rds/projects/c/chechlmy-chbh-mricn</code>. Inside the module’s RDS project, you will find that you have a folder labelled <code>xxx</code> (<code>xxx</code> = University of Birmingham ADF username). </p>
<p>If you navigate to that folder <code>(rds/projects/c/chechlmy-chbh-mricn/xxx)</code>, you will be able to perform the various file operations from there during workshops.</p>
<p><b>The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 02 workshop materials.</b></p>



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</div>
<p>We will be working with various previously acquired datasets (similar to the data acquired during the CHBH MRI Demonstration/Site visit). We will not go into details as to why and how specific sequence parameters and specific values of the default settings have been chosen. Some values should be clear to you from the lectures or assigned on Canvas readings, please check there, or if you are still unclear, feel free to ask. </p>
<p>Note that for your own projects, you are very likely to want to change some of these settings/parameters depending on your study aims and design. </p>
<p><b>The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 03 workshop materials.</b></p>



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<img src="../../assets/images/workshop4/intro/diffusion_mri_pipeline.png" alt="TBSS Pipeline" width="800" height="300">
</p>

<p><b>The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 04 workshop materials.</b></p>




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Expand Up @@ -1161,7 +1161,6 @@ <h1 id="workshop-5-first-level-fmri-analysis">Workshop 5 - First-level fMRI anal
<p>We will not go into details as to why and how specific values of the default settings have been chosen.
Some values should be clear to you from the lectures or resource list readings, please check there or if you are still unclear feel free to ask.
We will explore some general examples. Note that for your own projects you are very likely to want to change some of these settings/parameters depending on your study aims and design. </p>
<p><b>The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 05 workshop materials.</b></p>



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<p class="admonition-title">More information</p>
<p>The <a href="https://docs.bear.bham.ac.uk/">BEAR Technical Docs</a> provides guidance on submitting jobs to the cluster.</p>
</div>
<p><b>The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 06 workshop materials.</b></p>



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Expand Up @@ -1161,7 +1161,6 @@ <h1 id="workshop-7-higher-level-fmri-analysis">Workshop 7 - Higher-level fMRI an
<p class="admonition-title">More information</p>
<p>As always, you can also find more information on running higher-level fMRI analyses on the <a href="https://fsl.fmrib.ox.ac.uk/fsl/docs/#/">FSL website</a>.</p>
</div>
<p><b>The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 07 workshop materials.</b></p>



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