minor formatting changes for workshops 5 and 6, added course overview…

… to index
chbh-opensource · Dec 9, 2024 · f6399cf · f6399cf
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diff --git a/docs/index.md b/docs/index.md
@@ -55,6 +55,20 @@ This website contains workshop materials created for the MSc module 'Magnetic Re
 <div class="social-item"><a href="https://sohaamir.github.io/" target="_blank"><i class="fa-solid fa-globe fa-xl" style="color: #87CEEB;"></i> sohaamir.github.io</a></div>
 </div>
 
+## Course Overview
+
+| Workshop | Key Concepts/Tools Used |
+|----------|-------------------|
+| [Getting Started](https://chbh-opensource.github.io/mri-on-bear-edu/setting-up/) | BEAR Portal, BEAR Storage, BlueBEAR |
+| [Workshop 1](https://chbh-opensource.github.io/mri-on-bear-edu/workshop1/workshop1-intro/) | BlueBEAR GUI, Linux commands, Terminal basics |
+| [Workshop 2](https://chbh-opensource.github.io/mri-on-bear-edu/workshop2/workshop2-intro/) | NIFTI/DICOM format, FSLeyes viewer, MRI atlases |
+| [Workshop 3](https://chbh-opensource.github.io/mri-on-bear-edu/workshop3/workshop3-intro/) | DTI preprocessing, DTIfit, TBSS, BET |
+| [Workshop 4](https://chbh-opensource.github.io/mri-on-bear-edu/workshop4/workshop4-intro/) | Probabilistic tractography, BEDPOSTX, PROBTRACKX |
+| [Workshop 5](https://chbh-opensource.github.io/mri-on-bear-edu/workshop5/workshop5-intro/) | Advanced BET, FEAT, First-level GLM |
+| [Workshop 6](https://chbh-opensource.github.io/mri-on-bear-edu/workshop6/workshop6-intro/) | Group-level analysis, Fixed/Random effects |
+| [Workshop 7](https://chbh-opensource.github.io/mri-on-bear-edu/workshop7/scripting-fsl/) | Bash scripting, ROI analysis, Automated processing |
+| [Workshop 8](https://chbh-opensource.github.io/mri-on-bear-edu/workshop8/functional-connectivity/) | Resting-state fMRI, Functional connectivity, Neurosynth |
+
 <br>
 
 !!! info "Accessing additional course materials"

diff --git a/docs/workshop5/first-level-analysis.md b/docs/workshop5/first-level-analysis.md
@@ -169,7 +169,7 @@ The model should now be set up with all the correct details and be ready to be a
 !!! note "Running FSL on BlueBEAR"
     FSL jobs are now submitted in an automated way to a back-end high performance computing cluster on BlueBEAR for execution. Processing time for this analysis will vary but will probably be about 5 mins per run.
 
-## Monitoring and viewing the data
+## Monitoring and viewing the results
 
 FEAT has a built-in progress watcher, the 'FEAT Report', which you can open in a web browser. 
 
@@ -186,8 +186,6 @@ Watch the webpage for progress. Refresh the page to update and click the links (
 </p>
 <p align="center"><i style="font-size: 1.2em;">Example FEAT Reports for processes that are still running, and which have completed.</i></p>
 
-<br>
-
 After it has completed, first look at the webpage, click on the various links and try to understand what each part means.
 
 <p align="center">

diff --git a/docs/workshop5/preprocessing.md b/docs/workshop5/preprocessing.md
@@ -43,7 +43,7 @@ You now need to create a copy of the reconstructed fMRI data to be analysed duri
 
 <br>
 
-# Skull-stripping T1 scans using BET on the command-line
+## Skull-stripping T1 scans using BET on the command-line
 We will now look at how to ”skull-strip” the T1 image (remove the skull and non-brain areas), as this step is needed as part of the registration step in the fMRI analysis pipeline. 
 We will do this using FSL's BET on the command line. As you should know from previous workshops the basic command-line version of BET is: