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7 changes: 7 additions & 0 deletions AUTHORS
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# Names should be added to this file as:
# Name or Organization <email address>

Magdalena Chechlacz <m.chechlacz.1@bham.ac.uk>
Aamir Sohail <axs2210@bham.ac.uk>
Andrew Quinn <a.quinn@bham.ac.uk>
James Carpenter <j.j.carpenter@bham.ac.uk>
7 changes: 7 additions & 0 deletions CONTRIBUTORS
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# Names should be added to this file as:
# Name or Organization <email address>

Magdalena Chechlacz <m.chechlacz.1@bham.ac.uk>
Aamir Sohail <axs2210@bham.ac.uk>
Andrew Quinn <a.quinn@bham.ac.uk>
James Carpenter <j.j.carpenter@bham.ac.uk>
2 changes: 1 addition & 1 deletion docs/index.md
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Expand Up @@ -69,7 +69,7 @@ This website contains workshop materials created for the MSc module 'Magnetic Re
| [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/) | FEAT, First-level fMRI analysis |
| [Workshop 6](https://chbh-opensource.github.io/mri-on-bear-edu/workshop6/workshop6-intro) | Bash scripting, Submitting jobs, Containers |
| [Workshop 7](https://chbh-opensource.github.io/mri-on-bear-edu/workshop7/scripting-fsl/) | Higher-level fMRI analysis, FEATquery |
| [Workshop 7](https://chbh-opensource.github.io/mri-on-bear-edu/workshop7/workshop7-intro) | Higher-level fMRI analysis, FEATquery |
| [Workshop 8](https://chbh-opensource.github.io/mri-on-bear-edu/workshop8/functional-connectivity/) | Resting-state fMRI, Functional connectivity, Neurosynth |

<br>
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19 changes: 19 additions & 0 deletions docs/stylesheets/extra.css
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6 changes: 3 additions & 3 deletions docs/workshop1/intro-to-bluebear.md
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Expand Up @@ -40,21 +40,21 @@ If you navigate to that folder `rds/projects/c/chechlmy-chbh-mricn/xxx`, you wil

## Launching the BlueBEAR GUI

The BlueBEAR Portal options in the menu bar, 'Jobs', 'Clusters' and 'My Interactive Sessions' can be used to submit and edit jobs to run on the BlueBEAR cluster and to get information about your currently running jobs and interactive sessions. Some of these processes can be also executed using Code Server Editor (VS Code) accessible via Interactive Apps. We won’t explore these options in detail now but some of these will be introduced later when needed.
The BlueBEAR Portal options in the menu bar, 'Jobs', 'Clusters' and 'My Interactive Sessions' can be used to submit and edit jobs to run on the BlueBEAR cluster and to get information about your currently running jobs and interactive sessions. Some of these processes can be also executed using the Code Server Editor (VS Code) accessible via Interactive Apps. We won’t explore these options in detail now but some of these will be introduced later when needed.

<p align="center">
<img src="../../assets/images/workshop1/intro-to-bluebear/bluebear_tabs.png" alt="BEAR Tabs" width="900" height="300">
</p>

For example, from the 'Cluster' option you can jump directly on BlueBEAR terminal and by using this built-in terminal, submit data analysis jobs and/or employ own contained version of neuroimaging software rather than software already available on BlueBEAR. We will cover containers, scripting and submitting jobs in later workshops. <b>For now, just click on this option and see what happens; you can subsequently exit/close the terminal page.</b>
For example, from the 'Cluster' option you can jump directly on to the BlueBEAR terminal and by using this built-in terminal, submit data analysis jobs and/or employ your own contained version of neuroimaging software rather than software already available on BlueBEAR. We will cover containers, scripting and submitting jobs in [Workshop 6](https://chbh-opensource.github.io/mri-on-bear-edu/workshop6/workshop6-intro/). <b>For now, just click on this option and see what happens; you can subsequently exit/close the terminal page.</b>

Finally, from the BlueBEAR Portal menu bar you can select 'Interactive Apps' and from there access various GUI applications you wish to use, including [JupyterLab](https://jupyter.org/), [RStudio](https://posit.co/download/rstudio-desktop/), [MATLAB](https://uk.mathworks.com/products/matlab.html?requestedDomain=) and most importantly the <b>BlueBEAR GUI</b>, which we will be using to analyse MRI data in the subsequent workshops.

<p align="center">
<img src="../../assets/images/workshop1/intro-to-bluebear/bluebear_gui_dropdown.png" alt="BEAR GUI" width="900" height="300">
</p>

Please select 'BlueBEAR GUI'. This will bring up a page for you to specify options for your job to start the BlueBEAR GUI. You can leave some of these options as default. But please <b>change “Number of Hours” to 2</b> (our workshops will last 2 hours; for some other analysis tasks you might need more time) and make sure that the selected 'BEAR Project' is `chechlmy-chbh-mricn`. Next click on Launch.
Please select 'BlueBEAR GUI'. This will bring up a page for you to specify options for your job to start the BlueBEAR GUI. You can leave some of these options as default. But please <b>change “Number of Hours” to 2</b> (our workshops will last 2 hours; for some other analysis tasks you might need more time) and make sure that the selected 'BEAR Project' is `chechlmy-chbh-mricn`. Next click on 'Launch'.

<p align="center">
<img src="../../assets/images/workshop1/intro-to-bluebear/bluebear_gui_options.png" alt="BEAR GUI Options" width="400" height="1200">
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10 changes: 5 additions & 5 deletions docs/workshop1/intro-to-linux.md
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Expand Up @@ -7,7 +7,7 @@ Linux is a computer Operating System (OS) similar to Microsoft Windows or Mac OS

<b>If you work in neuroimaging, it is to your advantage to become familiar with Linux. The more familiar you are, the more productive you will become.</b> For some of you, this might be a challenge. The environment will present a new learning experience, one that will take time and effort to learn. But in the end, you should hopefully realize that the benefits of learning to work in this new computer environment are indeed worth the effort.

Linux is not like the Windows or Mac OSX environments. It is best used by typing commands into a Terminal client and by writing small batch command programs. Frequently you may not even need to use the mouse. Using the Linux environment alone may take some getting used to, but will become more familar throughout the course, as we use them to navigate through our file system and to script our analyses. <b>For now, we will simply explore using the Linux terminal and simple commands</b>.
Linux is not like Windows or Mac OSX environments. It is best used by typing commands into a Terminal client and by writing small batch command programs. Frequently you may not even need to use the mouse. Using the Linux environment alone may take some getting used to, but will become more familar throughout the course, as we use them to navigate through our file system and to script our analyses. <b>For now, we will simply explore using the Linux terminal and simple commands</b>.

## Using the Linux Terminal

Expand All @@ -16,13 +16,13 @@ BlueBEAR GUI enables to load various apps and applications by using the Linux en
Either by selecting from the drop-down menu:

<p align="center">
<img src="../../assets/images/workshop1/intro-to-linux/open_terminal1.png" alt="Open Terminal" width="700" height="300">
<img src="../../assets/images/workshop1/intro-to-linux/open_terminal1.png" alt="Open Terminal" width="900" height="300">
</p>
<br>
Or by selecting the folder at the bottom of the screen:

<p align="center">
<img src="../../assets/images/workshop1/intro-to-linux/open_terminal2.png" alt="Open Terminal 2" width="700" height="300">
<img src="../../assets/images/workshop1/intro-to-linux/open_terminal2.png" alt="Open Terminal 2" width="900" height="300">
</p>
<br>
In either case you will load the terminal:
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- `/rds/projects/c/chechlmy-chbh-mricn` (our module RDS project directory)

!!! note "Directory separators on Linux and Windows"
/ (forward slash) is the Linux directory separator. Note that this is different from Windows (where the backward slash \ is the directory separator).
`/` (forward slash) is the Linux directory separator. Note that this is different from Windows (where the backward slash `\` is the directory separator).

The current directory is always called `.` (i.e. a single dot).

Expand All @@ -81,7 +81,7 @@ Your home directory can always be accessed using the shortcut `~` (the tilde sym
## Basic Linux Commands

<p align="center">
<img src="../../assets/images/workshop1/intro-to-linux/linux_cheatsheet.png" alt="Linux Cheatsheet" width="600" height="600">
<img src="../../assets/images/workshop1/intro-to-linux/linux_cheatsheet.png" alt="Linux Cheatsheet" width="700" height="600">
</p>

<b>pwd (Print Working Directory) </b>
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8 changes: 3 additions & 5 deletions docs/workshop1/workshop1-intro.md
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Expand Up @@ -8,12 +8,10 @@ Linux OS is similar to other operating systems such as Mac OS and Windows, and c
!!! success "Overview of Workshop 1"
Topics for this workshop include:

- Introduction to BlueBEAR portal
- Introduction to the BEAR Portal
- Using the BlueBEAR Graphical User Interface (GUI) environment
- Files and Directories in BEAR Portal
- Introduction to Linux
- Using the Linux Terminal
- Basic Linux Commands
- Navigating files and directories in the BEAR Portal
- Introduction to Linux, and using basic Linux commands in the Terminal

!!! danger "Pre-requisites for the workshop"
Please ensure that you have completed the '[Setting Up](https://chbh-opensource.github.io/mri-on-bear-edu/setting-up/)' section of this course, as you will require access to the BEAR Portal for this workshop.
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