Introduction to Linux

Linux is a computer Operating System (OS) similar to Microsoft Windows or Mac OS. Linux is very widely used in the academic world especially in the sciences. It is derived from one of the oldest and most stable and used OS platforms around, Unix. We use Linux on BlueBEAR. Many versions of Linux are freely available to download and install, including CentOS (Community ENTerprise Operating System) and Debian, which you might be familiar with. You can also use these operating systems with Microsoft Windows in Dual Boot Environment on your laptop or desktop computer.

Linux and neuroimaging

Linux is particularly suited for clustering computers together and for efficient batch processing of data. All major neuroimaging software runs on Linux. This includes FSL, SPM, AFNI, and many others. Linux, or some version of Unix, is used in almost all leading neuroimaging centres. Both MATLAB and Python also run well in a Linux environment.

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. 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. For now, we will simply explore using the Linux terminal and simple commands.

Using the Linux Terminal

BlueBEAR GUI enables to load various apps and applications by using the Linux environment and a built-in Terminal client. Once you have launched the BlueBEAR GUI, you will see a new window and from there you can open the Terminal client. There are different ways to open Terminal in BlueBEAR GUI window as illustrated below.

Either by selecting from the drop-down menu:

Or by selecting the folder at the bottom of the screen:

In either case you will load the terminal:

Once you have started the terminal you, you will be able to load required applications (e.g., to start the FSL GUI). FSL (FMRIB Software Library) is a neuroimaging software package we will be using in our workshops for MRI data analysis.

When using the BlueBEAR GUI Linux desktop, you can simultaneously work in four separate spaces/windows. For example, if you are planning on using multiple apps, rather than opening multiple terminals and apps in the same space, you can move to another space. You can do that by clicking on “workspace manager” in Linux desktop window.

Linux is fundamentally a command line-based operating system, so although you can use the GUI interface with many applications, it is essential you get used to issuing commands through the Terminal interface to improve your work efficiency.

Make sure you have an open Terminal as per the instructions above. Note that a Terminal is a text-based interface, so generally the mouse is not much use. You need to get used to taking your hand off the mouse and letting go of it. Move it away, out of reach. You can then get used to using both hands to type into a Terminal client.

[chechlmy@bear-pg0210u07a ~]$ as shown above in the Terminal Client is known as the system prompt. The prompt usually identifies the user and the system hostname. You can type commands at the system prompt (press the Enter key after each command to make it run). The system then returns output based on your command to the same Terminal.

Try typing ls in the Terminal.

This command tells Linux to print a list of the current directory contents. We will get back later to basic Linux commands, which you should learn to use BlueBEAR for neuroimaging data analysis.

Why bother with Linux?

You may wonder why you should invest the time to learn the names of the various commands needed to copy files, change directories and to do general things such as run image analysis programs via the command line. This may seem rather clunky. However, the commands you learn to run on the command line in a terminal can alternatively be written in a text file. This text file can then be converted to a batch script that can be run on data sets using the BlueBEAR cluster, potentially looping over hundreds or thousands of different analyses, taking many days to run. This is vastly more efficient and far less error prone than using equivalent graphical tools to do the same thing, one at a time.

When you open a new terminal window it opens in a particular directory. By default, this will be your home directory:

/rds/homes/x/xxx

or the Desktop folder in your home directory:

/rds/homes/x/xxx/Desktop(where x is the first letter of your last name and xxx is your University of Birmingham ADF username).

On BlueBEAR files are stored in directories (folders) and arranged into a tree hierarchy.

Examples of directories on BlueBEAR include:

• /rds/homes/x/xxx (your home directory)
• /rds/projects/c/chechlmy-chbh-mricn (our module RDS project directory)

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).

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

The directory above the current directory is always called .. (i.e. dot dot)

Your home directory can always be accessed using the shortcut ~ (the tilde symbol). Note that this is the same as /rds/homes/x/xxx.

You need to remember this to use and understand basic Linux Commands.

Basic Linux Commands

pwd (Print Working Directory)

In a Terminal type pwd followed by the return (enter) key to find out the name of the directory where you are. You are always in a directory and can (usually) move to directories above you or below to subdirectories.

For example if you type pwd in your terminal you will see: /rds/homes/x/xxx (e.g., /rds/homes/c/chechlmy)

cd (Change Directory)

In a Terminal window, type cd followed by the name of a directory to gain access to it. Keep in mind that you are always in a directory and normally are allowed access to any directories hierarchically above or below.

Type in your terminal the examples below:

cd /rds/projects

cd /rds/homes/

cd .. (to change to the directory above using .. shortcut)

To find out where you are now, type pwd:

(answer: /rds)

If the directory is not located above or below the current directory, then it is often less confusing to write out the complete path instead. Try this in your terminal:

cd /rds/homes/x/xxx/Desktop (where x is the first letter of your last name and xxx is your ADF username)

Changing directories with full paths

Note that it does not matter what directory you are in when you execute this command, the directory will always be changed based on the full pathway you specified.

Remember that the tilde symbol ~ is a shortcut for your home directory. Try this:

cd /rds/projects 
cd ~ 
pwd

You should be now back in your home directory.

ls (List Files)

The ls command (lowercase L, S) allows you to see a summary list of the files and directories located in the current directory. Try this:

cd /rds/projects/c
ls

(you should now see a long list of various BEAR RDS projects)

Before moving to the next section, please close your terminal by clicking on “x” in the top right of the Terminal.

cp (Copy files/directories)

The cp command will copy files and/or directories FROM a source TO a destination in the current working directory. This command will create the destination file if it doesn't exist. In some cases, to do that you might need to specify a complete path to a file location.

Here are some examples (please do not type them, they are only examples):

Command	Function
cp myfile yourfile	Basic file copy (in current directory)
cp data data_copy	Copy a directory (but not sub-directories)
cp -r ~fred/data .	Recursively copy fred dir to current dir
cp ~fred/fredsfile myfile	Copy remote file and rename it
cp ~fred/* .	Copy all files from fred dir to current dir
cp ~fred/test* .	Copy all files that begin with test e.g. test, test1.txt

In the subsequent workshops we will practice using the cp command. For now, looking at the examples above to understand its usage. There are also some exercises below to check your understanding.

mv, rmdir and mkdir (Moving, removing and making files/directories)

The mv command will move files FROM a source TO a destination. It works like copy, except the file is actually moved. If applied to a single file, this effectively changes the name of the file. (Note there is no separate renaming command in Linux). The command also works on directories.

Here are some examples (again please do not type these in):

Command	Function
mv myfile yourfile	renames file
mv ~/data/somefile somefile	moves file
mv ~/data/somefile yourfile	moves and renames
mv ~/data/* .	moves multiple files

There are also the mkdir and rmdir commands:

• mkdir – to make a new directory e.g. mkdir testdir
• rmdir – to remove an empty directory e.g. rmdir testdir

You can try these two commands. Open a new Terminal and type:

mkdir testdir
ls

In your home directory you will see now a new directory testdir. Now type:

rmdir testdir
ls

You should notice that the testdir has been removed from your home directory.

To remove a file you can use the rm command. Note that once files are deleted at the command line prompt in a terminal window, unlike in Microsoft Windows, you cannot get files back from the wastebin.

e.g. rm junk.txt (this is just an example, do not type it in your terminal)

Clearing your terminal

Often when running many commands, your terminal will be full and difficult to understand. To clear the terminal screen type clear. This is an especially helpful command when you have been typing lots of commands and need a clean terminal to help you focus.

Linux commands in general

Note that most commands in Linux have a similar syntax: command name [modifiers/options] input output

The syntax of the command is very important. There must be spaces in between the different parts of the command. You need to specify input and output. The modifiers (in brackets) are optional and may or may not be needed depending on what you want to achieve.

For example, take the following command:

cp -r /rds/projects/f/fred/data ~/tmp (This is an example, do not type this)

In the above example -r is an option meaning 'recursive' often used with cp and other commands, used in this case to copy a directory including all its content from one directory to another directory.

Opening FSL on the BlueBEAR GUI

FSL (FMRIB Software Library) is a software library containing multiple tools for processing, statistical analyses, and visualisation of magnetic resonance imaging (MRI) data. Subsequent workshops will cover usage of some of the FSL tools for structural, functional and diffusion MRI data. This workshop only covers how to start FSL app on BlueBEAR GUI Linux desktop, and some practical aspects of using FSL, specifically running it in the terminal either in the foreground or in the background.

There are several different versions of FSL software available on BlueBEAR. You can search which versions of FSL are available on BlueBEAR as well as all other available software using the following link: https://bear-apps.bham.ac.uk

From there you will also find information how to load different software. Below you will find an example of loading one of the available versions of FSL.

To open FSL in terminal, you first need to load the FSL module. To do this, you need to type in the Terminal a specific command.

First, either close the Terminal you have been previously using and open a new one, or simply clean it. Next, type:

module load FSL/6.0.5.1-foss-2021a

You will see various processes running the terminal. Once these have stopped and you see a system prompt in the terminal, type:

fsl

This fsl command will initiate the FSL GUI as shown below.

Now try typing ls in the same terminal window and pressing return.

Notice how nothing appears to happen (your keystrokes are shown as being typed in but no actual event seems to be actioned). Indeed, nothing you type is being processed and the commands are being ignored. That is because the fsl command is running in the foreground in the terminal window. Because of that it is blocking other commands from being run in the same terminal.

• Now close FSL by clicking on the 'Exit' button in the FSL GUI.

Notice now that control has been returned to the Terminal and how commands you type are now being acted on. Try typing ls again; it should now work in the Terminal.

• Go back to the terminal window again, but this time type fsl & at the system prompt and press return. Again, you should see the FSL GUI pop up.

• Now try typing ls in the same Terminal.

Notice that your new commands are now being processed. The fsl command is now running in the background in the Terminal allowing you to run other commands in parallel from the same Terminal. Typing the & after any command makes it run in the background and keeps the Terminal free for you to use.

Sometimes you may forget to type & after a command.

• Close all open windows, open a new terminal and type fsl (without the &) so that it is running in the foreground.
• Now hold down the CTRL key and the z key together 'CTRL-z'.

You should get a message like “[1]+ Stopped fsl”. You will notice that the FSL GUI is now unresponsive (try clicking on some of the buttons). The fsl process has been suspended.

• To make it run again in the background type bg in the terminal window (followed by pressing the return key).

You should find the FSL GUI is now responsive again and input to the terminal now works once more. If you clicked the 'Exit' button when the FSL GUI was unresponsive, FSL might close now.

Running and killing commands in the terminal

If, for some reason, you want to make the command run in the foreground then rather than typing bg (for background) instead type fg (for foreground). If you want to kill (rather than suspend) a command that was running in the foreground, press CTRL-c (CTRL key and c key).

Linux: some final useful tips

TIP 1:

When typing a command - or the name of a directory or file - you never need to type everything out. The terminal will self-complete the command or file name if you type the TAB key as you go along. Try using TAB key when typing commands or complete path to specific directory.

TIP 2:

If you need help understanding what the options are, or how to use a command, try adding --help to the end of your command. For example, for better understanding of the du options, type:

du --help [enter]

TIP 3:

There are many useful online lists of these various commands, for example: www.ss64.com/bash

Exercise: Basic Linux commands

Please complete the following exercises, you should hopefully know which Linux commands to use!

• clean up your Terminal
• cd back to your home directory
• make sure you are in your home directory
• make a new directory called test
• rename this directory to test1 and make another directory called test2
• move or copy directory test1 to your folder on modules’s RDS project (i.e., rds/projects/c/chechlmy-chbh-mricn/xxx)
• delete the test1 and test2 directories and confirm it

If unsure, check your results with someone else or ask for help!

The correct commands are provided below. (click to reveal)

Linux Commands Exercise (Answers)

1. clear

2. cd ~ or cd /rds/homes/x/xxx

3. pwd

4. mkdir test

5. mv test test1
mkdir test2

6. cp -r test1 /rds/projects/c/chechlmy-chbh-mricn/xxx/ or mv test1 /rds/projects/c/chechlmy-chbh-mricn/xxx/

7. rm -r test1 test2
ls

Workshop 1: Further Reading and Reference Material

Here are some additional resources that introduce users to Linux:

• A useful textbook on essential Linux commands is the Linux Pocket Guide by Daniel J. Barratt.
• The Carpentries (an organisation providing free training for various software engineering and data science skills) have an introduction to UNIX course.
• Iowa State University also have a course introducing users to UNIX.

The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 01 workshop materials.