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BASH tutorial (Linux and MacOS command prompt)

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etiaum edited this page Jul 16, 2024 · 41 revisions

By Etienne Aumont

Table of content

  1. Basic BASH commands
    1.1 BASH cheatsheet
    1.1 Navigating through files
    1.2 Manipulating files
  2. For loops
    2.1 Rationale
    2.2 Basic loop structure + examples
    2.3 For loops with 2 variables

1. Basic BASH commands

1.1 BASH cheatsheet

Commands
cd Current Directory - to move around
pwd Prints what the current directory is
ls Lists files and directories
tree Show directory and file tree
mkdir Creates a directory
cp Copies a file or a directory
mv Moves a file (like cut and paste)
rm Deletes a file
rmdir Deletes a directory
echo Displays what comes after
tar For un-compression. (Use option -xzf for files ending in .tar.gz)

Action keys & tips

  • "Tab" key: Autocomplete (for files/directories)
  • Tab (twice): Displays options for autocomplete
  • CTRL + C: Interrupts current command (you can only copy + paste using the right mouse click)
  • Middle mouse click: Copies whatever is selected in the command prompt (faster than copy + paste)
  • -help: Type -help after any command to display the command's options

1.2 Navigating through files

In the command prompt, you are by default working from the home directory on your drive. Every command you use will be from the point of view of this directory.
First, to change your point of view, you can move through the directories with cd. For example:
cd /home/minc/Desktop/FEOBV/analyses/
This will bring me from the home directory to my FEOBV analyses directory.
You can always press TAB twice to autocomplete or display your options while typing the path
Files with spaces in their name will not work here, make sure you remove all spaces! cd alone will bring you back to the home directory To go back, use .., for example:
cd ../../MK6240/analyses/
This will bring me 2 directories out from the current directory - the Desktop - then into a different analyses folder.
If you ever wonder where you currently are, you can use pwd to display the path to the current directory

Next, you may list files in the current directory using ls
This will display everything, so the list may be long. If it's too long, you can always press CTRL + C to interrupt the current command.
It's also possible to display the content of another file with ls path/to/your/folder/
The content will by default be organized by name, but you can organize them by modification time by adding "-t" right after "ls". To see the file structure, you can use tree instead

1.3 Moving files around

You can create new directories using mkdir. For example:

 pwd 
 >/home/minc/Desktop/MK6240/analyses  
 mkdir hippocampus
 ls
 >hippocampus

You can copy this directory around using cp and including the option -r for directories. Then populate it with an image.Instead of copying a file, you can also move it using mv. This is also useful to rename your file

 cp -r hippocampus ../../FEOBV/analyses/
 cd ../../FEOBV/analyses/
 cp ../../FEOBV001_SUVR.mnc hippocampus/FEOBV001_SUVR.mnc
 mv hippocampus/FEOBV001_SUVR.mnc hippocampus/NEW_NAME001_SUVR.mnc

Instead of copying a file, you can also move it using mv
This is also useful to rename your file

To delete stuff, use rm for files or rmdir for directories.
Be careful with this action, as it is permanent
To limit mistakes, you can use echo first to make sure that you've got it right.

 echo rm hippocampus/NEW_NAME001_SUVR.mnc
 >rm hippocampus/NEW_NAME001_SUVR.mnc
 rm hippocampus/NEW_NAME001_SUVR.mnc
 rmdir hippocampus

The folder hippocampus no longer exists

Other uses for echo:

 echo content > patient_parameters.txt #a txt file containing the patient's weight and injected dose
 > 89.5
 > 6.5

2. For loops

2.1 Rationale

For loops allow you to perform operations on all objects that correspond to your criteria. This is a very efficient way of, for example, processing neuroimaging data. For loops require you to first define the objects you're interested in (eg. all MK6240 images).
In BASH, this usually means using something in the file's name to identify it. Using MINC functions, you can name an output based on the input. However, this process is based on the length of the file names, so this only works well if the files are named consistently. Ideally, all IDs should be the exact same length to allow you to name the outputs efficiently. Also, I recommend all of your files either be in the same folder or be nested into a subject folder. Your folder could therefore look like this:

PersonalFolder/MK/SUVR/

2.2 Basic for loop structure + examples

for [VarName] in [criteria for the specific files you want] ; 
do [The command you want to be executed on all selected files] ; 
done

You refer to your file in the command using $VarName When creating a new file based on parts of the existing file name, you can use the file name using

${VarName:0:18} #using 18 characters starting from character 0

Example: Display a series of images on Display (they will open 1 at a time, and the next one will automatically open when you close the previous one)

for file in * ; do Display -gray -range 50 900 "${file:0:10}"*.mnc -label ../Template_labels_Left/"${file:0:10}"*.mnc ; done

Example: obtain the mean SUVR within a mask File structure is [ID(7 character long)]/[ID+filetype]

for file in * ; 
do mincstats -mask ../WM_0.99_new.mnc -mask_binvalue 1 "${file:0:7}"/"${file:0:7}"-FEOBV-*avg_suv_autoreg_ST.mnc -mean ; 
done

The output will be a series of SUVR values based on the file's alphabetical order

FOR loops are also super useful to collect and move files around. For example:

for i in */*T2*.mnc ; #Collecting all T2 images in minc format nested 2 layers deeper than the current directory
do cp $i ../../../etienne/ ; #Copying all the images inside my folder
done

Adding one character to a file name to make it longer:
!!! If you modify a file like this, I recommend you run it with the echo function first to see if it's well built.

for i in MRT*.mnc ; #Collecting all files with "MRT" in the ID
do echo mv $i "${i:0:7}"O"${i:7:100}" ; #Adding an "O" at the end of the ID to bring it to 8 characters long
done
#output (1 line per file):
mv MRT6123_segmented_labels.mnc MRT6123O_segmented_labels.mnc

Also, remember that if something goes wrong, you can stop the for loop using the CTRL + C keys

The function looks good, we can now run it:

for i in MRT*.mnc ; #Collecting all files with "MRT" in the ID
do mv $i "${i:0:7}"O"${i:7:100}" ; #Adding an "O" at the end of the ID to bring it to 8 characters long
done

2.3 For loop with 2 variables

You can add variables in your for loop that is generated based on the text output of a command within the loop using something like

REF=$($echo [command you want the output of])

The output must ONLY be what you're interested in. In Minc commands, this generally implies using -quiet Echo means outputting the command's result as text

Example: Standardize a PET image based on the signal in a ROI

for file in * ; do REF=$($echo mincstats -mask ../../refMask_fullCG_res.mnc -mask_binvalue 1 $file -mean -quiet) ; 
mincmath -div -const $REF "${file:0:15}"*_ST.mnc "${file:0:18}"_SUVR_ST.mnc ; done

A second example of ref region SUVR

for i in FEOBV*.mnc ; do REF=$($echo mincstats -mask c2xSVBSS_er.mnc -mask_binvalue 1 $i -mean -quiet) ; 
mincmath -div -const $REF $i s"${i:0:13}"_PrevST_SUVR.mnc ; done

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