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File and Directory Paths in Linux

A file path is the human-readable representation of a file or directory location on a computer system. On Linux, this system is organized as a hierarchical tree of directories, starting at the root directory, indicated by a single forward slash /.

Path Syntax

Linux uses forward slashes / to separate directories in a path (unlike Windows, which uses backslashes \). Example:

/home/jdoe/example.txt

Each forward slash indicates that one item is located inside the one before it.

Linux is case-sensitive, meaning Subject1.jpg and subject1.JPG are different files. This differs from Windows and can cause naming issues when transferring files across systems.

All Files in a Single Hierarchy

On Linux, all files — even on remote shares — are part of a single directory tree. This differs from Windows, where each file system is accessed via a separate drive letter (e.g., C:).

Whitespace in File Names

Avoid using spaces in file and folder names. If you must use them, handle them properly with quotes or escape characters:

cp 'subject 1.txt' 'another file.txt'
cp subject\ 1.txt another\ file.txt

Wildcards

Wildcards allow you to reference multiple files easily:

Wildcard Description Example
* Any number of characters *.txt
? A single character file?.txt
[abc] One of the listed chars file[1-3].txt

Example commands:

ls *.txt
mv data/session?.nii /temp
rm data/subject[1-3]/*.tmp
gzip */*.nii

Further reading: The Grymoire – Bash Wildcards

Home Directory Shortcut ~/

~ (tilde) refers to the current user’s home directory.

ls -al ~/my-scratch

Note: ~ will not expand inside quotes.

Tab Completion

The Tab key autocompletes file names and paths in the terminal. It saves typing and reduces errors.

ls ~/my-s<TAB>

If multiple matches exist, press Tab again to list them. For environment variables like $FSLDIR, you may need:

  • Press ESC
  • Then Ctrl + Shift + E

To expand and enable tab completion.

Special Characters and Quotes

Special characters (like space, $, or !) can change how Bash interprets a command. Use quotes to handle names or strings with special characters.

  • Single Quotes ' ' preserve everything literally.

  • Cannot contain another single quote.

  • Double Quotes " " preserve most characters but allow variable expansion like $USER.

Example

cp 'My File.txt' "Another File.txt"
cp My\ File.txt Another\ File.txt

External Resources