BASIC LINUX COMMANDS

These are a few useful Linux terminal commands (independent of shell type):
  
  ls        : list contents of dir (short format, alphabetical)
  ls -l, ll : list contents of dir (long format, alphabetical)
  ls -ltr   : list contents of dir (long format, time-reversed--newest last)

  cd NAME   : change dir, "down" into NAME ("NAME" can be single dir or a path)
  cd ..     : change dir, "up" to parent dir
  cd -      : change dir, jump back to previous dir
  cd        : change dir, jump to user home dir

  pwd       : display present working dir
  ~         : ("tilde") abbreviation for user home dir, same as $HOME

  cat NAME  : display contents of NAME (likely a text file) in the terminal
              (just a dump of text, no paging)
  less NAME : display contents of NAME (likely a text file) in the terminal
              (with paging, scrolling, searching, etc.)
              NB: type 'q' to quit this, 'h' for help

  up arrow  : display previous command, e.g. to re-run or edit and run;
              can be hit repeatedly to go through command history

  history   : display record of all commands run in the terminal;
              can save it to a text file with redirect:  history > FILE.txt

  echo $0   : display current shell ('-' out front means it is the login shell)

... and see afni00_unix.pdf for more Linux commands and shell notes.

*Also note:*  Tab-autocompletion helps a lot when using the terminal.
              Directory, file, command and/or option names can be long
              and complicated.  Hit Tab often as you type, to either
              partially or fully complete strings:
              + Hit Tab once to autocomplete as far as uniquely possible.
              + Hit Tab a few times to be presented with possible completions
                if more than one exists.              

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OPENING FILES FROM THE TERMINAL

The following are commands to open text and other kinds of file. AFNI
contains some commands that work on any operating system (OS). Feel
free to use these, or any equivalent commands (we provide some common
but OS-specific programs, too, that may depend on the user's setup):

+ Open a text file NAME (e.g., *.txt, *.dat, *.1D) in a text editor:

    any OS  : afni_open -e NAME
    macOS   : open -t NAME
    linux   : gedit NAME

+ Open an image NAME (e.g., JPG, PNG, etc.) in a viewer:

    any OS  : aiv  NAME
    macOS   : open NAME
    linux   : eog  NAME

+ Open a PDF NAME.pdf:

    any OS  : afni_open NAME.pdf
    macOS   : open NAME.pdf
    linux   : evince NAME.pdf

+ Open an HTML file NAME.html in a web browser:

    any OS  : afni_open -b NAME.html
    macOS   : open NAME.html
    linux   : firefox NAME.html

  NB: When opening one or more APQC HTML files specifically, use: 
  
      open_apqc.py -infiles FILE1.html [FILE2.html FILE3.html ...]

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THE HELPFUL WILDCARD CHARACTER

Wildcards can be useful with Linux commands, particularly with 'ls'.

  * : a wildcard that can be filled by 0, 1 or more characters

      ls *.pdf         -> list any file ending in ".pdf", like:
                            FILE.pdf, 1.pdf, .pdf, ...
                          but not:
                            .pdf.jpg, FILE.pdf2, FILE.PDF, ...

      ls sub-*.nii.gz  -> list any zipped NIFTIs starting with "sub-", like:
                            sub-001.nii.gz, sub-7654321.nii.gz, ...
                          but not unzipped NIFTI files: 
                            sub-001.nii, sub-7654321.nii, ...

      ls sub-*.nii*    -> list any NIFTI files that start with "sub-", like:
                            sub-101.nii, sub-101.nii.gz, ...
                          but not: 
                            part-101.nii, sub-101.json, sub-101.HEAD, ...

  ? : a wildcard that is filled by exactly one character

      ls sub-00?.nii  -> list any unzipped NIFTI file with three 
                         characters in the label like: 
                           sub-000.nii, sub-001.nii, sub-009.nii, sub-00b.nii, ...
                         but not: 
                           sub-00.nii, sub-0000.nii, ...

      ls sub-???.nii  -> list any unzip NIFTI file that has three
                         characters after 'sub-', like: 
                           sub-000.nii, sub-101.nii, sub-999.nii, sub-ABC.nii, ...
                         but not: 
                           sub-0.nii, sub-1a2b3c.nii, ...