afni_open


A program to open various AFNI/SUMA files

  afni_open [OPTIONS] FILE1 [FILE2 ...]

Examples:
  afni_open  xmat.1D.xmat
  afni_open -aw roi_11.pdf
  afni_open -r driv

Options:
===========
  -w METHOD: Use METHOD to open FILES.
             Acceptable values for METHOD are:
             editor: Open with text editor.
             downloader: Fetch with wget or curl.
             browser: Open in browser
             afni: Open with AFNI
             suma: Open with SUMA
             1dplot: Open with 1dplot
             ExamineXmat: Open with ExamineXmat
             iviewer: Open with image viewer
             afniweb: Get from afni website.
             readme: Search for appropriate README
                     This option is in the same spirit of
                     apsearch -view_readme option. To see a list of
                     all readme files, run:
                     apsearch -list_all_afni_readmes
  -e: Same as -w editor
  -d: Same as -w downloader
  -x: Same as -w ExamineXmat
  -b: Same as -w browser
  -r: Same as -w readme
  -aw: Same as -w afniweb

     If no method is specifed, the program tries to guess
     from the filename.

  -global_help: Show help for global options.
  -gopts_help:  Show help for global options.
  -help: You're looking at it.

Global Options:
===============
  -h: Mini help, at time, same as -help in many cases.
  -help: The entire help output
  -HELP: Extreme help, same as -help in majority of cases.
  -h_view: Open help in text editor. AFNI will try to find a GUI editor
  -hview : on your machine. You can control which it should use by
           setting environment variable AFNI_GUI_EDITOR.
  -h_web: Open help in web browser. AFNI will try to find a browser.
  -hweb : on your machine. You can control which it should use by
          setting environment variable AFNI_GUI_EDITOR.
  -h_find WORD: Look for lines in this programs's -help output that match
                (approximately) WORD.
  -h_raw: Help string unedited
  -h_spx: Help string in sphinx loveliness, but do not try to autoformat
  -h_aspx: Help string in sphinx with autoformatting of options, etc.
  -all_opts: Try to identify all options for the program from the
             output of its -help option. Some options might be missed
             and others misidentified. Use this output for hints only.

   -overwrite: Overwrite existing output dataset.
               Equivalent to setting env. AFNI_DECONFLICT=OVERWRITE
   -ok_1D_text: Zero out uncommented text in 1D file.
                Equivalent to setting env. AFNI_1D_ZERO_TEXT=YES
   -Dname=val: Set environment variable 'name' to value 'val'
             For example: -DAFNI_1D_ZERO_TEXT=YES
   -Vname=: Print value of environment variable 'name' to stdout and quit.
            This is more reliable that the shell's env query because it would
            include envs set in .afnirc files and .sumarc files for SUMA
            programs.
             For example: -VAFNI_1D_ZERO_TEXT=
   -skip_afnirc: Do not read the afni resource (like ~/.afnirc) file.
   -pad_to_node NODE: Output a full dset from node 0 to MAX_NODE-1
                   ** Instead of directly setting NODE to an integer you
                      can set NODE to something like:
                   ld120 (or rd17) which sets NODE to be the maximum
                      node index on an Icosahedron with -ld 120. See
                      CreateIcosahedron for details.
                   d:DSET.niml.dset which sets NODE to the maximum node found
                      in dataset DSET.niml.dset.
                   ** This option is for surface-based datasets only.
                      Some programs may not heed it, so check the output if
                      you are not sure.
   -pif SOMETHING: Does absolutely nothing but provide for a convenient
                   way to tag a process and find it in the output of ps -a
   -echo_edu: Echos the entire command line to stdout (without -echo_edu)
              for edification purposes

   SPECIAL PURPOSE ARGUMENTS TO ADD *MORE* ARGUMENTS TO THE COMMAND LINE
------------------------------------------------------------------------
   Arguments of the following form can be used to create MORE command
   line arguments -- the principal reason for using these type of arguments
   is to create program command lines that are beyond the limit of
   practicable scripting. (For one thing, Unix command lines have an
   upper limit on their length.) This type of expanding argument makes
   it possible to input thousands of files into an AFNI program command line.

   The generic form of these arguments is (quotes, 'single' or "double",
   are required for this type of argument):
     '<<XY list'
   where X = I for Include (include strings from file)
      or X = G for Glob (wildcard expansion)
   where Y = M for Multi-string (create multiple arguments from multiple strings)
      or Y = 1 for One-string   (all strings created are put into one argument)

   Following the XY modifiers, a list of strings is given, separated by spaces.
   * For X=I, each string in the list is a filename to be read in and
       included on the command line.
   * For X=G, each string in the list is a Unix style filename wildcard
       expression to be expanded and the resulting filenames included
       on the command line.
   In each case, the '<<XY list' command line argument will be removed and
   replaced by the results of the expansion.

  * '<<GM wildcards'
    Each wildcard string will be 'globbed' -- expanded from the names of
    files -- and the list of files found this way will be stored in a
    sequence of new arguments that replace this argument:
      '<<GM ~/Alice/*.nii ~/Bob/*.nii'
    might expand into a list of hundreds of separate datasets.
    * Why use this instead of just putting the wildcards on the command
      line? Mostly to get around limits on the length of Unix command lines.

  * '<<G1 wildcards'
    The difference from the above case is that after the wildcard expansion
    strings are found, they are catenated with separating spaces into one
    big string. The only use for this in AFNI is for auto-catenation of
    multiple datasets into one big dataset.

  * '<<IM filenames'
    Each filename string will result in the contents of that text file being
    read in, broken at whitespace into separate strings, and the resulting
    collection of strings will be stored in a sequence of new arguments
    that replace this argument. This type of argument can be used to input
    large numbers of files which are listed in an external file:
      '<<IM Bob.list.txt'
    which could in principle result in reading in thousands of datasets
    (if you've got the RAM).
    * This type of argument is in essence an internal form of doing something
      like `cat filename` using the back-quote shell operator on the command
      line. The only reason this argument (or the others) was implemented is
      to get around the length limits on the Unix command line.

  * '<<I1 filenames'
    The difference from the above case is that after the files are read
    and their strings are found, they are catenated with separating spaces
    into one big string. The only use for this in AFNI is for auto-catenation
    of multiple datasets into one big dataset.

  * 'G', 'M', and 'I' can be lower case, as in '<<gm'.

  * 'glob' is Unix jargon for wildcard expansion:
    https://en.wikipedia.org/wiki/Glob_(programming)

  * If you set environment variable AFNI_GLOB_SELECTORS to YES,
    then the wildcard expansion with '<<g' will not use the '[...]'
    construction as a Unix wildcard. Instead, it will expand the rest
    of the wildcard and then append the '[...]' to the results:
      '<<gm fred/*.nii[1..100]'
    would expand to something like
      fred/A.nii[1..100] fred/B.nii[1..100] fred/C.nii[1..100]
    This technique is a way to preserve AFNI-style sub-brick selectors
    and have them apply to a lot of files at once.
    Another example:
      3dttest++ -DAFNI_GLOB_SELECTORS=YES -brickwise -prefix Junk.nii \
                -setA '<<gm sub-*/func/*rest_bold.nii.gz[0..100]'

  * However, if you want to put sub-brick selectors on the '<<im' type
    of input, you will have to do that in the input text file itself
    (for each input filename in that file).

   * BE CAREFUL OUT THERE!
------------------------------------------------------------------------


++ Compile date = Aug  5 2022 {AFNI_22.2.05:linux_ubuntu_16_64}