*NB:* Here and below, you can hit the "Tab" key as you type to help
autocomplete filenames, program names and even AFNI program options.

If autocomplete of AFNI program options does not work, run:
  apsearch -update_all_afni_help

---------------------------- display program help ----------------------------

To display help in the terminal, type the name of the program with no
options or '-help':

  3dinfo
  3dinfo -help

To display help in a text editor (which can be specified in ~/.afnirc), 
use '-hview':

  3dinfo -hview

----------------------------- open/view datasets ----------------------------

Move to the relevant directory looking at data with the AFNI GUI:

  cd ~/AFNI_data6/afni

Open the datasets there to visualize:

  afni

--------------------------- check dset header info --------------------------

Check header/meta information in a dataset (such as NIFTI, BRIK/HEAD,
or other formats);  all of the following are equivalent when reading
BRIK/HEAD files:

  3dinfo anat+orig
  3dinfo anat+orig.
  3dinfo anat+orig.HEAD
  3dinfo anat+orig.BRIK

... and to check just individual pieces, use some options:

  3dinfo -ad3 anat.nii.gz            (voxel dims)
  3dinfo -n4 anat.nii.gz             (matrix and time dims)
  3dinfo -history anat.nii.gz        (history of AFNI commands run)

... and to compare grids of two datasets:

  3dinfo -same_grid -prefix anat+orig. epi_r1+orig.      (yes/no form)  
  3dinfo -same_all_grid -prefix anat+orig. epi_r1+orig.  (item-by-item Y/N)

-------------------------- open/edit startup files -------------------------

AFNI and SUMA each have startup files where users can control a lot of
settings and behavior by providing "environment variable" values. Many
are populated by default.  Each time a GUI or program is run, this
file is checked---so these changes/settings last as long as you have
them set there.

To open one of these text files to view or edit: 

  afni_open -e ~/.afnirc
  afni_open -e ~/.sumarc

NB: if you don't have a pre-populated file (i.e., file appears empty
or doesn't exist), please run "afni_system_check.py -check_all" and
see the "Please fix" section at the bottom about creating one or both.

Examples of useful things to set in ~/.afnirc:

  Define a "global session" dir, whose datasets will always be
  appended to the  in the AFNI GUI:

    AFNI_GLOBAL_SESSION = ~/abin                (def: no dir set)

  In AFNI GUI, should image left correspond to dataset left?

    AFNI_LEFT_IS_LEFT = YES                     (def: YES)

See the full list of AFNI environment variables here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/afniandafni/readme_env_vars.html