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What the H*** is AFNI?
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AFNI is a suite of programs for looking at and analyzing 3D brain
images.  The emphasis is on FMRI, but AFNI can be used for other
purposes as well.  See http://afni.nimh.nih.gov/afni for more fun.

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AFNI directory
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doc/   = documentation for AFNI
src/   = source code for AFNI

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Relevant git-ology for AFNI
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###..... First time stuff .....###

#Make yourself known to git-land:
git config --global user.name   "Fred Mertz"
git config --global user.email  mertzf@bargle.argle
git config --global core.editor vim

#Create a copy of the repository on your machine:
git clone https://github.com/afni/afni.git

###..... Stuff to do as needed .....###

#Getting updates from the repository
git pull origin master

#Seeing what changes you have made locally
git status

#To commit some files to your LOCAL repository (preferred)
git commit -m "PLEASE comment"   FILE1 FILE2 ...

#To commit all tracked files with changes (locally):
git commit -a -m "PLEASE try to put a comment here"

#If you have new files to add into the repository;
#PLEASE PLEASE PLEASE, be careful with wildcards!!!
#The main thing is to avoid adding very large files (such as binaries)
#by mistake!
git add -f FILE1 FILE2 ...

#Sending the local updates to the master (github.com) repository
git push origin master

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Compilation of AFNI
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In src/, you need to choose one of the Makefile.* files that is closest
to your system, and cp it to be named Makefile.  Makefile is set up to
install into the INSTALLDIR location, defined in that file -- you should
probably change that to be appropriate for your use.

If you are using Mac OS X, choose one of the Makefile.macosx_* files.
  For later versions of Mac OS X, Apple's C compiler does not support
  OpenMP, so we recommend downloading and installing a version of gcc
  from http://hpc.sourceforge.net/ or purchasing a commercial C compiler
  (e.g., Intel's icc) that does support OpenMP.  Several important
  programs in the AFNI suite are parallelized via OpenMP, and will run
  much faster if compiled appropriately.

If you are using Linux, try Makefile.linux_openmp_64 first.

To make and install everything do
  make vastness
The command
  make cleanest
will remove all the *.o files, etc.