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 https://afni.nimh.nih.gov/afni for more fun.
Currently top directory contains three sub-directories
- doc/
- documentation for AFNI
- src/
- source code for AFNI
- tests/
- tests for AFNI
Make yourself known to git-land:
git config --global user.name "Fred Mertz" git config --global user.email [email protected] git config --global core.editor vim
Create a copy of the repository on your machine:
git clone https://github.com/afni/afni.git
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
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.