.TH \" Put title and section here, e.g. APE 1
.SH NAME    \" Section header
.PP
AFNI - Analysis of Functional NeuroImages

.SH SYNOPSIS
.PP
.nf 
.na 
afni [header file]
.ad
.fi

\" Optional sections
.SH "DESCRIPTION"
AFNI (Analysis of Functional NeuroImages) is a tool for viewing and
analyzing 3D brain images, usually from functional magnetic resonence
imaging scans.

The AFNI distribution consists of hundreds of programs, and 
is far too extensive to document as a man page.  

For quick usage info, type

afni -help

Full postscript documentation and READMEs can be found in 
%%PREFIX%%/share/doc/afni.

For more information visit the AFNI WEB site at

http://afni.nimh.nih.gov

.SH FILES
.nf
.na
 .afnirc, .cshrc, .tcshrc, .profile, .bashrc
.ad
.fi

.SH ENVIRONMENT
Users of this installation must have %%PREFIX%%/bin in their PATH.
AFNI_PLUGINPATH must include %%PREFIX%%/lib/afni so that AFNI can find plugins,
and %%PREFIX%%/share/afni so that AFNI can find startup images and
atlases.

For csh-compatible shells: 

setenv AFNI_PLUGINPATH %%PREFIX%%/lib/afni:%%PREFIX%%/share/afni

For sh-compatible shells:

.nf
AFNI_PLUGINPATH=%%PREFIX%%/lib/afni:%%PREFIX%%/share/afni
export AFNI_PLUGINPATH
.fi

If you plan to use the atlas files, set AFNI_GLOBAL_SESSION to
%%PREFIX%%/share/afni.

Note that these values are particular to this installation.  These
files may be located elsewhere on other machines.
There are many environment variables to control AFNI behavior.
See the full AFNI documentation, especially README.environment, for details.

.SH "SEE ALSO"
BrainVoyager, Caret, DTIQuery, FreeSurfer, FSL, SPM, SurfRelax

.SH AUTHOR
.nf
.na
RW Cox, PhD, et al.
National Institutes of Health