The following is the README file for the permutation test plugins written
by Matthew Belmonte.  This code has been released under the GPL.
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This directory contains plug_permtest.c and plug_threshold.c, source modules
for the AFNI Permutation Test and Threshold plugins, respectively.  The
threshold plugin separates brain from non-brain (with touch-up work being
handled by the Draw Dataset plugin), and the Permutation Test plugin evaluates
activations for statistical significance using a sensitive, nonparametric
algorithm.  To build both modules, place them in your AFNI source code
directory and type "make plug_permtest.so" and "make plug_threshold.so".
If you use this software in your research, please take a moment to send mail to
the author, belmonte@mit.edu, and cite the following paper in your report:

Matthew Belmonte and Deborah Yurgelun-Todd, `Permutation Testing Made Practical
for Functional Magnetic Resonance Image Analysis', IEEE Transactions on Medical
Imaging 20(3):243-248 (2001).

The permutation test takes a lot of memory and a lot of CPU.  You'll want to
use the fastest processor and system bus that you can lay your hands on, and at
least 256MB of memory.  If you're using Digital UNIX, you may find that the
plugin will be unable to allocate all the memory that it needs unless you
increase the values of the following kernel parameters:
max-per-proc-address-space, per-proc-data-size, max-per-proc-data-size,
per-proc-address-space, max-per-proc-address-space.  To change these parameters,
use the command-line tool "dxkerneltuner", or the graphical interface
"sysconfig".