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This is the directory for the extended neural network model
for short-term memory of long sequences of auditory stimuli 

Antonio Ulloa
National Institutes of Health
Wed Feb 13 12:28:51 EST 2002

It is assumed that a directory <weights> already exists. The 
<weights> directory contains all the connection weights 
between regions. This weights are contained in *.w files.
The *.w files were generated by executing the command
netgen1 <*.ws>
for each of the *.ws files. The shell script mkweights
can be used to execute netgen1 for each of those files.
The *.ws files can be modified by hand, similarly to most of 
the other input files for network generation and simulation.

NOTE: do NOT regenerate the *.w files. These weights were
generated by Fatima and copied to the <weights> directory. 
Apparently, they were generated by "netgenFatima". However,
generating weights with "netgenFatima" results in slightly
different results than with the original weight files. Using
"netgen1" to generate the weight files results in 
incativation of STG levels and up.

NOTE [Fri Mar  1 14:11:34 EST 2002]: "netgenFatima" is simply
called "netgen2" in the NETGEN directory and "netgen" in the bin 
directory.

a) Minimum set of files needed to run the simulation:

auseq.s               % Contains all the necessary information to 
		      % execute an experimental trial
ausimweightlist.txt   % Description of connections among regions 
auseq.rs              % Timeline of events in an exp. trial 

noinp_au.inp          % Useful for a no input stream
pethiattn.s

auseq<n>.inp          % Contains the time-varying input for
                      % a sound sequence.  

resetall_au.inp       % Useful to reset all the nodes


b) Steps to run the simulation:

bin/sim <auseq>  % where <auseq> is a file with extension '.s'


c) Output of the simulation:

auseq.out             % General output of the simulation 
debug.txt

mgns.out              % MGN units

ea1u.out              % Ai up-selective units
ea1d.out              % Ai down-selective units

ea2u.out              % Aii up-selective units
ea2c.out              % Aii contour-selective units
ea2d.out              % Aii down-selective units

estg.out              % STG units

efd1.out              % D1 units
efd2.out              % D2 units
exfr.out              %  R units
exfs.out              %  C units

spec_pet.m            % MatLab specification of PET

d) To plot raster files of the simulations

run plotoutput.m in MatLab

e) To simulate fMRI

copy <spect_pet.m> to directory <fMRI>
go to directory <fMRI> 
run 'runfm' from MatLab