PSPM v 1.1.0

-1. In the beginning...
stages supported:
coregister
reslice
slice-timing correction
spatial normalization (writing not estimation)
smoothing
statistics

Everything here is distributed under GPL.  You should
know the spiel by now.  Apologies for a less than
gainly distribution at the moment.  It'll be made
keen when I have the time.

LIMITATIONS:
-----------
1. Your data needs to be in the same place across all
computers.  Basically this means that your data needs
to be on mounted disks if you're using a workstation
cluster.

2. Your SPM has to be in the same place across all
computers, so does the PSPM (MATLAB bits).  UNLESS when
Matlab starts up, the SPM and PSPM can already be found
in the default path

3. A couple bits of it are not parallelized.  This is
just initialization stuff for a couple of the stages.
However, I would suggest running the interface off of
your fastest computer if you're using a workstation
cluster.

0. Prelude
You'll need an MPI implementation.  You can download
MPICH at http://www-unix.mcs.anl.gov/mpi/mpich/
or you can use LAM/MPI from http://www.lam-mpi.org.
Both are free.  Some pros and cons: 

LAM/MPI seems to work better with heterogenous systems.  
There were bugs with MPICH (at least older versions 
that I tested out) that wouldn't allow it to run more 
than 6 processes on a heterogenous system.

MPICH2 (the newest version of MPICH) will allow you to
run on Windows.  Supposedly you can also have MPI programs
that will run on Windows AND unix/linux machines (I haven't
personally tested it out).  Refer to the user/install manual
for the details.  You'll need to use the 'smpd' manager as 
opposed to the default mpd manager

1. Installing

Refer to the INSTALL document.  

2. running the thing... 

For starters, if you get an error message about not 
being able to find libeng.so or some such at runtime,
libeng.so is a MATLAB library.  You should be able to find
it in <MATLAB>/extern/lib/<ARCH> where MATLAB is whereever
you've installed MATLAB and ARCH is what sort of computer
MATLAB thinks you're on.  You'll need to add that directory
to your LD_LIBRARY_PATH environment variable.  Sorry
for the inconvenience. In the future, this should
be taken care of during compile.

It can be run via the command line but it requires
some mat files that are generated by the MATLAB
interface.  You should be able to fire it up
using:
PSPM
at the matlab prompt (obviously after adding the
directory to your path).  
a. the architectures and processes list show which
architectures you're going to run it on and how
many processes to launch per architecture.  The
architecture name HAS to match what your MPI
implementation uses.  

b. in the display thing, tell it what computer
you want the graphics sent to.  

c. it'll try to guess where your SPM is installed
and where PSPM (this) has been installed.  If it
doesn't guess correctly, edit the paths.  Refer to
the LIMITATIONS section point 2

d. add stages to your analysis 

e. click on 'Verbose' if you want a lot of debugging
output.  This is helpful if things aren't working.

f. click on 'No Display' if you would like to not output
graphics files

g. after stages are added, press 'Set Files' to
select the session that you'll be processing

h. click on 'Export command' if you want it to create
a text file with the command that it will be running.  It
will write a text file with a temporary name (something like
tp252232--this name is generated by matlab) in the directory
that your data is in

i. Press 'Run', this just uses the matlab function
system to run the binary.  In the future, there'll probably
be a mex file interface or something, god only knows.  Alternatively
once the options are set, you can go back to your shell and
simply type out (or use the text file from step h) the command


report any problems to:
koola@musc.edu
