Dear Tibor,

Have you been using the GUI?
There is a fairly detailed documentation page at:
   http://www.fmrib.ox.ac.uk/fsl/possum/
which takes you through the different inputs
required.  The GUI should also give you an
estimate of the running time at the bottom
right.  What did it say?  Doing a full fMRI
simulation is *very* intensive and I suspect
that with this kind of resolution you are looking
at a very long time on a single machine (much
more than a week!) but on a sizable cluster it
should be feasible.

I recommend trying a small scale test to begin
with (e.g. one slice) to check that you have
got things set up correctly.

We do not currently have a module devoted to
POSSUM in the FSL course and so it does not
have the same information there (i.e. Tutorial/Practical)
like many of the other tools have.

In the documentation at:
   http://www.fmrib.ox.ac.uk/fsl/possum/input.html#activation
it describes how the activation is modeled via T2* values
and points you to example files.  If you look at the  
activation3Dtimecourse
file you will see that it is a simple text file with two columns.
The first is time (in seconds) the second is the T2* value.
Here the T2* value has been fit experimentally and is quite
approximate, but theoretical values can be used too.  The
most important equation is S/S0 = exp(-TE/T2*) which tells
you how the signal (S), as a fraction of the baseline signal, S0,
varies as a function of TE (specified in the pulse sequence)
and T2* (which is variable and specified in the appropriate
file).  To get a certain change in intensity (S/S0) you can
work out what T2* change is required for a given TE.
The other input is a 3D image, specifying the weighting of
the T2* change at each voxel.  This is typically a map that
specifies the activation location, and can be a binary image
or a more realistic case where the "strength" of the activation
drops off at the boundaries.  Look at the example to see what
it looks like, although you'll need to reset the display range
in FSLView to -0.01 to 0.01 (or similar) as the values are
quite small (which modulates the T2* change, giving an
overall T2* change of approximately 6ms in the active regions).
Note that the T2* specified here is always added to the
base T2* value of that tissue type (which is 51ms for grey
matter at 3T and 83ms at 1.5T - see the $FSLDIR/data/possum/MRpar_3T
and $FSLDIR/data/possum/MRpar_1.5T files which are
also described in the documentation).

Note also that any timing can be specified and that it
linearly interpolates between T2* values at the specified
times.

I hope this is helpful.
All the best,
	Mark



On 16 Apr 2010, at 15:17, Auer, Tibor MD. Ph.D. wrote:

> Dear Experts,
>
> I am trying to find a software to perform fMRI simulations. I set up  
> 100 volumes each containing 18 slices with resolution of 2mmx2mm.
> In FSL-package,  there is POSSUM available. However, there is no  
> User Guide/Tutorial/Practical guide for POSSUM similar to that given  
> for other FSL tools. I also tried to look for MIDAS, but the given  
> website  (http://www.midas-online.org/) is some crap about printers  
> (?).
>
> I tried also to figure out POSSUM myself, so I gave simply the  
> parameters and the supplied activation maps. However, I do not know  
> how to set up the paradigm (control and active phases). It did not  
> give me any failure message (I have checked the logfile), but it  
> runs for almost a week.
> How can I define custom activation pattern (shape, size and  
> amplitude)? How can I define paradigm?
>
> Or is there any useful tool for fMRI-data simulation?
>
> Thanks,
>
> Auer, Tibor M.D. Ph.D.
> Biomedizinische NMR Forschungs GmbH
> am Max-Planck Institut für Biophysikalische Chemie
> Am Fassberg 11
> 37077 Göttingen
> Germany
> Phone/Work: +49-(0)551-201-1725
> Phone/Home: +49-(0)551-250-4576
> Mobile: +49-(0)176-8012-7921
> Mail: [log in to unmask]
>