Thanks for your advices

I still need to ask again, while the 3D activation is not enough for our
study. Possum does not have examples for 4D activation volumes and
timecourse.

If I understood right the timecourse in 4D activation includes only the time
points of the activation volumes (according of possum command).

The real question is then the format of the 4D activation volume. Does the
intensities in the activation volumes need to be scaled in some certain
level, for example [-1 1]? Are every volume in the 4D activation
independent or do they depend somehow from each others (for example, first
volume defines the activation intensities and the next just includes the
changes from the first)?

We need multiple different activation patterns in the same simulation and
so the 4D activation is our only choice. I have created CLI tool to use
possum easier with 4D activation without GUI, so the limitations of the
GUI are not a problem.

- Juha

> Dear Juha,
>
> What you need to specify in possum is the change in T2* values.
> This relates to the intensity of the signal (assuming nothing
> is moving) via the equation:
>    S = S0 * exp(-TE/T2*)
>
> Hence you need to specify time-varying T2* values.
> Look at the files $FSLDIR/data/possum/activation3D.nii.gz
> and $FSLDIR/data/possum/activation3Dtimecourse to see
> the format of the spatial map and timecourse.  The first
> column of the second file specifies values of time (in seconds)
> and the second specifies the change in T2* values (from
> the fixed, static value specified in the MR parameter file).
> The units for both of these things is seconds, not milliseconds.
>
> Note that the HRF is not added for you - it is necessary for
> you to specify a timecourse that already takes this into account.
>
> The specification of procnum works fine at our end, so I'm
> not sure why it is not working for you.  Feel free to modify it
> if that works for you.
>
> As for the memory and time requirements for possum - they
> can be very high if you specify very long time series and/or
> high resolutions.  I strongly recommend running a small test
> case first and then seeing how it scales up.
>
> I hope this helps.
> All the best,
> 	Mark
>
>
>
> On 15 Jun 2010, at 15:43, Juha Pajula wrote:
>
>> Hi!
>>
>> I am creating 4D activation sequences to POSSUM and now I need some
>> advices.
>>
>> I have fMRI data from previous studies and now we need to create
>> activations for POSSUM from the data. I found some instructions from
>> the POSSUM homepage, but could you give bit more detailed
>> instructions here; especially in the case of 4D activation.
>>
>> How the data should be scaled? Is the data impressed separately in
>> every volume or do the following volumes after the first one having
>> just the changes from the first activation?
>>
>> Do I need to consider the effect of haemodynamic response function?
>>
>> What does the following error truly means:
>> ------
>> Creating activation4D volume and timecourse vector...
>> 4D activation mode
>> Testing if the values in the activation volumes are smaller than the
>> T2* values
>> vol= 0
>> WARNING: Perturbation in the T2* values bigger than the T2* values.
>> ------
>>
>> I sent one email at last week about the memory consumption of the
>> POSSUM simulator processes in the SGE. Can you give any advices to
>> that now?
>>
>>
>> I think I found a bug in possumX in fsl version 4.1.4 from the line
>> 240:
>> procnum=0
>>
>> I guess it should be
>> procnum=1
>>
>> With the 0 the script creates one extra process to the SGE, which is
>> disturbing if the maximum amount of processes per user is limited in
>> the system. Could you check that it does not have any other effects
>> to the simulation?
>>
>>
>> --
>> Juha Pajula,
>> Research Assistant,
>> Methods and Models for Biological Signals and Images group of Signal
>> Processing department in Tampere University of Technology
>>
>