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Hello Bjorn,

yes you are right, you first specify activation and then you run  
POSSUM.  You can crate the activation file in many ways. One way  
would be if you combine the tissues types of your input phantom into  
one volume (you give them some weighting csf*1+gry*0.7+wht*0.5 so  
that you can see clearly where the different tissues are). This will  
give you a good feeling for the structure. Then, in fslview, you can  
draw a mask on the top of this structure, and then save it as your  
activation region (see ~/fsl/data/possum/activation3D.nii.gz). Once  
you have the region, you then create a timecourse file which defines  
the behavior of the T2* parameter for this region during the  
experiment (e.g. follows the stimulus in your experiment ). For an  
example of this file look at ~/fsl/data/possum/activation3Dtimecourse .

Then you run POSSUM with extra options

possum  ....     -a activation3D -t activation3Dtimecourse

Hope this helps,
Ivana


  You specify activation on your input phantom, which in POSSUM_gui  
is by default MNI Collin's brain ( $FSLDIR/data/possum/brain.nii.gz).  
There are many ways
On 21 Apr 2008, at 09:46, Bjorn Roelstraete wrote:

> Hi,
>
> In the POSSUM manual I read:
>
> "You can make your own files by drawing areas of interest in  
> fslview and then creating a modulation time-course file which  
> matches your experimental paradigm."
>
> In order to try this, I simulated images in possum without  
> activation. Instead, I drew areas of activation afterwards on my  
> images and created my time course matrix. But when analyzing the  
> data with FEAT, there seemed to be no opportunity to specify my  
> timecourse matrix. How can I make these two communicate?
> Or does the manual mean that I should first draw activation and  
> specify my timecourse before running possum? If this is the case,  
> how do I start from a "blank sheet" to draw activation on?
>
> Many thanks,
> Bjorn
>
>
>
> -- 
> Bjorn Roelstraete
> Ghent University
> Department of Data-analysis
> H. Dunantlaan 1, B-9000 Gent, Belgium
> Tel: 32-9-2646434
> E-mail: [log in to unmask]
>