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Dear Eric,

When you use possum the image it initially generates contains no noise at all.  The command systemnoise is used to add noise afterwards, and is _very_ quick to run, so you can make lots and lots of instances of the image with different amounts/realisations of noise very quickly and easily.  This is step 4 of the four main steps, as described in:
   http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/POSSUM/UserGuide

So just run systemnoise on the noise-free image after you've created it with possumX. 

All the best,
Mark


On 29 Mar 2013, at 22:45, Eric Walden <[log in to unmask]> wrote:

We need to run hundreds of POSSUM simulations, so we need to script it.  My understanding is that the system noise seed is automatically set to 1234.  Therefore, to get different outputs, I need to change the seed each run.  However, the command line to run POSSUM on the SGE is POSSUMX, and it does not allow mu to change the seed.

systemnoise allows me to change the seed, but it is not clear how it runs in POSSUMX.  Do I have to noise up each image before I run POSSUM or is there an easy way to adjust the random seed each time, for hundreds of simulations.