Hello

I am trying to make a simulated data-set with POSSUM, which contains different time 
course for every voxel. For the first step, I used the data-set that FSL have been provided 
for POSSUM simulation. I created a 4D activation map by combining the 3D activation 
map (activation3D) with the corresponding time course (activation3Dtimecourse), 
therefore the output is a 4D 181x217x181x23 image (I named it activation4D). I also 
generate a timing file which is only the first column of activation3Dtimecourse. Then I 
used the following possum command to do the simulation (in order to generate other files 
like MRpar and pulse, I used possum GUI, select parameters that I want, and upload 
activation4D and activation4Dtimecourse. Obviously it didn't work, but it generates the 
pulse, MRpar, ... files):
possum -i brain.nii.gz -x MRpar -m motion -p pulse -o Signal -f slcprof -q 
activation4D.nii.gz -u activation4Dtimecourse
but the output signal file is all "NaN" and therefore the final image is all zero.
then I ran the following command (which does not have the time-course file):
possum -i brain.nii.gz -x MRpar -m motion -p pulse -o Signal -f slcprof -q 
activation4D.nii.gz
now I have something in the signal file, but after running signal2image command, the 
time course in all of the voxels is just a constant and there is no activation signal in any 
of the voxels.
I don't know if I misunderstand some part of the 4D activation concept in possum or I am 
missing something in my simulation.
I would be very thankful if someone can help me to do my simulation.

Thanks
Ali Golestani





On 5-Sep-09, at 8:57 AM, Ivana Drobnjak wrote:

Hello Ali,

yes, there is a command line option -q 4Dactivationfile -u timefile (just write possum in 
the command line and it will give you more details ). This option allows you to specify a 
4D file which contains a different time course for every voxel. Timefile contains a 
timeline (in seconds ) when the activation curve was sampled e.g. 0 3 6 9 .....

Please note that running this is very memory consuming so try it first on just a few 
slices.

Ivana



On 4 Sep 2009, at 22:43, Ali Golestani wrote:

Hi;

is there anyway to define two activation location with different time courses in POSSUM?

Thanks
Ali