Dear Bjorn,

-p pulse /usr/share/fsl/data/possum/brain.nii.gz /home/bjorn/simdir/pulse

--te=0.030 --tr=3 --trslc=3.0 --nx=64 --ny=64 --dx=0.004 --dy=0.004

--maxG=0.055 --riset=0.00022 --bw=100000 --numvol=1 --numslc=1

--slcthk=0.001 --zstart=0.07 --seq=epi --slcdir=z+ --readdir=x

--phasedir=y --gap=0.0

should not be in POSSUM command line. You should generate the pulse sequence earlier by using pulse command. So you should do do this at the beginning

${FSLDIR}/bin/pulse -i ${FSLDIR}/data/possum/brain -o /home/bjorn/simdir/pulse --te=0.030 --tr=3 --trslc=3 --nx=64 --ny=64 --dx=0.004 --dy=0.004 --maxG=0.055 --riset=0.00022 --bw=100000 --numvol=1 --numslc=1 --slcthk=0.001 --zstart=0.07 --seq=epi --slcdir=z+ --readdir=x --phasedir=y --cover=${cover} --angle=90 --gap=0 -v

Once pulse.* files are generated in your simdir directory (there will be 5 or 6 of them) then you should run possum command:

$FSLDIR/bin/possum -i ${FSLDIR}/data/possum/brain -o /home/bjorn/simdir/signal -x /usr/share/fsl/data/possum/MRpar_3T -p /home/bjorn/simdir/pulse -f /usr/share/fsl/data/possum/slcprof -m

/usr/share/fsl/data/possum/zeromotion -f ${FSLDIR}/data/possum/slcprof

If using the POSSUM GUI, you can avoid having to deal with command lines.

Hope this helps,

Ivana

On 3 Apr 2008, at 12:19, Bjorn Roelstraete wrote:

possum -i /usr/share/fsl/data/possum/brain.nii.gz -o /home/bjorn/simdir/

-x /usr/share/fsl/data/possum/MRpar_3T -p pulse

/usr/share/fsl/data/possum/brain.nii.gz /home/bjorn/simdir/pulse

--te=0.030 --tr=3 --trslc=3.0 --nx=64 --ny=64 --dx=0.004 --dy=0.004

--maxG=0.055 --riset=0.00022 --bw=100000 --numvol=1 --numslc=1

--slcthk=0.001 --zstart=0.07 --seq=epi --slcdir=z+ --readdir=x

--phasedir=y --gap=0.0 -f /usr/share/fsl/data/possum/slcprof -m

/usr/share/fsl/data/possum/motionRzlarge_0.12s