Hi Dinesh,
I have met the same problem before. The problem is a small piece of code to
check environment variables which has not yet been patched.
To make things work all you need to do is the following: type
export POSSUMDIR=$FSLDIR
in your terminal to start with, and then run POSSUM from this
terminal afterwards. This should make sure it has the right
settings to run without error.
Best,
Zheng
On Wed, Nov 18, 2009 at 11:18 AM, Subscribe Fsl Dinesh Sam <
[log in to unmask]> wrote:
> Hi FSL,
>
> I can't seem to obtain a resulting image when running possum on default
> parameters. The following is what appears :
>
> ---------------------------------------------------------------------------
> Starting POSSUM...
>
> Creating the POSSUM directory...
>
> Generating the pulse sequence...
> Regular EPI. 100 % coverage
>
> /usr/local/fsl/bin/pulse -i /usr/local/fsl/data/possum/brain.nii.gz -
> o /home/fsl/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=3e-06 -v --cover=100 --angle=90
> >> /home/fsl/simdir/possum.log 2>&1
>
> Submitting the job...
>
> /usr/local/fsl/bin/possumX /home/fsl/simdir -n 1 -t 2
> >> /home/fsl/simdir/possum.log 2>&1
>
> Job submitted.
>
> You can follow the POSSUM process by looking at the possum.log file.
>
> If you want to see the individual processes see the logs directory.
>
> ---------------------------------------------------------------------------
>
> The process seems to stop at the above point and I can't see a resulting
> image file.
>
> Any feedaback will be much appreciated.
>
> Thanks,
> Dinesh
>
--
Dr. Zheng Liu
Postdoctoral student in Computer Vision and Image Analysis Lab
Department of Electrical and Computer Engineering
Texas Tech University, Lubbock, TX 79409
