The position of the option does not matter.

What version of FSL are you using?
I would try with FSL version >= 5.0.9

If that does not work, I would try to drop --network / --omatrix1
Do you need both matrices? Matrix1 can be computationally very expensive
omatrix1 : AllSeeds x AllSeeds matrix  (vertices or voxels)
network: AllSeedsMasks x ALLSeedsMasks

Moises

On Wed, 31 Oct 2018 at 10:11, Yingtian Hu <[log in to unmask]> wrote:
Hi Moises,

Thank you very much for you help. But I did not find the output extra files. Is there something wrong with my scripts?  Is the position where I put the --pd wrong?

/usr/local/fsl/bin/probtrackx2  \
--network -x ${save_path}/targets_Power.txt \
 -l -c 0.2 -S 2000  \
 --steplength=0.5 -P 5000 \
 --pd \
 --xfm=${pathproc}/${subject}/data_${method}.bedpostX/xfms/standard2diff.mat \
 --forcedir --opd -s ${bpx_path}/merged \
 -m ${bpx_path}/nodif_brain_mask \
 --dir=${save_path} \
 --avoid=/cbis/projects/brain/R01DPS/analysis/templates/CSF.nii \
 --omatrix1

Thank you very much.

Sincerely,
Yingtian








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