Dear Nabin,
I think you are just missing an "=" after --xfm option, so your command should be:
probtrackx2 --network -x /gpfs/fs1/home/nkoirala/trial_data/G_Babar/dti.bedpostX/masks.txt --targetmasks=/gpfs/fs1/home/nkoirala/trial_data/G_Babar/dti.bedpostX/masks.txt -V 1 --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /gpfs/fs1/home/nkoirala/Gesunde/HC001.bedpostX/merged -m /gpfs/fs1/home/nkoirala/Gesunde/HC001.bedpostX/nodif_brain_mask --xfm=/gpfs/fs1/home/nkoirala/Gesunde/HC001.bedpostX/xfms/diff2standard.mat --dir=/gpfs/fs1/home/nkoirala/Gesunde/HC001/tracktography
Hope that fixes your problem,
Vasilis