Hi - the multiple masks option had a little bug in FSL 501. This has been fixed for FSL502.
Sorry about that.
Cheers
Saad
On 17 Dec 2012, at 22:02, Yu Zhang wrote:
> Dear FSL experts,
>
> I and my PhD advisor are having troubles with PROBTRACKX2(FDTV3,FSL 5.0.1) with multiple masks as seeds/waypoints. We got images with all zeros after running PROBTRACKX2. The data was running very well on PROBTRACKX(FDTV2).
>
> Here's the GUI&logs:
>
> /usr/local/fsl/bin/probtrackx2 --network -x /mnt/hgfs/Final/Tracktography/test/masks.txt -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /mnt/hgfs/Final/BedpostX/SE.bedpostX/merged -m /mnt/hgfs/Final/BedpostX/SE.bedpostX/nodif_brain_mask --dir=/mnt/hgfs/Final/Tracktography/test
> Log directory is: /mnt/hgfs/Final/Tracktography/test
> Running in network mode
> load seeds
> Load bedpostx samples
> 1_1
> 1_2
> 1_3
>
> nfibres : 1
> nsamples : 50
>
> Done loading samples.
> Volume seeds
> volume 0
> volume 1
>
> time spent tracking: 275 seconds
>
> save results
> finished
> Done!
>
> Fdt.log:
>
>
> set tool probtrackx
> set probtrack(bedpost_dir) /mnt/hgfs/Final/BedpostX/SE.bedpostX
> set probtrack(xfm)
> set probtrack(mode) network
> set probtrack(exclude_yn) 0
> set probtrack(usereference_yn) 0
> set probtrack(verbose_yn) 0
> set probtrack(loopcheck_yn) 1
> set probtrack(modeuler_yn) 0
> set probtrack(curvature) 0.2
> set probtrack(nsteps) 2000
> set probtrack(steplength) 0.5
> set probtrack(nparticles) 5000
> set probtrack(fibthresh) 0.01
> set probtrack(distthresh) 0.0
> set probtrack(sampvox) 0.0
> set probtrack(oneway_yn) 1
> set probtrack(wayorder_yn) 0
> set probtrack(waycond) AND
> .fdt.data.seed.targets insert end /mnt/hgfs/Final/Mask-5/SE/cpL.nii.gz /mnt/hgfs/Final/Mask-5/SE/plicL.nii.gz
> set probtrack(reference)
> set probtrack(output) /mnt/hgfs/Final/Tracktography/test
>
> Masks:
> /mnt/hgfs/Final/Mask-5/SE/cpL.nii.gz
> /mnt/hgfs/Final/Mask-5/SE/plicL.nii.gz
>
>
> Thanks,
> Yu Zhang
> PhD Student, Biomedical Engineering, Northwestern University
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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