Hi Matt
When you say you don't get an image, I suppose you mean fdt_paths only
has zero values, right?
Did you also use the -f option when you were not using a waypoint mask?
Not sure what else might be happening, waypoint not in the right place
perhaps?
Cheers,
Saad.
On 1 Jun 2009, at 01:09, Matthew Hoptman wrote:
> Hi all,
> I'm doing some tractography using probtrackx and have gotten nice
> results.
> However, when I put a waypoint mask in an area where the tracts pass
> (to
> refine the tractography), I don't get an image. Has anyone else had
> this
> experience? The command I used was:
>
> /home/matt/fsl4.1/bin/probtrackx --mode=seedmask -
> x /home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/
> lpcc.nii.
> gz -V 1 -l -f --modeuler -c 0.2 -S 2000 --steplength=0.5 -P 5000 --
> avoid=/home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/exc
> lude.nii.gz --forcedir --opd -
> s /home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/./merge
> d -
> m /home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/./
> nodif_
> brain_mask --dir=l_cingulate --waypoints=l_cingulate/waypoints.txt
>
> Thanks,
> Matt
>
--
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
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